WorldWideScience

Sample records for structurally determined vacancies

  1. Vacancies in ordered and disordered titanium monoxide: Mechanism of B1 structure stabilization

    Energy Technology Data Exchange (ETDEWEB)

    Kostenko, M.G. [Institute of Solid State Chemistry, The Ural Branch of the Russian Academy of Sciences, Pervomayskaya 91, Ekaterinburg 620990 (Russian Federation); Lukoyanov, A.V. [Institute of Metal Physics, The Ural Branch of the Russian Academy of Sciences, S. Kovalevskoy 18, Ekaterinburg 620990 (Russian Federation); Ural Federal University named after First President of Russia B.N. Yeltsin, Mira 19, Ekaterinburg 620002 (Russian Federation); Zhukov, V.P. [Institute of Solid State Chemistry, The Ural Branch of the Russian Academy of Sciences, Pervomayskaya 91, Ekaterinburg 620990 (Russian Federation); Rempel, A.A., E-mail: rempel@ihim.uran.ru [Institute of Solid State Chemistry, The Ural Branch of the Russian Academy of Sciences, Pervomayskaya 91, Ekaterinburg 620990 (Russian Federation); Ural Federal University named after First President of Russia B.N. Yeltsin, Mira 19, Ekaterinburg 620002 (Russian Federation)

    2013-08-15

    The electronic structure and stability of three phases of titanium monoxide TiO{sub y} with B1 type of the basic structure have been studied. Cubic phase without structural vacancies, TiO, and two phases with structural vacancies, monoclinic Ti{sub 5}O{sub 5} and cubic disordered TiO{sub 1.0}, was treated by means of first-principles calculations within the density functional theory with pseudo-potential approach based on the plane wave's basis. The ordered monoclinic phase Ti{sub 5}O{sub 5} was found to be the most stable and the cubic TiO without vacancies the less stable one. The role of structural vacancies in the titanium sublattice is to decrease the Fermi energy, the role of vacancies in the oxygen sublattice is to contribute to the appearance of Ti–Ti bonding interactions through these vacancies and to reinforce the Ti–Ti interactions close to them. Listed effects are significantly pronounced if the vacancies in the titanium and oxygen sublattices are associated in the so called “vacancy channels” which determine the formation of vacancy ordered structure of monoclinic Ti{sub 5}O{sub 5}-type. - Graphical abstract: Changes in total DOS of titanium monoxide when going from vacancy-free TiO to TiO with disordered structural vacancies and to TiO with ordered structural vacancies. Highlights: • Ordered monoclinic Ti{sub 5}O{sub 5} is the most stable phase of titanium monoxide. • Vacancy-free TiO is the less stable phase of the titanium monoxide. • Ordering of oxygen vacancies leads to the appearance of Ti–Ti bonding interactions. • Titanium vacancies contribute significantly to the decreasing of the Fermi energy.

  2. Electronic Structures of Clusters of Hydrogen Vacancies on Graphene

    OpenAIRE

    Bi-Ru Wu; Chih-Kai Yang

    2015-01-01

    Hydrogen vacancies in graphane are products of incomplete hydrogenation of graphene. The missing H atoms can alter the electronic structure of graphane and therefore tune the electronic, magnetic, and optical properties of the composite. We systematically studied a variety of well-separated clusters of hydrogen vacancies in graphane, including the geometrical shapes of triangles, parallelograms, hexagons, and rectangles, by first-principles density functional calculation. The results indicate...

  3. Electronic Structures of Clusters of Hydrogen Vacancies on Graphene.

    Science.gov (United States)

    Wu, Bi-Ru; Yang, Chih-Kai

    2015-10-15

    Hydrogen vacancies in graphane are products of incomplete hydrogenation of graphene. The missing H atoms can alter the electronic structure of graphane and therefore tune the electronic, magnetic, and optical properties of the composite. We systematically studied a variety of well-separated clusters of hydrogen vacancies in graphane, including the geometrical shapes of triangles, parallelograms, hexagons, and rectangles, by first-principles density functional calculation. The results indicate that energy levels caused by the missing H are generated in the broad band gap of pure graphane. All triangular clusters of H vacancies are magnetic, the larger the triangle the higher the magnetic moment. The defect levels introduced by the missing H in triangular and parallelogram clusters are spin-polarized and can find application in optical transition. Parallelograms and open-ended rectangles are antiferromagnetic and can be used for nanoscale registration of digital information.

  4. Chemical expansion affected oxygen vacancy stability in different oxide structures from first principles calculations

    Energy Technology Data Exchange (ETDEWEB)

    Aidhy, Dilpuneet S.; Liu, Bin; Zhang, Yanwen; Weber, William J.

    2015-03-01

    We study the chemical expansion for neutral and charged oxygen vacancies in fluorite, rocksalt, perovskite and pyrochlores materials using first principles calculations. We show that the neutral oxygen vacancy leads to lattice expansion whereas the charged vacancy leads to lattice contraction. In addition, we show that there is a window of strain within which an oxygen vacancy is stable; beyond that range, the vacancy can become unstable. Using CeO2|ZrO2 interface structure as an example, we show that the concentration of oxygen vacancies can be manipulated via strain, and the vacancies can be preferentially stabilized. These results could serve as guiding principles in predicting oxygen vacancy stability in strained systems and in the design of vacancy stabilized materials.

  5. Size of oxide vacancies in fluorite and perovskite structured oxides

    DEFF Research Database (Denmark)

    Chatzichristodoulou, Christodoulos; Norby, Poul; Hendriksen, Peter Vang

    2015-01-01

    An analysis of the effective radii of vacancies and the stoichiometric expansion coefficient is performed on metal oxides with fluorite and perovskite structures. Using the hard sphere model with Shannon ion radii we find that the effective radius of the oxide vacancy in fluorites increases...... with increasing ion radius of the host cation and that it is significantly smaller than the radius of the oxide ion in all cases, from 37% smaller for HfO2 to 13 % smaller for ThO2. The perovskite structured LaGaO3 doped with Sr or Mg or both is analyzed in some detail. The results show that the effective radius...... of an oxide vacancy in doped LaGaO3 is only about 6 % smaller than the oxide ion. In spite of this the stoichiometric expansion coefficient (a kind of chemical expansion coefficient) of the similar perovskite, LaCrO3, is significantly smaller than the stoichiometric expansion coefficient of the fluorite...

  6. Computer simulation study of the structure of vacancies in grain boundaries

    Energy Technology Data Exchange (ETDEWEB)

    Brokman, A.; Bristowe, P.D.; Balluffi, R.W.

    1981-10-01

    The structure of vacancies in grain boundaries has been investigated by computer molecular statics employing pairwise potentials. In order to gain an impression of the vacancy structures which may occur generally, a number of variables was investigated, including metal type, boundary type, degree of lattice coincidence, and choice of boundary site. In all cases the vacancies remained as distinguishable point defects in the relatively irregular boundary structures. However, it was found that the vacancy often induced relatively large atomic displacements in the core of the boundary. These displacements often occurred only in the direct vicinity of the vacancy, but in certain cases they were widely distributed in the boundary, sometimes at surprisingly large distances. In certain cases the displacements included a large inward relaxation of one, or more, of the atoms neighboring the vacancy, and the initial vacant site became effectively ''split''.

  7. Effect of single vacancy on the structural, electronic structure and magnetic properties of monolayer graphyne by first-principles

    Energy Technology Data Exchange (ETDEWEB)

    Yun, Jiangni, E-mail: niniyun@nwu.edu.cn; Zhang, Yanni; Xu, Manzhang; Wang, Keyun; Zhang, Zhiyong

    2016-10-01

    The effect of single vacancy on the structural, electronic and magnetic properties of monolayer graphyne is investigated by the first-principles calculations. The calculated results reveal that single vacancy can result in the spin polarization in monolayer graphyne and the spin polarization is sensitive to local geometric structure of the vacancy. In the case of monolayer graphyne with one single vacancy at the sp{sup 2} hybridized C site, the vacancy introduces rather weakly spin-polarized, flat bands in the band gap. Due to the localization nature of the defect-induced bands, the magnetic moment is mainly localized at the vacancy site. As for the monolayer graphyne with one single vacancy at the sp hybridized C site, one defect-induced state which is highly split appears in the band gap. The spin-up band of the defect-induced state is highly dispersive and shows considerable delocalization, suggesting that the magnetic moment is dispersed around the vacancy site. The above magnetization in monolayer graphyne with one single vacancy is possibly explained in terms of the valence-bond theory. - Graphical abstract: Calculated band structure of the monolayer graphyne without (a) and with one single vacancy at Vb site (b) and at Vr site(c), respectively. Blue and red lines represent the spin-up and spin-down bands, respectively. For the sake of clarity, the band structure near the Fermi energy is also presented on the right panel. The Fermi level is set to zero on the energy scale. - Highlights: • A Jahn-Teller distortion occurs in monolayer graphyne with single vacancy. • The spin polarization is sensitive to local geometric structure of the vacancy. • Vacancy lying at sp{sup 2} hybridized C site introduces weakly spin-polarized defect bands. • A strong spin splitting occurs when the vacancy lies at sp hybridized C site. • The magnetization is explained in terms of the valence-bond theory.

  8. Positron annihilation in structural vacancies in Al-rich NiAl alloys

    Energy Technology Data Exchange (ETDEWEB)

    Morales, A.L.; Leon, L.A.; Raigoza, N.; Duque, C.A. [Instituto de Fisica, Universidad de Antioquia, Medellin (Colombia); Kuriplach, J. [Department of Low Temperature Physics, Faculty of Mathematics and Physics, Charles Univ., Prague (Czech Republic); Hou, M. [Physique des Solides Irradies et des Nanostructures, Universite Libre de Bruxelles, Brussels (Belgium)

    2007-07-01

    Positron annihilation in structural vacancies in B2 Al-rich NiAl alloys is studied theoretically. For this purpose we use the atomic superposition method combined with molecular dynamics employed for relaxations of random vacancy configurations. We found that the defect lifetime decreases with the increasing Ni vacancy concentration. Calculated positron lifetimes are discussed in terms of the 'vacancy-superstructure' effect and compared with experimental positron lifetime data available. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  9. Computer simulation study of the structure of vacancies in grain boundaries

    Energy Technology Data Exchange (ETDEWEB)

    Brokman, A.; Bristowe, P.D.; Balluffi, R.W.

    1981-01-01

    The structure of vacancies in grain boundaries has been investigated by computer molecular statics employing pairwise potentials. In order to gain an impression of the vacancy structures which may occur generally, a number of variables was investigated including: metal type, boundary type, degree of lattice coincidence and choice of boundary site. In all cases the vacancies remained as distinguishable point defects in the relatively irregular boundary structures. However, it was found that the vacancy often induced relatively large atomic displacements in the core of the boundary. These displacements often occurred only in the direct vicinity of the vacancy, but in certain cases they were widely distributed in the boundary, sometimes at surprisingly large distances.

  10. Computer simulation study of the structure of vacancies in grain boundaries

    Science.gov (United States)

    Brokman, A.; Bristowe, P. D.; Balluffi, R. W.

    1981-10-01

    The structure of vacancies in grain boundaries has been investigated by computer molecular statics employing pairwise potentials. In order to gain an impression of the vacancy structures which may occur generally, a number of variables was investigated, including metal type, boundary type, degree of lattice coincidence, and choice of boundary site. In all cases the vacancies remained as distinguishable point defects in the relatively irregular boundary structures. However, it was found that the vacancy often induced relatively large atomic displacements in the core of the boundary. These displacements often occurred only in the direct vicinity of the vacancy, but in certain cases they were widely distributed in the boundary, sometimes at surprisingly large distances. In certain cases the displacements included a large inward relaxation of one, or more, of the atoms neighboring the vacancy, and the initial vacant site became effectively ″split″. These results were classified and discussed in relation to the variables listed above. Several binding energies to the boundary were also calculated. Finally, the relevance of the results to the mechanism of boundary self-diffusion was discussed.

  11. Simulation of the structure of vacancies in high angle grain boundaries

    Science.gov (United States)

    Bristowe, P. D.

    1980-06-01

    A hard sphere dynamic model and a bubble raft model provided insight into the structure of a variety of defects in two dimensional crystalline and amorphous systems. The computed results form part of a wider investigation of vacancies and interstitials in various grain boundaries in which the binding energies are analyzed and related to the defect structure and form of the interatomic potential.

  12. Oxygen vacancies confined in SnO2 nanoparticles for desirable electronic structure and enhanced visible light photocatalytic activity

    Science.gov (United States)

    Yang, Yuanjie; Wang, Yuhua; Yin, Shu

    2017-10-01

    Electronic structure in principle determines the light absorbance, charge transfer and separation, and consequently, photocatalytic property of a photocatalyst. Herein, we report rutile SnO2 with a desirable electronic structure that exhibits a narrowed bandgap and an increased valence band width resulted from the introduction of homogeneous oxygen vacancies. XPS, Raman, ESR and PL spectra demonstrate the homogeneous oxygen vacancies confined in SnO2 nanoparticles. Moreover, the first principle calculations theoretically reveal the desirable electronic structure. The narrowed bandgap further contributes to extended light absorption range and the increased valence band width leads to efficient charge transfer and separation, hence facilitating the visible light photoreactivity. As a result, the defected SnO2 exhibits a superior visible light photocatalytic activity. More strikingly, the photodegration of methyl orange (MO) is completely accomplished within only 20 min under λ ≥ 420 nm. Briefly, this work both experimentally and theoretically indicates that homogeneous oxygen vacancies confined in SnO2 nanoparticles lead to the optimized electronic structure and, consequently, the remarkable visible light photocatalytic activity. This could open up an innovative strategy for designing potentially efficient photocatalysts.

  13. Nitrogen vacancy effects on the electronic structure of CrN

    Science.gov (United States)

    Rojas, Tomas; Ulloa, Sergio E.

    Chromium nitride (CrN) is believed to be a small indirect gap semiconductor with interesting electronic and magnetic properties. It exhibits a phase transition at T 280K in which both the electronic and magnetic structures change from a paramagnetic cubic rock-salt to an antiferromagnetic orthorhombic structure. However, the transport properties of CrN thin films are not fully settled, exhibiting metallic and semiconducting behavior at low temperatures in different situations. In particular, the impact of nitrogen vacancies and other defects on the transport properties are yet to be analyzed in detail. We have performed ab initio calculations using the LSDA+U method to examine the effect of N vacancies in bulk CrN. By replacing or removing a nitrogen atom in an appropriately large supercell, we study the accompanying deformations of the lattice structure as well as the energetics and spatial distribution of the associated charge and spin distribution of the defect state. We also study and compare less likely defects such as Cr, N-N and Cr-N vacancies. Our results indicate that a high percentage of N vacancies results in a transition towards a metallic phase, which produces strong defects on the local magnetic arrangements and may even create a small absolute magnetization. Supported by NSF-DMR 1508325, and the Ohio Supercomputer Center.

  14. Electronic structure of the substitutional vacancy in graphene: density-functional and Green's function studies

    Science.gov (United States)

    Nanda, B. R. K.; Sherafati, M.; Popović, Z. S.; Satpathy, S.

    2012-08-01

    We study the electronic structure of graphene with a single substitutional vacancy using a combination of the density-functional, tight-binding and impurity Green's function approaches. Density-functional studies are performed with the all-electron spin-polarized linear augmented plane wave (LAPW) method. The three sp2σ dangling bonds adjacent to the vacancy introduce localized states (Vσ) in the mid-gap region, which split due to the crystal field and a Jahn-Teller distortion, while the pzπ states introduce a sharp resonance state (Vπ) in the band structure. For a planar structure, symmetry strictly forbids hybridization between the σ and the π states, so that these bands are clearly identifiable in the calculated band structure. As to the magnetic moment of the vacancy, the Hund's rule coupling aligns the spins of the four localized Vσ1↑↓, Vσ2↑ and Vπ↑ electrons, resulting in an S = 1 state, with a magnetic moment of 2μB, which is reduced by about 0.3μB due to the anti-ferromagnetic spin polarization of the π band itinerant states in the vicinity of the vacancy. This results in the net magnetic moment of 1.7μB. Using the Lippmann-Schwinger equation, we reproduce the well-known ˜1/r decay of the localized Vπ wave function with distance, and in addition, find an interference term coming from the two Dirac points, previously unnoticed in the literature. The long-range nature of the Vπ wave function is a unique feature of the graphene vacancy and we suggest that this may be one of the reasons for the widely varying relaxed structures and magnetic moments reported from the supercell band calculations in the literature.

  15. Inhomogeneous Oxygen Vacancy Distribution in Semiconductor Gas Sensors: Formation, Migration and Determination on Gas Sensing Characteristics

    OpenAIRE

    Liu, Jianqiao; Gao, Yinglin; Wu, Xu; Jin, Guohua; Zhai, Zhaoxia; Liu, Huan

    2017-01-01

    The density of oxygen vacancies in semiconductor gas sensors was often assumed to be identical throughout the grain in the numerical discussion of the gas-sensing mechanism of the devices. In contrast, the actual devices had grains with inhomogeneous distribution of oxygen vacancy under non-ideal conditions. This conflict between reality and discussion drove us to study the formation and migration of the oxygen defects in semiconductor grains. A model of the gradient-distributed oxygen vacanc...

  16. Structure and electronic states of a graphene double vacancy with an embedded Si dopant

    Science.gov (United States)

    Nieman, Reed; Aquino, Adélia J. A.; Hardcastle, Trevor P.; Kotakoski, Jani; Susi, Toma; Lischka, Hans

    2017-11-01

    Silicon represents a common intrinsic impurity in graphene, bonding to either three or four carbon neighbors, respectively, in a single or double carbon vacancy. We investigate the effect of the latter defect (Si-C4) on the structural and electronic properties of graphene using density functional theory. Calculations based both on molecular models and with periodic boundary conditions have been performed. The two-carbon vacancy was constructed from pyrene (pyrene-2C) which was then expanded to circumpyrene-2C. The structural characterization of these cases revealed that the ground state is slightly non-planar, with the bonding carbons displaced from the plane by up to ±0.2 Å. This non-planar structure was confirmed by embedding the defect into a 10 × 8 supercell of graphene, resulting in 0.22 eV lower energy than the previously considered planar structure. Natural bond orbital analysis showed sp3 hybridization at the silicon atom for the non-planar structure and sp2d hybridization for the planar structure. Atomically resolved electron energy loss spectroscopy and corresponding spectrum simulations provide a mixed picture: a flat structure provides a slightly better overall spectrum match, but a small observed pre-peak is only present in the corrugated simulation. Considering the small energy barrier between the two equivalent corrugated conformations, both structures could plausibly exist as a superposition over the experimental time scale of seconds.

  17. Simulation of the structure of vacancies in high angle grain boundaries

    Energy Technology Data Exchange (ETDEWEB)

    Bristowe, P.D.; Brokman, A.; Spaepen, F.; Balluffi, R.W.

    1980-06-01

    Since the modeling approach used in an earlier work is used at an atomic level, this is the most appropriate and reliable technique available. To complement this study, however, we have also employed a hard sphere dynamic model and a bubble raft model because in the past they have provided useful qualitative insight into the structure of a variety of defects in two-dimensional crystalline and amorphous systems. The computed results form part of a wider investigation of vacancies and interstitials in various grain boundaries in which the binding energies are analyzed and related to the defect structure and form of the interatomic potential.

  18. Inhomogeneous Oxygen Vacancy Distribution in Semiconductor Gas Sensors: Formation, Migration and Determination on Gas Sensing Characteristics

    Science.gov (United States)

    Liu, Jianqiao; Gao, Yinglin; Wu, Xu; Jin, Guohua; Zhai, Zhaoxia; Liu, Huan

    2017-01-01

    The density of oxygen vacancies in semiconductor gas sensors was often assumed to be identical throughout the grain in the numerical discussion of the gas-sensing mechanism of the devices. In contrast, the actual devices had grains with inhomogeneous distribution of oxygen vacancy under non-ideal conditions. This conflict between reality and discussion drove us to study the formation and migration of the oxygen defects in semiconductor grains. A model of the gradient-distributed oxygen vacancy was proposed based on the effects of cooling rate and re-annealing on semiconductive thin films. The model established the diffusion equations of oxygen vacancy according to the defect kinetics of diffusion and exclusion. We described that the steady-state and transient-state oxygen vacancy distributions, which were used to calculate the gas-sensing characteristics of the sensor resistance and response to reducing gases under two different conditions. The gradient-distributed oxygen vacancy model had the applications in simulating the sensor performances, such as the power law, the grain size effect and the effect of depletion layer width. PMID:28796167

  19. Inhomogeneous Oxygen Vacancy Distribution in Semiconductor Gas Sensors: Formation, Migration and Determination on Gas Sensing Characteristics

    Directory of Open Access Journals (Sweden)

    Jianqiao Liu

    2017-08-01

    Full Text Available The density of oxygen vacancies in semiconductor gas sensors was often assumed to be identical throughout the grain in the numerical discussion of the gas-sensing mechanism of the devices. In contrast, the actual devices had grains with inhomogeneous distribution of oxygen vacancy under non-ideal conditions. This conflict between reality and discussion drove us to study the formation and migration of the oxygen defects in semiconductor grains. A model of the gradient-distributed oxygen vacancy was proposed based on the effects of cooling rate and re-annealing on semiconductive thin films. The model established the diffusion equations of oxygen vacancy according to the defect kinetics of diffusion and exclusion. We described that the steady-state and transient-state oxygen vacancy distributions, which were used to calculate the gas-sensing characteristics of the sensor resistance and response to reducing gases under two different conditions. The gradient-distributed oxygen vacancy model had the applications in simulating the sensor performances, such as the power law, the grain size effect and the effect of depletion layer width.

  20. Inhomogeneous Oxygen Vacancy Distribution in Semiconductor Gas Sensors: Formation, Migration and Determination on Gas Sensing Characteristics.

    Science.gov (United States)

    Liu, Jianqiao; Gao, Yinglin; Wu, Xu; Jin, Guohua; Zhai, Zhaoxia; Liu, Huan

    2017-08-10

    The density of oxygen vacancies in semiconductor gas sensors was often assumed to be identical throughout the grain in the numerical discussion of the gas-sensing mechanism of the devices. In contrast, the actual devices had grains with inhomogeneous distribution of oxygen vacancy under non-ideal conditions. This conflict between reality and discussion drove us to study the formation and migration of the oxygen defects in semiconductor grains. A model of the gradient-distributed oxygen vacancy was proposed based on the effects of cooling rate and re-annealing on semiconductive thin films. The model established the diffusion equations of oxygen vacancy according to the defect kinetics of diffusion and exclusion. We described that the steady-state and transient-state oxygen vacancy distributions, which were used to calculate the gas-sensing characteristics of the sensor resistance and response to reducing gases under two different conditions. The gradient-distributed oxygen vacancy model had the applications in simulating the sensor performances, such as the power law, the grain size effect and the effect of depletion layer width.

  1. The Effect of Atom Vacancy Defect on the Vibrational Behavior of Single-Walled Carbon Nanotubes: A Structural Mechanics Approach

    Directory of Open Access Journals (Sweden)

    S. K. Georgantzinos

    2014-04-01

    Full Text Available An atomistic structural mechanics method, which is based on the exclusive use of spring elements, is developed in order to study the effect of imperfections due to atom vacancy on the vibrational characteristics of single-walled carbon nanotubes (SWCNTs. The developed elements simulate the relative translations and rotations between atoms as well as the mass of the atoms. In this way, molecular mechanics theory can be applied directly because the atomic bonds are modeled by using exclusively physical variables such as bond stretching. The method is validated for its predictability comparing with vibration results found in the open literature for pristine nanotubes. Then, it is used for the vibration analysis of defective nanotubes. Imperfections such as one-atom vacancy, two-atom vacancy, and one carbon hexagonal cell vacancy are investigated. Their effect on vibrational behavior is explored for different defect positions, nanotube diameters, and support conditions. According to the obtained results, the fundamental frequency is decreased as the size of imperfection increases, and the percentage reduction in fundamental frequency due to the atomic vacancy defect is more affected for a single-clamped SWCNT than for a double-clamped one.

  2. The B35 cluster with a double-hexagonal vacancy: a new and more flexible structural motif for borophene.

    Science.gov (United States)

    Li, Wei-Li; Chen, Qiang; Tian, Wen-Juan; Bai, Hui; Zhao, Ya-Fan; Hu, Han-Shi; Li, Jun; Zhai, Hua-Jin; Li, Si-Dian; Wang, Lai-Sheng

    2014-09-03

    Elemental boron is electron-deficient and cannot form graphene-like structures. Instead, triangular boron lattices with hexagonal vacancies have been predicted to be stable. A recent experimental and computational study showed that the B36 cluster has a planar C6v structure with a central hexagonal hole, providing the first experimental evidence for the viability of atom-thin boron sheets with hexagonal vacancies, dubbed borophene. Here we report a boron cluster with a double-hexagonal vacancy as a new and more flexible structural motif for borophene. Photoelectron spectrum of B35(-) displays a simple pattern with certain similarity to that of B36(-). Global minimum searches find that both B35(-) and B35 possess planar hexagonal structures, similar to that of B36, except a missing interior B atom that creates a double-hexagonal vacancy. The closed-shell B35(-) is found to exhibit triple π aromaticity with 11 delocalized π bonds, analogous to benzo(g,h,i)perylene (C22H12). The B35 cluster can be used to build atom-thin boron sheets with various hexagonal hole densities, providing further experimental evidence for the viability of borophene.

  3. The Vacancy Formation Energy in Crystalline Adamantane Determined by Positron Annihilation Techniques

    DEFF Research Database (Denmark)

    Lightbody, D.; Sherwood, J. N.; Eldrup, Morten Mostgaard

    1980-01-01

    The injection of positrons into crystalline adamantane results in the formation of positronium (Ps). At temperatures T> 400 K the mean lifetime of the long-lived ortho-positronium exhibits a sigmoidal increase with temperature characteristic of the trapping of this species in thermally created de...... energy of lattice vacancies in adamantane derived from self-diffusion studies....

  4. Determination of vacancy mechanism for grain boundary self-diffusion by computer simulation

    Energy Technology Data Exchange (ETDEWEB)

    Balluffi, R.W.; Kwok, T.; Bristowe, P.D.; Brokman, A.; Ho, P.S.; Yip, S.

    1981-08-01

    This note reports efforts to establish the GB self-diffusion mechanism in a bcc iron /SIGMA/.5 (36.9/degree/) (001) (310) tilt boundary using the combined methods of computer molecular statics and molecular dynamics simulation to provide quantitative microscopic evidence in favor of the vacancy mechanism. 16 refs.

  5. Structural Engineering of Vacancy Defected Bismuth Tellurides for Thermo-electric Applications

    Directory of Open Access Journals (Sweden)

    Chumakov Y.

    2012-10-01

    Full Text Available Molecular Dynamics and ab-initio simulations are used to find the most stable stoichiometries of Bismuth Tellurides with vacancy defects. The interest is to decrease the thermal conductivity of these compounds a key point to achieve high figure of merits. A reduction of 70% of the thermal conductivity is observed with Te vacancies of only 5%.

  6. NMR study of vacancy and structure-induced changes in Cu2-xTe

    Science.gov (United States)

    Sirusi, Ali A.; Page, Alexander; Uher, Ctirad; Ross, Joseph H.

    2017-07-01

    We report Cu and Te NMR measurements on Cu2-xTe with x between 0.13 and 0.22. Aided by powder x-ray analysis and computed NMR quadrupole shifts, a structure change near x=0.20 was found consistent with structures reported by Baranova, with best fits to the β-I structure for x=0.22 and β-III for smaller x. NMR T1 and Hall effect results demonstrate p-type electronic behavior with filling of simple hole pockets induced by increased numbers of vacancies for both phases. Furthermore the Cu and Te chemical shifts are large and negative, as observed in topologically inverted semiconductors, with a splitting into two distinct local environments for both Cu and Te sites in the x=0.22 structure. Cu T1 results show a rapid decrease of the energy barrier for initiation of Cu ion hopping to 0.12 eV for x=0.22, considerably smaller than observed at higher temperatures, indicating a tail of relatively mobile Cu ions which may be of significance for potential device applications.

  7. All-Optical dc Nanotesla Magnetometry Using Silicon Vacancy Fine Structure in Isotopically Purified Silicon Carbide

    Directory of Open Access Journals (Sweden)

    D. Simin

    2016-07-01

    Full Text Available We uncover the fine structure of a silicon vacancy in isotopically purified silicon carbide (4H-^{28}SiC and reveal not yet considered terms in the spin Hamiltonian, originated from the trigonal pyramidal symmetry of this spin-3/2 color center. These terms give rise to additional spin transitions, which would be otherwise forbidden, and lead to a level anticrossing in an external magnetic field. We observe a sharp variation of the photoluminescence intensity in the vicinity of this level anticrossing, which can be used for a purely all-optical sensing of the magnetic field. We achieve dc magnetic field sensitivity better than 100  nT/sqrt[Hz] within a volume of 3×10^{-7}mm^{3} at room temperature and demonstrate that this contactless method is robust at high temperatures up to at least 500 K. As our approach does not require application of radio-frequency fields, it is scalable to much larger volumes. For an optimized light-trapping waveguide of 3  mm^{3}, the projection noise limit is below 100  fT/sqrt[Hz].

  8. Determination of vacancy mechanism for grain boundary self-diffusion by computer simulation

    Energy Technology Data Exchange (ETDEWEB)

    Balluffi, R. W.; Kwok, T.; Bristowe, P. D.; Brokman, A.; Ho, P. S.; Yip, S.

    1981-06-01

    It is currently well established that the fast self-diffusion which occurs along grain boundaries (GBs) in metals must occur by a point defect exchange mechanism. For example, it is known that rapid GB diffusion can transport a net current of atoms along GBs during both sintering and diffusional creep, and that the two species in a binary substitutional alloy diffuse at different rates in GBs. However, it has not been possible to establish firmly whether the defect mechanism involves the exchange of atoms with vacancy or interstitial point defects. It has been suspected that the vacancy exchange mechanism must apply but it has been difficult to prove this hypothesis because of a lack of detailed information at the atomistic level. The results are presented of an effort to establish the GB self-diffusion mechanism in a bcc iron ..sigma.. = 5 (36.9/sup 0/) (001) (310) tilt boundary using the combined methods of computer molecular statics and molecular dynamics simulation.

  9. Atomistic simulations of screw dislocations in bcc tungsten: From core structures and static properties to interaction with vacancies

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Ke [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Niu, Liang-Liang [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Department of Nuclear Engineering and Radiological Science, University of Michigan, Ann Arbor, MI 48109 (United States); Jin, Shuo, E-mail: jinshuo@buaa.edu.cn [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Shu, Xiaolin [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Xie, Hongxian [School of Mechanical Engineering, Hebei University of Technology, Tianjin 300132 (China); Wang, Lifang; Lu, Guang-Hong [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China)

    2017-02-15

    Atomistic simulations have been used to investigate the core structures, static properties of isolated 1/2 <1 1 1> screw dislocations, and their interaction with vacancies in bcc tungsten (W) based on three empirical interatomic potentials. Differential displacement maps show that only one embedded atom method potential is able to reproduce the compact non-degenerate core as evidenced by ab initio calculations. The obtained strain energy and stress distribution from atomistic simulations are, in general, consistent with elasticity theory predictions. In particular, one component of the calculated shear stress, which is not present according to elasticity theory, is non-negligible in the core region of our dislocation model. The differences between the results calculated from three interatomic potentials are in details, such as the specific value and the symmetry, but the trend of spatial distributions of static properties in the long range are close to each other. By calculating the binding energies between the dislocations and vacancies, we demonstrate that the dislocations act as vacancy sinks, which may be important for the nucleation and growth of hydrogen bubbles in W under irradiation.

  10. Annealing dependent oxygen vacancies in SnO{sub 2} nanoparticles: Structural, electrical and their ferromagnetic behavior

    Energy Technology Data Exchange (ETDEWEB)

    Mehraj, Sumaira, E-mail: sumairamehraj07@gmail.com [Department of Applied Physics, Aligarh Muslim University, Aligarh 202002 (India); Ansari, M. Shahnawaze, E-mail: shah.csengg@gmail.com [Center of Nanotechnology, King Abdulaziz University, Jeddah 21589 (Saudi Arabia); Al-Ghamdi, Attieh A. [Center of Nanotechnology, King Abdulaziz University, Jeddah 21589 (Saudi Arabia); Alimuddin [Department of Applied Physics, Aligarh Muslim University, Aligarh 202002 (India)

    2016-03-01

    The effect of annealing on structural, electrical and d0 ferromagnetism in SnO{sub 2} nanoparticles synthesized by solution combustion method is investigated. The as synthesized SnO{sub 2} nanoparticles were annealed at 500 °C–1300 °C for 2 h in ambient conditions. The crystallinity, grain size and morphology of the samples were studied using X-ray diffraction, Field emission scanning electron microscope, Transmission electron microscopy and energy dispersive X-ray spectroscopic studies. The annealing temperature resulted in grain growth as well as reduction in oxygen vacancies as confirmed by Raman spectroscopy. Resistivity measurement of all the samples showed the typical behavior of semiconductors. Dielectric spectroscopy showed that there is an improvement in electric properties of SnO{sub 2} nanoparticles as the annealing temperature is increased. The samples exhibited ferromagnetism at room temperature as well as at 5 K. However, the saturation magnetization at room temperature is decreasing from 0.019 emu/g to 0.001 emu/g whereas at 5 K, it is decreasing from 0.75 emu/g to 0.05 emu/g with increasing annealing temperature. The observed difference between ferromagnetism at 300 K and 5 K clearly indicates that oxygen vacancies become more active at 5 K and induce ferromagnetism with almost 40 times higher magnitude of saturation magnetization than that at 300 K in as synthesized and annealed SnO{sub 2} nanoparticles. In the light of this study electrical and magnetization values can be tuned by changing the relative concentration of oxygen vacancies which can be achieved by varying annealing temperature thus projecting their technological applications in spintronics. - Highlights: • Preparation of SnO{sub 2} nanoparticles using solution combustion method. • Effect of annealing temperature on oxygen vacancies. • Role of grains and grain boundaries in electrical properties. • Complex impedance analysis with respect to the average particle

  11. Electronic structure and vacancy formation in La(1 - x) B(x) CoO3 (B=Mg,Ca,Ba and x=0.125)

    Science.gov (United States)

    Salawu, Omotayo; Gan, Liyong; Schwingenschlogl, Udo

    2015-03-01

    The LaCoO3 class of materials is of interest for cathodes of solid oxide fuel cells. Spin-polarized density functional theory is applied to cubic La0.75(Mg/Ca/Ba)0.125CoO3. The effect of this cation doping on the electronic and magnetic properties as well as oxygen vacancy formation energy is studied. Oxygen vacancies with proximity to the dopant are energetically favourable in most cases. We discuss the effect of distortions of the CoO6 octahedron on the electronic structure and the formation energy of oxygen vacancies. The order of formation oxygen is found to be Mg > Ca > Ba. Cation doping incorporates holes to the Co-O network which enhances the oxygen vacancy formation.

  12. Vacancies in functional materials for clean energy storage and harvesting: the perfect imperfection.

    Science.gov (United States)

    Li, Guowei; Blake, Graeme R; Palstra, Thomas T M

    2017-03-21

    Vacancies exist throughout nature and determine the physical properties of materials. By manipulating the density and distribution of vacancies, it is possible to influence their physical properties such as band-gap, conductivity, magnetism, etc. This can generate exciting applications in the fields of water treatment, energy storage, and physical devices such as resistance-change memories. In this review, we focus on recent progress in vacancy engineering for the design of materials for energy harvesting applications. A brief discription of the concept of vacancies, the way to create and control them, as well as their fundamental properties, is first provided. Then, emphasis is placed on the strategies used to tailor vacancies for metal-insulator transitions, electronic structures, and introducing magnetism in non-magnetic materials. Finally, we present representative applications of different structures with vacancies as active electrode materials of lithium or sodium ion batteries, catalysts for water splitting, and hydrogen evolution.

  13. Electronic structural properties of BiOF crystal and its oxygen vacancy from first-principles calculations

    Science.gov (United States)

    Li, Sen; Zhang, Chao; Min, Fanfei; Dai, Xing; Pan, Chengling; Cheng, Wei

    2017-12-01

    First-principles calculations are performed to investigate the crystal and electronic structures of BiOF crystal and its oxygen vacancy BiO7/8F. By analyzing the energy band structures, the total density of states and the partial densities of states, it is found that the band gaps for the perfect BiOF and BiO7/8F are 3.12 and 2.65 eV, respectively, which are smaller than the experiment value of 3.64 eV. There is a new electronic state within the forbidden band in the BiO7/8F, which could serve as a capture center for excited electrons, consequently improves the effective separation of electron-hole pairs, and makes the optical absorption band edge red shift. The calculated results demonstrate that the BiOF crystal and its oxygen vacancy BiO7/8F could be the potential application as photocatalytic semiconductor materials.

  14. Structures and electrical properties of pure and vacancy-included ZnO NWs of different sizes

    Science.gov (United States)

    Yu, Xiao-Xia; Zhou, Yan; Liu, Jia; Jin, Hai-Bo; Fang, Xiao-Yong; Cao, Mao-Sheng

    2015-12-01

    The structures and electronic properties of ZnO nanowires (NWs) of different diameters are investigated by employing the first-principles density functional theory. The results indicate that the oxygen vacancy (VO) exerts a more evident influence on the band gap of the ZnO NWs. However, the effect will be weakened with the increase of the diameter. In addition, the energy band shifts downward due to the existence of VO and the offset decreases with the reduction of the VO concentration. As the concentration of surface Zn atoms decreases, the conduction band shifts downward, while 2p electrons are lost in the oxygen vacancy, resulting in the split of valence band and the formation of an impurity level. Our findings agree well with the previous observations and will be of great importance for theoretical research based on ZnO NWs. Project supported by the National Natural Science Foundation of China (Grant Nos. 51132002 and 11574261) and the Natural Science Foundation of Hebei Province, China (Grant No. A2015203261).

  15. The effects of a hydrogen pair in the electronic structure of the FCC iron containing a vacancy

    Energy Technology Data Exchange (ETDEWEB)

    Simonetti, S. [Departamento de Fisica, Universidad Nacional del Sur, Av. Alem 1253, 8000 Bahia Blanca (Argentina); Centro de Investigaciones en Mecanica Teorica y Aplicada, Universidad Tecnologica Nacional, 11 de Abril 461, 8000 Bahia Blanca (Argentina); Saravia, D. Rey [Departamento de Ingenieria, Universidad Nacional del Sur, Av. Alem 1253, 8000 Bahia Blanca (Argentina); Brizuela, G.; Juan, A. [Departamento de Fisica, Universidad Nacional del Sur, Av. Alem 1253, 8000 Bahia Blanca (Argentina)

    2010-06-15

    Fuel cell vehicles have been identified as the personal transportation technology of the future because of their high efficiency and very low emissions. To achieve the goal of road-ready fuel cell vehicles, great strides must be made in the development of fuel cells, hydrogen production and hydrogen storage technologies, that includes metal-H interaction studies and safety considerations. The interaction between two-hydrogen atoms and a {gamma}-Fe structure containing a vacancy has been studied using a cluster model and a theoretical method. For the study of the sequential absorption, the hydrogen atoms were positioned in their energy minima configurations, near the vacancy. The interactions mainly involve Fe 4s-H 1s atomic orbitals. The contribution of Fe 4p and Fe 3d orbitals is much less important. The Fe-Fe bond is weakened as new Fe-H-H and H-H pairs were formed. The effect of H atoms is limited to its first Fe neighbors. The Fe-Fe bond strength decreases with the introduction of the H atoms. Fe-H bonding is achieved at expense of weakening the metal-metal nearest bonds. There is not a real bond between the H atoms but some H-H interaction is observed. The detrimental effect of H atoms on the Fe-Fe bonds can be related to one of the aspect of embrittlement in {gamma}-Fe. (author)

  16. Band structure engineering and vacancy induced metallicity at the GaAs-AlAs interface

    KAUST Repository

    Upadhyay Kahaly, M.

    2011-09-20

    We study the epitaxial GaAs-AlAs interface of wide gap materials by full-potential density functional theory. AlAsthin films on a GaAs substrate and GaAsthin films on an AlAs substrate show different trends for the electronic band gap with increasing film thickness. In both cases, we find an insulating state at the interface and a negligible charge transfer even after relaxation. Differences in the valence and conduction band edges suggest that the energy band discontinuities depend on the growth sequence. Introduction of As vacancies near the interface induces metallicity, which opens great potential for GaAs-AlAs heterostructures in modern electronics.

  17. Vacancies in SiC nanopowders

    Energy Technology Data Exchange (ETDEWEB)

    Kityk, I.V.; Makowska-Janusik, M. [Technical Univ. of Czestochowa (Poland). Inst. of Phys.; Kassiba, A.; Charpentier, C. [Laboratoire de Physique de l' Etat Condense, UPRES-A6087, Universite du Maine, Avenue Olivier Messiaen, 72085 Cedex 9, LeMans (France); Tuesu, K. [Research Informatic Science Department, Tohoku University, 2-1-4 Katahira, Aoba-ku, 982-12, Sendai (Japan); Ling, Y. [Michigan Molecular Institute, 48640, Midland, MI (United States)

    2000-08-31

    Origin of vacancies in the large-sized SiC nanocrystals (higher than 10 nm) has been investigated using theoretical band structure calculations and experimental electronic paramagnetic resonance (EPR) measurements. Influence of geometry sizes on appearance of concrete vacancy has been studied. The theoretical approach includes self-consistent norm-conserving pseudopotential band energy calculations and geometry structure optimisation. The performed calculations show that the presence of the vacancies is a necessary attribute of the SiC nanocrystallites. Moreover, the type and concentration of the vacancies are dependent on the nanoparticle geometry. We have revealed that spin-polarised states of intracrystallite vacancies differ essentially from vacancies in the bulk crystals. A comparison between the performed theoretical simulations and obtained EPR experimental data shows the possibility of using the proposed methods for prediction of vacancy appearance in the binary nanocrystallites and possibility for their operation. (orig.)

  18. Electronic structure and O vacancy formation/migration in La0.825(Mg/Ca/Ba)0.125CoO3

    Science.gov (United States)

    Omotayo Akande, Salawu; Gan, Li-Yong; Schwingenschlögl, Udo

    2016-04-01

    The effect of A-site hole doping (Mg2+, Ca2+ or Ba2+) on the electronic and magnetic properties as well as the O vacancy formation and migration in perovskite LaCoO3 is studied using first-principles calculations. All three dopants are found to facilitate O vacancy formation. Substitution of La3+ with Ba2+/Mg2+ yields the lowest O vacancy formation energy for low/intermediate spin Co, implying that not only the structure but also the spin state of Co is a key parameter. Only for low spin Co the ionic radius is correlated with the O migration barrier. Enhanced migration for intermediate spin Co is ascribed to the availability of additional space at the transition state.

  19. Electronic structure and O vacancy formation/migration in La0.825(Mg/Ca/Ba)0.125CoO3

    KAUST Repository

    Omotayo Akande, Salawu

    2016-05-05

    The effect of A-site hole doping (Mg2+, Ca2+ or Ba2+) on the electronic and magnetic properties as well as the O vacancy formation and migration in perovskite LaCoO3 is studied using first-principles calculations. All three dopants are found to facilitate O vacancy formation. Substitution of La3+ with Ba2+/Mg2+ yields the lowest O vacancy formation energy for low/intermediate spin Co, implying that not only the structure but also the spin state of Co is a key parameter. Only for low spin Co the ionic radius is correlated with the O migration barrier. Enhanced migration for intermediate spin Co is ascribed to the availability of additional space at the transition state. © CopyrightEPLA, 2016.

  20. First-principles study of structure, electronic properties and stability of tungsten adsorption on TiC(111) surface with disordered vacancies

    Science.gov (United States)

    Ilyasov, Victor V.; Pham, Khang D.; Zhdanova, Tatiana P.; Phuc, Huynh V.; Hieu, Nguyen N.; Nguyen, Chuong V.

    2017-12-01

    In this paper, we systematically investigate the atomic structure, electronic and thermodynamic properties of adsorbed W atoms on the polar Ti-terminated TixCy (111) surface with different configurations of adsorptions using first principle calculations. The bond length, adsorption energy, and formation energy for different reconstructions of the atomic structure of the W/TixCy (111) systems were established. The effect of the tungsten coverage on the electronic structure and the adsorption mechanism of tungsten atom on the TixCy (111) are also investigated. We also suggest the possible mechanisms of W nucleation on the TixCy (111) surface. The effective charges on W atoms and nearest-neighbor atoms in the examined reconstructions were identified. Additionally, we have established the charge transfer from titanium atom to tungsten and carbon atoms which determine by the reconstruction of the local atomic and electronic structures. Our calculations showed that the charge transfer correlates with the electronegativity of tungsten and nearest-neighbor atoms. We also determined the effective charge per atom of titanium, carbon atoms, and neighboring adsorbed tungsten atom in different binding configurations. We found that, with reduction of the lattice symmetry associated with titanium and carbon vacancies, the adsorption energy increases by 1.2 times in the binding site A of W/TixCy systems.

  1. Electronic structure and oxygen vacancies in PdO and ZnO: validation of DFT models.

    Science.gov (United States)

    Bruska, Marta Kinga; Czekaj, Izabela; Delley, Bernard; Mantzaras, John; Wokaun, Alexander

    2011-09-21

    PdO is one of the most important catalytic materials currently used in the industry. In redox catalytic reactions involving PdO, the bulk phase is an additional source of oxygen. This leads to strong transformations not only at the surface of PdO but also in the near sub-surface and bulk regions. The redox process is, therefore, governed not only by the extent of PdO d-band filling, but also depends on the material properties of the PdO crystal--the ease with which its structure can be deformed. Methane oxidation is of key industrial interest, and therein the rate of CH(4) conversion depends strongly on the reversible oxygen defects formation on the surface and in the bulk of the catalyst. The present study gives a first insight into these complex phenomena at the atomistic level. Comparison of different density functional theory (DFT) approaches and their capacity to reproduce experimental values of the heat of formation as well as the band gap of the PdO are discussed in detail. Results from DFT calculations for an oxygen vacancy creation in the bulk and on the surface of PdO are presented and compared at the level of accuracy of the implemented approaches with defect calculations for ZnO. Many different modeling approaches based on functionals and pseudopotentials (non-modified PP and empirically tuned) have been evaluated in their aptness to capture key PdO properties. It was shown that simulations with the PP-115 pseudopotential gave the closest possible agreement to the relevant PdO thermodynamic data and energy of oxygen vacancy formation.

  2. Sc and Nb Dopants in SrCoO3 Modulate Electronic and Vacancy Structures for Improved Water Splitting and SOFC Cathodes

    KAUST Repository

    Tahini, Hassan A.

    2017-01-12

    SrCoO3 is a promising material in the field of electrocatalysis. Difficulties in synthesising the material in its cubic phase have been overcome by doping it with Sc and Nb ions [Mater. Horiz.2015, 2, 495–501]. Using ab initio calculations and special quasi random structures we undertake a systematic study of these dopants in order to elucidate the effect of doping on electronic structure of the SrCoO3 host and the formation of oxygen vacancies. We find that while the overall electronic structure of SrCoO3 is preserved, increasing the Sc fraction leads to a decrease of electrical conductivity, in agreement with earlier experimental work. For low Sc and Nb doping fractions we find that the oxygen vacancy formation increases relative to undoped SrCoO3. However, as the dopants concentration is increased the vacancy formation energy drops significantly, indicating a strong tendency to accommodate high concentration of oxygen vacancies and hence non-stoichiometry. This is explained based on the electronic instabilities caused by the presence of Sc ions which weakens the B-O interactions as well as the increased degree of electron delocalization on the oxygen sublattice. Sc dopants also shift the p-band centre closer to the Fermi level, which can be associated with experimentally reported improvements in oxygen evolution reactions. These findings provide crucial baseline information for the design of better electrocatalysts for oxygen evolution reactions as well as fuel-cell cathode materials.

  3. Electronic Structure and Ferromagnetism Modulation in Cu/Cu2O Interface: Impact of Interfacial Cu Vacancy and Its Diffusion

    Science.gov (United States)

    Li, Hao-Bo; Wang, Weichao; Xie, Xinjian; Cheng, Yahui; Zhang, Zhaofu; Dong, Hong; Zheng, Rongkun; Wang, Wei-Hua; Lu, Feng; Liu, Hui

    2015-01-01

    Cu/Cu2O composite structures have been discovered to show sizable ferromagnetism (FM) with the potential applications in spintronic devices. To date, there is no consensus on the FM origin in Cu/Cu2O systems. Here, first principles calculations are performed on the interface structure to explore the microscopic mechanism of the FM. It is found that only the Cu vacancy (VCu) adjacent to the outermost Cu2O layer induces a considerable magnetic moment, mostly contributed by 2p orbitals of the nearest-neighbor oxygen atom (ONN) with two dangling bonds and 3d orbitals of the Cu atoms bonding with the ONN. Meanwhile, the charge transfer from Cu to Cu2O creates higher density of states at the Fermi level and subsequently leads to the spontaneous FM. Furthermore, the FM could be modulated by the amount of interfacial VCu, governed by the interfacial Cu diffusion with a moderate energy barrier (~1.2 eV). These findings provide insights into the FM mechanism and tuning the FM via interfacial cation diffusion in the Cu/Cu2O contact. PMID:26478505

  4. Anion ordering, magnetic structure and properties of the vacancy ordered perovskite Ba{sub 3}Fe{sub 3}O{sub 7}F

    Energy Technology Data Exchange (ETDEWEB)

    Clemens, Oliver, E-mail: oliver.clemens@nano.tu-darmstadt.de [Technische Universität Darmstadt, Joint Research Laboratory Nanomaterials, Jovank a-Bontschits-Straße 2, 64287 Darmstadt (Germany); Karlsruher Institut für Technologie, Institut für Nanotechnologie, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); University of Birmingham, School of Chemistry, Birmingham B152TT (United Kingdom); Reitz, Christian; Witte, Ralf; Kruk, Robert [Karlsruher Institut für Technologie, Institut für Nanotechnologie, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); Smith, Ronald I. [ISIS Facility, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX (United Kingdom)

    2016-11-15

    This article describes a detailed investigation of the crystallographic and magnetic structure of perovskite type Ba{sub 3}Fe{sub 3}O{sub 7}F by a combined analysis of X-ray and neutron powder diffraction data. Complete ordering of vacancies within the perovskite lattice could be confirmed. In addition, the structure of the anion sublattice was studied by means of the valence bond method, which suggested partial ordering of the fluoride ions on two of the six crystallographically different anion sites. Moreover, the compound was found to show G-type antiferromagnetic ordering of Fe moments, in agreement with magnetometric measurements as well as previously recorded {sup 57}Fe Mössbauer spectroscopy data. - Graphical abstract: The vacancy and anion ordered structure of Ba{sub 3}Fe{sub 3}O{sub 7}F is described together with its magnetic properties. - Highlights: • Ba{sub 3}Fe{sub 3}O{sub 7}F possesses a unique vacancy order not found for other perovskite type compounds. • The valence bond method was used to locate oxide and fluoride ions. • Fluoride ions are distributed only on two of the six anion sites in Ba{sub 3}Fe{sub 3}O{sub 7}F. • The compound shows G-type antiferromagnetic ordering of magnetic moments. • The magnetic structure could be refined in one of the maximal magnetic subgroups of the nuclear structure.

  5. The effect of structural vacancies on the thermoelectric properties of (Cu₂Te){sub 1–x}(Ga₂Te₃)x

    Energy Technology Data Exchange (ETDEWEB)

    Ye, Zuxin; Young Cho, Jung; Tessema, Misle M. [Optimal Inc., Plymouth Township, MI 48170 (United States); Salvador, James R., E-mail: james.salvador@gm.com [GM Global R and D, Warren, MI 48090 (United States); Waldo, Richard A. [GM Global R and D, Warren, MI 48090 (United States); Wang, Hsin; Cai, Wei [Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States)

    2013-05-01

    We have studied the effects of structural vacancies on the thermoelectric properties of the ternary compounds (Cu₂Te)1–x(Ga₂Te₃)x (x=0.5, 0.55, 0.571, 0.6, 0.625, 0.667 and 0.75), which are solid solutions found in the pseudo-binary phase diagram for Cu₂Te and Ga₂Te₃, and possesses tunable structural vacancy concentrations. This materials system is not suitable due to the cost and scarcity of the constituent elements, but the vacancy behavior is well understood and will provide a valuable test case for other systems more suitable from the standpoint of cost and abundance of raw materials, which also possesses these vacancy features, but whose structural characterization is lacking at this stage. We find that the nominally defect free phase CuGaTe₂ possess the highest ZT (ZT=S²T/ρκ, where S is the Seebeck coefficient and ρ is the electrical resistivity κ is the thermal conductivity and T is the absolute temperature) which approaches 1 at 840 K and seems to continuously increase above this temperature. This result is due to the unexpectedly low thermal conductivity found for this material at high temperature. The low thermal conductivity was caused by strong Umklapp (thermally resistive scattering processes involving three phonons) phonon scattering. We find that due to the coincidentally strong scattering of carriers by the structural defects that higher concentrations of these features lead to poor electrical transport properties and decreased ZT. - Graphical abstract: Thermal conductivity and zT as a function of temperature for a series of compounds of the type (Cu₂Te)1–x(Ga₂Te₃)x (x=0.5, 0.55, 0.571, 0.6, 0.625, 0.667 and 0.75). Highlights: • All the samples show p-type semiconducting behavior in the temperature dependence of the Seebeck and Hall coefficients. • The increased carrier concentration and the introduction of vacancies diminish the carrier mobility and power factor. • The low

  6. A Mechanistic Analysis of Oxygen Vacancy Driven Conductive Filament Formation in Resistive Random Access Memory Metal/NiO/Metal Structures (Preprint)

    Science.gov (United States)

    2018-01-10

    metal -induced gap states to the electronic density of states were identified, accommodating oxygen vacancy states, and showing that the interface region...Electrically switchable resistive random access memories have drawn much interest as nonvolatile memory device candidates, based also metal -insulator... metal (MIM) structure concepts. However, atomic-level mechanisms that lead to conductive filament (CF) formation in MIMs are often lacking, such as

  7. Oxygen Evolution at Hematite Surfaces: The Impact of Structure and Oxygen Vacancies on Lowering the Overpotential

    NARCIS (Netherlands)

    Zhang, X.; Klaver, P.; van Santen, R.; van de Sanden, M. C. M.; Bieberle, A.

    2016-01-01

    Simulations of the oxygen evolution reaction (OER) are essential for understanding the limitations of water splitting. Most research has focused so far on the OER at flat metal oxide surfaces. The structure sensitivity of the OER has, however, recently been highlighted as a promising research

  8. First-principles calculations of vacancy effects on structural and electronic properties of TiC sub x and TiN sub x

    CERN Document Server

    Dridi, Z; Ruterana, P; Aourag, H

    2002-01-01

    First-principles calculations have been used to study the effect of vacancies on the structural and electronic properties in substoichiometric TiC sub x and TiN sub x. The effect of vacancies on equilibrium volumes, bulk moduli, electronic band structures and density of states of the substoichiometric phases was studied using a full-potential linear augmented plane-wave method. A model structure of eight-atom supercells with ordered vacancies within the carbon and nitrogen sublattices is used. We find that the lattice parameters of the studied stoichiometries in both TiC sub x and TiN sub x are smaller than that of ideal stoichiometric TiC and TiN. Our results for the variation of the lattice parameters and the bulk moduli for TiC sub x are found to be in good agreement with experiment. The variation of the energy gaps with the atomic concentration ratio shows that these compounds present the same trends. Results for TiC sub x are compared to a recent full-potential calculation with relaxed 16-atom supercells...

  9. Detecting neighborhood vacancy level in Detroit city using remote sensing

    Science.gov (United States)

    Li, X.; Wang, R.; Yang, A.; Vojnovic, I.

    2015-12-01

    With the decline of manufacturing industries, many Rust Belt cities, which enjoyed prosperity in the past, are now suffering from financial stress, population decrease and urban poverty. As a consequence, urban neighborhoods deteriorate. Houses are abandoned and left to decay. Neighborhood vacancy brings on many problems. Governments and agencies try to survey the vacancy level by going through neighborhoods and record the condition of each structure, or by buying information of active mailing addresses to get approximate neighborhood vacancy rate. But these methods are expensive and time consuming. Remote sensing provides a quick and comparatively cost-efficient way to access spatial information on social and demographical attributes of urban area. In our study, we use remote sensing to detect a major aspect of neighborhood deterioration, the vacancy levels of neighborhoods in Detroit city. We compared different neighborhoods using Landsat 8 images in 2013. We calculated NDVI that indicates the greenness of neighborhoods with the image in July 2013. Then we used thermal infrared information from image in February to detect human activities. In winter, abandoned houses will not consume so much energy and therefore neighborhoods with more abandoned houses will have smaller urban heat island effect. Controlling for the differences in terms of the greenness obtained from summer time image, we used thermal infrared from winter image to determine the temperatures of urban surface. We find that hotter areas are better maintained and have lower house vacancy rates. We also compared the changes over time for neighborhoods using Landsat 7 images from 2003 to 2013. The results show that deteriorated neighborhoods have increased NDVI in summer and get colder in winter due to abandonment of houses. Our results show the potential application of remote sensing as an easily accessed and efficient way to obtain data about social conditions in cities. We used the neighborhood

  10. Strain engineering of magnetic state in vacancy-doped phosphorene

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Jie [Hunan Provincial Key Laboratory of Micro–Nano Energy Materials and Devices, Xiangtan University, Xiangtan 411105, Hunan (China); Zhang, Chunxiao, E-mail: zhangchunxiao@xtu.edu.cn [Hunan Provincial Key Laboratory of Micro–Nano Energy Materials and Devices, Xiangtan University, Xiangtan 411105, Hunan (China); Li, Jin [Hunan Provincial Key Laboratory of Micro–Nano Energy Materials and Devices, Xiangtan University, Xiangtan 411105, Hunan (China); Guo, Zhixin [Department of Physics, Xiangtan University, Xiangtan 411105, Hunan (China); Xiao, Huaping, E-mail: hpxiao@xtu.edu.cn [Hunan Provincial Key Laboratory of Micro–Nano Energy Materials and Devices, Xiangtan University, Xiangtan 411105, Hunan (China); Zhong, Jianxin [Hunan Provincial Key Laboratory of Micro–Nano Energy Materials and Devices, Xiangtan University, Xiangtan 411105, Hunan (China)

    2016-09-23

    Inducing and manipulating the magnetism in two-dimensional materials play an important role for the development of the next-generation spintronics. In this letter, the effects of the biaxial strain on magnetic properties of vacancy-doped phosphorene are investigated using first-principles calculation. We find although only SV956 doping induces magnetism for unstrained phosphorene, the biaxial strain induces nonzero magnetic moment for SV5566 and DVa doped phosphorene. The biaxial strain also modulates the magnetic state for SV956, SV5566 and DVa doped phosphorene. The local magnetic moment derives from the spin polarization of the dangling bonds near the vacancy. The biaxial strain influences the local bonding configuration near the vacancy which determines the presence of dangling bonds, and then modulates the magnetic state. Our findings promise the synergistic effect of strain engineering and vacancy decoration is an effective method for the operation of phosphorene-based spintronic devices. - Highlights: • Investigation of the magnetic moment of vacancy-doped phosphorene by DFT calculation. • The modulation of the magnetic moment by the biaxial strain. • The analysis of the bonding configuration with the biaxial strain. • The analysis of the electronic structures to explain the evolution of the magnetic moment. • The effects of the biaxial strain on the band gap and doping levels.

  11. Oxygen vacancy induced structure change and interface reaction in HfO{sub 2} films on native SiO{sub 2}/Si substrate

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Kai [Institute of Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083 (China); Department of Chemistry, Tsinghua University, Beijing 100084 (China); Yao, Wenqing, E-mail: yaowq@tsinghua.edu.cn [Department of Chemistry, Tsinghua University, Beijing 100084 (China); Zhao, Yuanyuan [Institute of Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083 (China); Yang, Liping [Department of Chemistry, Tsinghua University, Beijing 100084 (China); Cao, Jiangli, E-mail: jlcao@mater.ustb.edu.cn [Institute of Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083 (China); Zhu, Yongfa [Department of Chemistry, Tsinghua University, Beijing 100084 (China)

    2016-12-30

    Graphical abstract: The diffusion of interfacial oxygen atoms was induced by the oxygen vacancies and the grain boundaries in the HfO{sub 2} films, which caused structural changes in the film-substrate interface layer. - Highlights: • The relationship between the defects formation and the change of the interface structure in HfO{sub 2} films was investigated. • The existence of oxygen vacancies in the surface layer of the HfO{sub 2} film was confirmed by Auger line shapes. • The mechanisms of interfacial oxygen diffusion and interface reactions were demonstrated. - Abstract: The HfO{sub 2} films were deposited on SiO{sub 2} (native)/n-Si (100) substrates by electron beam evaporation (EBE) technology. The structural evolution of the films during thermal annealing were studied by using grazing incidence X-ray diffraction (GIXRD), Raman spectra and Auger electron spectroscopy (AES), while the change of bonding structure and interface products were obtained by Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS). The existence of oxygen vacancies in the surface layer of the as-deposited HfO{sub 2} film was confirmed by Auger line shapes, which could facilitate the adsorption of ambient oxygen on the free surface and induce the diffusion of oxygen atoms to the surface layer during thermal annealing. Meanwhile, the newly formed defects in the films could provide more passageways for the diffusion of oxygen atoms to the film-substrate interface layer. The oxygen that diffused to the interface layer was the key factor of the change in the interface structure, which participated in the interface reaction. In addition, the formation amount and bonding structure of the interface products such as suboxide of silicon and hafnium silicate were influenced by the oxygen concentration of the external environment.

  12. Vacancy Concentration in Ice

    DEFF Research Database (Denmark)

    Mogensen, O. E.; Eldrup, Morten Mostgaard

    1977-01-01

    Based on the diffusion constant for self-diffusion in ice, which is believed to take place by a vacancy mechanism, we estimate the relative vacancy concentration near the melting point to be at least ∼ 10−6, i.e. much higher than previous estimates of about 10−10.......Based on the diffusion constant for self-diffusion in ice, which is believed to take place by a vacancy mechanism, we estimate the relative vacancy concentration near the melting point to be at least ∼ 10−6, i.e. much higher than previous estimates of about 10−10....

  13. The effect of Lanthanum vacancy on structural, electrical and magnetic properties of La1-xMnO3+δ manganite

    Directory of Open Access Journals (Sweden)

    A Hosseinzadeh

    2012-06-01

    Full Text Available  In this investigation, the effect of Lanthanum vacancy on the structural, electrical and magnetic properties of La1-xMnO3+δ manganite (x=0, 0.05 was studied. Decreasing La3+ amount in samples led to creation of some Mn4+ cations. By increasing the Mn4+content in atomic structure of samples, double exchange interaction was strengthened. Results of Ac magnetic susceptibility measurements indicated that both samples (x=0, 0.05 have spin glass-like behavior at low temperatures. Electrical transport measurements showed a decrease in resistivity of samples, which can be attributed to variation in Mn3+ to Mn4+ ratio and different kinds of magnetic interactions in the samples. Furthermore, it was shown that fast cooling (FC is an appropriate method in controlling the oxygen of samples. The samples prepared by FC method showed similar properties with stoichiometric La1-xMnO3.

  14. Structural characterization of a new vacancy ordered perovskite modification found for Ba{sub 3}Fe{sub 3}O{sub 7}F (BaFeO{sub 2.333}F{sub 0.333}): Towards understanding of vacancy ordering for different perovskite-type ferrites

    Energy Technology Data Exchange (ETDEWEB)

    Clemens, Oliver, E-mail: oliver.clemens@kit.edu [Technische Universität Darmstadt, Joint Research Laboratory Nanomaterials, Jovanka-Bontschits-Straße 2, 64287 Darmstadt (Germany); Karlsruher Institut für Technologie, Institut für Nanotechnologie, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany)

    2015-05-15

    The new vacancy ordered perovskite-type compound Ba{sub 3}Fe{sub 3}O{sub 7}F (BaFeO{sub 2.33}F{sub 0.33}) was prepared by topochemical low-temperature fluorination of Ba{sub 2}Fe{sub 2}O{sub 5} (BaFeO{sub 2.5}) using stoichiometric amounts of polyvinylidene difluoride (PVDF). The vacancy order was found to be unique so far for perovskite compounds, and the connectivity pattern can be explained by the formula Ba{sub 3}(FeX{sub 6/2}) (FeX{sub 5/2}) (FeX{sub 3/2}X{sub 1/1}), with X=O/F. Mössbauer measurements were used to confirm the structural analysis and agree with the presence of Fe{sup 3+} in the above mentioned coordination environments. Group–subgroup relationships were used to build a starting model for the structure solution and to understand the relationship to the cubic perovskite structure. Furthermore, a comparison of a variety of vacancy-ordered iron-containing perovskite-type structures is given, highlighting the factors which favour one structure type over the other depending on the composition. - Graphical abstract: The crystal structure of Ba{sub 3}Fe{sub 3}O{sub 7}F in comparison to other perovskite type ferrites. - Highlights: • The crystal structure of Ba{sub 3}Fe{sub 3}O{sub 7}F in comparison to other perovskite type ferrites. • Ba{sub 3}Fe{sub 3}O{sub 7}F was synthesized by low temperature fluorination of Ba{sub 2}Fe{sub 2}O{sub 5}. • Ba{sub 3}Fe{sub 3}O{sub 7}F shows a unique vacancy order not found for other perovskite type compounds. • The structure of Ba{sub 3}Fe{sub 3}O{sub 7}F was solved using group–subgroup relationships. • A systematic comparison to other ferrite type compounds reveals structural similarities and differences. • The A-site coordination of the cation is shown to play an important role for the type of vacancy order found.

  15. Direct Observation of Sr Vacancies in SrTiO_{3} by Quantitative Scanning Transmission Electron Microscopy

    Directory of Open Access Journals (Sweden)

    Honggyu Kim

    2016-12-01

    Full Text Available Unveiling the identity, spatial configuration, and microscopic structure of point defects is one of the key challenges in materials science. Here, we demonstrate that quantitative scanning transmission electron microscopy (STEM can be used to directly observe Sr vacancies in SrTiO_{3} and to determine the atom column relaxations around them. By combining recent advances in quantitative STEM, including variable-angle, high-angle annular dark-field imaging and rigid registration methods, with frozen phonon multislice image simulations, we identify which Sr columns contain vacancies and quantify the number of vacancies in them. Picometer precision measurements of the surrounding atom column positions show that the nearest-neighbor Ti atoms are displaced away from the Sr vacancies. The results open up a new methodology for studying the microscopic mechanisms by which point defects control materials properties.

  16. Structure determination of enterovirus 71

    Energy Technology Data Exchange (ETDEWEB)

    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G. (Purdue); (Sentinext)

    2013-02-20

    Enterovirus 71 is a picornavirus that causes hand, foot and mouth disease but may induce fatal neurological illness in infants and young children. Enterovirus 71 crystallized in a body-centered orthorhombic space group with two particles in general orientations in the crystallographic asymmetric unit. Determination of the particle orientations required that the locked rotation function excluded the twofold symmetry axes from the set of icosahedral symmetry operators. This avoided the occurrence of misleading high rotation-function values produced by the alignment of icosahedral and crystallographic twofold axes. Once the orientations and positions of the particles had been established, the structure was solved by molecular replacement and phase extension.

  17. Structural determinants of arrestin functions.

    Science.gov (United States)

    Gurevich, Vsevolod V; Gurevich, Eugenia V

    2013-01-01

    Arrestins are a small protein family with only four members in mammals. Arrestins demonstrate an amazing versatility, interacting with hundreds of different G protein-coupled receptor (GPCR) subtypes, numerous nonreceptor signaling proteins, and components of the internalization machinery, as well as cytoskeletal elements, including regular microtubules and centrosomes. Here, we focus on the structural determinants that mediate various arrestin functions. The receptor-binding elements in arrestins were mapped fairly comprehensively, which set the stage for the construction of mutants targeting particular GPCRs. The elements engaged by other binding partners are only now being elucidated and in most cases we have more questions than answers. Interestingly, even very limited and imprecise identification of structural requirements for the interaction with very few other proteins has enabled the development of signaling-biased arrestin mutants. More comprehensive understanding of the structural underpinning of different arrestin functions will pave the way for the construction of arrestins that can link the receptor we want to the signaling pathway of our choosing. Copyright © 2013 Elsevier Inc. All rights reserved.

  18. Ordered vacancies and their chemistry in metal-organic frameworks.

    Science.gov (United States)

    Tu, Binbin; Pang, Qingqing; Wu, Doufeng; Song, Yuna; Weng, Linhong; Li, Qiaowei

    2014-10-15

    Vacancies are common in solid materials, but it remains a challenge to introduce them at specific locations with controlled distributions. Here we report the creation of ordered metal vacancies and linker vacancies in a cubic metal-organic framework (MOF) based on Zn(II) and pyrazolecarboxylic acid by removing a quarter of the metal ions and half of the linkers. The MOF with ordered vacancies shows increased pore size, thus allowing large dye molecules to fit in the pores. Furthermore, by filling the vacancies with new metals and new linkers, eight new single-crystalline MOFs with multicomponents in absolute order are introduced. The capability of performing stepwise elimination and addition reactions systematically in extended solids without destroying the structural integrity has generated complex MOF structures which otherwise cannot be made.

  19. Electronic and magnetic properties of graphene, silicene and germanene with varying vacancy concentration

    Directory of Open Access Journals (Sweden)

    Muhammad Ali

    2017-04-01

    Full Text Available The experimental realization of two-dimensional materials such as graphene, silicene and germanene has attracted incredible interest ranging from understanding their physical properties to device applications. During the fabrication and processing of these two-dimensional materials, structural defects such as vacancies may be produced. In this work we have systemically investigated the formation energies, electronic and magnetic properties of graphene, silicene and germanene with vacancies in the framework of spin polarized density functional theory. It is found that the magnetic moment of graphene and silicene with vacancies decreases with the increase in the concentration of vacancies. However, germanene remains non-magnetic irrespective of the vacancy concentration. Low-buckled silicene and germanene with vacancies may possess remarkable band gaps, in contrast to planar graphene with vacancies. With the formation of vacancies silicene and germanene demonstrate a transition from semimetal to semiconductor, while graphene turns to be metallic.

  20. Theoretical perspective on structural, electronic and magnetic properties of 3d metal tetraoxide clusters embedded into single and di-vacancy graphene

    Energy Technology Data Exchange (ETDEWEB)

    Rafique, Muhammad [School of Energy Science and Engineering, Harbin Institute of Technology, 92 West Dazhi Street, Harbin 150001 (China); Mehran University of Engineering and Technology, S.Z.A.B, Campus Khairpur Mir' s, Sindh (Pakistan); Shuai, Yong, E-mail: shuaiyong@hit.edu.cn [School of Energy Science and Engineering, Harbin Institute of Technology, 92 West Dazhi Street, Harbin 150001 (China); Tan, He-Ping; Muhammad, Hassan [School of Energy Science and Engineering, Harbin Institute of Technology, 92 West Dazhi Street, Harbin 150001 (China)

    2017-06-30

    Highlights: • First-principles calculations are performed for TMO{sub 4} cluster-doped SV and DV monolayer graphene structures. • Ferromagnetism coupling behavior between TM atoms and neighboring C and O atoms was observed for all structural models. • The direction of charge transfer is always from graphene layer to TMO{sub 4} clusters. • CrO{sub 4} and MnO{sub 4} doped SV graphene systems display dilute magnetic semiconductor (DMS) behavior in their spin down channel. • CoO{sub 4}, CrO{sub 4}, FeO{sub 4} and MnO{sub 4} doped DV graphene systems exhibit DMS behavior in their spin up channel. - Abstract: Structural, electronic and magnetic properties of 3d transition metal tetraoxide TMO{sub 4} superhalogen clusters doped single vacancy (SV) and divacancy (DV) monolayer graphene have been studied using first-principles calculations. We found that in both cases of TMO{sub 4} cluster substitution, all the impurity atoms are tightly bonded with graphene, having significant formation energy and large charge transfer occurs from graphene to TMO{sub 4} clusters. CrO{sub 4} and MnO{sub 4} substituted SV graphene structures exhibit dilute magnetic semiconductor behavior in their spin down channel with 2.15 μ{sub B} and 3.51 μ{sub B} magnetic moment, respectively. However, CoO{sub 4}, FeO{sub 4}, TiO{sub 4} and NiO{sub 4} substitution into SV graphene, leads to Fermi level shifting to conduction band, thereby causing the Dirac cone to move into valence band and a band gap appears at high symmetric K-point. Interestingly, CoO{sub 4}, CrO{sub 4}, FeO{sub 4} and MnO{sub 4} substituted DV graphene structures exhibit dilute magnetic semiconductor behavior in their spin up channel with 1.74 μ{sub B}, 3.27 μ{sub B}, 3.09 μ{sub B} and 1.99 μ{sub B} magnetic moment, respectively. Detailed analysis of density of states (DOS) plots show that d orbitals of 3d TM atoms should be responsible for inducing magnetic moments in graphene. We believe that our results are

  1. Magnesium Vacancy Segregation and Fast Pipe Diffusion for the ½{110} Edge Dislocation in MgO

    Science.gov (United States)

    Walker, A. M.; Zhang, F.; Wright, K.; Gale, J. D.

    2009-12-01

    The movement of point defects in minerals plays a key role in determining their rheological properties, both by permitting diffusional creep and by allowing recovery by dislocation climb. Point defect diffusion can also control the kinetics of phase transitions and grain growth, and can determine the rate of chemical equilibration between phases. Because of this, and the difficulties associated with experimental studies of diffusion, the simulation of point defect formation and migration has been a subject of considerable interest in computational mineral physics. So far, studies have concentrated on point defects moving through otherwise perfect crystals. In this work we examine the behavior of magnesium vacancies close to the core of an edge dislocation in MgO and find that the dislocation dramatically changes the behavior of the point defect. An atomic scale model of the ½{110} edge dislocation in MgO was constructed by applying the anisotropic linear elastic displacement field to the crystal structure and subsequently minimizing the energy of the crystal close to the dislocation core using a parameterized potential model. This process yielded the structure of an isolated edge dislocation in an otherwise perfect crystal. The energy cost associated with introducing magnesium vacancies around the dislocation was then mapped and compared to the formation energy of an isolated magnesium vacancy in bulk MgO. We find that the formation energy of magnesium vacancies around the dislocation mirrors the elastic strain field. Above the dislocation line σxx and σyy are negative and the strain field is compressional. Atoms are squeezed together to make room for the extra half plane effectively increasing the pressure in this region. Below the dislocation line σxx and σyy are positive and the strain field is dilatational. Planes of atoms are pulled apart to avoid a discontinuity across the glide plane and the effective pressure is decreased. In the region with a

  2. Disordering of InGaAs/GaAs multiquantum well structure by impurity-free vacancy diffusion for advanced optoelectronic devices and their integration

    Science.gov (United States)

    Yu, Jae Su; Kim, Jong Min; Lee, Yong Tak; Song, Jin Dong; Lim, H.

    2005-03-01

    We studied the impurity-free vacancy diffusion (IFVD) of In0.2Ga0.8As/GaAs multi-quantum well (MQW) structures for advanced optoelectronic devices and their integration. To gain deeper insight in IFVD, the influence of the plasma enhanced chemical vapor deposition parameters, such as SiH4 flow rate, deposition temperature, deposition pressure and rf power, of SiOx and SiNx capping layers on the band gap energy shift induced by IFVD was investigated. We observed that the magnitude of the blue shift increases with the decrease of SiH4 flow rate for SiOx and SiNx capping layers. The blue shift of the PL peak energy increases greatly with the increase of deposition pressure and slightly with the decrease of deposition temperature. The influence of rf power was found to be negligible. All these dependences are related to the porosity in the dielectric capping layers in the QW intermixing. We fabricated the wavelength shifted ridge-waveguide InGaAs/GaAs MQW lasers with 967, 946 and 927 nm emission wavelengths that have undergone IFVD using SiO2 capping layers at different annealing temperatures of 850, 900 and 950 °C, respectively. Also, multi-wavelength InGaAs/GaAs MQW lasers by the area-selective IFVD using different stoichiometric SiOx capping layers were studied. The lasing wavelength difference of about 31 nm is obtained between the ridge-waveguide laser diodes fabricated with the MQWs that had undergone the same thermal treatments using the SiOx film provided with SiH4 flow rates of 20 and 300 sccm.

  3. HYDROGEN VACANCY INTERACTION IN TUNGSTEN

    NARCIS (Netherlands)

    FRANSENS, [No Value; ELKERIEM, MSA; PLEITER, F

    1991-01-01

    Hydrogen-vacancy interaction in tungsten was investigated by means of the perturbed angular correlation technique, using the isotope In-111 as a probe. Hydrogen trapping at an In-111-vacancy cluster manifests itself as a change of the local electric field gradient, which gives rise to an observable

  4. Determinants of Glycosaminoglycan (GAG Structure

    Directory of Open Access Journals (Sweden)

    Kristian Prydz

    2015-08-01

    Full Text Available Proteoglycans (PGs are glycosylated proteins of biological importance at cell surfaces, in the extracellular matrix, and in the circulation. PGs are produced and modified by glycosaminoglycan (GAG chains in the secretory pathway of animal cells. The most common GAG attachment site is a serine residue followed by a glycine (-ser-gly-, from which a linker tetrasaccharide extends and may continue as a heparan sulfate, a heparin, a chondroitin sulfate, or a dermatan sulfate GAG chain. Which type of GAG chain becomes attached to the linker tetrasaccharide is influenced by the structure of the protein core, modifications occurring to the linker tetrasaccharide itself, and the biochemical environment of the Golgi apparatus, where GAG polymerization and modification by sulfation and epimerization take place. The same cell type may produce different GAG chains that vary, depending on the extent of epimerization and sulfation. However, it is not known to what extent these differences are caused by compartmental segregation of protein cores en route through the secretory pathway or by differential recruitment of modifying enzymes during synthesis of different PGs. The topic of this review is how different aspects of protein structure, cellular biochemistry, and compartmentalization may influence GAG synthesis.

  5. Vacancy-Mediated Processes in the Oxidation of CO on PdO(101).

    Science.gov (United States)

    Weaver, Jason F; Zhang, Feng; Pan, Li; Li, Tao; Asthagiri, Aravind

    2015-05-19

    Metal oxide films can form on late transition-metal catalysts under sufficiently oxygen-rich conditions, and typically cause significant changes in the catalytic performance of these materials. Several investigations using sensitive in situ surface characterization techniques reveal that the CO oxidation activity of Pd and other late transition-metal catalysts increases abruptly under conditions at which metal oxide structures begin to develop. Findings such as these provide strong motivation for developing atomic-scale descriptions of oxidation catalysis over oxide films of the late transition-metals. Surface oxygen vacancies can play a central role in mediating oxidation catalysis promoted by metal oxides. In general, adsorbed reactants abstract oxygen atoms from the lattice of the oxide surface, thereby creating oxygen vacancies, while gaseous O2 replenishes the reactive surface oxygen atoms and eliminates oxygen vacancies. Oxygen vacancies also represent a distinct type of surface site on which the binding and reactivity of adsorbed species can differ compared with sites on the pristine oxide surface. Detailed characterization of vacancy-mediated rate processes is thus essential for developing reliable mechanistic descriptions of oxidation catalysis over reducible metal oxide films. Careful measurements performed in ultrahigh vacuum (UHV) using well-defined oxide surfaces in combination with molecular simulations afford the capability to isolate and characterize such reaction steps, and thus provide information that is needed for developing mechanistic models of oxidation catalysis over metal oxides. In this Account, we discuss vacancy-mediated processes that are involved in the oxidation of CO on the PdO(101) surface as determined from UHV surface science experiments and density functional theory (DFT) calculations. These studies show that CO binds strongly on Pd atoms that are located next to surface oxygen vacancies, and diffuses rapidly to these sites

  6. Surface structure determines dynamic wetting

    Science.gov (United States)

    Shiomi, Junichiro; Wang, Jiayu; Do-Quang, Minh; Cannon, James; Yue, Feng; Suzuki, Yuji; Amberg, Gustav

    2014-11-01

    Dynamic wetting, the spontaneous spreading process after droplet contacts a solid surface, is important in various engineering processes, such as in printing, coating, and lubrication. In the recent years, experiments and numerical simulations have greatly progressed the understanding in the dynamic wetting particularly on ``flat'' substrates. To gain further insight into the governing physics of the dynamic wetting, we perform droplet-wetting experiments on microstructured surfaces, just a few micrometers in size, with complementary numerical simulations, and investigate the dependence of the spreading rate on the microstructure geometries and fluid properties. We reveal that the influence of microstructures can be quantified in terms of a line friction coefficient for the energy dissipation rate at the contact line, and that this can be described in a simple formula in terms of the geometrical parameters of the roughness and the line-friction coefficient of the planar surface. The systematic study is also of practical importance since structures and roughness are omnipresent and their influence on spreading rate would give us additional degrees of freedom to control the dynamic wetting. This work was financially supported in part by, the Japan Society for the Promotion of Science (J.W., J.C., and J.S) and Swedish Governmental Agency for Innovation Systems (M.D.-Q. and G.A.).

  7. Vacancy-indium clusters in implanted germanium

    KAUST Repository

    Chroneos, Alexander I.

    2010-04-01

    Secondary ion mass spectroscopy measurements of heavily indium doped germanium samples revealed that a significant proportion of the indium dose is immobile. Using electronic structure calculations we address the possibility of indium clustering with point defects by predicting the stability of indium-vacancy clusters, InnVm. We find that the formation of large clusters is energetically favorable, which can explain the immobility of the indium ions. © 2010 Elsevier B.V. All rights reserved.

  8. Concurrent La and A-Site Vacancy Doping Modulates the Thermoelectric Response of SrTiO3: Experimental and Computational Evidence.

    Science.gov (United States)

    Azough, Feridoon; Jackson, Samuel S; Ekren, Dursun; Freer, Robert; Molinari, Marco; Yeandel, Stephen R; Panchmatia, Pooja M; Parker, Stephen C; Maldonado, David Hernandez; Kepaptsoglou, Demie M; Ramasse, Quentin M

    2017-12-06

    To help understand the factors controlling the performance of one of the most promising n-type oxide thermoelectric SrTiO3, we need to explore structural control at the atomic level. In Sr1-xLa2x/3TiO3 ceramics (0.0 ≤ x ≤ 0.9), we determined that the thermal conductivity can be reduced and controlled through an interplay of La-substitution and A-site vacancies and the formation of a layered structure. The decrease in thermal conductivity with La and A-site vacancy substitution dominates the trend in the overall thermoelectric response. The maximum dimensionless figure of merit is 0.27 at 1070 K for composition x = 0.50 where half of the A-sites are occupied with La and vacancies. Atomic resolution Z-contrast imaging and atomic scale chemical analysis show that as the La content increases, A-site vacancies initially distribute randomly (x site vacancies contributes to a nonuniform distribution of atomic scale features. This combination induces temperature stable behavior in the material and reduces thermal conductivity, an important route to enhancement of the thermoelectric performance. A computational study confirmed that the thermal conductivity of SrTiO3 is lowered by the introduction of La and A-site vacancies as shown by the experiments. The modeling supports that a critical mass of A-site vacancies is needed to reduce thermal conductivity and that the arrangement of La, Sr, and A-site vacancies has a significant impact on thermal conductivity only at high La concentration.

  9. Mesoscale modeling of vacancy-mediated Si segregation near an edge dislocation in Ni under irradiation

    Science.gov (United States)

    Li, Zebo; Trinkle, Dallas R.

    2017-04-01

    We use a continuum method informed by transport coefficients computed using self-consistent mean field theory to model vacancy-mediated diffusion of substitutional Si solutes in FCC Ni near an a/2 [1 1 ¯0 ] (111 ) edge dislocation. We perform two sequential simulations: first under equilibrium boundary conditions and then under irradiation. The strain field around the dislocation induces heterogeneity and anisotropy in the defect transport properties and determines the steady-state vacancy and Si distributions. At equilibrium both vacancies and Si solutes diffuse to form Cottrell atmospheres with vacancies accumulating in the compressive region above the dislocation core while Si segregates to the tensile region below the core. Irradiation raises the bulk vacancy concentration, driving vacancies to flow into the dislocation core. The out-of-equilibrium vacancy fluxes drag Si atoms towards the core, causing segregation to the compressive region, despite Si being an oversized solute in Ni.

  10. Effects of Ga substitution for Al and cation vacancy on microwave dielectric properties of spinel-structured Co1-3 z (Al1- x Ga x )2+ z O4 ceramics

    Science.gov (United States)

    Okazaki, Hiroto; Takahashi, Susumu; Kan, Akinori; Ogawa, Hirotaka

    2017-10-01

    The microwave dielectric properties and cation distribution of spinel-structured Co1-3 z (Al1- x Ga x )2+ z O4 (z = 0-0.25) ceramics, where z represents the concentration of the cation vacancy, were characterized in this study. Ga substitution for Al in the Co(Al1- x Ga x )2O4 ceramics was effective in increasing the quality factor (Q · f) values from 27,000 to 103,000 GHz, making the Co2+, Al3+, and Ga3+ cations randomly occupy both the tetrahedral and octahedral sites to form an intermediate spinel. A similar result was also obtained by the introduction of the cation vacancy for the Co1-3 z Al2+ z O4 (x = 0) ceramic and the highest Q · f value of 120,000 GHz was obtained for z = 0.25 at which the degree of inversion, y, was estimated to be 0.5 from 27Al NMR spectra. Further improvement in Q · f value was achieved by the introduction of cation vacancy and Ga substitution for Al in Co0.25(Al1- x Ga x )2.5O4 ceramics. 71Ga NMR spectra showed that Ga3+ cations occupied both the tetrahedral and octahedral sites, while a single peak was observed from 27Al NMR spectra, implying that Al3+ cations occupied only the octahedral site. The preferential site occupancy of Al in the an octahedral site led to the formation of ordered spinel structure with the space group P4332 and the Q · f value of the Co0.25(Al0.4Ga0.6)2.5O4 (z = 0.25 and x = 0.6) ceramic was 170,000 GHz.

  11. Ordering of vacancies on Si(001)

    NARCIS (Netherlands)

    Zandvliet, Henricus J.W.

    1997-01-01

    Missing dimer vacancies are always present on the clean Si(001) surface. The vacancy density can be increased by ion bombardment (Xe+, Ar+), etching (O2, Br2, I2, etc.) or Ni contamination. The equilibrium shape at low vacancy concentrations (<0.2¿0.3 monolayers) of these vacancy islands is

  12. Non-classical behaviour of higher valence dopants in chromium (III) oxide by a Cr vacancy compensation mechanism

    Science.gov (United States)

    Carey, John J.; Nolan, Michael

    2017-10-01

    Modification of metal oxides with dopants that have a stable oxidation in their parent oxides which is higher than the host system is expected to introduce extra electrons into the material to improve carrier mobility. This is essential for applications in catalysis, SOFCs and solar energy materials. Density functional theory calculations are used to investigate the change in electronic and geometric structure of chromium (III) oxide by higher valence dopants, namely; Ce, Ti, V and Zr. For single metal doping, we find that the dopants with variable oxidation states, Ce, Ti and V, adopt a valence state of  +3, while Zr dopant has a  +4 oxidation state and reduces a neighbouring Cr cation. Chromium vacancy formation is greatly enhanced for all dopants, and favoured over oxygen vacancy formation. The Cr vacancies generate holes which oxidise Ce, Ti and V from  +3 to  +4, while also oxidising lattice oxygen sites. For Zr doping, the generated holes oxidise the reduced Cr2+ cation back to Cr3+ and also two lattice oxygen atoms. Three metal atoms in the bulk lattice facilitate spontaneous Cr vacancy from charge compensation. A non-classical compensation mechanism is observed for Ce, Ti and V; all three metals are oxidised from  +3 to  +4, which explains experimental observations that these metals have a  +4 oxidation state in Cr2O3. Charge compensation of the three Zr metals proceeds by a classical higher valence doping mechanism; the three dopants reduce three Cr cations, which are subsequently charge compensated by a Cr vacancy oxidising three Cr2+ to Cr3+. The compensated structures are the correct ground state electronic structure for these doped systems, and used as a platform to investigate cation/anion vacancy formation. Unlike the single metal doped bulks, preference is now given for oxygen vacancy formation over Cr vacancy formation, indicating that the dopants increase the reducibility of Cr2O3 with Ce doping showing the strongest

  13. Determining and visualizing flexibility in protein structures.

    Science.gov (United States)

    Scott, Walter R P; Straus, Suzana K

    2015-05-01

    How to compare the structures of an ensemble of protein conformations is a fundamental problem in structural biology. As has been previously observed, the widely used RMSD measure due to Kabsch, in which a rigid-body superposition minimizing the least-squares positional deviations is performed, has its drawbacks when comparing and visualizing a set of flexible protein structures. Here, we develop a method, fleximatch, of protein structure comparison that takes flexibility into account. Based on a distance matrix measure of flexibility, a weighted superposition of distance matrices rather than of atomic coordinates is performed. Subsequently, this allows a consistent determination of (a) a superposition of structures for visualization, (b) a partitioning of the protein structure into rigid molecular components (core atoms), and (c) an atomic mobility measure. The method is suitable for highlighting both particularly flexible and rigid parts of a protein from structures derived from NMR, X-ray diffraction or molecular simulation. © 2015 Wiley Periodicals, Inc.

  14. Characterisation and modelling of vacancy dynamics in Ni–Mn–Ga ferromagnetic shape memory alloys

    Energy Technology Data Exchange (ETDEWEB)

    Merida, D., E-mail: david.merida@ehu.es [Fisika Aplikatua II Saila, Euskal Herriko Unibertsitatea UPV/EHU, p.k. 644, 48080 Bilbao (Spain); Elektrizitate eta Elektronika Saila, Euskal Herriko Unibertsitatea UPV/EHU, p.k. 644, 48080 Bilbao (Spain); García, J.A. [Fisika Aplikatua II Saila, Euskal Herriko Unibertsitatea UPV/EHU, p.k. 644, 48080 Bilbao (Spain); BC Materials (Basque Centre for Materials, Application and Nanostructures), 48040 Leioa (Spain); Sánchez-Alarcos, V. [Departamento de Física, Universidad Pública de Navarra, Campus de Arrosadia, 31006 Pamplona (Spain); Pérez-Landazábal, J.I.; Recarte, V. [Departamento de Física, Universidad Pública de Navarra, Campus de Arrosadia, 31006 Pamplona (Spain); Institute for Advanced Materials (INAMAT), Universidad Pública de Navarra, Campus de Arrosadía, 31006 Pamplona (Spain); Plazaola, F. [Elektrizitate eta Elektronika Saila, Euskal Herriko Unibertsitatea UPV/EHU, p.k. 644, 48080 Bilbao (Spain)

    2015-08-05

    Highlights: • We study the dynamics of vacancies for three different Ni–Mn–Ga alloy samples. • The formation and migration energies have been obtained experimentally. • The entropic factor and the distance a vacancy has to reach a sink are measured. • We present a theoretical model to explain the dynamics of vacancies. • Results are applicable for any thermal treatment and extensible to other alloys. - Abstract: The dynamics of vacancies in Ni–Mn–Ga shape memory alloys has been studied by positron annihilation lifetime spectroscopy. The temperature evolution of the vacancy concentration for three different Ni–Mn–Ga samples, two polycrystalline and one monocrystalline, have been determined. The formation and migration energies and the entropic factors are quite similar in all cases, but vary slightly according to composition. However, the number of jumps a vacancy has to overtake to reach a sink is five times higher in the single crystal. This is an expected result, due to the role that surfaces and grain boundaries should play in balancing the vacancy concentration. In all cases, the initial vacancy concentration for the samples quenched from 1173 K lies between 1000 ppm and 2000 ppm. A phenomenological model able to explain the dynamics of vacancies has been developed in terms of the previous parameters. The model can reproduce the vacancy dynamics for any different kind of thermal history and can be easily extended to other alloys.

  15. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes...... chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure...... is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

  16. Capital Structure Determinants and Governance Structure Variety in Franchising

    NARCIS (Netherlands)

    T. Jiang (Tao)

    2009-01-01

    textabstractThis thesis investigates two questions: the determinants of capital structure in franchising and its subsequent impact on the franchise financing decisions; and the efficient governance structure choice in franchising. We posit that firms franchise in order to benefit from the reduced

  17. Evaluating protein structures determined by structural genomics consortia.

    Science.gov (United States)

    Bhattacharya, Aneerban; Tejero, Roberto; Montelione, Gaetano T

    2007-03-01

    Structural genomics projects are providing large quantities of new 3D structural data for proteins. To monitor the quality of these data, we have developed the protein structure validation software suite (PSVS), for assessment of protein structures generated by NMR or X-ray crystallographic methods. PSVS is broadly applicable for structure quality assessment in structural biology projects. The software integrates under a single interface analyses from several widely-used structure quality evaluation tools, including PROCHECK (Laskowski et al., J Appl Crystallog 1993;26:283-291), MolProbity (Lovell et al., Proteins 2003;50:437-450), Verify3D (Luthy et al., Nature 1992;356:83-85), ProsaII (Sippl, Proteins 1993;17: 355-362), the PDB validation software, and various structure-validation tools developed in our own laboratory. PSVS provides standard constraint analyses, statistics on goodness-of-fit between structures and experimental data, and knowledge-based structure quality scores in standardized format suitable for database integration. The analysis provides both global and site-specific measures of protein structure quality. Global quality measures are reported as Z scores, based on calibration with a set of high-resolution X-ray crystal structures. PSVS is particularly useful in assessing protein structures determined by NMR methods, but is also valuable for assessing X-ray crystal structures or homology models. Using these tools, we assessed protein structures generated by the Northeast Structural Genomics Consortium and other international structural genomics projects, over a 5-year period. Protein structures produced from structural genomics projects exhibit quality score distributions similar to those of structures produced in traditional structural biology projects during the same time period. However, while some NMR structures have structure quality scores similar to those seen in higher-resolution X-ray crystal structures, the majority of NMR structures

  18. Membrane protein structure determination in membrana.

    Science.gov (United States)

    Ding, Yi; Yao, Yong; Marassi, Francesca M

    2013-09-17

    The two principal components of biological membranes, the lipid bilayer and the proteins integrated within it, have coevolved for specific functions that mediate the interactions of cells with their environment. Molecular structures can provide very significant insights about protein function. In the case of membrane proteins, the physical and chemical properties of lipids and proteins are highly interdependent; therefore structure determination should include the membrane environment. Considering the membrane alongside the protein eliminates the possibility that crystal contacts or detergent molecules could distort protein structure, dynamics, and function and enables ligand binding studies to be performed in a natural setting. Solid-state NMR spectroscopy is compatible with three-dimensional structure determination of membrane proteins in phospholipid bilayer membranes under physiological conditions and has played an important role in elucidating the physical and chemical properties of biological membranes, providing key information about the structure and dynamics of the phospholipid components. Recently, developments in the recombinant expression of membrane proteins, sample preparation, pulse sequences for high-resolution spectroscopy, radio frequency probes, high-field magnets, and computational methods have enabled a number of membrane protein structures to be determined in lipid bilayer membranes. In this Account, we illustrate solid-state NMR methods with examples from two bacterial outer membrane proteins (OmpX and Ail) that form integral membrane β-barrels. The ability to measure orientation-dependent frequencies in the solid-state NMR spectra of membrane-embedded proteins provides the foundation for a powerful approach to structure determination based primarily on orientation restraints. Orientation restraints are particularly useful for NMR structural studies of membrane proteins because they provide information about both three-dimensional structure

  19. Numerical Modeling of the Stability of Face-Centered Cubic Metals with High Vacancy Concentration

    Energy Technology Data Exchange (ETDEWEB)

    Brian P. Somerday; M. I. Baskes

    1998-12-01

    The objective of this research is to assess the possibility of forming an atomically porous structure in a low-density metal, e.g., Al with vacancies up to 0.20/lattice site; and to examine the effects of hydrogen and vacancy concentration on the stability of an atomically porous structure that has been experimentally produced in nickel. The approach involves numerical modeling using the Embedded-Atom Method (EAM). High vacancy concentrations cause the Al lattice to disorder at 300K. In contrast, Ni retains the face-centered-cubic structure at 300K for vacancy concentrations up to 0.15 Vac/lattice site. Unexpectedly, the lattice with 0.15 Vac/lattice site is more stable than the lattice with 0.10 or 0.20 Vac/lattice site. The Ni systems with 0.10 and 0.15 Vac/lattice site exhibit domains consisting of uniform lattice rotations. The Ni lattice with 0.15 Vac/lattice site is more stable with an initial distribution of random vacancies compared to ordered vacancies. The equilibrium lattice structures of Ni a d Al containing vacancies and H are less ordered to structures with vacancies only at 300K.

  20. Science achievement determinants: factorial structure of family ...

    African Journals Online (AJOL)

    Personality and Social Psychology. Bulletin. 19:474-480. Wetchler JL 1990. Family treatment of a fifteen year old social isolate. Journal of. Family Psychotherapy, 1:29-38. Science achievement determinants: factorial structure of family variables. Elias Oupa Mashile. Faculty of Education, University of South Africa, P.O. Box ...

  1. Representing Personal Determinants in Causal Structures.

    Science.gov (United States)

    Bandura, Albert

    1984-01-01

    Responds to Staddon's critique of the author's earlier article and addresses issues raised by Staddon's (1984) alternative models of causality. The author argues that it is not the formalizability of causal processes that is the issue but whether cognitive determinants of behavior are reducible to past stimulus inputs in causal structures.…

  2. Method of fan sound mode structure determination

    Science.gov (United States)

    Pickett, G. F.; Sofrin, T. G.; Wells, R. W.

    1977-01-01

    A method for the determination of fan sound mode structure in the Inlet of turbofan engines using in-duct acoustic pressure measurements is presented. The method is based on the simultaneous solution of a set of equations whose unknowns are modal amplitude and phase. A computer program for the solution of the equation set was developed. An additional computer program was developed which calculates microphone locations the use of which results in an equation set that does not give rise to numerical instabilities. In addition to the development of a method for determination of coherent modal structure, experimental and analytical approaches are developed for the determination of the amplitude frequency spectrum of randomly generated sound models for use in narrow annulus ducts. Two approaches are defined: one based on the use of cross-spectral techniques and the other based on the use of an array of microphones.

  3. HYDROGEN VACANCY INTERACTION IN MOLYBDENUM

    NARCIS (Netherlands)

    Abd El Keriem, M.S.; van der Werf, D.P.; Pleiter, F

    1993-01-01

    Vacancy-hydrogen interaction in molybdenum was investigated by means of the perturbed angular correlation technique, using the isotope In-111 as a probe. The complex InV2 turned out to trap up to two hydrogen atoms: trapping of a single hydrogen atom gives rise to a decrease of the quadrupole

  4. Determination of DNA structural detail using radioprobing.

    Science.gov (United States)

    Girard, Peter M; Laughton, Charles; Nikjoo, Hooshang

    2012-01-01

    To put radioprobing into context as a relatively new method of determining structural detail in deoxyribonucleic acid (DNA), and to review its use since first proposed in 1997. The key feature of the method is that, by experiment or simulation, a radionuclide such as iodine-125 ((125)I) is placed near the DNA at a known point relative to the DNA base sequence, and the number of resulting strand breaks in each nucleotide is determined. As the intensity of damage declines consistently with distance from the radionuclide, relative distances between the emitter and the nucleotides can be deduced, and hence potentially the topology or structural detail of the DNA. For simulation, appropriate software includes a Molecular Dynamics package, analysis and visualization tools, and a Monte Carlo track structure program. A review of published work and our own recent unpublished studies have shown that radioprobing is sufficiently sensitive and consistent to determine structural detail such as internal folding topology and flexing behavior, and can be applied to DNA or a DNA-protein complex in an approximation to its normal biological environment.

  5. Relaxation of vacancy depth profiles in silicon wafers: A low apparent diffusivity of vacancy species

    OpenAIRE

    Voronkov, Vladimir V.; Falster, Robert; Pichler, Peter

    2014-01-01

    Vacancy depth profiles in silicon wafersinstalled by Rapid Thermal Annealing and monitored by Pt diffusionshow, upon subsequent annealing at 975 or 950 °C, a peculiar evolution: the concentration profile goes down without any trace of vacancy out-diffusion. The estimated apparent diffusivity is less than 1E7 cm2/s at 975 °C. The monitored vacancy species is tentatively identified as a "slow vacancy" that was recently concluded to exist along with other (highly mobile) vacancy species.

  6. Vacancies in functional materials for clean energy storage and harvesting : the perfect imperfection

    NARCIS (Netherlands)

    Li, Guowei; Blake, Graeme R; Palstra, Thomas T M

    2017-01-01

    Vacancies exist throughout nature and determine the physical properties of materials. By manipulating the density and distribution of vacancies, it is possible to influence their physical properties such as band-gap, conductivity, magnetism, etc. This can generate exciting applications in the fields

  7. Vacancies and defect levels in III–V semiconductors

    KAUST Repository

    Tahini, H. A.

    2013-08-13

    Using electronic structure calculations, we systematically investigate the formation of vacancies in III-V semiconductors (III = Al, Ga, and In and V = P, As, and Sb), for a range of charges ( −3≤q≤3 ) as a function of the Fermi level and under different growth conditions. The formation energies were corrected using the scheme due to Freysoldt et al. [Phys. Rev. Lett. 102, 016402 (2009)] to account for finite size effects. Vacancy formation energies were found to decrease as the size of the group V atom increased. This trend was maintained for Al-V, Ga-V, and In-V compounds. The negative-U effect was only observed for the arsenic vacancy in GaAs, which makes a charge state transition from +1 to –1. It is also found that even under group III rich conditions, group III vacancies dominate in AlSb and GaSb. For InSb, group V vacancies are favoured even under group V rich conditions.

  8. Simultaneous determination of protein structure and dynamics

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.

    2005-01-01

    at the atomic level about the structural and dynamical features of proteins-with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout......We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information...... the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant...

  9. Using a spherical crystallite model with vacancies to relate local atomic structure to irradiation defects in ZrC and ZrN

    Energy Technology Data Exchange (ETDEWEB)

    Olive, Daniel T.; Ganegoda, Hasitha [Department of Physics, Illinois Institute of Technology, Chicago, IL 60616 (United States); Allen, Todd [Department of Engineering Physics, University of Wisconsin-Madison, WI 53706 (United States); Yang, Yong [Nuclear Engineering Program, University of Florida, Gainsville, FL 32611 (United States); Dickerson, Clayton [Material Science Program, University of Wisconsin-Madison, WI 53706 (United States); Terry, Jeff, E-mail: terryj@iit.edu [Department of Physics, Illinois Institute of Technology, Chicago, IL 60616 (United States)

    2016-07-15

    Zirconium carbide and zirconium nitride are candidate materials for new fuel applications due to several favorable physicochemical properties. ZrC and ZrN samples were irradiated at the Advanced Test Reactor National Scientific User Facility with neutrons at 800 °C to a dose of 1 dpa. Structural examinations have been made of the ZrC samples using high resolution transmission electron microscopy, and the findings compared with a previous study of ZrC irradiated with protons at 800 °C. The use of X-ray absorption fine structure spectroscopy (XAFS) to characterize the radiation damage was also explored including a model based on spherical crystallites that can be used to relate EXAFS measurements to microscopy observations. A loss of coordination at more distant coordination shells was observed for both ZrC and ZrN, and a model using small spherical crystallites suggested this technique can be used to study dislocation densities in future studies of irradiated materials. - Highlights: • ZrC and ZrN were irradiated at the ATR NSUF reactor to 1 dpa at 800 °C. • Dislocation loop size and density determined with TEM. • Defects in ZrC are similar to proton irradiated ZrC under similar conditions. • EXAFS modeling of radiation damage using a spherical crystallite model.

  10. Interaction of oxygen vacancies in yttrium germanates

    KAUST Repository

    Wang, Hao

    2012-01-01

    Forming a good Ge/dielectric interface is important to improve the electron mobility of a Ge metal oxide semiconductor field-effect transistor. A thin yttrium germanate capping layer can improve the properties of the Ge/GeO 2 system. We employ electronic structure calculations to investigate the effect of oxygen vacancies in yttrium-doped GeO 2 and the yttrium germanates Y 2Ge 2O 7 and Y 2GeO 5. The calculated densities of states indicate that dangling bonds from oxygen vacancies introduce in-gap states, but the system remains insulating. However, yttrium-doped GeO 2 becomes metallic under oxygen deficiency. Y-doped GeO 2, Y 2Ge 2O 7 and Y 2GeO 5 are calculated to be oxygen substoichiometric under low Fermi energy conditions. The use of yttrium germanates is proposed as a way to effectively passivate the Ge/dielectric interface. This journal is © 2012 the Owner Societies.

  11. Interaction of carbon–vacancy complex with minor alloying elements of ferritic steels

    Energy Technology Data Exchange (ETDEWEB)

    Bakaev, A., E-mail: abakaev@sckcen.be [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, Mol B2400 (Belgium); Center for Molecular Modeling, Department of Physics and Astronomy, Ghent University, Technologiepark 903, 9052 Zwijnaarde (Belgium); Department of Experimental Nuclear Physics K-89, Institute of Physics, Nanotechnology and Telecommunications, St. Petersburg State Polytechnical University, 29 Polytekhnicheskaya Str., 195251 St. Petersburg (Russian Federation); Terentyev, D. [SCK-CEN, Nuclear Materials Science Institute, Boeretang 200, Mol B2400 (Belgium); He, X. [China Institute of Atomic Energy, P.O. Box 275-51, 102413 Beijing (China); Zhurkin, E.E. [Department of Experimental Nuclear Physics K-89, Institute of Physics, Nanotechnology and Telecommunications, St. Petersburg State Polytechnical University, 29 Polytekhnicheskaya Str., 195251 St. Petersburg (Russian Federation); Van Neck, D. [Center for Molecular Modeling, Department of Physics and Astronomy, Ghent University, Technologiepark 903, 9052 Zwijnaarde (Belgium)

    2014-08-01

    Interstitial carbon, dissolved in bcc matrix of ferritic steels, plays an important role in the evolution of radiation-induced microstructure since it exhibits strong interaction with vacancies. Frequent formation and break-up of carbon–vacancy pairs, occurring in the course of irradiation, affect both kinetics of the accumulation of point defect clusters and carbon spatial distribution. The interaction of typical alloying elements (Mn, Ni, Cu, Si, Cr and P) in ferritic steels used as structural materials in nuclear reactors with a carbon–vacancy complex is analyzed using ab initio techniques. It is found that all the considered solutes form stable triple clusters resulting in the increase of the total binding energy by 0.2–0.3 eV. As a result of the formation of energetically favourable solute–carbon–vacancy triplets, the dissociation energy for vacancy/carbon emission is also increased by ∼0.2–0.3 eV, suggesting that the solutes enhance thermal stability of carbon–vacancy complex. Association of carbon–vacancy pairs with multiple solute clusters is found to be favorable for Ni, Cu and P. The energetic stability of solute(s)–carbon–vacancy complexes was rationalized on the basis of pairwise interaction data and by analyzing the variation of local magnetic moments on atoms constituting the clusters.

  12. Tailored cellulose esters: synthesis and structure determination.

    Science.gov (United States)

    Liebert, Tim F; Heinze, Thomas

    2005-01-01

    A broad variety of cellulose esters with complex and sensitive (against hydrolysis and light) structures was synthesized homogeneously in N,N-dimethylacetamide (DMAc)/LiCl and in the new solvent dimethyl sulfoxide (DMSO)/tetrabutylammonium fluoride (TBAF) via in situ activation of the carboxylic acids with N,N'-carbonyldiimidazole (CDI). New esters of chiral (-)-menthyloxyacetic acid, of unsaturated 3-(2-furyl)-acrylcarboxylic- and furane-2-carboxylic acid, acids with crownether moieties (4'-carboxybenzo-18-crown-6), and with carboxymethyl-beta-cyclodextrin were accessible in a one-pot reaction. Because of the mild conditions and the efficiency of the reaction via imidazolides, very pure and highly functionalized cellulose derivatives were obtained up to a degree of substitution of 2.5 possessing a degree of polymerization in the range of the starting cellulose. Structure determination was carried out by different one- and two-dimensional NMR techniques confirming the high purity of the esters and a pronounced regioselectivity for the primary OH function. The structural features, the purity, the solubility, and the film forming properties, make these materials desired products for the preparation of membranes with tailored separation characteristics.

  13. Electronic and optical properties of vacancy-doped WS2 monolayers

    Directory of Open Access Journals (Sweden)

    Jian-wei Wei

    2012-12-01

    Full Text Available Monolayers of tungsten disulfide doped with atomic vacancies have been investigated for the first time by density functional theory calculations. The results reveal that the atomic vacancy defects affect the electronic and optical properties of the tungsten disulfide monolayers. The strongly ionic character of the W-S bonds and the non-bonding electrons of the vacancy defects result in spin polarization near the defects. Moreover, the spin polarization of single W atomic vacancies has a larger range than for one or two S atomic vacancies. In particular, increased intensity of absorption and red shift of optical absorption are universally observed in the presence of these atomic defects, which are shown to be a fundamental factor in determining the spin transport and optical absorption of tungsten disulfide monolayers.

  14. Switch 'on' and 'off' ferromagnetic ordering through the induction and removal of oxygen vacancies and carriers in doped ZnO: A magnetization and electronic structure study

    Energy Technology Data Exchange (ETDEWEB)

    Singhal, R.K.; Samariya, A.; Dolia, S.N. [Department of Physics, University of Rajasthan, Jaipur 302004 (India); Kumar, S. [Department of Physics, ML Sukhadia University, Udaipur 313002 (India); Xing, Y.T.; Saitovitch, Elisa B. [CBPF, Rua Dr. Xavier Sigaud 150, Rio de Janeiro (Brazil); Deshpande, U.P.; Shripathi, T. [UGC-DAE CSR, University Campus, Indore 452001 (India)

    2010-10-15

    The electronic structure and magnetic properties of cobalt-doped (7.5%) and manganese co-doped (2.5%) ZnO polycrystalline samples have been investigated to understand the mechanism of room temperature ferromagnetism (RTFM) in dilute magnetic semiconductors. The samples in powder form were annealed in argon and hydrogen atmospheres followed by their repressing into pellets and reheating in air. Rietveld analysis of X-ray diffraction patterns confirmed the single-phase nature of the samples in the wurtzite type hexagonal (P6{sub 3}mc) ZnO structure. The X-ray photoelectron spectroscopy (XPS) results indicate that the Co and Mn atoms are in +2 oxidation states, which incorporate at the Zn{sup 2+} site, with no signature of metallic clusters. The Co-doped sample prepared in air displays a paramagnetic state while the sample annealed in Ar atmosphere shows a weak ferromagnetic ordering at 300 K. The co-doping of Mn further enhances the ferromagnetic ordering, indicating that Co and Mn ions play an additive role in inducing the ferromagnetic ordering in the ZnO matrix. Interestingly, the Co- and (Co+Mn)-doped ZnO samples annealed in hydrogen atmosphere show a huge increment in the magnetic moment, however, the Mn ions seem to stay passive towards the hydrogen induced magnetization. Notably, the samples reheated in air show suppression of the induced ferromagnetism (FM). The resistance measurements suggest that the additional carriers induced upon hydrogenation also play some role in mediating the exchange coupling. The O 1s XPS and the XRD results show clear evidence of oxygen depletion in the samples upon hydrogenation, followed by a recovery upon their reheating in air. The observed FM is explained in terms of composite effect of the oxygen vacancies and the carrier density. Our results point out that the ferromagnetic ordering could be switched between 'on' and 'off' by introducing (through hydrogenation) and by removing (through reheating in air

  15. Icosahedral Quasicrystal Structure Determination: Aluminum-Copper

    Science.gov (United States)

    Qiu, Shi-Yue

    This dissertation reports the theoretical study of the determination of quasicrystal atomic structures. A new method is developed for phasing the quasicrystal diffraction data (neutron, X-ray diffraction). A mathematical model is built which explicitly relates quasicrystals to their related periodic crystals. A test of the method is made on a simple theoretical system, the icosahedral quasiperiodic Ammann tiling decorated with point scatterers (Dirac delta scattering potential) on vertices. A success is achieved in reconstructing the phases of the quasicrystal. The method is applied to a real quasicrystal system, the icosahedral quasicrystal i(Al_{.570 }Cu_{.108}Li _{.322}), where single -grain X-ray as well as neutron diffraction data are available, and the structure of the related large-unit-cell crystal of R(Al_{.564}Cu _{.116}Li_{.320 }), is well known. The reconstructed phases give the density of scatterers, which can then be used in the analysis of the atomic structure, and provide a guide to the final structure modeling. The validity of the method is evaluated with respect to the non-negativity of the resulting electron densities. In order to identify the negativity due to the intensity cut -off, the negativity is evaluated as a function of the cut -off and compared with the exact and reconstructed quasiperiodic Ammann tilings as well as with the experimental and model crystal data of R(Al_{.564}Cu _{.116}Li_ {.320}). It is concluded that the negativity of the reconstructed quasiperiodic electron density of i(Al_{.570}Cu _{.108}Li_{.322 }) is consistent with a cut-off effect. Modeling of the i(Al_{.570 }Cu_{.108}Li _{.322}) atomic structure in six-dimensional hyperspace is discussed. It is assumed that atomic surfaces can be modeled by polyhedra which can be described by a finite number of parameters. Under the conditions that the structure model should produce right density, stoichiometry, no unphysically short interatomic distances, we successfully

  16. Image-Based Chemical Structure Determination.

    Science.gov (United States)

    Ofner, Johannes; Brenner, Florian; Wieland, Karin; Eitenberger, Elisabeth; Kirschner, Johannes; Eisenmenger-Sittner, Christoph; Török, Szilvia; Döme, Balazs; Konegger, Thomas; Kasper-Giebl, Anne; Hutter, Herbert; Friedbacher, Gernot; Lendl, Bernhard; Lohninger, Hans

    2017-07-28

    Chemical imaging is a powerful tool for understanding the chemical composition and nature of heterogeneous samples. Recent developments in elemental, vibrational, and mass-spectrometric chemical imaging with high spatial resolution (50-200 nm) and reasonable timescale (a few hours) are capable of providing complementary chemical information about various samples. However, a single technique is insufficient to provide a comprehensive understanding of chemically complex materials. For bulk samples, the combination of different analytical methods and the application of statistical methods for extracting correlated information across different techniques is a well-established and powerful concept. However, combined multivariate analytics of chemical images obtained via different imaging techniques is still in its infancy, hampered by a lack of analytical methodologies for data fusion and analysis. This study demonstrates the application of multivariate statistics to chemical images taken from the same sample via various methods to assist in chemical structure determination.

  17. Structure determination by X-ray crystallography

    CERN Document Server

    Ladd, M F C

    1977-01-01

    Crystallography may be described as the science of the structure of materi­ als, using this word in its widest sense, and its ramifications are apparent over a broad front of current scientific endeavor. It is not surprising, therefore, to find that most universities offer some aspects of crystallography in their undergraduate courses in the physical sciences. It is the principal aim of this book to present an introduction to structure determination by X-ray crystal­ lography that is appropriate mainly to both final-year undergraduate studies in crystallography, chemistry, and chemical physics, and introductory post­ graduate work in this area of crystallography. We believe that the book will be of interest in other disciplines, such as physics, metallurgy, biochemistry, and geology, where crystallography has an important part to play. In the space of one book, it is not possible either to cover all aspects of crystallography or to treat all the subject matter completely rigorously. In particular, certain ...

  18. Electronic signature of the vacancy ordering in NbO (Nb3O3)

    Science.gov (United States)

    Efimenko, A. K.; Hollmann, N.; Hoefer, K.; Weinen, J.; Takegami, D.; Wolff, K. K.; Altendorf, S. G.; Hu, Z.; Rata, A. D.; Komarek, A. C.; Nugroho, A. A.; Liao, Y. F.; Tsuei, K.-D.; Hsieh, H. H.; Lin, H.-J.; Chen, C. T.; Tjeng, L. H.; Kasinathan, D.

    2017-11-01

    We investigated the electronic structure of the vacancy-ordered 4 d -transition-metal monoxide NbO (Nb3O3) using angle-integrated soft- and hard-x-ray photoelectron spectroscopies as well as ultraviolet angle-resolved photoelectron spectroscopy. We found that density-functional-based band-structure calculations can describe the spectral features accurately provided that self-interaction effects are taken into account. In the angle-resolved spectra we were able to identify the so-called `vacancy' band that characterizes the ordering of the vacancies. This together with the band-structure results indicate the important role of the very large inter-Nb-4 d hybridization for the formation of the ordered vacancies and the high thermal stability of the ordered structure of niobium monoxide.

  19. Determination of surface structure of cleaved (001) USb2 single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Shao-ping [Los Alamos National Laboratory; Hawley, Marilyn [Los Alamos National Laboratory; Bauer, Eric D [Los Alamos National Laboratory; Stockum, Phil B [STANFORD UNIV; Manoharan, Hari C [STANFORD UNIV

    2009-01-01

    We have achieved what we believe to be the first atomic resolution STM images for a uranium compound taken at room temperature. The a, b, and c lattice parameters in the images confirm that the USb{sub 2} crystals cleave on the (001) basal plane as expected. The a and b dimensions were equal, with the atoms arranged in a cubic pattern. Our calculations indicate a symmetric cut between Sb planes to be the most favorable cleavage plane and U atoms to be responsible for most of the DOS measured by STM. Some strange features associated with vacancies were observed in the STM win be discussed in conjunction with ab initio calculations. The purpose of this work is to demonstrate the power of scanning tunneling microscopy (STM) techniques combined with a theoretical underpinning to determine the surface atomic structure and properties of actinide materials, such as the quasi 2-dimensional uranium dipnictide USb{sub 2} single crystal, thereby contributing to the understanding of their surface structural and electronic properties. The members of this interesting UX{sub 2} (X=P, As, Sb, Bi) series of compounds display dual localized and itinerant 5f electron behavior within the same compound due to the hybridization of the 5f orbitals with the conduction band. With the exception of UO{sub 2}, which has to be studied at elevated temperature to generate enough carriers for STM imaging, STM techniques have not been applied successfully to the characterization of the surface atomic structure of any other single crystal actinide compound, to the best of our knowledge. However, STM has been used to a limited extent for the study of some cerium compounds. STM probes electronic properties at the atomic level and can directly provide information about the local density of filled and empty states (LDOS) states simultaneously. A STM topograph provides the local atomic arrangement and spacing of the atoms on the surface, local defect structures (e.g. steps, vacancies, and kink sites

  20. First-principles study for vacancy-induced magnetism in nonmagnetic ferroelectric BaTiO3.

    Science.gov (United States)

    Cao, D; Cai, M Q; Zheng, Yue; Hu, W Y

    2009-12-14

    The possibilities of vacancy-induced magnetism in perovskite BaTiO(3) are investigated by first-principles calculations. Calculated results show that both titanium and oxygen vacancies could induce magnetism, but the barium vacancy did not induce magnetism. New and interesting magnetic properties of half-metallic magnetism are found in BaTiO(3) induced by the Ti-vacancy. Based on the density of states and the spin charge density distribution of BaTiO(3), we discuss the different origins of magnetism induced by the partial spin-polarized O 2p states around Ti vacancies and the partially filled d-states Ti around the oxygen vacancies. The discrepancy between the magnetic moments in the cubic phase and the tetragonal phase is due to anisotropic spin polarization induced by structure distortions. Our calculations would enable exploring magneto-electric coupling in nonmagnetic ferroelectric oxides.

  1. Fast-switching electrochromic properties of mesoporous WO3 films with oxygen vacancy defects.

    Science.gov (United States)

    Koo, Bon-Ryul; Ahn, Hyo-Jin

    2017-11-08

    In this study, mesoporous WO3 films with oxygen vacancy defects have been fabricated using the camphene-assisted sol-gel method. By controlling the optimized weight ratio of camphene on the WO3 films, we developed a unique film structure of the WO3 phase with both mesoporous morphology and oxygen vacancy defects due to the distinctive effect of camphene. The mesoporous WO3 films with oxygen vacancy defects fabricated using 10 wt% camphene showed superb multifunctional electrochromic (EC) properties with both fast switching speeds (5.8 s for coloration speed and 1.0 s for bleaching speed) and high coloration efficiency (CE, 51.4 cm(2) C(-1)), which include the most prominent properties, particularly for switching speeds among WO3-based films reported so far. The attractive EC properties are due to the synergistic effects of the mesoporous morphology and oxygen vacancy defects on the WO3. The fast switching speeds are mainly caused by the reduced Li(+) diffusion pathway due to the mesoporous morphology and increased electrical conductivity due to the oxygen vacancy defects. In addition, the increased CE value is due to the large transmittance modulation as a result of a more effective electrostatic contact of the mesoporous morphology and an increased optical bandgap of the oxygen vacancy defects on the WO3. Therefore, this unique film structure of the mesoporous WO3 films with oxygen vacancy defects can be potentially regarded as a novel EC material for high-performance EC devices.

  2. Intrinsic vacancy chalcogenides as dilute magnetic semiconductors: Theoretical investigation of transition-metal doped gallium selenide

    Science.gov (United States)

    Gatuna, Ngigi Wa

    Incorporating magnetism into semiconductors has been a major goal of research efforts aimed at achieving control of both spin and charge of carriers. An entirely new class of electronic materials known as dilutes magnetic semiconductors (DMS) has been synthesized and closely studied. This has led to a deeper understanding of semiconductor physics and the development of new magnetic mechanisms. Unfortunately, most DMS materials retain their magnetic ordering below room temperatures and have only limited solubility and structural compatibility with standard semiconductors. We investigate transition metal doped vacancy-ordered Ga 2Se3 as a material that can address these shortcomings. The intrinsic vacancies of this III-VI, zinc-blende-based semiconductor open possibilities for self-compensation as well as supply highly anistropic and polarizable band edge states. Ga2Se3 is also closely lattice matched to Si and may be grown heteroepitaxially on Si with high quality interfaces. Our first principles computations of X: Ga2Se3 (X = Mn, V, Cr, concentrations 5% to 16%) reveal that X atoms hybridize with neighboring Se in the p-d hybridization typical of III-V and II-VI DMS materials. This hybridization spin-polarizes states near the Fermi level in these T =0 calculations, and lowers the energy of the Se lone-pair orbitals that neighbor vacancies, reducing their prominent role in determining the properties of intrinsic Ga 2Se3. There are distinct differences between substitution on a vacancy or for a Ga. Anisotropic, hole-like conductivity is predicted when X is located in a Ga site, while for X situated in a vacancy, a half-metallic state with an isotropic conductivity appears likely. Our calculations suggest that Mn offers the best choice for the dopant, perhaps because its 3d 5 electronic configuration offers a large (˜0.5 eV) separation of spin up and spin down states near the Fermi level, reducing the metallic densities of states at the Fermi level for all doping

  3. Electronic structure and evidence for La vacancies in the misfit layer compound (La1-xS)(1.20)CrS2

    NARCIS (Netherlands)

    Fang, C.M.; Groot, R.A. de; Wiegers, G.A.; Haas, C.

    Ab initio spin-polarized band structure calculations using the LSW method were performed for an incommensurate misfit layer compound (LaS)(1.20)CrS2 in the supercell approximation. The electronic structure of (LaS)(1.20)CrS2 can be regarded as that of LaS intercalated into the host CrS2. There is a

  4. 38 CFR 1.896 - Publicizing vacancies.

    Science.gov (United States)

    2010-07-01

    ... PROVISIONS Part-Time Career Employment Program § 1.896 Publicizing vacancies. When applicants from outside the Federal service are desired, part-time vacancies may be publicized through various recruiting means, such as: (a) Federal Job Information Centers. (b) State Employment offices. (c) VA Recruiting...

  5. 22 CFR 506.6 - Publicizing vacancies.

    Science.gov (United States)

    2010-04-01

    ... Foreign Relations BROADCASTING BOARD OF GOVERNORS PART-TIME CAREER EMPLOYMENT PROGRAM § 506.6 Publicizing vacancies. When applicants from outside the Federal service are desired, part-time vacancies may be publicized through various recruiting means, such as: (a) Federal Job Information Centers. (b) State...

  6. Generation of Nitrogen-Vacancy Centers in Diamond with Ion Implantation

    Science.gov (United States)

    Cui, Jin-Ming; Chen, Xiang-Dong; Fan, Le-Le; Gong, Zhao-Jun; Zou, Chong-Wen; Sun, Fang-Wen; Han, Zheng-Fu; Guo, Guang-Can

    2012-03-01

    Nitrogen-vacancy defect color centers are created in a high purity single crystal diamond by nitrogen-ion implantation. Both optical spectrum and optically detected magnetic resonance are measured for these artificial quantum emitters. Moreover, with a suitable mask, a lattice composed of nitrogen-vacancy centers is fabricated. Rabi oscillation driven by micro-waves is carried out to show the quality of the ion implantation and potential in quantum manipulation. Along with compatible standard lithography, such an implantation technique shows high potential in future to make structures with nitrogen-vacancy centers for diamond photonics and integrated photonic quantum chip.

  7. Vacancy formation in MoO3: hybrid density functional theory and photoemission experiments

    KAUST Repository

    Salawu, Omotayo Akande

    2016-09-29

    Molybdenum oxide (MoO3) is an important material that is being considered for numerous technological applications, including catalysis and electrochromism. In the present study, we apply hybrid density functional theory to investigate O and Mo vacancies in the orthorhombic phase. We determine the vacancy formation energies of different defect sites as functions of the electron chemical potential, addressing different charge states. In addition, we investigate the consequences of defects for the material properties. Ultraviolet photoemission spectroscopy is employed to study the valence band of stoichiometric and O defective MoO3. We show that O vacancies result in occupied in-gap states.

  8. Energy band modulation of graphane by hydrogen-vacancy chains: A first-principles study

    Directory of Open Access Journals (Sweden)

    Bi-Ru Wu

    2014-08-01

    Full Text Available We investigated a variety of configurations of hydrogen-vacancy chains in graphane by first-principles density functional calculation. We found that graphane with two zigzag H-vacancy chains segregated by one or more H chain is generally a nonmagnetic conductor or has a negligible band gap. However, the same structure is turned into a semiconductor and generates a magnetic moment if either one or both of the vacancy chains are blocked by isolated H atoms. If H-vacancy chains are continuously distributed, the structure is similar to a zigzag graphene nanoribbon embedded in graphane. It was also found that the embedded zigzag graphene nanoribbon is antiferromagnetic, and isolated H atoms left in the 2-chain nanoribbon can tune the band gap and generate net magnetic moments. Similar effects are also obtained if bare carbon atoms are present outside the nanoribbon. These results are useful for designing graphene-based nanoelectronic circuits.

  9. Oxygen vacancy diffusion in bare ZnO nanowires

    Science.gov (United States)

    Deng, Bei; Luisa da Rosa, Andreia; Frauenheim, Th.; Xiao, J. P.; Shi, X. Q.; Zhang, R. Q.; van Hove, Michel A.

    2014-09-01

    Oxygen vacancies (VO) are known to be common native defects in zinc oxide (ZnO) and to play important roles in many applications. Based on density functional theory, we present a study for the migration of oxygen vacancies in ultra-thin ZnO nanowires (NWs). We find that under equilibrium growth conditions VO has a higher formation energy (Ef) inside the wire than that at shallow sites and surface sites, with different geometric relaxations and structural reconstructions. The migration of VO has lower barriers in the NW than in the bulk and is found to be energetically favorable in the direction from the bulk to the surface. These results imply a higher concentration of VO at surface sites and also a relative ease of diffusion in the NW structure. Our results support the previous experimental observations and are important for the development of ZnO-based devices in photocatalysis and optoelectronics.

  10. Formation and Migration of Oxygen Vacancies in SrCoO3 and their effect on Oxygen Evolution Reactions

    KAUST Repository

    Tahini, Hassan A.

    2016-07-18

    Perovskite SrCoO3 is a potentially useful material for promoting the electrocatalytic oxygen evolution reaction, with high activities predicted theoretically and observed experimentally for closely related doped perovskite materials. However, complete stoichiometric oxidation is very difficult to realize experimentally – in almost all cases there are significant fractions of oxygen vacancies present. Here, using first principles calculations we study oxygen vacancies in perovskite SrCoO3 from thermodynamic, electronic and kinetic points of view. We find that an oxygen vacancy donates two electrons to neighboring Co sites in the form of localized charge. The formation energy of a single vacancy is very low and estimated to be 1.26 eV in the dilute limit. We find that a vacancy is quite mobile with a migration energy of ~0.5 eV. Moreover, we predict that oxygen vacancies exhibit a tendency towards clustering which is in accordance with the material’s ability to form a variety of oxygen-deficient structures. These vacancies have a profound effect on the material’s ability to facilitate OER, increasing the overpotential from ~0.3 V for the perfect material to ~0.7 for defective surfaces. A moderate compressive biaxial strain (2%) is predicted here to increase the surface oxygen vacancy formation energy by ca. 30%, thus reducing the concentration of surface vacancies and thereby preserving the OER activity of the material.

  11. Molecular dynamics simulation of grain-boundary diffusion of vacancies in bcc iron

    Science.gov (United States)

    Kwok, T.; Ho, P. S.; Yip, S.; Balluffi, R.; Brokman, A. W.; Bristowe, P. D.

    1981-06-01

    The jumping of vacancies in a bcc iron sigma = 5 tilt boundary was simulated by computer molecular dynamics. The data yielded a reasonable value of the activation energy for migration and showed that the jump processes are highly structure dependent. The use of a temperature dependent transition probability matrix to describe the diffusion of the vacancies in the grain boundary is suggested. Formation of one type of boundary interstitial was observed which was found to be immobile.

  12. Molecular dynamics simulation of grain-boundary diffusion of vacancies in bcc iron

    Energy Technology Data Exchange (ETDEWEB)

    Kwok, T.; Ho, P. S.; Yip, S.; Balluffi, R. W.; Bristowe, P. D.; Brokman, A.

    1981-06-01

    The jumping of vacancies in a bcc iron ..sigma.. = 5 tilt boundary was simulated by computer molecular dynamics. The data yielded a reasonable value of the activation energy for migration and showed that the jump processes are highly structure-dependent. The use of a temperature dependent transition probability matrix to describe the diffusion of the vacancies in the grain boundary is suggested. Formation of one type of boundary interstitial was observed which was found to be immobile.

  13. Determining crystal structures through crowdsourcing and coursework

    Science.gov (United States)

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Roque, Paulo Sergio Silveira Belo Nascimento; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

    2016-01-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552

  14. Determining crystal structures through crowdsourcing and coursework

    Science.gov (United States)

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Silveira Belo Nascimento Roque, Paulo Sergio; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K.; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

    2016-09-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  15. Effect of the property of dielectric capping layers on impurity-free vacancy diffusion in InGaAs/InGaAsP MQW structures

    Science.gov (United States)

    Yu, Jae Su; Chung, Kwan Soo

    2007-08-01

    A dependence of the interdiffusion in InGaAs/InGaAsP multiple quantum well (MQW) structures on the stoichiometry of SiOx and SiNx capping layers, which were deposited with different SiH4 flow rates by plasma enhanced chemical vapor deposition (PECVD), has been studied. Decreasing the SiH4 flow rate during PECVD deposition produces relatively more voids inside SiOx or SiNx film. For both SiOx and SiNx capping layers, the blue shift of intermixed samples after rapid thermal annealing (RTA) becomes larger due to the enhancement of the interdiffusion of well/barrier caused by the increased porosity of dielectric capping layers as SiH4 flow rate decreases from 300 sccm to 20 sccm. Using SiOx (SiNx) deposited with different SiH4 flow rates, the magnitude of blue shift is varied by about 98 nm (75 nm) for the samples annealed at 850 °C for 30 s. The blue shifts of 138 nm and 98 nm of photoluminescence peak wavelength for the SiOx (deposited with 20 sccm SiH4) capped MQWs without and with an InGaAs cap layer, respectively, are observed after RTA of 850 °C for 30 s. A possible mechanism is discussed for these phenomena.

  16. Determinants of the detrital arthropod community structure

    DEFF Research Database (Denmark)

    Lessard, J.P.; Sackett, Tara E.; Reynolds, William N.

    2011-01-01

    Understanding the factors that shape community structure, and whether those factors vary geographically, has a long history in ecology. Because the abiotic environment often varies in predictable ways along elevational gradients, montane systems are ideal to study geographic variation in the dete......Understanding the factors that shape community structure, and whether those factors vary geographically, has a long history in ecology. Because the abiotic environment often varies in predictable ways along elevational gradients, montane systems are ideal to study geographic variation...

  17. Improving the optoelectronic property and photoactivity of nano-structured titanuim dioxide: Effect of particle size, oxygen vacancy, and nitrogen doping

    Science.gov (United States)

    Lin, Hong-Ying

    Titanium dioxide (TiO2) has been proven to be one of the most important and widely used photocatalyst for applications such as gas/liquid phase environmental cleaning, solar hydrogen generation, sensitized solar cell, UV filtration, etc. The biggest challenge in the applications of this semiconductor photocatalyst is its large band gap (˜ 3.2 eV) which limits the utilizable spectrum of photons from the solar light (˜ 4 to 5 %). To improve the optical sensitivity of TiO2 in the visible light region, the band gap of TiO2 needs to be tailored. The reduction of TiO2 band gap can be achieved by controlling of its electronic structure via two routes: changing the particle size and doping it with impurities. To precisely control the size of TiO2 particles, anatase TiO 2 nanocrystallines (17 to 29 nm) were synthesized by metallo-organic chemical vapor deposition (MOCVD) method with moderate control on system parameters (i.e. pressure and gas flow rates). The results of band gap change as a function of particle size agreed well with what was predicted using the Brus' effective mass model (EMM). However, the observations from photocatalytic oxidation of 2-chlorophenol (2-CP) showed that the smaller the particle size, the faster the degradation rate. This is attributed in part to the combined effect of band gap change relative to the spectrum of the light source and the specific surface area (or particle size) of the photocatalysts. Our results indicate that the gain in specific surface area due to the smaller particle size outweighs the improvement on its optical property (e.g. reduction in bandgap) under similar experimental condition. Our observation also showed the secondary particle size to be time dependent due to the aggregation and is highly correlated with its primary particle size. The nitrogen doped TiO2 thin film synthesis was carried out with two different approaches: (1) oxidation of the titanium nitride (TiN) thin film and (2) reactive pulsed laser deposition

  18. Structural determinants in the bulk heterojunction.

    Science.gov (United States)

    Acocella, Angela; Höfinger, Siegfried; Haunschmid, Ernst; Pop, Sergiu C; Narumi, Tetsu; Yasuoka, Kenji; Yasui, Masato; Zerbetto, Francesco

    2018-02-21

    Photovoltaics is one of the key areas in renewable energy research with remarkable progress made every year. Here we consider the case of a photoactive material and study its structural composition and the resulting consequences for the fundamental processes driving solar energy conversion. A multiscale approach is used to characterize essential molecular properties of the light-absorbing layer. A selection of bulk-representative pairs of donor/acceptor molecules is extracted from the molecular dynamics simulation of the bulk heterojunction and analyzed at increasing levels of detail. Significantly increased ground state energies together with an array of additional structural characteristics are identified that all point towards an auxiliary role of the material's structural organization in mediating charge-transfer and -separation. Mechanistic studies of the type presented here can provide important insights into fundamental principles governing solar energy conversion in next-generation photovoltaic devices.

  19. Structure determination by X-ray crystallography

    CERN Document Server

    Ladd, M F C

    1995-01-01

    X-ray crystallography provides us with the most accurate picture we can get of atomic and molecular structures in crystals. It provides a hard bedrock of structural results in chemistry and in mineralogy. In biology, where the structures are not fully crystalline, it can still provide valuable results and, indeed, the impact here has been revolutionary. It is still an immense field for young workers, and no doubt will provide yet more striking develop­ ments of a major character. It does, however, require a wide range of intellectual application, and a considerable ability in many fields. This book will provide much help. It is a very straightforward and thorough guide to every aspect of the subject. The authors are experienced both as research workers themselves and as teachers of standing, and this is shown in their clarity of exposition. There are plenty of iliustrations and worked examples to aid the student to obtain a real grasp of the subject.

  20. Some structural determinants of melody recall.

    Science.gov (United States)

    Boltz, M

    1991-05-01

    Sophisticated musicians were asked to recall, using musical notation, a set of unfamiliar folk tunes that varied in rhythmic structure and referents of tonality. The results showed that memory was facilitated by tonic triad members marking phrase endings, but only when their presence was highlighted by a corresponding pattern of temporal accents. Conversely, recall significantly declined when tonal information was either absent or obscured by rhythmic structure. Error analyses further revealed that the retention of overall pitch contour and information at phrase ending points varied as a function of these manipulations. The results are discussed in terms of a framework that links the acts of perceiving and remembering to a common attentional scheme.

  1. Magnetic behavior in LiNbO{sub 3} nanocrystallites caused by oxygen vacancies

    Energy Technology Data Exchange (ETDEWEB)

    Díaz-Moreno, C.A. [Centro de Investigación en Materiales Avanzados S.C., Laboratorio Nacional de Nanotecnología, Miguel de Cervantes 120, Complejo Industrial Chihuahua, Chihuahua, Apdo. Postal 31109, México (Mexico); Farías-Mancilla, R. [Instituto de Ingeniería y Tecnología, Departamento de Física y Matemáticas, Ave. del Charro #450, Cd. Juarez C.P., 32310 Chihuahua (Mexico); Matutes-Aquino, J.A. [Centro de Investigación en Materiales Avanzados S.C., Laboratorio Nacional de Nanotecnología, Miguel de Cervantes 120, Complejo Industrial Chihuahua, Chihuahua, Apdo. Postal 31109, México (Mexico); Elizalde-Galindo, J. [Instituto de Ingeniería y Tecnología, Departamento de Física y Matemáticas, Ave. del Charro #450, Cd. Juarez C.P., 32310 Chihuahua (Mexico); Espinosa-Magaña, F.; González-Hernández, J. [Centro de Investigación en Materiales Avanzados S.C., Laboratorio Nacional de Nanotecnología, Miguel de Cervantes 120, Complejo Industrial Chihuahua, Chihuahua, Apdo. Postal 31109, México (Mexico); Hurtado-Macías, A., E-mail: abel.hurtado@cimav.edu.mx [Centro de Investigación en Materiales Avanzados S.C., Laboratorio Nacional de Nanotecnología, Miguel de Cervantes 120, Complejo Industrial Chihuahua, Chihuahua, Apdo. Postal 31109, México (Mexico)

    2014-04-01

    Ferromagnetism is observed in LiNiO{sub 3} nanocrystals exposed to a reducing atmosphere intended to create oxygen vacancies. The existence of vacancies is confirmed by measuring the oxygen depletion across the selected nanoparticles by TEM. The magnetism shows no temperature dependence in the range of 4–300 K. The density functional theory was used to perform spin polarized electronic structure calculations for LiNiO{sub 3} with and without oxygen vacancies. The calculated magnetic data qualitatively support the observed magnetic behavior. - Highlights: • Oxygen vacancies were formed at the surface of LiNiO{sub 3} nanocrystals by a temperature programmed reduction process. • The observed ferromagnetism in LiNbO{sub 3} nanocrystals after a treatment in a reducing atmosphere shows no temperature dependence in the range of 4–300 K. • Magnetization based on density functional theory calculations was compared with the experimental data.

  2. Mechanism of dopant-vacancy association in α-quartz GeO2

    KAUST Repository

    Wang, Hao

    2013-02-28

    Improving the electron mobility of devices such as Ge metal oxide semiconductor field effect transistors requires good Ge/dielectric interfaces. GeO2 thus is reconsidered as a passivation layer for Ge. However, O-vacancies need to be controlled as they have a deleterious impact on the properties. We employ electronic structure calculations to investigate the introduction of trivalent ions (Al, Y, and La) in α-quartz GeO2. The binding energies of the dopant-vacancy pairs reveal that dopants can be used to control the O-vacancies and reduce the induced dangling bonds. It is proposed that the introduction of Al will limit the concentration of O-vacancies at low Fermi energy.

  3. Vacancy induced half-metallicity in half-Heusler semiconductors

    KAUST Repository

    Zhu, Zhiyong

    2011-09-28

    First-principles calculations are performed to investigate the effect of vacancies on the electronic structure and magnetic properties of the two prototypical half-Heusler semiconductors NiTiSn and CoTiSb. The spin degeneracy of the host materials is broken for all types of isolated vacancies under consideration, except for Ni-deficient NiTiSn. A half-metallic character is identified in Sn-deficient NiTiSn and Co/Ti/Sb-deficient CoTiSb. We can explain our findings by introducing an extending Slater-Pauling rule for systems with defects. A ferromagnetic ordering of the local moments due to double exchange appears to be likely.

  4. Electronic properties of graphene with single vacancy and Stone-Wales defects

    Energy Technology Data Exchange (ETDEWEB)

    Zaminpayma, Esmaeil [Physics Group, Qazvin Branch, Islamic Azad University, Qazvin (Iran, Islamic Republic of); Razavi, Mohsen Emami, E-mail: razavi246@gmail.com [Plasma Physics Research Center, Science and Research Branch, Islamic Azad University, P.O. Box 14665-678, Tehran (Iran, Islamic Republic of); Nayebi, Payman [Department of Physics, College of Technical and Engineering, Saveh Branch, Islamic Azad University, Saveh (Iran, Islamic Republic of)

    2017-08-31

    Highlights: • The electronic properties of graphene device with single vacancy (SV) and Stone-Wales (SW) defect have been studied. • The first principles calculations have been performed based on self-consistent charge density functional tight-binding. • The density of state, current voltage curves of pure graphene and graphene with SV and SW defects have been investigated. • Transmission spectrum of pristine graphene device and graphene with SV and SW defects has been examined. - Abstract: The first principles calculations have been performed based on self-consistent charge density functional tight-binding in order to examine the electronic properties of graphene with single vacancy (SV) and Stone-Wales (SW) defects. We have optimized structures of pristine graphene and graphene with SV and SW defects. The bond lengths, current-voltage curve and transmission probability have been calculated. We found that the bond length for relaxed graphene is 1.43 Å while for graphene with SV and SW defects the bond lengths are 1.41 Å and 1.33 Å, respectively. For the SV defect, the arrangement of atoms with three nearest neighbors indicates sp{sub 2} bonding. While for SW defect, the arrangement of atoms suggests nearly sp bonding. From the current-voltage curve for graphene with defects we have determined that the behavior of the I–V curves is nonlinear. It is also found that the SV and SW defects cause to decrease the current compared to the pristine graphene case. Furthermore, the single vacancy defect reduces the current more than the Stone-Wales defect. Moreover, we observed that by increasing the voltage from zero to 1 V new peaks near Fermi level in the transmission probability curves have been created.

  5. determination of verticality of reservoir engineering structure

    African Journals Online (AJOL)

    user

    Terrestrial laser scanners (TLS) are used nowadays as Geomatics instruments for various applications. One of these applications is 3D survey and management of oil and gas facilities and other engineering structures. This recent attention is due to the fact that laser scanner has the ability to generate massive amounts of ...

  6. Electron Diffraction Determination of Nanoscale Structures

    Energy Technology Data Exchange (ETDEWEB)

    Parks, Joel H

    2013-03-01

    Dominant research results on adsorption on gold clusters are reviewed, including adsorption of H{sub 2}O and O{sub 2} on gold cluster cations and anions, kinetics of CO adsorption to middle sized gold cluster cations, adsorption of CO on Au{sub n}{sup +} with induced changes in structure, and H{sub 2}O enhancement of CO adsorption.

  7. Vacancy Duration, Wage Offers, and Job Requirements

    DEFF Research Database (Denmark)

    Eriksson, Tor Viking; Chen, Long-Hwa

    is concerned with how vacancy durations vary with firms' minimum wage offers and minimum job requirements (regarding education, skills, age, gender and earlier work experience). The empirical analysis is based on ten employer surveys carried out by the DGBAS on Taiwan during the period 1996-2006. We estimate...... logistic discrete hazard models with a rich set of job and firm characteristics as explanatory variables. The results show that vacancies associated with higher wage offers take, ceteris paribus, longer to be filled. The impact of firms' wage offers and credential requirements does not vary over...... the business cycle. However, firms vary their skills requirements over the business cycle: our empirical analysis shows that, for a given wage offer, requirements are stricter in recessions and downturns. Separating between reasons for posting vacancies turned out important in explaining differences in vacancy...

  8. Oxygen vacancies dependent phase transition of Y2O3 films

    Science.gov (United States)

    Yu, Pengfei; Zhang, Kan; Huang, Hao; Wen, Mao; Li, Quan; Zhang, Wei; Hu, Chaoquan; Zheng, Weitao

    2017-07-01

    Y2O3 films have great application potential in high-temperature metal matrix composite and nuclear engineering, used as interface diffusion and reaction barrier coating owing to their excellent thermal and chemical stability, high melting point and extremely negative Gibbs formation energy, and thus their structural and mechanical properties at elevated temperature are especially important. Oxygen vacancies exist commonly in yttrium oxide (Y2O3) thin films and act strongly on the phase structure and properties, but oxygen vacancies dependent phase transition at elevated temperature has not been well explored yet. Y2O3 thin films with different oxygen vacancy concentrations have been achieved by reactive sputtering through varying substrate temperature (Ts), in which oxygen vacancies increase monotonously with increasing Ts. For as-deposited Y2O3 films, oxygen vacancies present at high Ts can promote the nucleation of monoclinic phase, meanwhile, high Ts can induce the instability of monoclinic phase. Thus their competition results in forming mixed phases of cubic and monoclinic at high Ts. During vacuum annealing at 1000 °C, a critical oxygen vacancy concentration is observed, below which phase transition from monoclinic to cubic takes place, and above which phase transfer from monoclinic to the oxygen defective phase (ICDD file no. 39-1063), accompanying by stress reversal from compressive to tensile and maintenance of high hardness.

  9. Engineering of optical and electrical properties of ZnO by non-equilibrium thermal processing: The role of zinc interstitials and zinc vacancies

    Science.gov (United States)

    Prucnal, S.; Wu, Jiada; Berencén, Y.; Liedke, M. O.; Wagner, A.; Liu, F.; Wang, M.; Rebohle, L.; Zhou, S.; Cai, Hua; Skorupa, W.

    2017-07-01

    A controlled manipulation of defects in zinc oxide (ZnO) and the understanding of their electronic structure can be a key issue towards the fabrication of p-type ZnO. Zn vacancy (VZn), Zn interstitials (IZn), and O vacancy (VO) are mainly native point defects, determining the optoelectronic properties of ZnO. The electronic structure of these defects still remains controversial. Here, we experimentally demonstrate that the green emission in ZnO comes from VZn-related deep acceptor and VZn-VO clusters, which is accompanied by the radiative transition between the triplet and the ground singlet state with the excited singlet state located above the CB minimum. Moreover, the IZn is identified to be a shallow donor in ZnO, being mainly responsible for the n-type conductivity of non-intentionally doped ZnO.

  10. Determination of micro structural corrosion by BN

    Energy Technology Data Exchange (ETDEWEB)

    Zergoug, M.; Kamel, G.; Benchaala, A. [Laboratoire d' Electronique et d' Electrotechnique, Centre de soudage et de controle, Route de Dely Ibrahim, B.P:64, Cheraga (Algeria)

    2004-07-01

    The quality control of industrial components requires adaptation and the development of new material characterization and particular non destructive testing techniques. To characterize steel, it would be useful to know its chemical composition, physic-chemical constitution, metallurgical state (annealed, hammered) and other parameters (superficial and chemical processing, etc.). The testing method using Barkhausen noise (B.N.) is a particular method, which can be applied on ferromagnetic materials. It is a magnetic non destructive evaluation (NDE) method and can provide very important information about the material microstructure. The work here presented documents the ability to determine the metallurgical state of steel submitted to the corrosive attack by electrochemical process. The samples are characterized by Barkhausen noise as non destructive methods and are compared with methods as metallography, micro hardness measurement, and toughness determination. (authors)

  11. δ-Doping of oxygen vacancies dictated by thermodynamics in epitaxial SrTiO3 films

    Directory of Open Access Journals (Sweden)

    Fengmiao Li

    2017-06-01

    Full Text Available Homoepitaxial SrTiO3(110 film is grown by molecular beam epitaxy in ultra-high vacuum with oxygen diffusing from substrate as the only oxidant. The resulted oxygen vacancies (VOs are found to be spatially confined within few subsurface layers only, forming a quasi-two-dimensional doped region with a tunable high concentration. Such a δ-function distribution of VOs is essentially determined by the thermodynamics associated with the surface reconstruction, and facilitated by the relatively high growth temperature. Our results demonstrate that it is feasible to tune VOs distribution at the atomic scale by controlling the lattice structure of oxide surfaces.

  12. How structure determines correlations in neuronal networks.

    Directory of Open Access Journals (Sweden)

    Volker Pernice

    2011-05-01

    Full Text Available Networks are becoming a ubiquitous metaphor for the understanding of complex biological systems, spanning the range between molecular signalling pathways, neural networks in the brain, and interacting species in a food web. In many models, we face an intricate interplay between the topology of the network and the dynamics of the system, which is generally very hard to disentangle. A dynamical feature that has been subject of intense research in various fields are correlations between the noisy activity of nodes in a network. We consider a class of systems, where discrete signals are sent along the links of the network. Such systems are of particular relevance in neuroscience, because they provide models for networks of neurons that use action potentials for communication. We study correlations in dynamic networks with arbitrary topology, assuming linear pulse coupling. With our novel approach, we are able to understand in detail how specific structural motifs affect pairwise correlations. Based on a power series decomposition of the covariance matrix, we describe the conditions under which very indirect interactions will have a pronounced effect on correlations and population dynamics. In random networks, we find that indirect interactions may lead to a broad distribution of activation levels with low average but highly variable correlations. This phenomenon is even more pronounced in networks with distance dependent connectivity. In contrast, networks with highly connected hubs or patchy connections often exhibit strong average correlations. Our results are particularly relevant in view of new experimental techniques that enable the parallel recording of spiking activity from a large number of neurons, an appropriate interpretation of which is hampered by the currently limited understanding of structure-dynamics relations in complex networks.

  13. Enzymatically Controlled Vacancies in Nanoparticle Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Barnaby, Stacey N.; Ross, Michael B.; Thaner, Ryan V.; Lee, Byeongdu; Schatz, George C.; Mirkin, Chad A.

    2016-08-01

    In atomic systems, the mixing of metals results in distinct phase behavior that depends on the identity and bonding characteristics of the atoms. In nanoscale systems, the use of oligonucleotides as programmable “bonds” that link nanoparticle “atoms” into superlattices allows for the decoupling of atom identity and bonding. While much research in atomic systems is dedicated to understanding different phase behavior of mixed metals, it is not well understood on the nanoscale how changes in the nanoscale “bond” affect the phase behavior of nanoparticle crystals. In this work, the identity of the atom is kept the same but the chemical nature of the bond is altered, which is not possible in atomic systems, through the use of DNA and RNA bonding elements. These building blocks assemble into single crystal nanoparticle superlattices with mixed DNA and RNA bonding elements throughout. The nanoparticle crystals can be dynamically changed through the selective and enzymatic hydrolysis of the RNA bonding elements, resulting in superlattices that retain their crystalline structure and habit, while incorporating up to 35% random vacancies generated from the nanoparticles removed. Therefore, the bonding elements of nanoparticle crystals can be enzymatically and selectively addressed without affecting the nature of the atom.

  14. Ga2O3 doping and vacancy effect in KNN—LT lead-free piezoceramics

    Science.gov (United States)

    Tan, Zhi; Xing, Jie; Jiang, Laiming; Zhu, Jianguo; Wu, Bo

    2017-12-01

    Ga2O3 was doped into 0.95(K0.48Na0.52)NbO3—0.05LiTaO3 (KNN—LT) ceramics and its influences on the sintering behavior, phase structure and electrical properties of ceramics were studied. Firstly, SEM observation exhibits that more and more glass phase appears in ceramics with the gradual addition of Ga2O3, which determines the continuous decrease in sintering temperatures. And the addition of Ga2O3 is also found to increase the orthorhombic—tetragonal transition temperature ( T O—T) of system to a higher level. Secondly, both the density and the coercive field ( E C) of ceramics increase firstly and then decrease with increasing the Ga2O3 content, and the KNN—LT— xGa sample at x = 0.004 shows a pinched P— E hysteresis loop. Finally, the impedance characteristics of KNN—LT— xGa ceramics were investigated at different temperatures, revealing a typical vacancy related conduction mechanism. This work demonstrates that Ga2O3 is a good sintering aid for KNN-based ceramics, and the vacancy plays an important role in the sintering and electrical behaviors of ceramics.

  15. Electronic properties of graphene with single vacancy and Stone-Wales defects

    Science.gov (United States)

    Zaminpayma, Esmaeil; Razavi, Mohsen Emami; Nayebi, Payman

    2017-08-01

    The first principles calculations have been performed based on self-consistent charge density functional tight-binding in order to examine the electronic properties of graphene with single vacancy (SV) and Stone-Wales (SW) defects. We have optimized structures of pristine graphene and graphene with SV and SW defects. The bond lengths, current-voltage curve and transmission probability have been calculated. We found that the bond length for relaxed graphene is 1.43 Å while for graphene with SV and SW defects the bond lengths are 1.41 Å and 1.33 Å, respectively. For the SV defect, the arrangement of atoms with three nearest neighbors indicates sp2 bonding. While for SW defect, the arrangement of atoms suggests nearly sp bonding. From the current-voltage curve for graphene with defects we have determined that the behavior of the I-V curves is nonlinear. It is also found that the SV and SW defects cause to decrease the current compared to the pristine graphene case. Furthermore, the single vacancy defect reduces the current more than the Stone-Wales defect. Moreover, we observed that by increasing the voltage from zero to 1 V new peaks near Fermi level in the transmission probability curves have been created.

  16. Memristive properties of hexagonal WO3 nanowires induced by oxygen vacancy migration

    Science.gov (United States)

    2013-01-01

    Tungsten trioxide (WO3) is always oxygen-deficient or non-stoichiometric under atmospheric conditions. Positively charged oxygen vacancies prefer to drift as well as electrons when the electric field is strong enough, which will alter the distribution of oxygen vacancies and then endow WO3 with memristive properties. In Au/WO3 nanowire/Au sandwich structures with two ohmic contacts, the axial distribution of oxygen vacancies and then the electrical transport properties can be more easily modulated by bias voltage. The threshold electric field for oxygen vacancy drifting in single-crystal hexagonal WO3 nanowire is about 106 V/m, one order of magnitude less than that in its granular film. At elevated temperatures, the oxygen vacancy drifts and then the memristive effect can be enhanced remarkably. When the two metallic contacts are asymmetric, the WO3 nanowire devices even demonstrate good rectifying characteristic at elevated temperatures. Based on the drift of oxygen vacancies, nanoelectronic devices such as memristor, rectifier, and two-terminal resistive random access memory can be fabricated on individual WO3 nanowires. PMID:23347429

  17. Structural determinants of criticality in biological networks.

    Science.gov (United States)

    Valverde, Sergi; Ohse, Sebastian; Turalska, Malgorzata; West, Bruce J; Garcia-Ojalvo, Jordi

    2015-01-01

    Many adaptive evolutionary systems display spatial and temporal features, such as long-range correlations, typically associated with the critical point of a phase transition in statistical physics. Empirical and theoretical studies suggest that operating near criticality enhances the functionality of biological networks, such as brain and gene networks, in terms for instance of information processing, robustness, and evolvability. While previous studies have explained criticality with specific system features, we still lack a general theory of critical behavior in biological systems. Here we look at this problem from the complex systems perspective, since in principle all critical biological circuits have in common the fact that their internal organization can be described as a complex network. An important question is how self-similar structure influences self-similar dynamics. Modularity and heterogeneity, for instance, affect the location of critical points and can be used to tune the system toward criticality. We review and discuss recent studies on the criticality of neuronal and genetic networks, and discuss the implications of network theory when assessing the evolutionary features of criticality.

  18. Structural Determinants of Criticality in Biological Networks

    Directory of Open Access Journals (Sweden)

    Sergi eValverde

    2015-05-01

    Full Text Available Many adaptive evolutionary systems display spatial and temporal features, such as long-range correlations, typically associated with the critical point of a phase transition in statistical physics. Empirical and theoretical studies suggest that operating near criticality enhances the functionality of biological networks, such as brain and gene networks, in terms for instance of information processing, robustness and evolvability. While previous studies have explained criticality with specific system features, we still lack a general theory of critical behaviour in biological systems. Here we look at this problem from the complex systems perspective, since in principle all critical biological circuits have in common the fact that their internal organisation can be described as a complex network. An important question is how self-similar structure influences self-similar dynamics. Modularity and heterogeneity, for instance, affect the location of critical points and can be used to tune the system towards criticality. We review and discuss recent studies on the criticality of neuronal and genetic networks, and discuss the implications of network theory when assessing the evolutionary features of criticality.

  19. Recombination Cross Section for Interstitials and Vacancies as a Function of Vacancy Concentration

    DEFF Research Database (Denmark)

    Leffers, Torben; Singh, Bachu Narain

    1981-01-01

    the actual recombination event. This makes it possible to cover the range of vacancy concentrations from very high values down to 10−6 and to include the case where interstitials and vacancies are equally mobile. We are therefore in a position to establish the dependence of Ziv, on the various relevant...

  20. Language structure is partly determined by social structure.

    Directory of Open Access Journals (Sweden)

    Gary Lupyan

    Full Text Available BACKGROUND: Languages differ greatly both in their syntactic and morphological systems and in the social environments in which they exist. We challenge the view that language grammars are unrelated to social environments in which they are learned and used. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a statistical analysis of >2,000 languages using a combination of demographic sources and the World Atlas of Language Structures--a database of structural language properties. We found strong relationships between linguistic factors related to morphological complexity, and demographic/socio-historical factors such as the number of language users, geographic spread, and degree of language contact. The analyses suggest that languages spoken by large groups have simpler inflectional morphology than languages spoken by smaller groups as measured on a variety of factors such as case systems and complexity of conjugations. Additionally, languages spoken by large groups are much more likely to use lexical strategies in place of inflectional morphology to encode evidentiality, negation, aspect, and possession. Our findings indicate that just as biological organisms are shaped by ecological niches, language structures appear to adapt to the environment (niche in which they are being learned and used. As adults learn a language, features that are difficult for them to acquire, are less likely to be passed on to subsequent learners. Languages used for communication in large groups that include adult learners appear to have been subjected to such selection. Conversely, the morphological complexity common to languages used in small groups increases redundancy which may facilitate language learning by infants. CONCLUSIONS/SIGNIFICANCE: We hypothesize that language structures are subjected to different evolutionary pressures in different social environments. Just as biological organisms are shaped by ecological niches, language structures appear to adapt to the

  1. Understanding the presence of vacancy clusters in ZnO from a kinetic perspective

    Science.gov (United States)

    Bang, Junhyeok; Kim, Youg-Sung; Park, C. H.; Gao, F.; Zhang, S. B.

    2014-06-01

    Vacancy clusters have been observed in ZnO by positron-annihilation spectroscopy (PAS), but detailed mechanisms are unclear. This is because the clustering happens in non-equilibrium conditions, for which theoretical method has not been well established. Combining first-principles calculation and kinetic Monte Carlo simulation, we determine the roles of non-equilibrium kinetics on the vacancies clustering. We find that clustering starts with the formation of Zn and O vacancy pairs (VZn - Vo), which further grow by attracting additional mono-vacancies. At this stage, vacancy diffusivity becomes crucial: due to the larger diffusivity of VZn compared to VO, more VZn-abundant clusters are formed than VO-abundant clusters. The large dissociation energy barriers, e.g., over 2.5 eV for (VZn - Vo), suggest that, once formed, it is difficult for the clusters to dissociate. By promoting mono-vacancy diffusion, thermal annealing will increase the size of the clusters. As the PAS is insensitive to VO donor defects, our results suggest an interpretation of the experimental data that could not have been made without the in-depth calculations.

  2. Determination of atomic cluster structure with cluster fusion algorithm

    DEFF Research Database (Denmark)

    Obolensky, Oleg I.; Solov'yov, Ilia; Solov'yov, Andrey V.

    2005-01-01

    We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters.......We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters....

  3. Structure of catalase determined by MicroED

    Science.gov (United States)

    Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir

    2014-01-01

    MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. DOI: http://dx.doi.org/10.7554/eLife.03600.001 PMID:25303172

  4. Ab initio structure determination via powder X-ray diffraction

    Indian Academy of Sciences (India)

    Although the method of structure completion when once the starting model is provided is facile through the Rietveld refinement technique, the structure solution ab initio os still not push-button technology. In this article a survey of the recent development in this area is provided with an illustration of the structure determination ...

  5. Determinants of Capital Structure: Empirical Evidence From UK

    OpenAIRE

    Xu, Wenjing

    2010-01-01

    This paper investigates the determinants of capital structure for the companies in the United Kingdom. The aim of this study is to determine which capital structure is more appropriate to UK listed companies. Results obtained will be compared against previous empirical and theoretical predictions. Panel data set containing 342 UK public quoted companies across 8 industries during the period from 2000-2009 is employed. A Pooled OLS regression is constructed to discuss what the determinants...

  6. Interlayer vacancy defects in AA-stacked bilayer graphene: density functional theory predictions.

    Science.gov (United States)

    Vuong, A; Trevethan, T; Latham, C D; Ewels, C P; Erbahar, D; Briddon, P R; Rayson, M J; Heggie, M I

    2017-04-20

    AA-stacked graphite and closely related structures, where carbon atoms are located in registry in adjacent graphene layers, are a feature of graphitic systems including twisted and folded bilayer graphene, and turbostratic graphite. We present the results of ab initio density functional theory calculations performed to investigate the complexes that are formed from the binding of vacancy defects across neighbouring layers in AA-stacked bilayers. As with AB stacking, the carbon atoms surrounding lattice vacancies can form interlayer structures with sp 2 bonding that are lower in energy than in-plane reconstructions. The sp 2 interlayer bonding of adjacent multivacancy defects in registry creates a type of stable sp 2 bonded 'wormhole' or tunnel defect between the layers. We also identify a new class of 'mezzanine' structure characterised by sp 3 interlayer bonding, resembling a prismatic vacancy loop. The V 6 hexavacancy variant, where six sp 3 carbon atoms sit midway between two carbon layers and bond to both, is substantially more stable than any other vacancy aggregate in AA-stacked layers. Our focus is on vacancy generation and aggregation in the absence of extreme temperatures or intense beams.

  7. Engineering oxygen vacancies towards self-activated BaLuAl(x)Zn(4-x)O(7-(1-x)/2) photoluminescent materials: an experimental and theoretical analysis.

    Science.gov (United States)

    Ma, Lan; Xia, Zhiguo; Atuchin, Victor; Molokeev, Maxim; Auluck, S; Reshak, A H; Liu, Quanlin

    2015-12-14

    Novel self-activated yellow-emitting BaLuAlxZn4-xO7-(1-x)/2 photoluminescent materials were investigated by a combined experimental and theoretical analysis. The effects of Al/Zn composition modulation, calcination atmosphere and temperature on the crystal structure and photoluminescence properties have been studied via engineering oxygen vacancies. Accordingly, BaLuAl0.91Zn3.09O7 prepared in an air atmosphere was found to be the stable crystalline phase with optimal oxygen content and gave a broad yellow emission band with a maximum at 528 nm. The self-activated luminescence mechanism is ascribed to the O-vacancies based on the density functional theory (DFT) calculation. A theoretical model originating from the designed oxygen vacancies has been proposed in order to determine the influence of O-vacancies on the band structure and self-activated luminescence. Therefore, the appearance of a new local energy level in the band gap will cause the wide-band optical transitions in the studied BaLuAlxZn4-xO7-(1-x)/2 materials.

  8. Target Selection and Determination of Function in Structural Genomics

    Science.gov (United States)

    Watson, James D.; Todd, Annabel E.; Bray, James; Laskowski, Roman A.; Edwards, Aled; Joachimiak, Andrzej; Orengo, Christine A.; Thornton, Janet M.

    2011-01-01

    Summary The first crucial step in any structural genomics project is the selection and prioritization of target proteins for structure determination. There may be a number of selection criteria to be satisfied, including that the proteins have novel folds, that they be representatives of large families for which no structure is known, and so on. The better the selection at this stage, the greater is the value of the structures obtained at the end of the experimental process. This value can be further enhanced once the protein structures have been solved if the functions of the given proteins can also be determined. Here we describe the methods used at either end of the experimental process: firstly, sensitive sequence comparison techniques for selecting a high-quality list of target proteins, and secondly the various computational methods that can be applied to the eventual 3D structures to determine the most likely biochemical function of the proteins in question. PMID:12880206

  9. Exchange and Dzyaloshinskii-Moriya interactions in bulk FeGe: Effects of atomic vacancies

    Directory of Open Access Journals (Sweden)

    G. C. Loh

    2017-05-01

    Full Text Available We examine the effects of atomic vacancies on the (1 spin interaction, and (2 electronic character in the cubic B20 chiral magnet FeGe. For the former, Heisenberg exchange and Dzyaloshinskii-Moriya (DM interactions are studied. The latter is done via a particular Wannier flavor of the Hamiltonian in the form of maximally-localized Wannier functions (MLWFs. Using first-principles calculations based on full-potential linearized augmented plane-wave (FLAPW-based density functional theory (DFT, the spin order of bulk FeGe, in its pristine form, and with a Fe (Fe75%Ge100% or Ge vacancy (Fe100%Ge75% is investigated. Despite the presence of vacancies, the ground state of FeGe remains helimagnetic, i.e. spin spirals in FeGe are fairly robust. The energetic stability of FeGe increases in the presence of the vacancies. The spiral size is increased by approximately 40%, suggesting that vacancies can be introduced to manipulate the chiral order. The vacancies lift the band degeneracy in the valence manifold of the Wannier-interpolated band structures. Only the spin-down Fermi surfaces are substantially different between the pristine and defective FeGe; it is electron-like in the pristine case, but largely hole-like in the defective ones. The Ge vacancy splits the Fermi surface more than the Fe vacancy. The Heisenberg exchange between nearest Fe pairs is ferromagnetic in pristine FeGe. This Fe-Fe interaction remains ferromagnetic, albeit a slight decrease in strength, in the presence of a Fe vacancy. In contrast, a Ge vacancy in FeGe induces anti-ferromagnetism between nearest Fe pairs. By including spin-orbit coupling effects, we find that the DM interaction of defective FeGe is reversed in sign, and it is more uniform in strength along the three highly symmetric directions, relative to that in pristine FeGe. All in all, the versatility of FeGe makes it an excellent functional material, especially in data storage and spintronics applications.

  10. Exchange and Dzyaloshinskii-Moriya interactions in bulk FeGe: Effects of atomic vacancies

    Science.gov (United States)

    Loh, G. C.; Gan, C. K.

    2017-05-01

    We examine the effects of atomic vacancies on the (1) spin interaction, and (2) electronic character in the cubic B20 chiral magnet FeGe. For the former, Heisenberg exchange and Dzyaloshinskii-Moriya (DM) interactions are studied. The latter is done via a particular Wannier flavor of the Hamiltonian in the form of maximally-localized Wannier functions (MLWFs). Using first-principles calculations based on full-potential linearized augmented plane-wave (FLAPW)-based density functional theory (DFT), the spin order of bulk FeGe, in its pristine form, and with a Fe (Fe75%Ge100%) or Ge vacancy (Fe100%Ge75%) is investigated. Despite the presence of vacancies, the ground state of FeGe remains helimagnetic, i.e. spin spirals in FeGe are fairly robust. The energetic stability of FeGe increases in the presence of the vacancies. The spiral size is increased by approximately 40%, suggesting that vacancies can be introduced to manipulate the chiral order. The vacancies lift the band degeneracy in the valence manifold of the Wannier-interpolated band structures. Only the spin-down Fermi surfaces are substantially different between the pristine and defective FeGe; it is electron-like in the pristine case, but largely hole-like in the defective ones. The Ge vacancy splits the Fermi surface more than the Fe vacancy. The Heisenberg exchange between nearest Fe pairs is ferromagnetic in pristine FeGe. This Fe-Fe interaction remains ferromagnetic, albeit a slight decrease in strength, in the presence of a Fe vacancy. In contrast, a Ge vacancy in FeGe induces anti-ferromagnetism between nearest Fe pairs. By including spin-orbit coupling effects, we find that the DM interaction of defective FeGe is reversed in sign, and it is more uniform in strength along the three highly symmetric directions, relative to that in pristine FeGe. All in all, the versatility of FeGe makes it an excellent functional material, especially in data storage and spintronics applications.

  11. Rapid and reliable protein structure determination via chemical shift threading.

    Science.gov (United States)

    Hafsa, Noor E; Berjanskii, Mark V; Arndt, David; Wishart, David S

    2017-12-01

    Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often structure) and to significantly outperform other shift-based or threading-based structure determination methods (in terms of top template model accuracy)-with an average TM-score performance of 0.68 (vs. 0.50-0.62 for other methods). Coupled with recent developments in chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

  12. Trapping of oxygen vacancies on twin walls of CaTiO sub 3 : a computer simulation study

    CERN Document Server

    Calleja, M; Salje, E K H

    2003-01-01

    We have studied the atomic structure of [001] 90 deg. rotation twin walls in orthorhombic CaTiO sub 3 (symmetry Pbnm) at low temperature (10 K) and their effects on oxygen vacancies. The wall thickness was found to be 2.3 nm at T || T sub c and it was found that it is energetically favourable for such vacancies to reside in the wall, particularly when bridging titania ions in the (001) plane. The binding energy of an oxygen vacancy in the wall with respect to the bulk is calculated to be <= 1.2 eV.

  13. Nanoscale NMR and NQR with Nitrogen Vacancy Centers

    Science.gov (United States)

    Urbach, Elana; Lovchinsky, Igor; Sanchez-Yamagishi, Javier; Choi, Soonwon; Bylinskii, Alexei; Dwyer, Bo; Andersen, Trond; Sushkov, Alex; Park, Hongkun; Lukin, Mikhail

    2016-05-01

    Nuclear quadrupole resonance (NQR) is a powerful tool which is used to detect quadrupolar interaction in nuclear spins with I > 1/2. Conventional NQR and NMR technology, however, rely on measuring magnetic fields from a macroscopic number of spins. Extending NMR and NQR techniques to the nanoscale could allow us to learn structural information about interesting materials and biomolecules. We present recent progress on using Nitrogen-Vacancy (NV) centers in diamond to perform room temperature nanoscale NMR and NQR spectroscopy on small numbers of nuclear spins in hexagonal boron nitride.

  14. Effect of random vacancies on the electronic properties of graphene and T graphene: a theoretical approach

    Science.gov (United States)

    Sadhukhan, B.; Nayak, A.; Mookerjee, A.

    2017-12-01

    In this communication we present together four distinct techniques for the study of electronic structure of solids: the tight-binding linear muffin-tin orbitals, the real space and augmented space recursions and the modified exchange-correlation. Using this we investigate the effect of random vacancies on the electronic properties of the carbon hexagonal allotrope, graphene, and the non-hexagonal allotrope, planar T graphene. We have inserted random vacancies at different concentrations, to simulate disorder in pristine graphene and planar T graphene sheets. The resulting disorder, both on-site (diagonal disorder) as well as in the hopping integrals (off-diagonal disorder), introduces sharp peaks in the vicinity of the Dirac point built up from localized states for both hexagonal and non-hexagonal structures. These peaks become resonances with increasing vacancy concentration. We find that in presence of vacancies, graphene-like linear dispersion appears in planar T graphene and the cross points form a loop in the first Brillouin zone similar to buckled T graphene that originates from π and π* bands without regular hexagonal symmetry. We also calculate the single-particle relaxation time, τ (ěc {q}) of ěc {q} labeled quantum electronic states which originates from scattering due to presence of vacancies, causing quantum level broadening.

  15. Protein Structure Determination Using Protein Threading and Sparse NMR Data

    Energy Technology Data Exchange (ETDEWEB)

    Crawford, O.H.; Einstein, J.R.; Xu, D.; Xu, Y.

    1999-11-14

    It is well known that the NMR method for protein structure determination applies to small proteins and that its effectiveness decreases very rapidly as the molecular weight increases beyond about 30 kD. We have recently developed a method for protein structure determination that can fully utilize partial NMR data as calculation constraints. The core of the method is a threading algorithm that guarantees to find a globally optimal alignment between a query sequence and a template structure, under distance constraints specified by NMR/NOE data. Our preliminary tests have demonstrated that a small number of NMR/NOE distance restraints can significantly improve threading performance in both fold recognition and threading-alignment accuracy, and can possibly extend threading's scope of applicability from structural homologs to structural analogs. An accurate backbone structure generated by NMR-constrained threading can then provide a significant amount of structural information, equivalent to that provided by the NMR method with many NMR/NOE restraints; and hence can greatly reduce the amount of NMR data typically required for accurate structure determination. Our preliminary study suggests that a small number of NMR/NOE restraints may suffice to determine adequately the all-atom structure when those restraints are incorporated in a procedure combining threading, modeling of loops and sidechains, and molecular dynamics simulation. Potentially, this new technique can expand NMR's capability to larger proteins.

  16. The vacancies formation and agglomeration under centrifugal force

    Science.gov (United States)

    Wierzba, Bartek

    2017-10-01

    In this paper the vacancies formation and agglomeration under centrifugal force - sedimentation will be analyzed. The evolutionary algorithm for diffusion and vacancy evolution will be shown. The model predicts the location of vacancies agglomeration during the sedimentation process - the most probably place of voids formation. The computed results will be compared with experiments in Cu-brass diffusion couple. The influence of the centrifugal force on the vacancies migration will be presented.

  17. Determination of Velocity And Acceleration of Structural Deformation ...

    African Journals Online (AJOL)

    Journal of the Nigerian Association of Mathematical Physics ... Objects and engineering structures are subject to displacements resulting from ... is possible on the basis of cyclic measurements of changes in position of points determining the ...

  18. Determination of Structures of Proteins in Solution using Nuclear ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 8; Issue 8. Determination of Structures of Proteins in Solution using Nuclear Magnetic Resonance. Siddhartha P Sarma. Research News Volume 8 Issue 8 August 2003 pp 86-99 ...

  19. Nitrogen-vacancy ensemble magnetometry based on pump absorption

    DEFF Research Database (Denmark)

    Ahmadi, Sepehr; El-Ella, Haitham A. R.; Wojciechowski, Adam M.

    2018-01-01

    We demonstrate magnetic-field sensing using an ensemble of nitrogen-vacancy centers by recording the variation in the pump-light absorption due to the spin-polarization dependence of the total ground-state population. Using a 532 nm pump laser, we measure the absorption of native nitrogen-vacancy...... the nitrogen-vacancy concentration and the detection method....

  20. 45 CFR 1176.7 - Publicizing vacancies.

    Science.gov (United States)

    2010-10-01

    ... HUMANITIES NATIONAL ENDOWMENT FOR THE HUMANITIES PART-TIME CAREER EMPLOYMENT § 1176.7 Publicizing vacancies. When applicants from outside the Federal service are desired, part-time vacanies may be publicized through various recruiting means, such as: (a) Federal Job Information Centers. (b) State Employment...

  1. 7 CFR 915.26 - Vacancies.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 8 2010-01-01 2010-01-01 false Vacancies. 915.26 Section 915.26 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements and Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE AVOCADOS GROWN IN SOUTH FLORIDA Order...

  2. 7 CFR 1219.36 - Vacancies.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Vacancies. 1219.36 Section 1219.36 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (MARKETING AGREEMENTS AND ORDERS; MISCELLANEOUS COMMODITIES), DEPARTMENT OF AGRICULTURE HASS AVOCADO PROMOTION, RESEARCH...

  3. 7 CFR 1207.324 - Vacancies.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Vacancies. 1207.324 Section 1207.324 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (MARKETING AGREEMENTS AND ORDERS; MISCELLANEOUS COMMODITIES), DEPARTMENT OF AGRICULTURE POTATO RESEARCH AND PROMOTION PLAN...

  4. Transaction cost determinants of credit governance structures of ...

    African Journals Online (AJOL)

    This paper explores transaction cost determinants of credit governance structures (CGS) of commercial banks in Tanzania. Descriptive statistics, linear regression model, binary and multinomial logistic regression models were employed for analysis. Findings revealed four modes of credit governance structures that are ...

  5. Determination of conduction and valence band electronic structure ...

    Indian Academy of Sciences (India)

    Electronic structures of rutile and anatase polymorph of TiO2 were determined by resonant inelastic X-ray scattering measurements and FEFF9.0 calculations. Difference between crystalline structures led to shifts in the rutile Ti -band to lower energy with respect to anatase, i.e., decrease in band gap. Anatase possesses ...

  6. Food web structure in three contrasting estuaries determined using ...

    African Journals Online (AJOL)

    Food web structure in three contrasting estuaries determined using stable isotope (δ 13 C) analysis. ... African Journal of Aquatic Science ... Food web structure in three contrasting estuaries, the freshwater-deprived Kariega, the freshwater-dominated Great Fish River and the temporarily open/closed Kasouga estuary, along ...

  7. Magnetism in Sc-doped ZnO with zinc vacancies: A hybrid density functional and GGA + U approaches

    KAUST Repository

    Kanoun, Mohammed

    2012-04-01

    We investigate the zinc vacancy effects on the electronic structures and magnetic properties of Sc-doped ZnO, by performing first-principles calculations within both GGA + U and Heyd-Scuseria-Ernzerhof hybrid functional methods. We find that Sc impurities stabilize considerably Zn vacancies. The electronic and magnetic analysis shows a half metallic ferromagnetic character with a total magnetic moment of 2.01 μ B. The magnetism mainly stems from the O 2p states around the Zn vacancies. Calculations with the hybrid density functional agree with the GGA + U results but give an accurate description of the electronic structure for pure ZnO and Sc-doped ZnO with Zn vacancies. © 2012 Elsevier B.V. All rights reserved.

  8. Mass Spectrometric Determination of Gas Phase Structures of Amino Acids

    OpenAIRE

    Rožman, Marko; Srzić, Dunja

    2005-01-01

    In the past two decades mass spectrometry became an important tool in the structural investigations of biomolecules (amino acids). Although, the primary focus of mass spectrometry is on compound identification and sequence information (primary structure), some mass spectrometry based methods as ion chromatography, hydrogen/deuterium exchange, and kinetic method are able to determine secondary gas phase structure of the amino acids. For example, it is possible to distinguish the zwitterionic a...

  9. Oxygen vacancies dependent phase transition of Y{sub 2}O{sub 3} films

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Pengfei; Zhang, Kan [Department of Materials Science, State Key Laboratory of Superhard Materials, and Key Laboratory of Automobile Materials, MOE, Jilin University, Changchun 130012 (China); Huang, Hao [Titanium Alloys Lab. Beijing Institute of Aeronautical Materials, Beijing 81-15 100095 (China); Wen, Mao, E-mail: Wenmao225@jlu.edu.cn [Department of Materials Science, State Key Laboratory of Superhard Materials, and Key Laboratory of Automobile Materials, MOE, Jilin University, Changchun 130012 (China); Li, Quan; Zhang, Wei; Hu, Chaoquan [Department of Materials Science, State Key Laboratory of Superhard Materials, and Key Laboratory of Automobile Materials, MOE, Jilin University, Changchun 130012 (China); Zheng, Weitao, E-mail: WTZheng@jlu.edu.cn [Department of Materials Science, State Key Laboratory of Automotive Simulation and Control and Key Laboratory of Automobile Materials, MOE, Jilin University, Changchun 130012 (China)

    2017-07-15

    Highlights: • Oxygen vacancies for Y{sub 2}O{sub 3} films increase monotonously with increasing T{sub s}. • Oxygen vacancies can promote the nucleation of monoclinic phase. • That monoclinic phase with oxygen deficiency is not thermodynamic stable at high temperature. • Phase transition from monoclinic to oxygen defective occurs at high concentrations of oxygen vacancies. • High hardness just appears in Y{sub 2}O{sub 3} films with mixed phase configurations. - Abstract: Y{sub 2}O{sub 3} films have great application potential in high-temperature metal matrix composite and nuclear engineering, used as interface diffusion and reaction barrier coating owing to their excellent thermal and chemical stability, high melting point and extremely negative Gibbs formation energy, and thus their structural and mechanical properties at elevated temperature are especially important. Oxygen vacancies exist commonly in yttrium oxide (Y{sub 2}O{sub 3}) thin films and act strongly on the phase structure and properties, but oxygen vacancies dependent phase transition at elevated temperature has not been well explored yet. Y{sub 2}O{sub 3} thin films with different oxygen vacancy concentrations have been achieved by reactive sputtering through varying substrate temperature (T{sub s}), in which oxygen vacancies increase monotonously with increasing T{sub s}. For as-deposited Y{sub 2}O{sub 3} films, oxygen vacancies present at high T{sub s} can promote the nucleation of monoclinic phase, meanwhile, high T{sub s} can induce the instability of monoclinic phase. Thus their competition results in forming mixed phases of cubic and monoclinic at high T{sub s}. During vacuum annealing at 1000 °C, a critical oxygen vacancy concentration is observed, below which phase transition from monoclinic to cubic takes place, and above which phase transfer from monoclinic to the oxygen defective phase (ICDD file no. 39-1063), accompanying by stress reversal from compressive to tensile and

  10. Denotational, Causal, and Operational Determinism in Event Structures

    NARCIS (Netherlands)

    Rensink, Arend; Kirchner, H.

    1996-01-01

    Determinism of labelled transition systems and trees is a concept of theoretical and practical importance. We study its generalisation to event structures. It turns out that the result depends on what characterising property of tree determinism one sets out to generalise. We present three distinct

  11. Denotational, Causal, and Operational Determinism in Event Structures

    NARCIS (Netherlands)

    Rensink, Arend

    Determinism is a theoretically and practically important concept in labelled transition systems and trees. We study its generalisation to event structures. It turns out that the result depends on what characterising property of tree determinism one sets out to generalise. We present three distinct

  12. Integral membrane protein structure determination using pseudocontact shifts.

    Science.gov (United States)

    Crick, Duncan J; Wang, Jue X; Graham, Bim; Swarbrick, James D; Mott, Helen R; Nietlispach, Daniel

    2015-04-01

    Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary strategies highly beneficial for successful structure elucidation. Recently, lanthanide-induced pseudocontact shifts (PCSs) have been established as a structural tool for globular proteins. Here, we demonstrate that a PCS-based approach can be successfully applied for the structure determination of integral membrane proteins. Using the 7TM α-helical microbial receptor pSRII, we show that PCS-derived restraints from lanthanide binding tags attached to four different positions of the protein facilitate the backbone structure determination when combined with a limited set of NOEs. In contrast, the same set of NOEs fails to determine the correct 3D fold. The latter situation is frequently encountered in polytopical α-helical membrane proteins and a PCS approach is thus suitable even for this particularly challenging class of membrane proteins. The ease of measuring PCSs makes this an attractive route for structure determination of large membrane proteins in general.

  13. Integral membrane protein structure determination using pseudocontact shifts

    Energy Technology Data Exchange (ETDEWEB)

    Crick, Duncan J.; Wang, Jue X. [University of Cambridge, Department of Biochemistry (United Kingdom); Graham, Bim; Swarbrick, James D. [Monash University, Monash Institute of Pharmaceutical Sciences (Australia); Mott, Helen R.; Nietlispach, Daniel, E-mail: dn206@cam.ac.uk [University of Cambridge, Department of Biochemistry (United Kingdom)

    2015-04-15

    Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary strategies highly beneficial for successful structure elucidation. Recently, lanthanide-induced pseudocontact shifts (PCSs) have been established as a structural tool for globular proteins. Here, we demonstrate that a PCS-based approach can be successfully applied for the structure determination of integral membrane proteins. Using the 7TM α-helical microbial receptor pSRII, we show that PCS-derived restraints from lanthanide binding tags attached to four different positions of the protein facilitate the backbone structure determination when combined with a limited set of NOEs. In contrast, the same set of NOEs fails to determine the correct 3D fold. The latter situation is frequently encountered in polytopical α-helical membrane proteins and a PCS approach is thus suitable even for this particularly challenging class of membrane proteins. The ease of measuring PCSs makes this an attractive route for structure determination of large membrane proteins in general.

  14. Structure Determination of Natural Products by Mass Spectrometry

    Science.gov (United States)

    Biemann, Klaus

    2015-07-01

    I review laboratory research on the development of mass spectrometric methodology for the determination of the structure of natural products of biological and medical interest, which I conducted from 1958 to the end of the twentieth century. The methodology was developed by converting small peptides to their corresponding polyamino alcohols to make them amenable to mass spectrometry, thereby making it applicable to whole proteins. The structures of alkaloids were determined by analyzing the fragmentation of a known alkaloid and then using the results to deduce the structures of related compounds. Heparin-like structures were investigated by determining their molecular weights from the mass of protonated molecular ions of complexes with highly basic, synthetic peptides. Mass spectrometry was also employed in the analysis of lunar material returned by the Apollo missions. A miniaturized gas chromatograph mass spectrometer was sent to Mars on board of the two Viking 1976 spacecrafts.

  15. Structural determination of intact proteins using mass spectrometry

    Science.gov (United States)

    Kruppa, Gary [San Francisco, CA; Schoeniger, Joseph S [Oakland, CA; Young, Malin M [Livermore, CA

    2008-05-06

    The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

  16. Lattice Effects on the Formation of Oxygen Vacancies in Perovskite Thin Films

    Science.gov (United States)

    Cazorla, Claudio

    2017-04-01

    We use first-principles methods to investigate the effects of collective lattice excitations on the formation of oxygen vacancies in perovskite thin films. We find that phonons play a crucial role in the strain-mediated control of defect chemistry at finite temperatures. Specifically, zero-temperature oxygen-vacancy formation trends deduced as a function of epitaxial strain can be fully reversed near room temperature. Our first-principles calculations evidence a direct link between the lattice contribution to the oxygen-vacancy free energy and the volume expansion that the system undergoes when it is chemically reduced: The larger the resulting volume expansion, the more favorable thermal excitations are to point-defect formation. However, the interplay between the vibrational vacancy entropy—or, equivalently, chemical expansion—and epitaxial strain is difficult to generalize, as it can be strongly influenced by underlying structural and magnetic transitions. In addition, we find that vacancy ordering can be largely hindered by the thermal lattice excitations.

  17. Role of vacancies in tuning the electronic properties of Au-MoS{sub 2} contact

    Energy Technology Data Exchange (ETDEWEB)

    Su, Jie, E-mail: sujie0105@mail.nwpu.edu.cn, E-mail: lpfeng@nwpu.edu.cn; Li, Ning; Zhang, Yingying; Feng, Liping, E-mail: sujie0105@mail.nwpu.edu.cn, E-mail: lpfeng@nwpu.edu.cn; Liu, Zhengtang [State Key Lab of Solidification Processing, College of Materials Science and Engineering, Northwestern Polytechnical University, Xi’an, Shaanxi, 710072 (China)

    2015-07-15

    Understanding the electronic properties between molybdenum disulfide (MoS{sub 2}) and metal electrodes is vital for the designing and realization of nanoelectronic devices. In this work, influence of intrinsic vacancies in monolayer MoS{sub 2} on the electronic structure and electron properties of Au-MoS{sub 2} contacts is investigated using first-principles calculations. Upon formation of vacancies in monolayer MoS{sub 2}, both tunnel barriers and Schottky Barriers between metal Au and monolayer MoS{sub 2} are decreased. Perfect Au-MoS{sub 2} top contact exhibits physisorption interface with rectifying character, whereas Au-MoS{sub 2} contact with Mo-vacancy shows chemisorption interface with Ohmic character. Partial density of states and electron density of defective Au-MoS{sub 2} top contacts are much higher than those of perfect one, indicating the lower contact resistance and higher electron injection efficiency of defective Au-MoS{sub 2} top contacts. Notably, Mo-vacancy in monolayer MoS{sub 2} is beneficial to get high quality p-type Au-MoS{sub 2} top contact, whereas S-vacancy in monolayer MoS{sub 2} is favorable to achieve high quality n-type Au-MoS{sub 2} top contact. Our results provide guidelines for designing and fabrication of novel 2D nanoelectronic devices.

  18. Role of vacancies in tuning the electronic properties of Au-MoS2 contact

    Directory of Open Access Journals (Sweden)

    Jie Su

    2015-07-01

    Full Text Available Understanding the electronic properties between molybdenum disulfide (MoS2 and metal electrodes is vital for the designing and realization of nanoelectronic devices. In this work, influence of intrinsic vacancies in monolayer MoS2 on the electronic structure and electron properties of Au-MoS2 contacts is investigated using first-principles calculations. Upon formation of vacancies in monolayer MoS2, both tunnel barriers and Schottky Barriers between metal Au and monolayer MoS2 are decreased. Perfect Au-MoS2 top contact exhibits physisorption interface with rectifying character, whereas Au-MoS2 contact with Mo-vacancy shows chemisorption interface with Ohmic character. Partial density of states and electron density of defective Au-MoS2 top contacts are much higher than those of perfect one, indicating the lower contact resistance and higher electron injection efficiency of defective Au-MoS2 top contacts. Notably, Mo-vacancy in monolayer MoS2 is beneficial to get high quality p-type Au-MoS2 top contact, whereas S-vacancy in monolayer MoS2 is favorable to achieve high quality n-type Au-MoS2 top contact. Our results provide guidelines for designing and fabrication of novel 2D nanoelectronic devices.

  19. Determination of the Crystal Structure of Lead Tungstate by Neutron Diffraction

    CERN Document Server

    Cousson, A; Paulus, W

    1999-01-01

    The crystal structure of lead tungstate, PbWO4, is tetragonal, scheelite type, space group I4/a. This compound, due to the difference in the vapour pressure of the two raw oxides, WO3 and PbO, used in the crystal growth, is frequently subjected to lead deficiency. It has been reported by one group that lead vacancies can order in a crystal structure derived from the scheelite type, but of lower symmetry and described by the space group P4/nnc or P-4. We report here on neutron diffraction measurements performed on three different single crystals, two of them being presented to us as possibly presenting the lead deficient phase. Our measurements do not show any indication of structural distortion, even at 70 K for one of the samples. The existence of a lead deficient structure remains unconfirmed.

  20. O-vacancies in (i) nano-crystalline HfO2 and (i) non-crystalline SiO2 and Si3N4 studied by X-ray absorption spectroscopy.

    Science.gov (United States)

    Lucovsky, Gerald; Miotti, Leonardo; Bastos, Karen Paz

    2012-06-01

    Performance and reliability in semiconductor devices are limited by electronically active defects, primarily O-atom and N-atom vacancies. Synchrotron X-ray spectroscopy results, interpreted in the context of two-electron multiplet theories, have been used to analyze conduction band edge, and O-vacancy defect states in nano-crystalline transition metal oxides, e.g., HfO2, and the noncrystalline dielectrics, SiO2, Si3N4 and Si-oxynitride alloys. Two-electron multiplet theory been used to develop a high-spin state equivalent d2 model for O-vacancy allowed transitions and negative ion states as detected by X-ray absorption spectroscopy in the O K pre-edge regime. Comparisons between theory and experiment have used Tanabe-Sugano energy level diagrams for determining the symmetries and relative energies of intra-d-state transitions for an equivalent d2 ground state occupancy. Trap-assisted-tunneling, Poole-Frenkel hopping transport, and the negative bias temperature instability have been explained in terms of injection and/or trapping into O-atom and N-atom vacancy sites, and applied to gate dielectric, and metal-insulator-metal structures.

  1. PHENIX: building new software for automated crystallographic structure determination.

    Science.gov (United States)

    Adams, Paul D; Grosse-Kunstleve, Ralf W; Hung, Li Wei; Ioerger, Thomas R; McCoy, Airlie J; Moriarty, Nigel W; Read, Randy J; Sacchettini, James C; Sauter, Nicholas K; Terwilliger, Thomas C

    2002-11-01

    Structural genomics seeks to expand rapidly the number of protein structures in order to extract the maximum amount of information from genomic sequence databases. The advent of several large-scale projects worldwide leads to many new challenges in the field of crystallographic macromolecular structure determination. A novel software package called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is therefore being developed. This new software will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model and to facilitate structure solution for both the novice and expert crystallographer.

  2. Vacancy induced metallicity at the CaHfO3/SrTiO3 interface

    KAUST Repository

    Nazir, Safdar

    2011-03-31

    Density functional theory is used to study the electronic properties of the oxide heterointerfaceCaHfO3/SrTiO3. Structural relaxation is carried out with and without O vacancies. As compared to related interfaces, strongly reduced octahedral distortions are found. Stoichiometric interfaces between the wide band gap insulatorsCaHfO3 and SrTiO3 turn out to exhibit an insulating state. However, interface metallicity is introduced by O vacancies, in agreement with experiment. The reduced octahedral distortions and necessity of O deficiency indicate a less complicated mechanism for the creation of the interfacial electron gas.

  3. Phase stability and the arsenic vacancy defect in InxGa1−xAs

    KAUST Repository

    Murphy, S. T.

    2011-11-18

    The introduction of defects, such as vacancies, into InxGa1−xAs can have a dramatic impact on the physical and electronic properties of the material. Here we employ ab initio simulations of quasirandom supercells to investigate the structure of InxGa1−xAs and then examine the energy and volume changes associated with the introduction of an arsenic vacancy defect. We predict that both defect energies and volumes for intermediate compositions of InxGa1−xAs differ significantly from what would be expected by assuming a simple linear interpolation of the end member defect energies/volumes.

  4. Evidence for Vacancy Mechanism in Grain Boundary Diffusion in bcc Iron: A Molecular-Dynamics Study

    Science.gov (United States)

    Kwok, Thomas; Ho, P. S.; Yip, Sidney; Balluffi, R. W.; Bristowe, P. D.; Brokman, A.

    1981-10-01

    The dominance of vacancy migration in grain boundary self-diffusion has been established by molecular-dynamics simulation of a bcc iron Σ=5 tilt boundary. The data yielded a reasonable value of the activation energy for migration and showed that the jump processes are highly structure dependent. The use of a temperature-dependent transition-probability matrix to describe the diffusion of the vacancies in the grain boundary is suggested. Formation of one type of boundary interstitial was observed, and the interstitial was found to be immobile during its lifetime.

  5. Mössbauer and DLTS Investigations of Impurity-Vacancy Complexes in Semiconductors

    CERN Multimedia

    Nylandsted larsen, A

    2002-01-01

    % IS321 \\\\ \\\\ The structure and electronic states of impurity-vacancy complexes formed in silicon-based semiconductors are proposed to be studied by Mössbauer and DLTS techniques utilizing implanted radioactive $^{119}$Sb isotopes. Impurity-vacancy complexes are created thermally at high temperatures, but can also be produced by electron and ion irradiation at low temperatures. By comparing complexes created by both methods we expect to be able to understand the newly discovered, extremely fast diffusion of dopants in n-type extrinsic silicon.

  6. High temperature thermoelectric properties of strontium titanate thin films with oxygen vacancy and niobium doping

    KAUST Repository

    Sarath Kumar, S. R.

    2013-08-14

    We report the evolution of high temperature thermoelectric properties of SrTiO3 thin films doped with Nb and oxygen vacancies. Structure-property relations in this important thermoelectric oxide are elucidated and the variation of transport properties with dopant concentrations is discussed. Oxygen vacancies are incorporated during growth or annealing in Ar/H2 above 800 K. An increase in lattice constant due to the inclusion of Nb and oxygen vacancies is found to result in an increase in carrier density and electrical conductivity with simultaneous decrease in carrier effective mass and Seebeck coefficient. The lattice thermal conductivity at 300 K is found to be 2.22 W m-1 K-1, and the estimated figure of merit is 0.29 at 1000 K. © 2013 American Chemical Society.

  7. Three-dimensional structure determination from a single view.

    Science.gov (United States)

    Raines, Kevin S; Salha, Sara; Sandberg, Richard L; Jiang, Huaidong; Rodríguez, Jose A; Fahimian, Benjamin P; Kapteyn, Henry C; Du, Jincheng; Miao, Jianwei

    2010-01-14

    The ability to determine the structure of matter in three dimensions has profoundly advanced our understanding of nature. Traditionally, the most widely used schemes for three-dimensional (3D) structure determination of an object are implemented by acquiring multiple measurements over various sample orientations, as in the case of crystallography and tomography, or by scanning a series of thin sections through the sample, as in confocal microscopy. Here we present a 3D imaging modality, termed ankylography (derived from the Greek words ankylos meaning 'curved' and graphein meaning 'writing'), which under certain circumstances enables complete 3D structure determination from a single exposure using a monochromatic incident beam. We demonstrate that when the diffraction pattern of a finite object is sampled at a sufficiently fine scale on the Ewald sphere, the 3D structure of the object is in principle determined by the 2D spherical pattern. We confirm the theoretical analysis by performing 3D numerical reconstructions of a sodium silicate glass structure at 2 A resolution, and a single poliovirus at 2-3 nm resolution, from 2D spherical diffraction patterns alone. Using diffraction data from a soft X-ray laser, we also provide a preliminary demonstration that ankylography is experimentally feasible by obtaining a 3D image of a test object from a single 2D diffraction pattern. With further development, this approach of obtaining complete 3D structure information from a single view could find broad applications in the physical and life sciences.

  8. Ordered-vacancy-compound semiconductors: Pseudocubic CdIn2Se4

    Science.gov (United States)

    Bernard, James E.; Zunger, Alex

    1988-04-01

    Whereas substitutional adamantine compounds AnB4-nC4 (e.g., ABC2 chalcopyrites for n=2, or the AC and BC zinc-blende compounds for n=4 and 0) have four metal atoms around each nonmetal atom and vice versa, ordered-vacancy compounds OVC's) AB2C4 have but three metal atoms (one A and two B's) around each nonmetal site (C) while the fourth (unoccupied) site forms an ordered array of vacancies. An example for OVC's is ``pseudocubic'' CdIn2Se4 which can be structurally derived from the layered alternate monolayer superlattice of CdSe and InSe (along the [001] direction) by removing half of the Cd atoms from each Cd plane. Such OVC's form a natural bridge between crystal and impurity physics. Much like the metal vacancy in II-VI compounds (e.g., CdSe), the vacancy in CdIn2Se4 has associated with it (nonmetal) ``dangling bonds'' and ``lone-pair'' electrons, which, however, form a dispersed band in the crystal. Using all-electron mixed-basis electronic-structure techniques, we study the properties of such an ordered array of vacancies in CdIn2Se4 vis-a$ga--vis the experimental data. We find vacancy-induced atomic relaxations (Se moves towards the vacant site), resonant broadening of the lone-pair dangling-bond states into a ~=3-eV band, and that the total charge density around the vacant site has little density and shows scant evidence of dangling bonds. We discuss the nature of the bonding in this system, comparing it to other covalent selenides and to the observed photoemission and optical data. A number of possible order-disorder transitions, including the disordering of cations on the vacant sites, are identified.

  9. Investigation of vacancy damage influence on He diffusion in apatite: implication for the (U-Th)/He thermochronometer

    Science.gov (United States)

    Gautheron, Cécile; Gerin, Chloé; Bachelet, Cyril; Mbongo Djimbi, Duval; Seydoux-Guillaume, Anne-Magali; Tassan-Got, Laurent; Roques, Jérôme; Garrido, Frédérico

    2017-04-01

    Helium diffusion in minerals rich in actinides, especially apatite, is considered as strongly impacted by damage, even at low U-Th content. However, no direct evidence exists neither about such an impact nor the damage topology. To better understand the impact of damage on He diffusion, we conducted a study on vacancy damage in apatite, at nanometric to atomic scales, using several methodologies [1]. We investigate the role of vacancy damage that are the one created during alpha decay. Firstly, Transmission Electron Microscopy (TEM) was used to image the damage structure done by He implantation in the first 200 nm below the surface of apatite crystal. TEM images present no visible damage zone at nano-scale, implying that the created damage corresponds well to Frenkel defects (vacancies and interstitials). Secondly, to test the damage impact on diffusion and the trapping efficiency, we conduct both experimental and theoretical studies. Diffusion experiments were performed on He implanted samples by mapping He concentration vs. depth profiles using Elastic Recoil Detection Analysis (ERDA). After measurement of implanted-He profiles and He concentrations, the samples were heated in order to diffuse the implanted profile. The obtained He vs. depth heated profiles and He concentrations reveal the impact of damage on He diffusivity. The results can only be explained by a model where diffusion depends on damage dose, taking into account He trapping in vacancies and damage interconnectivity at higher damage dose. Thirdly, Density Functional Theory (DFT) calculations were performed to simulate a vacancy in a F-apatite crystal, and results are compared with an undamaged apatite cell [2]. The structure becomes slightly deformed by the vacancy and the insertion energy of a He atom in the vacancy is lower than for an usual insertion site. Accordingly, the additional energy for a He atom to jump out of the vacancy is in good agreement with published estimates. This calculation

  10. A study on determinants of capital structure in India

    Directory of Open Access Journals (Sweden)

    Anshu Handoo

    2014-09-01

    Full Text Available The paper identifies the most important determinants of capital structure of 870 listed Indian firms comprising both private sector companies and government companies for the period 2001–2010. Ten independent variables and three dependent variables have been tested using regression analysis. It has been concluded that factors such as profitability, growth, asset tangibility, size, cost of debt, tax rate, and debt serving capacity have significant impact on the leverage structure chosen by firms in the Indian context.

  11. Determinants of Market Structure and the Airline Industry

    Science.gov (United States)

    Raduchel, W.

    1972-01-01

    The general economic determinants of market structure are outlined with special reference to the airline industry. Included are the following facets: absolute size of firms; distributions of firms by size; concentration; entry barriers; product and service differentiation; diversification; degrees of competition; vertical integration; market boundaries; and economies of scale. Also examined are the static and dynamic properties of market structure in terms of mergers, government policies, and economic growth conditions.

  12. Optimizing an emperical scoring function for transmembrane protein structure determination.

    Energy Technology Data Exchange (ETDEWEB)

    Young, Malin M.; Sale, Kenneth L.; Gray, Genetha Anne; Kolda, Tamara Gibson

    2003-10-01

    We examine the problem of transmembrane protein structure determination. Like many other questions that arise in biological research, this problem cannot be addressed by traditional laboratory experimentation alone. An approach that integrates experiment and computation is required. We investigate a procedure which states the transmembrane protein structure determination problem as a bound constrained optimization problem using a special empirical scoring function, called Bundler, as the objective function. In this paper, we describe the optimization problem and some of its mathematical properties. We compare and contrast results obtained using two different derivative free optimization algorithms.

  13. Organizational Structure as a Determinant of Job Burnout.

    Science.gov (United States)

    Bilal, Atif; Ahmed, Hafiz Mushtaq

    2017-03-01

    This exploratory study determined the impact of organizational structure, particularly participation in decision making, instrumental communication, formalization, integration, and promotional opportunity, on burnout among Pakistani pediatric nurses. Data were collected from pediatric nurses working for Punjab's largest state-run hospital. The findings revealed that participation in decision making, instrumental communication, and promotional opportunity prevented burnout. Formalization contributed to burnout but integration was not related to burnout. Quite interestingly, except for supervisory status, most control variables for this study were not significantly related to emotional burnout. Hence, the hypothesis that organizational structure is a determinant of job burnout was accepted.

  14. Optomechanics with levitating nitrogen-vacancy centers

    OpenAIRE

    Ahmed Abobeih, Mohamed

    2015-01-01

    Levitated nanoparticles in high vacuum have recently demonstrated unique capabilities to advance the field of optomechanics, by providing a new platform for ultra high quality factors nanomechanical oscillators, thanks to the absence of supporting substrates. At the same time, nitrogen-vacancy (NV) centers in nanodiamonds have shown outstanding properties as individual quantum objects, acting as artificial atoms. Therefore, the levitation of NV centers in high vacuum is expected to open a new...

  15. Novel genetic algorithm search procedure for LEED surface structure determination.

    Science.gov (United States)

    Viana, M L; dos Reis, D D; Soares, E A; Van Hove, M A; Moritz, W; de Carvalho, V E

    2014-06-04

    Low Energy Electron Diffraction (LEED) is one of the most powerful experimental techniques for surface structure analysis but until now only a trial-and-error approach has been successful. So far, fitting procedures developed to optimize structural and nonstructural parameters-by minimization of the R-factor-have had a fairly small convergence radius, suitable only for local optimization. However, the identification of the global minimum among the several local minima is essential for complex surface structures. Global optimization methods have been applied to LEED structure determination, but they still require starting from structures that are relatively close to the correct one, in order to find the final structure. For complex systems, the number of trial structures and the resulting computation time increase so rapidly that the task of finding the correct model becomes impractical using the present methodologies. In this work we propose a new search method, based on Genetic Algorithms, which is able to determine the correct structural model starting from completely random structures. This method-called here NGA-LEED for Novel Genetic Algorithm for LEED-utilizes bond lengths and symmetry criteria to select reasonable trial structures before performing LEED calculations. This allows a reduction of the parameter space and, consequently of the calculation time, by several orders of magnitude. A refinement of the parameters by least squares fit of simulated annealing is performed only at some intermediate stages and in the final step. The method was successfully tested for two systems, Ag(1 1 1)(4 × 4)-O and Au(1 1 0)-(1 × 2), both in theory versus theory and in theory versus experiment comparisons. Details of the implementation as well as the results for these two systems are presented.

  16. Vacancy-impurity centers in diamond: prospects for synthesis and applications

    Science.gov (United States)

    Ekimov, E. A.; Kondrin, M. V.

    2017-06-01

    The bright luminescence of impurity-vacancy complexes, combined with high chemical and radiation resistance, makes diamond an attractive platform for the production of single-photon emitters and luminescent biomarkers for applications in nanoelectronics and medicine. Two representatives of this kind of defects in diamond, silicon-vacancy (SiV) and germanium-vacancy (GeV) centers, are discussed in this review; their similarities and differences are demonstrated in terms of the more thoroughly studied nitrogen-vacancy (NV) complexes. The recent discovery of GeV luminescent centers opens a unique opportunity for the controlled synthesis of single-photon emitters in nanodiamonds. We demonstrate prospects for the high-pressure high-temperature (HPHT) technique to create single-photon emitters, not only as an auxiliary to chemical vapor deposition (CVD) and ion-implantation methods but also as a primary synthesis tool for producing color centers in nanodiamonds. Besides practical applications, comparative studies of these two complexes, which belong to the same structural class of defects, have a fundamental importance for deeper understanding of shelving levels, the electronic structure, and optical properties of these centers. In conclusion, we discuss several open problems regarding the structure, charge state, and practical application of these centers, which still require a solution.

  17. Skills and Vacancy Analysis with Data Mining Techniques

    Directory of Open Access Journals (Sweden)

    Izabela A. Wowczko

    2015-11-01

    Full Text Available Through recognizing the importance of a qualified workforce, skills research has become one of the focal points in economics, sociology, and education. Great effort is dedicated to analyzing labor demand and supply, and actions are taken at many levels to match one with the other. In this work we concentrate on skills needs, a dynamic variable dependent on many aspects such as geography, time, or the type of industry. Historically, skills in demand were easy to evaluate since transitions in that area were fairly slow, gradual, and easy to adjust to. In contrast, current changes are occurring rapidly and might take an unexpected turn. Therefore, we introduce a relatively simple yet effective method of monitoring skills needs straight from the source—as expressed by potential employers in their job advertisements. We employ open source tools such as RapidMiner and R as well as easily accessible online vacancy data. We demonstrate selected techniques, namely classification with k-NN and information extraction from a textual dataset, to determine effective ways of discovering knowledge from a given collection of vacancies.

  18. A Laboratory Exercise in the Determination of Carbohydrate Structures.

    Science.gov (United States)

    White, Bernard J.; Robyt, John F.

    1988-01-01

    Describes an experiment in which students are given a naturally occurring oligosaccharide as an unknown and are asked to determine both its monosaccharide composition and its structure. Discusses methods and experimental techniques including thin layer chromatography and the use of enzymes. (CW)

  19. Birthday Cake Activity Structured Arrangement for Helping Children Determining Quantities

    Science.gov (United States)

    Mariana, Neni

    2010-01-01

    Few researches have been concerned about relation between children's spatial thinking and number sense. Narrowing for this small research, we focused on one component of spatial thinking, that is structuring objects, and one component of number senses, that is cardinality by determining quantities. This study focused on a design research that was…

  20. Determining the Cognitive Structures of Geography Teacher Candidates on "Earthquake"

    Science.gov (United States)

    Kaya, Bastürk; Aladag, Caner

    2017-01-01

    The objective of this study is to determine the cognitive structures of the students of geography teaching department by identifying their conceptual frameworks about the concept of earthquake. A case study design from qualitative research approaches was used in this research. Sample group of the study constitutes 155 students from the Department…

  1. X-ray structure determination and analysis of hydrogen interactions ...

    Indian Academy of Sciences (India)

    The crystal structure of 3,3′-dimethoxybiphenyl has been determined by X-ray diffraction methods with an aim of describing the hydrogen interaction in biphenyl derivatives. The title compound crystallizes in monoclinic space group 21/ with unit cell dimensions, = 7.706(1), = 11.745(2), = 12.721(2) Å, ...

  2. Determining modulus of elasticity of ancient structural timber

    Science.gov (United States)

    Houjiang Zhang; Lei Zhu; Yanliang Sun; Xiping Wang; Haicheng Yan

    2011-01-01

    During maintenance of ancient timber architectures, it is important to determine mechanical properties of the wood component materials non-destructively and effectively, so that degraded members may be replaced or repaired to avoid structural failure. Experimental materials are four larch (Larix principis-rupprechtii Mayr.) components, which were taken down from the...

  3. Determining carrier mobility with a metal–insulator–semiconductor structure

    NARCIS (Netherlands)

    Stallinga, P.; Benvenho, A.R.V.; Smits, E.C.P.; Mathijssen, S.G.J.; Colle, M.; Gomes, H.L.; Leeuw, D.M. de

    2008-01-01

    The electron and hole mobility of nickel-bis(dithiolene) (NiDT) are determined in a metal– insulator–semiconductor (MIS) structure using admittance spectroscopy. The relaxation times found in the admittance spectra are attributed to the diffusion time of carriers to reach the insulator interface and

  4. The determinants of financial structure in the algerian enterprises: A ...

    African Journals Online (AJOL)

    The aim of this work is to identify the determinants of the financing structure of the Algerian companies, using the financial statements of 83 large companies and 165 SMEs over the period 2008-2010. This is done through a comparative study between SMEs and large companies in order to verify the existence of a size ...

  5. Determination of bone structural parameters from multiple projection DXA images

    Science.gov (United States)

    Spisz, Thomas S.; Beck, Thomas J.; Feldmesser, Howard S.; Chen, Michelle H.; Magee, Thomas C.; Bade, Paul R.; Charles, Harry K., Jr.

    2004-04-01

    To more precisely measure and monitor bone health, The Johns Hopkins University Applied Physics Lab and School of Medicine have developed the Advanced Multiple Projection Dual-Energy X-Ray Absorptiometry (AMPDXA) scanner. This system provides improvements over conventional DXA scanners in image resolution and multiple projection capability. These improvements allow us to determine structural information about the bone in addition to the standard bone mineral density (BMD) measurements. Algorithms and software were developed to process data acquired from the AMPDXA scanner and to determine important structural parameters, such as the center of mass axis in three dimensions and cross-sectional moments of inertia. The analysis operates on three projections about 15 degrees apart, calculates BMD for each projection, and then combines the data into a three dimensional coordinate system. By knowing the patient position in three dimensions, bone structural parameters are calculated more precisely. Using repeated testing of cadaver bones, the precision of determining these structural parameters is approximately the detector pixel size of 0.127 mm. Data on artificial bone cylinders indicate accuracy of about 3%. Comparisons between bone structural parameters derived from AMPDXA and CT scans show very similar results.

  6. Electronic and optical properties of vacancy defects in single-layer transition metal dichalcogenides

    Science.gov (United States)

    Khan, M. A.; Erementchouk, Mikhail; Hendrickson, Joshua; Leuenberger, Michael N.

    2017-06-01

    A detailed first-principles study has been performed to evaluate the electronic and optical properties of single-layer (SL) transition metal dichalcogenides (TMDCs) (M X 2 ; M = transition metal such as Mo, W, and X = S, Se, Te), in the presence of vacancy defects (VDs). Defects usually play an important role in tailoring electronic, optical, and magnetic properties of semiconductors. We consider three types of VDs in SL TMDCs: (i) X vacancy, (ii) X2 vacancy, and (iii) M vacancy. We show that VDs lead to localized defect states (LDS) in the band structure, which in turn gives rise to sharp transitions in in-plane and out-of-plane optical susceptibilities, χ∥ and χ⊥. The effects of spin-orbit coupling (SOC) are also considered. We find that SOC splitting in LDS is directly related to the atomic number of the transition metal atoms. Apart from electronic and optical properties we also find magnetic signatures (local magnetic moment of ˜μB ) in MoSe2 in the presence of the Mo vacancy, which breaks the time-reversal symmetry and therefore lifts the Kramers degeneracy. We show that a simple qualitative tight-binding model (TBM), involving only the hopping between atoms surrounding the vacancy with an on-site SOC term, is sufficient to capture the essential features of LDS. In addition, the existence of the LDS can be understood from the solution of the two-dimensional Dirac Hamiltonian by employing infinite mass boundary conditions. In order to provide a clear description of the optical absorption spectra, we use group theory to derive the optical selection rules between LDS for both χ∥ and χ⊥.

  7. Macromolecular structure determination in the post-genome era

    CERN Document Server

    Kuhn, P

    2001-01-01

    Recent advances in genetics, molecular biology and crystallographic instrumentation and methodology have led to a revolution in the field of Structural Molecular Biology (SMB). These combined advances have paved the way to a more complete and detailed understanding of the biological macromolecules that make up an organism, both in terms of their individual functions and also the interactions between them. In this paper we describe a large-scale, genomic approach to the three-dimensional structure determination of macromolecules and their complexes, using high-throughput methodology to streamline all aspects of the process. This task requires the development of automated high-intensity synchrotron beam lines for X-ray diffraction data collection from single crystal samples. Furthermore, these beam lines must be operated within a sophisticated software and hardware environment, which is capable of delivering a completely automated structure determination pipeline. The SMB resource at SSRL is developing a system...

  8. The determinants of capital structure of microfinance institutions in Ghana

    Directory of Open Access Journals (Sweden)

    Anthony Kyereboah-Coleman

    2013-04-01

    Full Text Available Using a panel data methodology, this study examines the determinants of capital structure of 52 microfinance institutions (MFIs in Ghana. The empirical results show that the MFIs are highly leveraged and that their capital structure is explained partly by standard finance theory and by other unconventional variables. Specifically, the study confirms that leverage is positively related to asset tangibility, with small MFIs using short-term and large MFIs using long-term debt. Though, the findings confirm that leverage is inversely related to risk, they also suggest that some MFIs enjoy long-term debt in spite of risk, while profitability is irrelevant in explaining the capital structure decisions of MFIs. Finally, the study shows that the reputation and board independence of MFIs significantly and positively affect their capital structure decisions.

  9. Tunable Se vacancy defects and the unconventional charge density wave in 1 T -TiSe2 -δ

    Science.gov (United States)

    Huang, S. H.; Shu, G. J.; Pai, Woei Wu; Liu, H. L.; Chou, F. C.

    2017-01-01

    A systematic study of polycrystalline 1 T -TiSe2 -δ with controlled Se loss indicates that the unconventional charge density wave (CDW) phase is found to be most pronounced in samples with δ ˜0.12 , instead of being Se vacancy free. The level of Se vacancy defects and temperature determines whether 1 T -TiSe2 -δ should be categorized as a semiconductor, a semimetal, or an excitonic insulator. An interpretation using a general band picture of p -type doped narrow-band-gap semiconductor with an impurity band (IB) in proximity to the valence band (VB) is proposed to explain the evolution of electronic structures for 1 T -TiSe2 -δ , from the intermediate doping of δ ˜0.08 , to the critical doping of δ ˜0.12 showing an anomalous resistivity peak between ˜100 -200 K , and to the heavily doped of δ ˜0.17 as an n -type degenerate semiconductor. Integrated chemical analysis and physical property characterization, including electron probe microanalysis (EPMA), synchrotron x-ray diffraction, resistivity, and Seebeck coefficient measurement results are provided for the polycrystalline samples prepared via vacuum-sealed high temperature annealing route.

  10. Theoretical analytical model of vacancy formation energy with simultaneous dependence on surface orientation, temperature, and material size

    Science.gov (United States)

    Zhang, Xuyao; Li, Weiguo; Deng, Yong; Shao, Jiaxing; Kou, Haibo; Ma, Jianzuo; Zhang, Xianhe; Li, Ying

    2018-02-01

    From the perspectives of bond energy theory, the bond–order–length–strength correlation mechanism, and the core–surface configuration for nanomaterials, a physics-based model, free of any adjustable parameters and simultaneously considering the coupling effects of surface orientation, temperature, and size on the vacancy formation energy of metal materials is developed. To confirm our present model, the temperature-dependent vacancy formation energies of six face-centered cubic metals and the size-dependent vacancy formation energies of gold particles are predicted, which are in reasonable agreement with the simulation results. In particular, the model can provide a convenient method to predict the temperature-dependent vacancy formation energy of nanomaterials with different surface orientations, and also can provide a new method to study the structural relaxation. The study shows that the size effect on the vacancy formation energy depends on the stronger bond energy in the surface layers compared with those in the core interior, and the temperature-dependent vacancy formation energy arises from cohesive energy weakening, with the opposite trend to that induced by size reduction.

  11. X-ray structure determination and deuteration of nattokinase

    Energy Technology Data Exchange (ETDEWEB)

    Yanagisawa, Yasuhide [Chiba Institute of Science, 15-8 Shiomi-cho, Cho-shi, Chiba 288-025 (Japan); Chatake, Toshiyuki, E-mail: chatake@rri.kyoto-u.ac.jp [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan); Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki [Kurashiki University of Science and the Arts, 2640 Nishinoura, Tsurajima-cho, Kurashiki, Okayama 712-8505 (Japan); Kawaguchi, Akio [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan); Chiba-Kamosida, Kaori [Nippon Advanced Technology Co. Ltd, J-PARC, 2-4 Shirane Shirakata, Tokai, Ibaraki 319-1195 (Japan); Ogawa, Megumi; Adachi, Tatsumi [Chiba Institute of Science, 15-8 Shiomi-cho, Cho-shi, Chiba 288-025 (Japan); Morimoto, Yukio [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan)

    2013-11-01

    X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis. Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D{sub 2}O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D{sub 2}O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

  12. Experimental and theoretical investigations of cadmium diffusion in vacancy-rich Cu(In, Ga)Se2 material

    Science.gov (United States)

    Biderman, Norbert J.

    Copper indium gallium selenide (Cu(In,Ga)Se2 or CIGS) has become a significant topic of research and development for photovoltaic application. CIGS photovoltaic devices have demonstrated record conversion efficiencies however are still below the maximum solar conversion efficiency. Losses in performance have been attributed structural defects including vacancies, doping, grain boundaries, and compositional non-uniformity that are poorly understood and controlled. The cadmium sulfide (CdS) buffer layer plays a critical role in high-performance CIGS photovoltaic devices, serving as the n-type component of the p-n junction formed with the p-type CIGS absorber layer. Cadmium diffusion into the CIGS surface during CdS deposition creates a buried p-n homojunction in addition to the CIGS/CdS p-n heterojunction. CdS is believed to assist in reducing carrier recombination at the CIGS/CdS interface, an important attribute of high-efficiency solar cells. In the present work, cadmium diffusion mechanisms in CIGS are experimentally investigated via secondary ion mass spectroscopy (SIMS) and Auger electron spectroscopy (AES). Two cadmium diffusion profiles with distinct Arrhenius diffusion kinetics within a single depth profile of the CIGS thin film are observed with SIMS and AES: an intense first-stage diffusion profile directly below the CIGS/CdS interface and a long-range, second-stage diffusion profile that extends deep into the thin film. Cadmium grain boundary diffusion is also detected in fine-grain CIGS samples. These multiple diffusion processes are quantified in the present work, and the two-stage cadmium diffusion profiles suggest distinctive lattice diffusion mechanisms. Calculations and modeling of general impurity diffusion via interstitial sites in CIGS are also conducted via numerical including cadmium, iron, and zinc. In the numerical simulations, the standard diffusion-reaction kinetics theory is extended to vacancy-rich materials like CIGS that contain 1 at

  13. Regional Mechanics Determine Collagen Fiber Structure in Healing Myocardial Infarcts

    Science.gov (United States)

    Fomovsky, Gregory M.; Rouillard, Andrew D.; Holmes, Jeffrey W.

    2012-01-01

    Following myocardial infarction, the mechanical properties of the healing infarct are an important determinant of heart function and the risk of progression to heart failure. In particular, mechanical anisotropy (having different mechanical properties in different directions) in the healing infarct can preserve pump function of the heart. Based on reports of different collagen structures and mechanical properties in various animal models, we hypothesized that differences in infarct size, shape, and/or location produce different patterns of mechanical stretch that guide evolving collagen fiber structure. We tested the effects of infarct shape and location using a combined experimental and computational approach. We studied mechanics and collagen fiber structure in cryoinfarcts in 53 Sprague-Dawley rats and found that regardless of shape or orientation, cryoinfarcts near the equator of the left ventricle stretched primarily in the circumferential direction and developed circumferentially aligned collagen, while infarcts at the apex stretched similarly in the circumferential and longitudinal direction and developed randomly oriented collagen. In a computational model of infarct healing, an effect of mechanical stretch on fibroblast and collagen alignment was required to reproduce the experimental results. We conclude that mechanical environment determines collagen fiber structure in healing myocardial infarcts. Our results suggest that emerging post-infarction therapies that alter regional mechanics will also alter infarct collagen structure, offering both potential risks and novel therapeutic opportunities. PMID:22418281

  14. Sulfated oligosaccharide structures, as determined by NMR techniques

    Energy Technology Data Exchange (ETDEWEB)

    Noseda, M.D.; Duarte, M.E.R.; Tischer, C.A.; Gorin, P.A.J. [Parana Univ., Curitiba, PR (Brazil). Dept. De Bioquimica; Cerezo, A.S. [Buenos Aires Univ. Nacional (Argentina). Dept. de Quimica Organica

    1997-12-31

    Carrageenans are sulfated polysaccharides, produced by red seaweeds (Rhodophyta), that have important biological and physico-chemical properties. Using partial autohydrolysis, we obtained sulfated oligosaccharides from a {lambda}-carrageenan (Noseda and Cerezo, 1993). These oligosaccharides are valuable not only for the study of the structures of the parent carrageenans but also for their possible biological activities. In this work we determined the chemical structure of one of the sulfated oligosaccharides using 1D and 2D NMR techniques. (author) 4 refs., 8 figs., 1 tabs.

  15. Structural studies on A-cation-deficient perovskite-related phases. I. ThNb/sub 4/O/sub 12/. Thorium/vacancy ordering in slow-cooled samples

    Energy Technology Data Exchange (ETDEWEB)

    Alario-Franco, M.A. (Universidad Complutense de Madrid (Spain). Facultad de Ciencias Quimicas); Grey, I.E.; Joubert, J.C.; Vincent, H. (Centre National de la Recherche Scientifique, 38 - Grenoble (France)); Labeau, M. (Institut National Polytechnique, 38 - Grenoble (France))

    1982-03-01

    The A-cation-deficient perovskite, Thsub(0.25)NbO/sub 3/, i.e. ThNb/sub 4/O/sub 12/, when slowly cooled from the melt, presents an interesting hierachy of ordering phenomena. The associated diffraction effects have been studied with electron microscopy/diffraction and X-ray diffraction techniques. Three main types of ordering processes occur, with different degrees of long-range order. Independent models for thorium/vacancy ordering and octahedral tilts have been refined with the intensities of the corresponding groups of satellites measured from precession photographs. The complete model for ThNb/sub 4/O/sub 12/ can be described in the unit cell 3..sqrt..2asub(p) x ..sqrt..2bsub(p) x 4csub(p), P2mm. The superlattice reflections arising from the octahedral tilts are split into groups of four satellites in the form of crosses, owing to microdomain formation in ThNb/sub 4/O/sub 12/, with domain boundaries parallel to (100)sub(p) and (010)sub(p) and with average widths of approximately25 A.

  16. Effects of oxygen vacancies on polarization stability of barium titanate

    Science.gov (United States)

    Wang, Jun; Shen, YaoGen; Song, Fan; Ke, FuJiu; Bai, YiLong; Lu, ChunSheng

    2016-03-01

    Oxygen vacancy, a kind of native point defects in ferroelectric ceramics, usually causes an increase of the dielectric loss. Based on experimental observations, it is believed that all of the oxygen vacancies are an unfavorable factor for energy saving. By using molecular dynamics simulations, we show that the increase of coercive and saturated electric fields is due to the difficulty to switch local polarization near an oxygen vacancy, and so that a ferroelectric device has to sustain the rising consumption of energy. The simulation results also uncover how oxygen vacancies influence ferroelectric properties.

  17. The potential for biological structure determination with pulsed neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, C.C. [CLRC Rutherford Appleton Laboratory, Chilton Didcot Oxon (United Kingdom)

    1994-12-31

    The potential of pulsed neutron diffraction in structural determination of biological materials is discussed. The problems and potential solutions in this area are outlined, with reference to both current and future sources and instrumentation. The importance of developing instrumentation on pulsed sources in emphasized, with reference to the likelihood of future expansion in this area. The possibilities and limitations of single crystal, fiber and powder diffraction in this area are assessed.

  18. Determination of the Basin Structure Beneath European Side of Istanbul

    Science.gov (United States)

    Karabulut, Savas; Cengiz Cinku, Mulla; Thomas, Michael; Lamontagne, Maurice

    2016-04-01

    Istanbul (near North Anatolian Fault Zone:NAFZ, Turkey) is located in northern part of Sea of Marmara, an area that has been influenced by possible Marmara Earthquakes. The general geology of Istanbul divided into two stratigraphic unit such as sedimentary (from Oligocene to Quaternary Deposits) and bedrock (Paleozoic and Eocene). The bedrock units consists of sand stone, clay stone to Paleozoic age and limestone to Eocene age and sedimentary unit consist of sand, clay, mil and gravel from Oligocene to Quaternary age. Earthquake disaster mitigation studies divided into two important phases, too. Firstly, earthquake, soil and engineering structure problems identify for investigation area, later on strategic emergency plan can prepare for these problems. Soil amplification play important role the disaster mitigation and the site effect analysis and basin structure is also a key parameter for determining of site effect. Some geophysical, geological and geotechnical measurements are requeired to defined this relationship. Istanbul Megacity has been waiting possible Marmara Earthquake and their related results. In order to defined to possible damage potential related to site effect, gravity measurements carried out for determining to geological structure, basin geometry and faults in Istanbul. Gravity data were collected at 640 sites by using a Scientrex CG-5 Autogravity meter Standard corrections applied to the gravity data include those for instrumental drift, Earth tides and latitude, and the free-air and Bouguer corrections. The corrected gravity data were imported into a Geosoft database to create a grid and map of the Bouguer gravity anomaly (grid cell size of 200 m). As a previously results, we determined some lineminants, faults and basins beneath Istanbul City. Especially, orientation of faults were NW-SE direction and some basin structures determined on between Buyukcekmece and Kucukcekmece Lake.

  19. Regional Mechanics Determine Collagen Fiber Structure in Healing Myocardial Infarcts

    OpenAIRE

    Fomovsky, Gregory M.; Rouillard, Andrew D; Holmes, Jeffrey W.

    2012-01-01

    Following myocardial infarction, the mechanical properties of the healing infarct are an important determinant of heart function and the risk of progression to heart failure. In particular, mechanical anisotropy (having different mechanical properties in different directions) in the healing infarct can preserve pump function of the heart. Based on reports of different collagen structures and mechanical properties in various animal models, we hypothesized that differences in infarct size, shap...

  20. Geophysical determination of buried structural features at Ovbiogie ...

    African Journals Online (AJOL)

    Computer iterated data from the study area made the structural determination possible with resistivity values ranging from 85ohm-m to 735ohm-m and depth ... soil at a depth of 1.0m, sandy soil at a depth of 3.0m, clay and mart at a depth of 12.6m, river sand and gravel at a depth of 35.1m and basalt at a depth of infinity.

  1. MOTIVATION INTERNALIZATION AND SIMPLEX STRUCTURE IN SELF-DETERMINATION THEORY.

    Science.gov (United States)

    Ünlü, Ali; Dettweiler, Ulrich

    2015-12-01

    Self-determination theory, as proposed by Deci and Ryan, postulated different types of motivation regulation. As to the introjected and identified regulation of extrinsic motivation, their internalizations were described as "somewhat external" and "somewhat internal" and remained undetermined in the theory. This paper introduces a constrained regression analysis that allows these vaguely expressed motivations to be estimated in an "optimal" manner, in any given empirical context. The approach was even generalized and applied for simplex structure analysis in self-determination theory. The technique was exemplified with an empirical study comparing science teaching in a classical school class versus an expeditionary outdoor program. Based on a sample of 84 German pupils (43 girls, 41 boys, 10 to 12 years old), data were collected using the German version of the Academic Self-Regulation Questionnaire. The science-teaching format was seen to not influence the pupils' internalization of identified regulation. The internalization of introjected regulation differed and shifted more toward the external pole in the outdoor teaching format. The quantification approach supported the simplex structure of self-determination theory, whereas correlations may disconfirm the simplex structure.

  2. Wide-Field Imaging Using Nitrogen Vacancies

    Science.gov (United States)

    Englund, Dirk Robert (Inventor); Trusheim, Matthew Edwin (Inventor)

    2017-01-01

    Nitrogen vacancies in bulk diamonds and nanodiamonds can be used to sense temperature, pressure, electromagnetic fields, and pH. Unfortunately, conventional sensing techniques use gated detection and confocal imaging, limiting the measurement sensitivity and precluding wide-field imaging. Conversely, the present sensing techniques do not require gated detection or confocal imaging and can therefore be used to image temperature, pressure, electromagnetic fields, and pH over wide fields of view. In some cases, wide-field imaging supports spatial localization of the NVs to precisions at or below the diffraction limit. Moreover, the measurement range can extend over extremely wide dynamic range at very high sensitivity.

  3. GPR determination of physical parameters of railway structural layers

    Science.gov (United States)

    Khakiev, Zelimkhan; Shapovalov, Vladimir; Kruglikov, Alexander; Yavna, Victor

    2014-07-01

    The paper studies the possibility of quantitative processing of the GPR data for determining the refractive index and conductivity of motor road and railway constructional layers. The main objective of the work is to develop a method of obtaining quantitative information on chosen physical properties of soil layers from regular GPR surveys. Theoretical study of plane electromagnetic wave propagation is made for the model of layered soil structure. As a result of the study appropriate equation systems are derived for the calculations of refractive index and conductivity of structural layers. Based on these equations the method of quantitative processing of radargrams is proposed. The method includes the GPR data processing algorithm and theoretical techniques for determination of refractive index and conductivity of the structural layers. The applicability of the proposed method was initially validated by lab experiments using radargrams of the soil samples with specified values of moisture and conductivity and reliable results were achieved. The methods were also successfully used while monitoring the long term seasonal changes in structural layers of several Russian railways sections. The contamination of ballast material is also evaluated by this method in addition to the refractive index and conductivity.

  4. Oxygen Vacancy-Mediated Photocatalysis of BiOCl: Reactivity, Selectivity, and Perspectives.

    Science.gov (United States)

    Li, Hao; Li, Jie; Ai, Zhihui; Jia, Falong; Zhang, Lizhi

    2018-01-02

    Semiconductor photocatalysis is a trustworthy approach to harvest clean solar light for energy conversions, while state-of-the-art catalytic efficiencies are unsatisfactory because of the finite light response and/or recombination of robust charge carriers. Along with the development of modern material characterization techniques and electronic-structure computations, oxygen vacancies (OVs) on the surface of real photocatalysts, even in infinitesimal concentration, are found to play a more decisive role in determining the kinetics, energetics, and mechanisms of photocatalytic reactions. This Review endeavors to clarify the inherent functionality of OVs in photocatalysis at the surface molecular level using 2D BiOCl as the platform. Structure sensitivity of OVs on reactivity and selectivity of photocatalytic reactions is intensely discussed via confining OVs onto prototypical BiOCl surfaces of different structures. The critical understanding of OVs chemistry can help consolidate and advance the fundamental theories of photocatalysis, and also offer new perspectives and guidelines for the rational design of catalysts with satisfactory performance. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Non-invasively improving the Schottky barriers of metal-MoS2 interfaces: effects of atomic vacancies in a BN buffer layer.

    Science.gov (United States)

    Su, Jie; Feng, Liping; Liu, Siyang; Liu, Zhengtang

    2017-08-09

    Using first-principles calculations within density functional theory, vacancies in the BN buffer layer have been predicted to improve the Schottky barrier of the metal-MoS2 interface without deteriorating the intrinsic properties of the MoS2 layer. Here, the effects of concentrations, sizes and types of vacancies on the contact properties of metal/BN-MoS2 sandwich interfaces are comparatively studied. The results show that vacancies in the BN buffer layer not only don't deteriorate the charge scatterings and electronic properties of the MoS2 layer at the metal/BN-MoS2 interface, but also improve the charge density and contact resistance between the metal surface and the BN layer. Although these vacancies have a negligible influence on the Fermi level pinning effect of the metal/BN-MoS2 interface, both N-vacancies and B-vacancies significantly change the position of the Fermi level of the metal/BN-MoS2 interface and then tune the Schottky barriers. Moreover, the Schottky barriers of metal/BN-MoS2 interfaces can decrease at first with the increasing concentrations and sizes of vacancies. When the concentration of vacancies increases to 4%, the Schottky barriers of metal/BN-MoS2 interfaces can reduce to the minimum value. The lowest n-type and p-type Schottky barriers of Au/BN-MoS2 and Pt/BN-MoS2 interfaces can reduce to -0.16 and 0.28 eV, respectively. However, the Schottky barriers are deteriorated when the sizes and concentrations of vacancies continue to increase because vacancies with large sizes and concentrations obviously change the interfacial structures of metal/BN-MoS2 interfaces and disarrange the directions of interface dipoles. The predictions in this work provide a non-invasive method to achieve high performance metal-MoS2 interfaces with low Schottky barriers.

  6. Determination of organic crystal structures by X ray powder diffraction

    CERN Document Server

    McBride, L

    2000-01-01

    The crystal structure of Ibuprofen has been solved from synchrotron X-ray powder diffraction data using a genetic algorithm (GA). The performance of the GA is improved by incorporating prior chemical information in the form of hard limits on the values that can be taken by the flexible torsion angles within the molecule. Powder X-ray diffraction data were collected for the anti-convulsant compounds remacemide, remacemide nitrate and remacemide acetate at 130 K on BM 16 at the X-ray European Synchrotron Radiation Facility (ESRF) at Grenoble. High quality crystal structures were obtained using data collected to a resolution of typically 1.5 A. The structure determinations were performed using a simulated annealing (SA) method and constrained Rietveld refinements for the structures converged to chi sup 2 values of 1.64, 1.84 and 1.76 for the free base, nitrate and acetate respectively. The previously unknown crystal structure of the drug famotidine Form B has been solved using X-ray powder diffraction data colle...

  7. A computational modelling study of oxygen vacancies at LaCoO3 perovskite surfaces.

    Science.gov (United States)

    Khan, S; Oldman, R J; Corà, F; Catlow, C R A; French, S A; Axon, S A

    2006-11-28

    Atomistic computational modelling of the surface structure of the catalytically-active perovskite LaCoO(3) has been undertaken in order to develop better models of the processes involved during catalytic oxidation processes. In particular, the energetics of creating oxygen ion vacancies at the surface have been investigated for the three low index faces (100), (110) and (111). Two mechanisms for vacancy creation have been considered involving dopant Sr(2+) cations at the La(3+) site and reduction of Co(3+) to Co(2+). For both mechanisms, there is a general tendency that the smaller the cation defect separation, the lower the energy of the cluster, as would be expected from simple electrostatic considerations. In addition, there are clear indications that oxygen vacancies are more easily created at the surface than in the bulk. The results also confirm that the presence of defects strongly influences crystal morphology and surface chemistry. The importance of individual crystal surfaces in catalysis is discussed in terms of the energetics for the creation of oxygen vacancies.

  8. Extinction of light and coherent scattering by a single nitrogen-vacancy center in diamond

    Science.gov (United States)

    Tran, Thai Hien; Siyushev, Petr; Wrachtrup, Jörg; Gerhardt, Ilja

    2017-05-01

    The efficient interaction of light and a single quantum system is required to implement a photon to spin interface. It is important to determine the amount of coherent and incoherent photons in such a scheme, since it is based on coherent scattering. In this paper an external laser field is efficiently coupled to a single nitrogen vacancy center in diamond. We detect the direct extinction signal and estimate the nitrogen vacancy's extinction cross section. The exact amount of coherent and incoherent photons is determined against the saturation parameter. This reveals the optimal point of interaction for further experiments. A theoretical model allows us to explain the deviation to an atom in free space. The introduced experimental techniques are used to determine the properties of the tight focusing in an interference experiment and allow for a direct determination of the Gouy phase in a strongly focused beam.

  9. X-ray structure determination and deuteration of nattokinase.

    Science.gov (United States)

    Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

    2013-11-01

    Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

  10. Effects of Oxygen Vacancy on Optical and Electrical Properties of ZnO Bulks and Nanowires

    Science.gov (United States)

    Yu, Xiao-Xia; Zheng, Hong-Mei; Fang, Xiao-Yong; Jin, Hai-Bo; Cao, Mao-Sheng

    2014-11-01

    Based on the generalized gradient approximation (GGA) in density functional theory (DFT) and using the first-principle plane wave ultrasoft pseudopotential method, we construct and optimize the structures of intrinsic and oxygen vacancy (VO) ZnO bulks and nanowires (NWs) in the Castep module. Moreover, the calculation of band structures and the optical properties are carried out. The calculated results exhibit that the oxygen vacancy exerts a more significant influence on the electronic structures of the ZnO bulks instead of the NWs. What is more, the influences of the VO on the optical properties are mainly embodied in the ultraviolet region, and the main optical parameters of ZnO bulks and NWs with VO are anisotropic.

  11. Thermal stability of helium-vacancy clusters in iron

    CERN Document Server

    Morishita, K; Wirth, B D; Díaz de la Rubia, T

    2003-01-01

    Molecular dynamics calculations were performed to evaluate the thermal stability of helium-vacancy clusters (He sub n V sub m) in Fe using the Ackland Finnis-Sinclair potential, the Wilson-Johnson potential and the Ziegler-Biersack-Littmark-Beck potential for describing the interactions of Fe-Fe, Fe-He and He-He, respectively. Both the calculated numbers of helium atoms, n, and vacancies, m, in clusters ranged from 0 to 20. The binding energies of an interstitial helium atom, an isolated vacancy and a self-interstitial iron atom to a helium-vacancy cluster were obtained from the calculated formation energies of clusters. All the binding energies do not depend much on cluster size, but they primarily depend on the helium-to-vacancy ratio (n/m) of clusters. The binding energy of a vacancy to a helium-vacancy cluster increases with the ratio, showing that helium increases cluster lifetime by dramatically reducing thermal vacancy emission. On the other hand, both the binding energies of a helium atom and an iron ...

  12. 29 CFR 511.5 - Vacancies and dissolution of committees.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Vacancies and dissolution of committees. 511.5 Section 511.5 Labor Regulations Relating to Labor (Continued) WAGE AND HOUR DIVISION, DEPARTMENT OF LABOR REGULATIONS WAGE ORDER PROCEDURE FOR AMERICAN SAMOA § 511.5 Vacancies and dissolution of committees. The...

  13. Brownian Motion of Vacancy Islands on Ag(111)

    NARCIS (Netherlands)

    Morgenstern, Karina; Rosenfeld, G.; Poelsema, Bene; Comsa, George

    1995-01-01

    The motion of monatomic deep vacancy islands on crystal surfaces is studied both theoretically and experimentally. We develop a new theoretical model which allows us to deduce the microscopic mechanism of mass transport from measuring the diffusion coefficients of the vacancy islands as a function

  14. Diffusion and aggregation of oxygen vacancies in amorphous silica

    Science.gov (United States)

    Munde, Manveer S.; Gao, David Z.; Shluger, Alexander L.

    2017-06-01

    Using density functional theory (DFT) calculations, we investigated oxygen vacancy diffusion and aggregation in relation to dielectric breakdown in amorphous silicon dioxide (a-SiO2). Our calculations indicate the existence of favourable sites for the formation of vacancy dimers and trimers in the amorphous network with maximum binding energies of approximately 0.13 eV and 0.18 eV, respectively. However, an average energy barrier height for neutral vacancy diffusion is found to be about 4.6 eV, rendering this process unfeasible. At Fermi level positions above 6.4 eV with respect to the top of the valence band, oxygen vacancies can trap up to two extra electrons. Average barriers for the diffusion of negative and double negatively charged vacancies are found to be 2.7 eV and 2.0 eV, respectively. These barriers are higher than or comparable to thermal ionization energies of extra electrons from oxygen vacancies into the conduction band of a-SiO2. In addition, we discuss the competing pathways for electron trapping in oxygen deficient a-SiO2 caused by the existence of intrinsic electron traps and oxygen vacancies. These results provide new insights into the role of oxygen vacancies in degradation and dielectric breakdown in amorphous silicon oxides.

  15. Hydrogen vacancies facilitate hydrogen transport kinetics in sodium hydride nanocrystallites

    NARCIS (Netherlands)

    Singh, S.; Eijt, S.W.H.

    2008-01-01

    We report ab initio calculations based on density-functional theory, of the vacancy-mediated hydrogen migration energy in bulk NaH and near the NaH(001) surface. The estimated rate of the vacancy mediated hydrogen transport, obtained within a hopping diffusion model, is consistent with the reaction

  16. The Phenix software for automated determination of macromolecular structures.

    Science.gov (United States)

    Adams, Paul D; Afonine, Pavel V; Bunkóczi, Gábor; Chen, Vincent B; Echols, Nathaniel; Headd, Jeffrey J; Hung, Li-Wei; Jain, Swati; Kapral, Gary J; Grosse Kunstleve, Ralf W; McCoy, Airlie J; Moriarty, Nigel W; Oeffner, Robert D; Read, Randy J; Richardson, David C; Richardson, Jane S; Terwilliger, Thomas C; Zwart, Peter H

    2011-09-01

    X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favor of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface. Copyright © 2011 Elsevier Inc. All rights reserved.

  17. Computational determination of radiation damage effects on DNA structure

    Science.gov (United States)

    Pinak, Miroslav

    2003-03-01

    Molecular dynamics (MD) studies of several radiation originated lesions on the DNA molecules are presented. The pyrimidine lesions (cytosinyl radical, thymine dimer, thymine glycol) and purine lesion (8-oxoguanine) were subjected to the MD simulations for several hundred picoseconds using MD simulation code AMBER 5.0 (4.0). The simulations were performed for fully dissolved solute molecules in water. Significant structural changes in the DNA double helical structure were observed in all cases which may be categorized as: a) the breaking of hydrogen bonds network between complementary bases and resulted opening of the double helix (cytosinyl, radical, 8-oxoguanine); b) the sharp bending of the DNA helix centered at the lesion site (thymine dimer, thymine glycol); and c) the flippingout of adenine on the strand complementary to the lesion (8-oxoguanine). These changes related to the overall collapsing of the double helical structure around the lesion, are expected to facilitate the docking of the repair enzyme into the DNA in the formation of DNA-enzyme complex. The stable DNA-enzyme complex is a necessary condition for the onset of the enzymatic repair process. In addition to structural changes, specific values of electrostatic interaction energy were determined at several lesion sites (thymine dimer, thymine glycol and 8-oxoguanine). This lesion-specific electrostatic energy is a factor that enables repair enzyme to discriminate lesion from the native site during the scanning of the DNA surface.

  18. Structure determination of spider silk from X-ray images

    Energy Technology Data Exchange (ETDEWEB)

    Ulrich, Stephan; Zippelius, Annette [Universitaet Goettingen, Institut fuer Theoretische Physik (Germany); Meling, Martin [Max-Planck-Institut fuer biophysikalische Chemie, Goettingen (Germany); Glisovic, Anja; Salditt, Tim [Universitaet Goettingen, Institut fuer Roentgenphysik (Germany)

    2008-07-01

    Spider silk consists of interconnected crystallites, which are typically aligned along the fiber axis. We present a method to systematically determine the structure of these crystallites. Hereby we introduce a model that calculates the scattering function G(q) which is fitted to the measured X-ray image (silk from nephila clavipes). With it, the crystallites' size, the constitution and dimensions of their unit cell, as well as their tilt with respect to the fiber axis is identified, and furthermore the effect of coherent scattering from different crystallites is investigated. The shown methods and the presented model can easily be generalized to a wide class of composite materials.

  19. Total structure determination of thiolate-protected Au38 nanoparticles.

    Science.gov (United States)

    Qian, Huifeng; Eckenhoff, William T; Zhu, Yan; Pintauer, Tomislav; Jin, Rongchao

    2010-06-23

    We report the total structure of Au(38)(SC(2)H(4)Ph)(24) nanoparticles determined by single crystal X-ray crystallography. This nanoparticle is based upon a face-fused Au(23) biicosahedral core, which is further capped by three monomeric Au(SR)(2) staples at the waist of the Au(23) rod and six dimeric staples with three on the top icosahedron and other three on the bottom icosahedron. The six Au(2)(SR)(3) staples are arranged in a staggered configuration, and the Au(38)S(24) framework has a C(3) rotation axis.

  20. Statistical distribution of thermal vacancies close to the melting point

    Energy Technology Data Exchange (ETDEWEB)

    José Pozo, María, E-mail: mariaj.pozom@gmail.com [Grupo de Nanomateriales, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago (Chile); Davis, Sergio, E-mail: sdavis@gnm.cl [Grupo de Nanomateriales, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago (Chile); Peralta, Joaquín, E-mail: joaquin.peralta@unab.cl [Departamento de Ciencias Físicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, Santiago (Chile)

    2015-01-15

    A detailed description of the statistical distribution of thermal vacancies in an homogeneous crystal near its melting point is presented, using the embedded atom model for copper as an example. As the temperature increase, the average number of thermal vacancies generated by atoms migrating to neighboring sites increases according to Arrhenius’ law. We present for the first time a model for the statistical distribution of thermal vacancies, which according to our atomistic computer simulations follow a Gamma distribution. All the simulations are carried out by classical molecular dynamics and the recognition of vacancies is achieved via a recently developed algorithm. Our results could be useful in the further development of a theory explaining the mechanism of homogeneous melting, which seems to be mediated by the accumulation of thermal vacancies near the melting point.

  1. Vacancy Effects on the Electronic Properties of Silicene Nanoribbons under Uniaxial Tension

    Science.gov (United States)

    Hernández-Tecorralco, J.; Chávez-Castillo, M. R.; Meza-Montes, L.

    During the recent emergence of two-dimensional materials, scientists have shown great interest in graphene-like systems. Silicene, the silicon counterpart of graphene, has gained much attention due to its similarity to graphene. As a result, silicene could be used for applications not only in nano-electronics but also in nano-electromechanical systems. Nanoribbons (NRs) exhibit different edge geometries, i. e., armchair and zig-zag chiralities, their properties could be determined by the width and chirality of the NR. Moreover, properties could also be manipulated by doping, strain and defects. In this work, we study the response of electronic and mechanical properties of silicene-NRs to the presence of a monovacancy defect. The Quantum Espresso package is employed to perform calculations. The structural parameters, band structure, and electronic density of states are analyzed in pristine and vacancy-defective silicene-NRs without strain, for both chirality directions. Since the electronic properties could be affected by strain, we also performed calculations when tensile strain is applied. We found our results are in good agreement with previous results for the pristine case. Partially supported by VIEP-BUAP. We also thank LNS where the calculations were performed.

  2. Correlation between structural, magnetic and electrical transport properties of barium vacancies in the La{sub 0.67}Ba{sub 0.33−x□x}MnO{sub 3} (x = 0, 0.05, and 0.1) manganite

    Energy Technology Data Exchange (ETDEWEB)

    Oumezzine, Marwène, E-mail: Oumezzine@hotmail.co.uk [Laboratoire de Physico-chimie des Matériaux, Département de Physique, Faculté des Sciences de Monastir, Université de Monastir, 5019 (Tunisia); Institut des Sciences Chimiques de Rennes, UMR 6226, Université de Rennes 1, 35042 Rennes cedex (France); Kallel, Sami [Laboratoire de Physico-chimie des Matériaux, Département de Physique, Faculté des Sciences de Monastir, Université de Monastir, 5019 (Tunisia); Peña, Octavio [Institut des Sciences Chimiques de Rennes, UMR 6226, Université de Rennes 1, 35042 Rennes cedex (France); Kallel, Nabil [Laboratoire de Physico-chimie des Matériaux, Département de Physique, Faculté des Sciences de Monastir, Université de Monastir, 5019 (Tunisia); Guizouarn, Thierry [Institut des Sciences Chimiques de Rennes, UMR 6226, Université de Rennes 1, 35042 Rennes cedex (France); Gouttefangeas, Francis [C.M.E.B.A (Centre de Microscopie Electronique à Balayage et Microanalyse), Université de Rennes 1, 35042 Rennes cedex (France); Oumezzine, Mohamed [Laboratoire de Physico-chimie des Matériaux, Département de Physique, Faculté des Sciences de Monastir, Université de Monastir, 5019 (Tunisia)

    2014-01-05

    Highlights: • La{sub 0.67}Ba{sub 0.33x}□{sub x}MnO{sub 3} manganites crystallize in the rhombohedral structure. • Barium vacancies modify the structural parameters such as the volume, the Mn–O bond length and the Mn–O–Mn angles. • La{sub 0.67}Ba{sub 0.33x}□{sub x}MnO{sub 3} exhibit a PM-semiconducting state at high temperatures and a FM-metallic state at low temperatures. • The resistivity is described in terms of percolation phase theory in the whole range of temperatures. • The Curie temperature T{sub C} and the electrical transition temperature T{sub M-SC} decrease with increasing barium deficiencies. -- Abstract: We investigate the effects of barium vacancies on the physical properties of the La{sub 0.67}Ba{sub 0.33−x□x}MnO{sub 3} (x = 0, 0.05, and 0.1) manganite. The X-ray diffraction studies show that all samples crystallize in the rhombohedral structure within the space group R-3c (No. 167). Rietveld refinement shows that the barium vacancies modify the structural parameters such as the volume, the Mn–O bond length and the Mn–O–Mn angles. An increase of the Mn–O bond length with increasing barium deficiencies leads to the decrease of the one-electron bandwidth W, which results in a decrease of the Curie temperature (T{sub C}) and of the metal–semiconductor transition temperature (T{sub M-SC}). Magnetic measurements showed a paramagnetic to ferromagnetic transition at T = T{sub C}. The temperature dependence of the resistivity shows that all samples undergo a sharp metal–semiconductor transition at T{sub M-SC} accompanying the ferromagnetic-paramagnetic transition. Metallic resistivity ρ(T) = ρ{sub 0} + ρ{sub 2}T{sup 2} + ρ{sub 4.5}T{sup 4.5} is observed below T{sub M-SC}. Above T{sub M-SC} the electrical conductivity is dominated by adiabatic small polaron hopping model (ASPH), giving the electrical resistivity in the paramagnetic region as ρ = BT exp (E{sub a}/k{sub B}T). Based on the idea that the doped manganites

  3. Structural determinants of the eosinophil cationic protein antimicrobial activity.

    Science.gov (United States)

    Boix, Ester; Salazar, Vivian A; Torrent, Marc; Pulido, David; Nogués, M Victòria; Moussaoui, Mohammed

    2012-08-01

    Antimicrobial RNases are small cationic proteins belonging to the vertebrate RNase A superfamily and endowed with a wide range of antipathogen activities. Vertebrate RNases, while sharing the active site architecture, are found to display a variety of noncatalytical biological properties, providing an excellent example of multitask proteins. The antibacterial activity of distant related RNases suggested that the family evolved from an ancestral host-defence function. The review provides a structural insight into antimicrobial RNases, taking as a reference the human RNase 3, also named eosinophil cationic protein (ECP). A particular high binding affinity against bacterial wall structures mediates the protein action. In particular, the interaction with the lipopolysaccharides at the Gram-negative outer membrane correlates with the protein antimicrobial and specific cell agglutinating activity. Although a direct mechanical action at the bacteria wall seems to be sufficient to trigger bacterial death, a potential intracellular target cannot be discarded. Indeed, the cationic clusters at the protein surface may serve both to interact with nucleic acids and cell surface heterosaccharides. Sequence determinants for ECP activity were screened by prediction tools, proteolysis and peptide synthesis. Docking results are complementing the structural analysis to delineate the protein anchoring sites for anionic targets of biological significance.

  4. Electric manipulation of the Mn-acceptor binding energy and the Mn-Mn exchange interaction on the GaAs (110) surface by nearby As vacancies

    Science.gov (United States)

    Mahani, M. R.; MacDonald, A. H.; Canali, C. M.

    2015-07-01

    We investigate theoretically the effect of nearby As (arsenic) vacancies on the magnetic properties of substitutional Mn (manganese) impurities on the GaAs (110) surface, using a microscopic tight-binding model which captures the salient features of the electronic structure of both types of defects in GaAs. The calculations show that the binding energy of the Mn acceptor is essentially unaffected by the presence of a neutral As vacancy, even at the shortest possible VAs-Mn separation. On the other hand, in contrast to a simple tip-induced-band-bending theory and in agreement with experiment, for a positively charged As vacancy the Mn-acceptor binding energy is significantly reduced as the As vacancy is brought closer to the Mn impurity. For two Mn impurities aligned ferromagnetically, we find that nearby charged As vacancies enhance the energy level splitting of the associated coupled acceptor levels, leading to an increase of the effective exchange interaction. Neutral vacancies leave the exchange splitting unchanged. Since it is experimentally possible to switch reversibly between the two charge states of the vacancy, such a local electric manipulation of the magnetic dopants could result in an efficient real-time control of their exchange interaction.

  5. Determining Subsurface Structure From Microtremors Using a Passive Circular Array

    Science.gov (United States)

    Folger, D. S.; Doser, D. I.; Velasco, A. A.

    2005-12-01

    The amount of damage to a structure during an earthquake is related to the ground motion at that site. Therefore, it is important to study seismic waves that propagate through specific soil types to understand site response. However, active seismic surveys are susceptible to noise interference and are limited due to spatial need while boreholes are costly. We develop a method using a passive array to study Rayleigh waves from microtremors, waves originating from building appliances, cars, pedestrians walking, etc. By using everyday noises as the source, site-specific analysis can be done in urban areas without worrying about noise interference or disturbing the public with explosions or other loud active sources. The array is comprised of short period Texans, self contained geophones, which record continuously for 24 hours. Our technique differs slightly from traditional SPAC (SPatial Auto-Correlation) methods used in passive arrays. We first cross correlate time windows between two receivers then stack the correlations to determine a phase delay. Performing the correlation at different frequencies will create a dispersion curve that can be inverted for shear velocity. This approach is similar to the two-station phase delay method used in regional tomography studies at much longer periods. Stacking removes off-azimuth energy, so we do not need to assume a source direction. Preliminary results from a previous passive array survey conducted near El Paso, Texas show 1-D velocity models can be created by cross-correlating noise at various frequencies. We will conduct another survey in alluvium sands at Rio Bosque Park east of El Paso. We will validate the results with active seismic refraction and surface wave survey results as well as other geophysical techniques to determine if a passive array using microtremors is an accurate method of determining subsurface structure.

  6. Effective bandstructures from unfolding supercells with vacancies

    Science.gov (United States)

    Boykin, Timothy B.; Ajoy, Arvind

    2018-02-01

    We study how vacancies alter the effective primitive cell bands projected out of supercell eigenstates via Brillouin zone unfolding. Two types of vacant primitive cells are of particular interest: Fully vacant, in which all atoms in a single cell are missing; and net fully vacant, in which the atoms comprising a full set for a single cell are missing from more than one cell. We find that a fully vacant primitive cell and a net fully vacant primitive cell have the same effect on the primitive cell bands. We show that the probability reduction for any primitive cell band is the same, regardless of band or wavevector in the primitive cell Brillouin zone, for both fully and net fully vacant primitive cells. We illustrate these results with a two-band model.

  7. Structural determination of new solid solutions [Y2-x Mx ][Sn2-x Mx ]O7-3x/2 (M = Mg or Zn by Rietveld method

    Directory of Open Access Journals (Sweden)

    Mohamed Douma

    2010-12-01

    Full Text Available New [Y2-x Mx][Sn2-x Mx]O7-3x/2 (0 ≤x≤ 0.30 for M = Mg and 0 ≤x≤ 0.36 for M = Zn solid solutions with the pyrochlore structure were synthesized via high-temperature solid-state reaction method. Powder X-ray diffraction (PXRD patterns and Fourier transform infrared (FT-IR spectra showed that these materials are new non-stoichiometric solid solutions with the pyrochlore type structure. The structural parameters for the solids obtained were successfully determined by Rietveld refinement based on the analysis of the PXRD diagrams. Lattice parameter (a of these solid solutions decreases when x increases in both series. All samples obtained have the pyrochlore structure Fd-3m, no. 227 (origin at center -3m with M2+ (M = Mg2+ or Zn2+ cations in Y3+ and Sn4+ sites, thus creating vacancies in the anionic sublattice.

  8. Lithium Insertion Mechanism in Iron-Based Oxyfluorides with Anionic Vacancies Probed by PDF Analysis.

    Science.gov (United States)

    Dambournet, Damien; Chapman, Karena W; Duttine, Mathieu; Borkiewicz, Olaf; Chupas, Peter J; Groult, Henri

    2015-08-01

    The mechanism of lithium insertion that occurs in an iron oxyfluoride sample with a hexagonal-tungsten-bronze (HTB)-type structure was investigated by the pair distribution function. This study reveals that upon lithiation, the HTB framework collapses to yield disordered rutile and rock salt phases followed by a conversion reaction of the fluoride phase toward lithium fluoride and nanometer-sized metallic iron. The occurrence of anionic vacancies in the pristine framework was shown to strongly impact the electrochemical activity, that is, the reversible capacity scales with the content of anionic vacancies. Similar to FeOF-type electrodes, upon de-lithiation, a disordered rutile phase forms, showing that the anionic chemistry dictates the atomic arrangement of the re-oxidized phase. Finally, it was shown that the nanoscaling and structural rearrangement induced by the conversion reaction allow the in situ formation of new electrode materials with enhanced electrochemical properties.

  9. Vacancy Ordering In Co3AlCx Alloys: A First Principles Study

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Chao [Los Alamos National Laboratory

    2008-01-01

    Ordering of structural vacancies in non-stoichiometric Co{sub 3}AlC{sub x} alloys has been studied using a combination of first-principles total energy calculations, a cluster expansion technique, and Monte-Carlo simulations. In the proximity of the experimental1y observed composition of x {approx} 0.59, our exhaustive ground state search yields two stable vacancy-ordered structures: a cubic Co{sub 3}AlC{sub 0.5} phase and a trigonal Co{sub 3}AlC{sub 0.667} phase. By performing finite-temperature Monte-Carlo simulations, the order-disorder transition temperatures of Co{sub 3}AlC{sub 0.5} and CO{sub 3}AlC{sub 0.667} are predicted to be {approx}1925K and {approx}1630K, respectively.

  10. Oxygen vacancy clusters on ceria: Decisive role of cerium f electrons

    Science.gov (United States)

    Zhang, Changjun; Michaelides, Angelos; King, David A.; Jenkins, Stephen J.

    2009-02-01

    Defects such as oxygen vacancies dominate the electronic and chemical properties of ceria. However, fundamental understanding of such defects, especially clusters of vacancies, is sparse. In this work, we use density-functional theory with the addition of the Hubbard U term to investigate various oxygen vacancies, including the vacancy monomer, dimer, trimer, and tetramer, in which subsurface vacancies can also be involved. We show that the individual surface and subsurface vacancies have very similar stabilities; the vacancy dimer consisting of two surface vacancies, which is not reported experimentally, is stable in theory; between the two vacancy trimers observed in experiments, the triangular surface vacancy cluster is more stable than the double linear surface vacancy cluster containing a subsurface vacancy, which agrees with some experiments but disagrees with some others; and the linear vacancy tetramer emerges as the most stable among the possible tetramers containing subsurface vacancies, although it is less stable than those containing no subsurface vacancies. These findings are rationalized in terms of the electronic change upon the removal of oxygen, namely, the localization of resulting excess electrons on Cef orbitals. We identify a correlation between the energy levels of the occupied f states of reduced Ce ions and their coordination numbers, which proves pivotal in interpreting formation energy and stability of various vacancies. Comparisons are made with experiments and apparent discrepancies are discussed. Results for gold adsorption on the vacancy clusters are presented, and the implications these have in catalysis are briefly discussed.

  11. Zn vacancy ferromagnetism in ZnS nanocrystals

    Science.gov (United States)

    Proshchenko, Vitaly; Dahnovsky, Yuri

    2017-12-01

    To explain three order of magnitude discrepancy between the experimental and calculated magnetic moments due to Zn vacancies in ZnS nanocrystals we study the effect of Zn vacancy distribution in a nanocrystal (NC). We consider small, intermediate, and large quantum dots. For the latter we employ the surface-bulk model. To study Zn vacancy distributions we choose aggregates and uniformly distributed gas in an NC core, on a surface, and both core + surface. From the investigation we find that the uniform distribution of vacancies on a surface is the most favorable configuration for quantum dots of all sizes. Then we investigate the detailed vacancy arrangement on an NC surface. We find that the most likely arrangement if the vacancies are placed along the diagonal of the unit cell square rather than along the square side. The former has the zero magnetic moment what explains the huge reduction in the total magnetization. The small nonvanishing magnetization is probably due to the presence of a small amount of Zn vacancies in the side configuration in a metastable state.

  12. Persistence of strong and switchable ferroelectricity despite vacancies

    Science.gov (United States)

    Raeliarijaona, Aldo; Fu, Huaxiang

    2017-01-01

    Vacancies play a pivotal role in affecting ferroelectric polarization and switching properties, and there is a possibility that ferroelectricity may be utterly eliminated when defects render the system metallic. However, sufficient quantitative understandings of the subject have been lacking for decades due to the fact that vacancies in ferroelectrics are often charged and polarization in charged systems is not translationally invariant. Here we perform first-principles studies to investigate the influence of vacancies on ferroelectric polarization and polarization switching in prototypical BaTiO3 of tetragonal symmetry. We demonstrate using the modern theory of polarization that, in contrast to common wisdom, defective BaTiO3 with a large concentration of vacancies (or , or ) possesses a strong nonzero electric polarization. Breaking of Ti-O bonds is found to have little effect on the magnitude of polarization, which is striking. Furthermore, a previously unrecognized microscopic mechanism, which is particularly important when vacancies are present, is proposed for polarization switching. The mechanism immediately reveals that (i) the switching barrier in the presence of is small with ΔE = 8.3 meV per bulk formula cell, and the polarization is thus switchable even when vacancies exist; (ii) The local environment of vacancy is surprisingly insignificant in polarization switching. These results provide profound new knowledge and will stimulate more theoretical and experimental interest on defect physics in FEs.

  13. Structural Determinants of Clostridium difficile Toxin A Glucosyltransferase Activity

    Energy Technology Data Exchange (ETDEWEB)

    Pruitt, Rory N.; Chumbler, Nicole M.; Rutherford, Stacey A.; Farrow, Melissa A.; Friedman, David B.; Spiller, Ben; Lacy, D. Borden (Vanderbilt)

    2012-03-28

    The principle virulence factors in Clostridium difficile pathogenesis are TcdA and TcdB, homologous glucosyltransferases capable of inactivating small GTPases within the host cell. We present crystal structures of the TcdA glucosyltransferase domain in the presence and absence of the co-substrate UDP-glucose. Although the enzymatic core is similar to that of TcdB, the proposed GTPase-binding surface differs significantly. We show that TcdA is comparable with TcdB in its modification of Rho family substrates and that, unlike TcdB, TcdA is also capable of modifying Rap family GTPases both in vitro and in cells. The glucosyltransferase activities of both toxins are reduced in the context of the holotoxin but can be restored with autoproteolytic activation and glucosyltransferase domain release. These studies highlight the importance of cellular activation in determining the array of substrates available to the toxins once delivered into the cell.

  14. Kinetic Monte Carlo Investigation of the Effects of Vacancy Pairing on Oxygen Diffusivity in Yttria-Stabilized Zirconia

    Science.gov (United States)

    Good, Brian S.

    2011-01-01

    Yttria-stabilized zirconia s high oxygen diffusivity and corresponding high ionic conductivity, and its structural stability over a broad range of temperatures, have made the material of interest for use in a number of applications, for example, as solid electrolytes in fuel cells. At low concentrations, the stabilizing yttria also serves to increase the oxygen diffusivity through the presence of corresponding oxygen vacancies, needed to maintain charge neutrality. At higher yttria concentration, however, diffusivity is impeded by the larger number of relatively high energy migration barriers associated with yttrium cations. In addition, there is evidence that oxygen vacancies preferentially occupy nearest-neighbor sites around either dopant or Zr cations, further affecting vacancy diffusion. We present the results of ab initio calculations that indicate that it is energetically favorable for oxygen vacancies to occupy nearest-neighbor sites adjacent to Y ions, and that the presence of vacancies near either species of cation lowers the migration barriers. Kinetic Monte Carlo results from simulations incorporating this effect are presented and compared with results from simulations in which the effect is not present.

  15. A Determination of the Neutron Spin Structure Function

    Energy Technology Data Exchange (ETDEWEB)

    Hughes, Emlyn W

    2003-08-18

    The authors report the results of the experiment E142 which measured the spin dependent structure function of the neutron, g{sub 1}{sup n}(x, Q{sup 2}). The experiment was carried out at the Stanford Linear Accelerator Center by measuring an asymmetry in the deep inelastic scattering of polarized electrons from a polarized {sup 3}He target, at electron energies from 19 to 26 GeV. The structure function was determined over the kinematic range 0.03 < BJorken x < 0.6 and 1.0 < Q{sup 2} < 5.5 (GeV/c){sup 2}. An evaluation of the integral {integral}{sub 0}{sup 1} g{sub 1}{sup n}(x,Q{sup 2})dx at fixed Q{sup 2} = 2 (GeV/c){sup 2} yields the final result {Lambda}{sub 1}{sup n} = -0.032 {+-} 0.006 (stat.) {+-} 0.009 (syst.). This result, when combined with the integral of the proton spin structure function measured in other experiments, confirms the fundamental Bjorken sum rule with O({alpha}{sub s}{sup 3}) corrections to within one standard deviation. This is a major success for perturbative Quantum Chromodynamics. Some ancillary results include the findings that the Ellis-Jaffe sum rule for the neutron is violated at the 2 {sigma} level, and that the total contribution of the quarks to the helicity of the nucleon is 0.36 {+-} 0.10. The strange sea polarization is estimated to be small and negative, {Delta}s = -0.07 {+-} 0.04.

  16. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline

    Science.gov (United States)

    Lesley, Scott A.; Kuhn, Peter; Godzik, Adam; Deacon, Ashley M.; Mathews, Irimpan; Kreusch, Andreas; Spraggon, Glen; Klock, Heath E.; McMullan, Daniel; Shin, Tanya; Vincent, Juli; Robb, Alyssa; Brinen, Linda S.; Miller, Mitchell D.; McPhillips, Timothy M.; Miller, Mark A.; Scheibe, Daniel; Canaves, Jaume M.; Guda, Chittibabu; Jaroszewski, Lukasz; Selby, Thomas L.; Elsliger, Marc-Andre; Wooley, John; Taylor, Susan S.; Hodgson, Keith O.; Wilson, Ian A.; Schultz, Peter G.; Stevens, Raymond C.

    2002-01-01

    Structural genomics is emerging as a principal approach to define protein structure–function relationships. To apply this approach on a genomic scale, novel methods and technologies must be developed to determine large numbers of structures. We describe the design and implementation of a high-throughput structural genomics pipeline and its application to the proteome of the thermophilic bacterium Thermotoga maritima. By using this pipeline, we successfully cloned and attempted expression of 1,376 of the predicted 1,877 genes (73%) and have identified crystallization conditions for 432 proteins, comprising 23% of the T. maritima proteome. Representative structures from TM0423 glycerol dehydrogenase and TM0449 thymidylate synthase-complementing protein are presented as examples of final outputs from the pipeline. PMID:12193646

  17. On features ov vacancies generation at low temperature

    CERN Document Server

    Magomedov, M N

    2001-01-01

    The expressions for calculating the thermodynamic potential, enthalpy, entropy (s subnu) and vacancies generation volume in the simple matter crystal at the temperatures close to 0 K are obtained. It is established that the vacancies concentration (PHI) as the temperature function (T) has the minimum by the certain T sub 0 value. The PHI(T) function by T < T sub 0 increases with decrease in T, therefore by T sub 0 the s subnu(T) function changes its sign, and by T < T sub 0 the s subnu-value becomes negative. It is shown that availability of the zero vacancies does not violate the third principle of thermodynamics

  18. Vacancy Migration and Void Formation in gamma-irradiated Ice

    DEFF Research Database (Denmark)

    Eldrup, Morten Mostgaard

    1976-01-01

    are ascribed to Ps inhibition and conversion by radiation created OH radicals. Heating above −165°C makes both effects disappear in agreement with radiation chemistry results on OH. Heating also increases the longest lifetime up to 11 nsec at −130°C. This is explained as vacancy migration leading to void...... formation. A vacancy migration energy is obtained, Em=0.34±0.07 eV, around three times higher than the previously assumed value. The advantage in this kind of study of using PAT, which are specifically sensitive to vacancy type defects, is pointed out....

  19. Thermal Motion of Steps and Vacancies in SILICON(001) by Scanning Tunneling Microscopy

    Science.gov (United States)

    Kitamura, Nobuyoshi

    Thermal motion of steps and vacancies plays important roles in surface kinetic processes. Using a scanning tunneling microscope with the new capability to image heated samples, we have conducted direct observations of the motion of monatomic-height steps and vacancies on Si(001) at the atomic level in the temperature range of 490 to 530K. We clarify behaviors of steps and vacancies specific to the Si(001) surface. The tip-to-sample drift caused by the sample heating has been reduced to about 0.01 A/sec by applying linear voltage ramps with a precisely adjusted rate to the piezo tube scanner. The low drift rate allows detailed analyses of individual structural changes at steps and vacancies within the same region for ~ 1 hour. We find that motion of vacancies is predominantly along the dimer rows, and that creation and annihilation events occur in the terraces rather than at steps. In particular, diffusion of the single-dimer vacancy has been analyzed in detail, and an activation energy of 1.7 +/- 0.4 eV has been measured for its diffusion. Structural changes at steps are observed at the ends of dimer rows as either additions or deletions of a pair of dimers. We observe that changes mainly occur nearby kinks and those of the same sign are clustered together. It is shown that these changes involve nucleation or dissociation of dimers and long range transport of monomers, and that they are inconsistent with random nucleation and dissociation of dimers. All the observations are quantitatively reproduced by a Metropolis Monte Carlo simulation with a Hamiltonian containing only kink and corner energies. By classifying the elementary reactions at steps based on the same Hamiltonian, we find that hopping of a unit kink along the step is the predominant type of reactions. This finding leads to a simple explanation for all the observations. At our temperatures, changes at steps are governed by energy differences among local configurations, which are only on the order of 0

  20. Vacancy migration energy dependence on local chemical environment in Fe–Cr alloys: A Density Functional Theory study

    Energy Technology Data Exchange (ETDEWEB)

    Costa, D., E-mail: davide.costa.ge@gmail.com [Unité Matériaux et Transformations, CNRS UMR8207, Université de Lille 1, F-59655 Villeneuve d’Ascq Cédex (France); EDF-R and D Département MMC, Les Renardières, F-77818 Moret sur Loing Cédex (France); Laboratoire commun (EDF–CNRS): Etude et Modélisation des Microstructures pour le Vieillissement des Matériaux (EM2VM) (France); Adjanor, G. [EDF-R and D Département MMC, Les Renardières, F-77818 Moret sur Loing Cédex (France); Laboratoire commun (EDF–CNRS): Etude et Modélisation des Microstructures pour le Vieillissement des Matériaux (EM2VM) (France); Becquart, C.S. [Unité Matériaux et Transformations, CNRS UMR8207, Université de Lille 1, F-59655 Villeneuve d’Ascq Cédex (France); Laboratoire commun (EDF–CNRS): Etude et Modélisation des Microstructures pour le Vieillissement des Matériaux (EM2VM) (France); Olsson, P. [Laboratoire commun (EDF–CNRS): Etude et Modélisation des Microstructures pour le Vieillissement des Matériaux (EM2VM) (France); KTH Royal Institute of Technology, Reactor Physics, Roslagstullsbacken 21, 106 91 Stockholm (Sweden); and others

    2014-09-15

    The first step towards the understanding and the modelling of the Fe–Cr alloy kinetic properties consists in estimating the migration energies related to the processes that drive the microstructure evolution. The vacancy’s migration barrier is expected to depend on the vacancy–migrating atom pair atomic environment as pointed out by Nguyen-Manh et al. or Bonny et al. In this paper, we address the issue of the dependence on the vacancy’s local atomic environment of both the vacancy migration energy and the configurational energy change ΔE that occurs when the vacancy jumps towards one of its nearest neighbour sites. A DFT approach is used to determine the ground state energy associated to a given configuration of the system. The results are interpreted in the light of the chromium–chromium and chromium–vacancy binding energies as well as the substitutional chromium atoms magnetic properties.

  1. Anisotropic behavior and inhomogeneity of atomic local densities of states in graphene with vacancy groups

    Directory of Open Access Journals (Sweden)

    V.V. Eremenko

    2016-06-01

    Full Text Available The electron local density of states (LDOS are calculated for graphene with isolated vacancies, divacancies and vacancy group of four nearest-neighbor vacancies. A strong anisotropy of behavior of LDOS near Fermi level is demonstrated for atoms near defect. Effect of next-to-nearest neighbor interaction on the properties of graphene with vacancies is established.

  2. Induced ferromagnetic and gas sensing properties in ZnO-nanostructures by altering defect concentration of oxygen and zinc vacancies

    CSIR Research Space (South Africa)

    Motaung, DE

    2015-01-01

    Full Text Available We report on the effect of the synthesis reaction-time on the structural, optical, magnetic and sensing properties of ZnO-nanostructures. Electron paramagnetic resonance and photoluminescence analyses reveal that singly ionized oxygen vacancies (VþO...

  3. Influences of vacancy defects on tensile failure of open-tip carbon nanocones

    OpenAIRE

    Ming-Liang Liao

    2017-01-01

    This paper studied influences of vacancy defects on tensile failure of open-tip carbon nanocones (CNCs) by molecular dynamics simulations. Carbon nanocones, perfect and containing mono-vacancy defects (including CNCs with the upper-vacancy, the middle-vacancy, and the lower-vacancy), were simulated in order to understand the influence of the presence and location of the vacancy defects on the CNCs tensile behavior. Some findings were obtained. It was found that the upper-vacancy CNC has the g...

  4. 75 FR 71721 - Pittsburgh Area Maritime Security Committee; Vacancies

    Science.gov (United States)

    2010-11-24

    ... SECURITY Coast Guard Pittsburgh Area Maritime Security Committee; Vacancies AGENCY: Coast Guard, DHS... the Pittsburgh Area Maritime Security Committee to submit their application for membership, to the Captain of the Port, Pittsburgh, Pennsylvania. DATES: Applications for membership should reach the...

  5. Controlling vacancies in chalcogenides as energy harvesting materials

    NARCIS (Netherlands)

    Li, Guowei

    2016-01-01

    Recent years witnessed fruitful results on tailoring properties and application performance, especially in the field of clean energy storage and harvesting materials. Defects, especially elemental vacancies, exist universally and are inevitable in materials. Due to the difficulties to precisely map

  6. 76 FR 33773 - Navigation Safety Advisory Council; Vacancies

    Science.gov (United States)

    2011-06-09

    ... the Road, navigation regulations and equipment, routing measures, marine information, diving safety... SECURITY Coast Guard Navigation Safety Advisory Council; Vacancies AGENCY: Coast Guard, DHS. ACTION: Request for applications. SUMMARY: The Coast Guard seeks applications for membership on the Navigation...

  7. 78 FR 32412 - Navigation Safety Advisory Council; Vacancies

    Science.gov (United States)

    2013-05-30

    ... the Road; navigation regulations and equipment, routing measures, marine information, diving safety... SECURITY Coast Guard Navigation Safety Advisory Council; Vacancies AGENCY: Coast Guard, DHS. ACTION: Request for applications. SUMMARY: The Coast Guard seeks applications for membership on the Navigation...

  8. Nitrogen-vacancy ensemble magnetometry based on pump absorption

    DEFF Research Database (Denmark)

    Ahmadi, Sepehr; El-Ella, Haitham A.R.; Hansen, Jørn B.

    2017-01-01

    We demonstrate magnetic field sensing by recording the variation in the pump light absorption with nitrogen-vacancy center ensemble. At a frequency of 10 mHz we obtain a noise floor of ~30 nT/√Hz....

  9. Annular dark field transmission electron microscopy for protein structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Koeck, Philip J.B., E-mail: Philip.Koeck@ki.se

    2016-02-15

    Recently annular dark field (ADF) transmission electron microscopy (TEM) has been advocated as a means of recording images of biological specimens with better signal to noise ratio (SNR) than regular bright field images. I investigate whether and how such images could be used to determine the three-dimensional structure of proteins given that an ADF aperture with a suitable pass-band can be manufactured and used in practice. I develop an approximate theory of ADF-TEM image formation for weak amplitude and phase objects and test this theory using computer simulations. I also test whether these simulated images can be used to calculate a three-dimensional model of the protein using standard software and discuss problems and possible ways to overcome these. - Highlights: • I present theory and simulations for imaging proteins using annular dark field transmission electron microscopy and investigate its suitability for 3D-reconstruction. • I show that the images are approximately proportional to the square of the projected electrostatic potential within a given passband ). • 3D-reconstructions show errors in the interior of the molecule. More accurate maps might be calculated by reconstruction algorithms that take into account non-linear image formation.

  10. High-performance gas sensing achieved by mesoporous tungsten oxide mesocrystals with increased oxygen vacancies

    KAUST Repository

    Wang, Dong

    2013-01-01

    The inner structure of W18O49 mesocrystals was observed by electron microscopy with the help of ultramicrotomy and focused ion beam techniques. The results showed that these mesocrystals contain irregular mesopores formed through partial fusion of self-assembled nanowires, and consequently have long-range structural ordering in one dimension and short-range ordering in the other two dimensions. The W18O 49 mesocrystals exhibit superior performance in gas sensing applications, which is considered to be associated with the presence of more oxygen vacancy sites in the unique mesoporous structure. © 2013 The Royal Society of Chemistry.

  11. Hydrogen-vacancy-dislocation interactions in α-Fe

    Science.gov (United States)

    Tehranchi, A.; Zhang, X.; Lu, G.; Curtin, W. A.

    2017-02-01

    Atomistic simulations of the interactions between dislocations, hydrogen atoms, and vacancies are studied to assess the viability of a recently proposed mechanism for the formation of nanoscale voids in Fe-based steels in the presence of hydrogen. Quantum-mechanics/molecular-mechanics method calculations confirm molecular statics simulations based on embedded atom method (EAM) potential showing that individual vacancies on the compressive side of an edge dislocation can be transported with the dislocation as it glides. Molecular dynamics simulations based on EAM potential then show, however, that vacancy clusters in the glide plane of an approaching dislocation are annihilated or reduced in size by the creation of a double-jog/climb process that is driven by the huge reduction in energy accompanying vacancy annihilation. The effectiveness of annihilation/reduction processes is not reduced by the presence of hydrogen in the vacancy clusters because typical V-H cluster binding energies are much lower than the vacancy formation energy, except at very high hydrogen content in the cluster. Analysis of a range of configurations indicates that hydrogen plays no special role in stabilizing nanovoids against jog formation processes that shrink voids. Experimental observations of nanovoids on the fracture surfaces of steels must be due to as-yet undetermined processes.

  12. Crystal Structure of the 30S Ribosomal Subunit from Thermus Thermophilus. Purification, Crystallization and Structure Determination

    Energy Technology Data Exchange (ETDEWEB)

    Clemons, William M.; Brodersen, Ditlev E.; McCutcheonn, John P.; May, Joanna L.C.; Carter, Andrew P.; Morgan-Warren, Robert J.; Wimberly, Brian T.; Ramakrishnan, Venki (MRC); (Utah); (MRC)

    2009-10-07

    We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 {angstrom} resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 {angstrom} resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.

  13. Decoupling structural and environmental determinants of sap velocity

    Science.gov (United States)

    Caylor, K. K.; Dragoni, D.

    2007-12-01

    Characterization of transpiration based on the water use of individual tress has the advantage of preserving vital information on the plant-environment functional links and flux partitioning between species and landscape areas. Whole-tree transpiration has been estimated by means of sap velocity probes, which offer the dual advantages of practicality and repeatability. However, the assumptions underlying the technique require careful verification in order to determine total sap flow from point-based estimates of sap velocity. Our work presents a novel theoretical framework for the study of individual tree sap flow that incorporates both spatial and temporal variability in sap velocities. The instantaneous sap velocity at any point in the radial profile of xylem tissue is defined as the product of two components: (1) a time-invariant sap velocity distribution linked to the species- specific anatomical and structural properties of the conducting xylem, and (2) a time-varying term linked to the dynamics of the atmospheric water demand and available soil moisture. The separation of structural and temporal variation in sap velocity observations provides a direct mechanism for investigating how sap flow is governed by variation in environmental conditions as well as a means for comparing characteristic rates of plant water use among individuals of varying size. Most critically, this approach allows for a consistent and physically meaningful method for extrapolating point observations of sap velocity across the entire depth of conducting xylem. Experimental evidence supports our theoretical framework in the case of a population of sugar maples in a mixed deciduous forest, where observations were taken from a wide range of tree sizes, under varying soil water availability and atmospheric transpiration demand. We have also applied our approach to a small homogeneous sample of dwarf apple trees in a managed orchard, with favorable results. While these results require further

  14. Discovery and Structure Determination of the Orphan Enzyme Isoxanthopterin Deaminase

    Energy Technology Data Exchange (ETDEWEB)

    Hall, R.S.; Swaminathan, S.; Agarwal, R.; Hitchcock, D.; Sauder, J. M.; Burley, S. K.; Raushel, F. M.

    2010-05-25

    Two previously uncharacterized proteins have been identified that efficiently catalyze the deamination of isoxanthopterin and pterin 6-carboxylate. The genes encoding these two enzymes, NYSGXRC-9339a (gi|44585104) and NYSGXRC-9236b (gi|44611670), were first identified from DNA isolated from the Sargasso Sea as part of the Global Ocean Sampling Project. The genes were synthesized, and the proteins were subsequently expressed and purified. The X-ray structure of Sgx9339a was determined at 2.7 {angstrom} resolution (Protein Data Bank entry 2PAJ). This protein folds as a distorted ({beta}/{alpha}){sub 8} barrel and contains a single zinc ion in the active site. These enzymes are members of the amidohydrolase superfamily and belong to cog0402 within the clusters of orthologous groups (COG). Enzymes in cog0402 have previously been shown to catalyze the deamination of guanine, cytosine, S-adenosylhomocysteine, and 8-oxoguanine. A small compound library of pteridines, purines, and pyrimidines was used to probe catalytic activity. The only substrates identified in this search were isoxanthopterin and pterin 6-carboxylate. The kinetic constants for the deamination of isoxanthopterin with Sgx9339a were determined to be 1.0 s{sup -1}, 8.0 {micro}M, and 1.3 x 10{sup 5} M{sup -1} s{sup -1} (k{sub cat}, K{sub m}, and k{sub cat}/K{sub m}, respectively). The active site of Sgx9339a most closely resembles the active site for 8-oxoguanine deaminase (Protein Data Bank entry 2UZ9). A model for substrate recognition of isoxanthopterin by Sgx9339a was proposed on the basis of the binding of guanine and xanthine in the active site of guanine deaminase. Residues critical for substrate binding appear to be conserved glutamine and tyrosine residues that form hydrogen bonds with the carbonyl oxygen at C4, a conserved threonine residue that forms hydrogen bonds with N5, and another conserved threonine residue that forms hydrogen bonds with the carbonyl group at C7. These conserved active site

  15. Tuning interfacial thermal conductance of graphene embedded in soft materials by vacancy defects.

    Science.gov (United States)

    Liu, Ying; Hu, Chongze; Huang, Jingsong; Sumpter, Bobby G; Qiao, Rui

    2015-06-28

    Nanocomposites based on graphene dispersed in matrices of soft materials are promising thermal management materials. Their effective thermal conductivity depends on both the thermal conductivity of graphene and the conductance of the thermal transport across graphene-matrix interfaces. Here, we report on molecular dynamics simulations of the thermal transport across the interfaces between defected graphene and soft materials in two different modes: in the "across" mode, heat enters graphene from one side of its basal plane and leaves through the other side; in the "non-across" mode, heat enters or leaves graphene simultaneously from both sides of its basal plane. We show that as the density of vacancy defects in graphene increases from 0% to 8%, the conductance of the interfacial thermal transport in the "across" mode increases from 160.4 ± 16 to 207.8 ± 11 MW/m(2) K, while that in the "non-across" mode increases from 7.2 ± 0.1 to 17.8 ± 0.6 MW/m(2) K. The molecular mechanisms for these variations of thermal conductance are clarified using the phonon density of states and structural characteristics of defected graphene. On the basis of these results and effective medium theory, we show that it is possible to enhance the effective thermal conductivity of thermal nanocomposites by tuning the density of vacancy defects in graphene despite the fact that graphene's thermal conductivity always decreases as vacancy defects are introduced.

  16. Unequivocal determination of complex molecular structures using anisotropic NMR measurements.

    Science.gov (United States)

    Liu, Yizhou; Saurí, Josep; Mevers, Emily; Peczuh, Mark W; Hiemstra, Henk; Clardy, Jon; Martin, Gary E; Williamson, R Thomas

    2017-04-07

    Assignment of complex molecular structures from nuclear magnetic resonance (NMR) data can be prone to interpretational mistakes. Residual dipolar couplings and residual chemical shift anisotropy provide a spatial view of the relative orientations between bonds and chemical shielding tensors, respectively, regardless of separation. Consequently, these data constitute a reliable reporter of global structural validity. Anisotropic NMR parameters can be used to evaluate investigators' structure proposals or structures generated by computer-assisted structure elucidation. Application of the method to several complex structure assignment problems shows promising results that signal a potential paradigm shift from conventional NMR data interpretation, which may be of particular utility for compounds not amenable to x-ray crystallography. Copyright © 2017, American Association for the Advancement of Science.

  17. The American Society for Clinical Pathology's 2014 vacancy survey of medical laboratories in the United States.

    Science.gov (United States)

    Garcia, Edna; Ali, Asma M; Soles, Ryan M; Lewis, D Grace

    2015-09-01

    To determine the extent and distribution of workforce shortages within the nation's medical laboratories. Historically, the results of this biennial survey have served as a basis for additional research on laboratory recruitment, retention, education, marketing, certification, and advocacy. The 2014 Vacancy Survey was conducted through collaboration between American Society for Clinical Pathology's Institute of Science, Technology, and Policy in Washington, DC, and the Evaluation, Measurement, and Assessment Department and Board of Certification in Chicago, Illinois. Data were collected via an Internet survey that was distributed to individuals who were able to report on staffing and certifications for their laboratories. Data reveal increased overall vacancy rates since 2012 for all departments surveyed except cytology and cytogenetics. Also, results show higher anticipated retirement rates for both staff and supervisors. Overall certification rates are highest among laboratory personnel in cytogenetics, hematology/coagulation, and flow cytometry departments and lowest among phlebotomy, specimen processing, and anatomic pathology. Factors such as retirement and the improving economy are driving the need for more laboratory professionals. Recruitment of qualified laboratory professionals in the workforce and students in laboratory programs will be the key in fulfilling the higher vacancies revealed from the survey results in 2014. Copyright© by the American Society for Clinical Pathology.

  18. Equilibration of experimentally determined protein structures for molecular dynamics simulation.

    Science.gov (United States)

    Walton, Emily B; Vanvliet, Krystyn J

    2006-12-01

    Preceding molecular dynamics simulations of biomolecular interactions, the molecule of interest is often equilibrated with respect to an initial configuration. This so-called equilibration stage is required because the input structure is typically not within the equilibrium phase space of the simulation conditions, particularly in systems as complex as proteins, which can lead to artifactual trajectories of protein dynamics. The time at which nonequilibrium effects from the initial configuration are minimized-what we will call the equilibration time-marks the beginning of equilibrium phase-space exploration. Note that the identification of this time does not imply exploration of the entire equilibrium phase space. We have found that current equilibration methodologies contain ambiguities that lead to uncertainty in determining the end of the equilibration stage of the trajectory. This results in equilibration times that are either too long, resulting in wasted computational resources, or too short, resulting in the simulation of molecular trajectories that do not accurately represent the physical system. We outline and demonstrate a protocol for identifying the equilibration time that is based on the physical model of Normal Mode Analysis. We attain the computational efficiency required of large-protein simulations via a stretched exponential approximation that enables an analytically tractable and physically meaningful form of the root-mean-square deviation of atoms comprising the protein. We find that the fitting parameters (which correspond to physical properties of the protein) fluctuate initially but then stabilize for increased simulation time, independently of the simulation duration or sampling frequency. We define the end of the equilibration stage--and thus the equilibration time--as the point in the simulation when these parameters attain constant values. Compared to existing methods, our approach provides the objective identification of the time at

  19. CCDC 1416891: Experimental Crystal Structure Determination : Methyl-triphenyl-germanium

    KAUST Repository

    Bernatowicz, Piotr

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  20. CCDC 1408042: Experimental Crystal Structure Determination : 6,13-dimesitylpentacene

    KAUST Repository

    Shi, Xueliang

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  1. Determining the Mechanical Properties of Lattice Block Structures

    Science.gov (United States)

    Wilmoth, Nathan

    2013-01-01

    Lattice block structures and shape memory alloys possess several traits ideal for solving intriguing new engineering problems in industries such as aerospace, military, and transportation. Recent testing at the NASA Glenn Research Center has investigated the material properties of lattice block structures cast from a conventional aerospace titanium alloy as well as lattice block structures cast from nickel-titanium shape memory alloy. The lattice block structures for both materials were sectioned into smaller subelements for tension and compression testing. The results from the cast conventional titanium material showed that the expected mechanical properties were maintained. The shape memory alloy material was found to be extremely brittle from the casting process and only compression testing was completed. Future shape memory alloy lattice block structures will utilize an adjusted material composition that will provide a better quality casting. The testing effort resulted in baseline mechanical property data from the conventional titanium material for comparison to shape memory alloy materials once suitable castings are available.

  2. Protein Structure Determination by Assembling Super-Secondary Structure Motifs Using Pseudocontact Shifts.

    Science.gov (United States)

    Pilla, Kala Bharath; Otting, Gottfried; Huber, Thomas

    2017-03-07

    Computational and nuclear magnetic resonance hybrid approaches provide efficient tools for 3D structure determination of small proteins, but currently available algorithms struggle to perform with larger proteins. Here we demonstrate a new computational algorithm that assembles the 3D structure of a protein from its constituent super-secondary structural motifs (Smotifs) with the help of pseudocontact shift (PCS) restraints for backbone amide protons, where the PCSs are produced from different metal centers. The algorithm, DINGO-PCS (3D assembly of Individual Smotifs to Near-native Geometry as Orchestrated by PCSs), employs the PCSs to recognize, orient, and assemble the constituent Smotifs of the target protein without any other experimental data or computational force fields. Using a universal Smotif database, the DINGO-PCS algorithm exhaustively enumerates any given Smotif. We benchmarked the program against ten different protein targets ranging from 100 to 220 residues with different topologies. For nine of these targets, the method was able to identify near-native Smotifs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. WHAT DETERMINES THE CAPITAL STRUCTURE OF LISTED FIRMS IN ROMANIA

    Directory of Open Access Journals (Sweden)

    Floriniţa Duca

    2012-10-01

    Full Text Available This paper examines the relative importance of four factors in the capital structure decisions of Romanian listed firms. The existing empirical research on capital structure has been largely confined to developed countries. The Romanian Financial Market has been developing at an exponential rate and dedicated research in the field is required. We used 100 firms listed in 2010 at the Bucharest Stock Exchange. The objective of this paper is to build on previous studies model all the important factors affecting capital structure decisions. We find that factors such as tangibility of assets, firm size, liquidity, and profitability have significant influences on the leverage structure chosen by firms.These results are believed to have significant implications for the theory of finance and to be of importance to the corporate treasure in choice of new financing and to the financial analyst.

  4. Structural determinants of reductive terpene cyclization in iridoid biosynthesis

    DEFF Research Database (Denmark)

    Kries, Hajo; Caputi, Lorenzo; Stevenson, Clare E M

    2016-01-01

    The carbon skeleton of ecologically and pharmacologically important iridoid monoterpenes is formed in a reductive cyclization reaction unrelated to canonical terpene cyclization. Here we report the crystal structure of the recently discovered iridoid cyclase (from Catharanthus roseus) bound...

  5. Origin of Nanobubbles Electrochemically Formed in a Magnetic Field: Ionic Vacancy Production in Electrode Reaction

    Science.gov (United States)

    Aogaki, Ryoichi; Sugiyama, Atsushi; Miura, Makoto; Oshikiri, Yoshinobu; Miura, Miki; Morimoto, Ryoichi; Takagi, Satoshi; Mogi, Iwao; Yamauchi, Yusuke

    2016-07-01

    As a process complementing conventional electrode reactions, ionic vacancy production in electrode reaction was theoretically examined; whether reaction is anodic or cathodic, based on the momentum conservation by Newton’s second law of motion, electron transfer necessarily leads to the emission of original embryo vacancies, and dielectric polarization endows to them the same electric charge as trans- ferred in the reaction. Then, the emitted embryo vacancies immediately receive the thermal relaxation of solution particles to develop steady-state vacancies. After the vacancy production, nanobubbles are created by the collision of the vacancies in a vertical magnetic field.

  6. Urban Structure as Determinant of Short Distance Goods Transport

    National Research Council Canada - National Science Library

    Holmgren, Johan

    2012-01-01

    In this study, data on short distance goods transports is analysed in order to determine if variations in the amounts of goods generated could be explained by geographical and demographical variables...

  7. Local factors determine plant community structure on closely neighbored islands.

    Directory of Open Access Journals (Sweden)

    Jianbo Lu

    Full Text Available Despite the recent popularity of the metacommunity concept, ecologists have not evaluated the applicability of different metacommunity frameworks to insular organisms. We surveyed 50 closely spaced islands in the Thousand-Island Lake of China to examine the role of local (environmental and regional (dispersal factors in structuring woody plant assemblages (tree and shrub species on these islands. By partitioning the variation in plant community structure into local and regional causes, we showed that local environmental conditions, specifically island morphometric characteristics, accounted for the majority of the variation in plant community structure among the studied islands. Spatial variables, representing the potential importance of species dispersal, explained little variation. We conclude that one metacommunity framework-species sorting-best characterizes these plant communities. This result reinforces the idea that the traditional approach of emphasizing the local perspective when studying ecological communities continues to hold its value.

  8. Local factors determine plant community structure on closely neighbored islands.

    Science.gov (United States)

    Lu, Jianbo; Jiang, Lin; Yu, Lin; Sun, Que

    2011-05-10

    Despite the recent popularity of the metacommunity concept, ecologists have not evaluated the applicability of different metacommunity frameworks to insular organisms. We surveyed 50 closely spaced islands in the Thousand-Island Lake of China to examine the role of local (environmental) and regional (dispersal) factors in structuring woody plant assemblages (tree and shrub species) on these islands. By partitioning the variation in plant community structure into local and regional causes, we showed that local environmental conditions, specifically island morphometric characteristics, accounted for the majority of the variation in plant community structure among the studied islands. Spatial variables, representing the potential importance of species dispersal, explained little variation. We conclude that one metacommunity framework-species sorting-best characterizes these plant communities. This result reinforces the idea that the traditional approach of emphasizing the local perspective when studying ecological communities continues to hold its value.

  9. RNA structure determination by solid-state NMR spectroscopy.

    Science.gov (United States)

    Marchanka, Alexander; Simon, Bernd; Althoff-Ospelt, Gerhard; Carlomagno, Teresa

    2015-05-11

    Knowledge of the RNA three-dimensional structure, either in isolation or as part of RNP complexes, is fundamental to understand the mechanism of numerous cellular processes. Because of its flexibility, RNA represents a challenge for crystallization, while the large size of cellular complexes brings solution-state NMR to its limits. Here, we demonstrate an alternative approach on the basis of solid-state NMR spectroscopy. We develop a suite of experiments and RNA labeling schemes and demonstrate for the first time that ssNMR can yield a RNA structure at high-resolution. This methodology allows structural analysis of segmentally labelled RNA stretches in high-molecular weight cellular machines—independent of their ability to crystallize—and opens the way to mechanistic studies of currently difficult-to-access RNA-protein assemblies.

  10. Structure determination of T-cell protein-tyrosine phosphatase

    DEFF Research Database (Denmark)

    Iversen, L.F.; Møller, K. B.; Pedersen, A.K.

    2002-01-01

    homologous T cell protein-tyrosine phosphatase (TC-PTP) has received much less attention, and no x-ray structure has been provided. We have previously co-crystallized PTP1B with a number of low molecular weight inhibitors that inhibit TC-PTP with similar efficiency. Unexpectedly, we were not able to co...... the high degree of functional and structural similarity between TC-PTP and PTP1B, we have been able to identify areas close to the active site that might be addressed to develop selective inhibitors of each enzyme....

  11. Nitrogen-vacancy ensemble magnetometry based on pump absorption

    Science.gov (United States)

    Ahmadi, Sepehr; El-Ella, Haitham A. R.; Wojciechowski, Adam M.; Gehring, Tobias; Hansen, Jørn O. B.; Huck, Alexander; Andersen, Ulrik L.

    2018-01-01

    We demonstrate magnetic-field sensing using an ensemble of nitrogen-vacancy centers by recording the variation in the pump-light absorption due to the spin-polarization dependence of the total ground-state population. Using a 532 nm pump laser, we measure the absorption of native nitrogen-vacancy centers in a chemical-vapor-deposited diamond placed in a resonant optical cavity. For a laser pump power of 0.4 W and a cavity finesse of 45, we obtain a noise floor of ˜100 nT /√{Hz } spanning a bandwidth up to 125 Hz. We project a photon shot-noise-limited sensitivity of ˜1 pT /√{Hz } by optimizing the nitrogen-vacancy concentration and the detection method.

  12. Multiple deuterium occupancy of vacancies in Pd and related metals

    DEFF Research Database (Denmark)

    Nordlander, P.; Nørskov, Jens Kehlet; Besenbacher, F.

    1989-01-01

    The binding energies of up to six deuterium atoms into monovacancies of Pd, Ni, Fe, Cu, Nb, and Mo have been calculated using the effective-medium theory. For all metals it is found that at least six D atoms can be accommodated in the vacancy. Of the systems studied the deuterium-deuterium intera......The binding energies of up to six deuterium atoms into monovacancies of Pd, Ni, Fe, Cu, Nb, and Mo have been calculated using the effective-medium theory. For all metals it is found that at least six D atoms can be accommodated in the vacancy. Of the systems studied the deuterium......-deuterium interaction is found to be least repulsive for Pd. This multiple occupancy of the vacancy defect can have potentially significant implications for the recently proposed fusion of D atoms in Pd....

  13. Probing superheavy quasimolecular collisions with incoming inner shell vacancies

    Energy Technology Data Exchange (ETDEWEB)

    Verma, P. [Atomphysik, GSI, Planckstrasse 1, D-64291 Darmstadt (Germany) and JMI University, New Delhi (India) and Vaish College, Rohtak (India)]. E-mail: P.Verma@gsi.de; Mokler, P.H. [Atomphysik, GSI, Planckstrasse 1, D-64291 Darmstadt (Germany); J. Liebig University, Giessen (Germany); Braeuning-Demian, A. [Atomphysik, GSI, Planckstrasse 1, D-64291 Darmstadt (Germany); Braeuning, H. [J. Liebig University, Giessen (Germany); Kozhuharov, C. [Atomphysik, GSI, Planckstrasse 1, D-64291 Darmstadt (Germany); Bosch, F. [Atomphysik, GSI, Planckstrasse 1, D-64291 Darmstadt (Germany); Liesen, D. [Atomphysik, GSI, Planckstrasse 1, D-64291 Darmstadt (Germany); Hagmann, S. [Atomphysik, GSI, Planckstrasse 1, D-64291 Darmstadt (Germany); J.W. Goethe University, Frankfurt (Germany); Stoehlker, Th. [Atomphysik, GSI, Planckstrasse 1, D-64291 Darmstadt (Germany); Stachura, Z. [Institute for Nuclear Physics, Cracow (Poland); Banas, D. [Atomphysik, GSI, Planckstrasse 1, D-64291 Darmstadt (Germany); Swietokrzyska Academy, Kielce (Poland); Orsic-Muthig, A. [Atomphysik, GSI, Planckstrasse 1, D-64291 Darmstadt (Germany); Schoeffler, M. [J.W. Goethe University, Frankfurt (Germany); Sierpowski, D. [Jagellonian University, Cracow (Poland); Spillmann, U. [Atomphysik, GSI, Planckstrasse 1, D-64291 Darmstadt (Germany); Tashenov, S. [Atomphysik, GSI, Planckstrasse 1, D-64291 Darmstadt (Germany); Toleikis, S. [Atomphysik, GSI, Planckstrasse 1, D-64291 Darmstadt (Germany); Wahab, M.A. [JMI University, New Delhi (India)

    2006-04-15

    With the advanced accelerator technologies used at the SIS/ESR heavy ion facility at GSI, the highest charge states (bare, H-like, etc.) even for the heaviest ions can be provided for experiments at moderate collision velocities (v {sub ion} < v {sub K}). Hence, inner shell vacancies can be provided prior to collisions for the innermost shells of transiently formed superheavy quasimolecules. However, projectile K-vacancies may be destroyed while penetrating solids. The goal of the present investigation is to establish how far at relatively low collision velocities, high incoming ionic charge states do survive in thin solid targets and hence, how far thin solid targets can be utilized for studying superheavy quasimolecules with well-defined, open, incoming, inner shell vacancy channels. The dependence of quasimolecular collisions on projectile charge state (q) and target thickness (t) is studied in very thin Au solid targets for 69 MeV/u U {sup q+} ions (73 {<=} q {<=} 91)

  14. Induced conductivity in sol-gel ZnO films by passivation or elimination of Zn vacancies

    Directory of Open Access Journals (Sweden)

    D. J. Winarski

    2016-09-01

    Full Text Available Undoped and Ga- and Al- doped ZnO films were synthesized using sol-gel and spin coating methods and characterized by X-ray diffraction, high-resolution scanning electron microscopy (SEM, optical spectroscopy and Hall-effect measurements. SEM measurements reveal an average grain size of 20 nm and distinct individual layer structure. Measurable conductivity was not detected in the unprocessed films; however, annealing in hydrogen or zinc environment induced significant conductivity (∼10−2 Ω.cm in most films. Positron annihilation spectroscopy measurements provided strong evidence that the significant enhancement in conductivity was due to hydrogen passivation of Zn vacancy related defects or elimination of Zn vacancies by Zn interstitials which suppress their role as deep acceptors. Hydrogen passivation of cation vacancies is shown to play an important role in tuning the electrical conductivity of ZnO, similar to its role in passivation of defects at the Si/SiO2 interface that has been essential for the successful development of complementary metal–oxide–semiconductor (CMOS devices. By comparison with hydrogen effect on other oxides, we suggest that hydrogen may play a universal role in oxides passivating cation vacancies and modifying their electronic properties.

  15. Cationic Vacancy Defects in Iron Phosphide: A Promising Route toward Efficient and Stable Hydrogen Evolution by Electrochemical Water Splitting.

    Science.gov (United States)

    Kwong, Wai Ling; Gracia-Espino, Eduardo; Lee, Cheng Choo; Sandström, Robin; Wågberg, Thomas; Messinger, Johannes

    2017-11-23

    Engineering the electronic properties of transition metal phosphides has shown great effectiveness in improving their intrinsic catalytic activity for the hydrogen evolution reaction (HER) in water splitting applications. Herein, we report for the first time, the creation of Fe vacancies as an approach to modulate the electronic structure of iron phosphide (FeP). The Fe vacancies were produced by chemical leaching of Mg that was introduced into FeP as "sacrificial dopant". The obtained Fevacancy-rich FeP nanoparticulate films, which were deposited on Ti foil, show excellent HER activity compared to pristine FeP and Mg-doped FeP, achieving a current density of 10 mA cm -2 at overpotentials of 108 mV in 1 m KOH and 65 mV in 0.5 m H 2 SO 4 , with a near-100 % Faradaic efficiency. Our theoretical and experimental analyses reveal that the improved HER activity originates from the presence of Fe vacancies, which lead to a synergistic modulation of the structural and electronic properties that result in a near-optimal hydrogen adsorption free energy and enhanced proton trapping. The success in catalytic improvement through the introduction of cationic vacancy defects has not only demonstrated the potential of Fe-vacancy-rich FeP as highly efficient, earth abundant HER catalyst, but also opens up an exciting pathway for activating other promising catalysts for electrochemical water splitting. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  16. The determination of turbulent structures in the atmospheric surface layer

    NARCIS (Netherlands)

    Schols, J.L.J.

    1984-01-01

    The turbulent flow in the atmospheric surface layer (ASL) contains turbulent structures, which are defined as spatially coherent, organized flow motions. 'Organized' means that characteristic patterns, observed at a point in space, occur almost simultaneously in more than one turbulence signal and

  17. Determination of conduction and valence band electronic structure ...

    Indian Academy of Sciences (India)

    insufficient to study in-depth unoccupied states of investigated materials because it overlooks the shallow traps. Keywords. Photo-catalysis; high-resolution RIXS; electronic structure. 1. Introduction. Photocatalysis is an emerging field that offers poten- tial to address some of the energy and waste manage- ment challenges.

  18. The internal structure of magnetic nanoparticles determines the magnetic response

    Czech Academy of Sciences Publication Activity Database

    Pacáková, Barbara; Kubíčková, Simona; Salas, G.; Mantlíková, Alice; Marciello, M.; Morales, M.P.; Nižňanský, D.; Vejpravová, Jana

    2017-01-01

    Roč. 9, č. 16 (2017), s. 5129-5140 ISSN 2040-3364 R&D Projects: GA ČR(CZ) GA15-01953S Institutional support: RVO:68378271 Keywords : nanoparticles * single-domain * internal structure Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 7.367, year: 2016

  19. Generative probabilistic models extend the scope of inferential structure determination

    DEFF Research Database (Denmark)

    Olsson, Simon; Boomsma, Wouter; Frellsen, Jes

    2011-01-01

    demonstrate that the use of generative probabilistic models instead of physical forcefields in the Bayesian formalism is not only conceptually attractive, but also improves precision and efficiency. Our results open new vistas for the use of sophisticated probabilistic models of biomolecular structure...

  20. Structural Determinants of Intergroup Association: Interracial Marriage and Crime.

    Science.gov (United States)

    South, Scott J.; Messner, Steven F.

    1986-01-01

    Using data from a sample of 25 U. S. metropolitan cities, this study investigates the relationship between interracial marriage and violent interracial crime. Results show a positive relationship, one which was predicted by Blau's macrosociological theory of social structure. (Author/JDH)

  1. Determination of verticality of reservoir engineering structure from ...

    African Journals Online (AJOL)

    Terrestrial laser scanners (TLS) are used nowadays as Geomatics instruments for various applications. One of these applications is 3D survey and management of oil and gas facilities and other engineering structures. This recent attention is due to the fact that laser scanner has the ability to generate massive amounts of ...

  2. Host Proteins Determine MRSA Biofilm Structure and Integrity

    DEFF Research Database (Denmark)

    Dreier, Cindy; Nielsen, Astrid; Jørgensen, Nis Pedersen

    Human extracellular matrix (hECM) proteins aids the initial attachment and initiation of an infection, by specific binding to bacterial cell surface proteins. However, the importance of hECM proteins in structure, integrity and antibiotic resilience of a biofilm is unknown. This study aims to det...

  3. Effect of transition metal Fe adsorption on CeO2 (110) surface in the methane activation and oxygen vacancy formation: A density functional theory study

    Science.gov (United States)

    Tian, Dong; Zeng, Chunhua; Wang, Hua; Cheng, Xianming; Zheng, Yane; Xiang, Chao; Wei, Yonggang; Li, Kongzhai; Zhu, Xing

    2017-09-01

    Methane activation and oxygen vacancy formation over transition metal Fe adsorption on CeO2 (110) are studied by using the method of density functional theory (DFT) + U method. A set of model configurations are generated by placing Fe at five surface sites, viz., O-top site, O-bridge site, Ce-bridge site, Ce-top and double oxygen-bridge sites. The study shows that the energetically most favorable configuration is Fe adsorption at the double oxygen-bridge site. Based on the calculated surface, subsurface and the second oxygen vacancies formation energy with (or without) Fe adsorption, it shows that the Fe adsorption is in favor of the surface, subsurface and second oxygen vacancies formation. For the surface and subsurface oxygen vacancy on the Fe/CeO2 (110) surface, the main factor responsible for lowering of Evac is that the adsorption induces structural distortions, whereas, for the second oxygen vacancy, half can be attributed to the large structural relaxation, half can be attributed to the electronic effects. After calculating and discussing about the CH4 activation on CeO2 (110) and Fe/CeO2 (110) surface with (or without) the surface or subsurface oxygen vacancies at the possible adsorption sites, the results show that when the CH4 adsorbed on the Fe/CeO2 (110) with the surface oxygen vacancy at the Ce1 and Ce2 sites, the CH4 decomposed into the CH(ads) and H(ads), its belongs to the chemical absorption, whereas, when the CH4 adsorbed on the other possible sites, the mentioned phenomenon is not occurred, its belongs to the physical absorption. This study reveals the correlation between surface reducibility and catalytic activity for methane oxidation on cerium-based materials, which might be beneficial in developing improved catalysts for methane combustion.

  4. Vacancy Mediated Mechanism of Nitrogen Substitution in Carbon Nanotubes

    Science.gov (United States)

    Srivastava, Deepak; Menon, Madhu; Sadanadan, Bindu; Rao, Apparao M.

    2003-01-01

    Nitrogen substitution reaction in a graphene sheet and carbon nanotubes of different diameter are investigated using the generalized tight-binding molecular dynamics method. The formation of a vacancy in curved graphene sheet or a carbon nanotube is found to cause a curvature dependent local reconstruction of the surface. Our simulations and analysis show that vacancy mediated N substitution (rather than N chemisorption) is favored on the surface of nanotubes with diameter larger than 8 nm. This predicted value of the critical minimum diameter for N incorporation is confirmed by experimental results presented.

  5. Structure Determination of Unknown Organic Liquids Using NMR and IR Spectroscopy: A General Chemistry Laboratory

    Science.gov (United States)

    Pavel, John T.; Hyde, Erin C.; Bruch, Martha D.

    2012-01-01

    This experiment introduced general chemistry students to the basic concepts of organic structures and to the power of spectroscopic methods for structure determination. Students employed a combination of IR and NMR spectroscopy to perform de novo structure determination of unknown alcohols, without being provided with a list of possible…

  6. Gap-closing test structures for temperature budget determination

    NARCIS (Netherlands)

    Faber, Erik Jouwert; Wolters, Robertus A.M.; Schmitz, Jurriaan

    2011-01-01

    We present the extension of a method for determining the temperature budget of the process side of silicon substrates and chips, employing silicide formation reactions. In this work, silicon-on-insulator type substrates are used instead of bulk silicon wafers. By an appropriate choice of the layer

  7. Determination of Velocity And Acceleration of Structural Deformation ...

    African Journals Online (AJOL)

    This paper outlines the procedure of geodetic monitoring system of circular oil storage tanks and presents the analysis of the resulted observations to determine the values of their deformation. At the Forcados Tank Farm, there are eighteen tanks currently used for crude oil storage. In this study, only tank 6 was used as case ...

  8. Algebraic algorithms for structure determination in biological chemistry

    Science.gov (United States)

    Emiris, Ioannis Z.; Fritzilas, Epaminondas D.; Manocha, Dinesh

    Several problems in computational chemistry, structural molecular biology, and biological chemistry can be solved by symbolic-numerical algorithms. We introduce suitable algebraic tools and then survey their usage in concrete applications. In particular, questions on molecular structure can be modeled by systems of polynomial equations, mainly by drawing on techniques from robot kinematics. Resultant-based algorithms, including sparse resultants and their matrix formulae, are described in order to reduce the solving of polynomial systems to numerical linear algebra. As an illustration, we focus on computing all conformations of cyclic molecules and on matching pharmacophores under distance constraints; in both cases, the number of independent degrees of freedom is relatively small. We summarize some existing results as well as sketch some original work. Both lead to complete and accurate solutions for those problems in the sense that our algorithms output all solutions with sufficiently high precision for the needs of biochemical applications.

  9. High performance computing in structural determination by electron cryomicroscopy.

    Science.gov (United States)

    Fernández, J J

    2008-10-01

    Computational advances have significantly contributed to the current role of electron cryomicroscopy (cryoEM) in structural biology. The needs for computational power are constantly growing with the increasing complexity of algorithms and the amount of data needed to push the resolution limits. High performance computing (HPC) is becoming paramount in cryoEM to cope with those computational needs. Since the nineties, different HPC strategies have been proposed for some specific problems in cryoEM and, in fact, some of them are already available in common software packages. Nevertheless, the literature is scattered in the areas of computer science and structural biology. In this communication, the HPC approaches devised for the computation-intensive tasks in cryoEM (single particles and tomography) are retrospectively reviewed and the future trends are discussed. Moreover, the HPC capabilities available in the most common cryoEM packages are surveyed, as an evidence of the importance of HPC in addressing the future challenges.

  10. Determination of the Structural Basis of Antibody Diversity Using NMR

    Science.gov (United States)

    1988-09-15

    diversity found in these anti- Lewitter, F. I., Rindone. W. P., Swindell , C. D. & Tung, C. S. DNP-SL antibodies provides a rich source for structural...matching heavy and light chains combi- Genetics il5. 169-176. natorially increases the number of related antibodies within 16. Jardetzky, 0. & Roberts . G. C...relative peak amplitudes & Roberts , 1981), giving an r- dependence for the effect that are consistent with those observed in the spectra. Using (Solomon

  11. Lifestyle and biomechanical determinants of knee joint structure and symptoms

    OpenAIRE

    Teichtahl, Andrew

    2017-01-01

    Osteoarthritis (OA) is the most common form of arthritis and commonly affects weight-bearing joints, such as the knee. With the growing obesity endemic and aging population, the prevalence of knee OA will increase over the coming decades. Since the advent of Magnetic resonance imaging (MRI), OA is now considered a whole-organ disease, affecting multiple articular structures. No cure exists for knee OA and the only definitive management is joint replacement surgery, indicated for painful end-s...

  12. X-ray structure determination and analysis of hydrogen interactions ...

    Indian Academy of Sciences (India)

    Unknown

    with an aim of describing the hydrogen interaction in biphenyl derivatives. The title compound crystallizes in monoclinic space group P21/c with unit cell dimensions, a = 7⋅706(1), b = 11⋅745(2), c = 12⋅721(2) Å, β = 92⋅31(1)°,. Z = 4 and its structure has been refined up to the reliability index of 3⋅8%. The average torsion ...

  13. Determining the Optimal Work Breakdown Structure for Defense Acquisition Contracts

    Science.gov (United States)

    2016-03-24

    reported in a format consistent with governing regulations and guidelines (DoD, 2011; Fitzpatrick, Meyer , & Stubbs, 2016). These programs can be...Fitzpatrick, Meyer , & Stubbs, 2016), a metric that can be applied reactively to a program’s Work Breakdown Structure, highlighting those leaf elements that...Hicks, 2008), program rebaselining (Ruter & Philip , 2007), and technological difficulties causing cost and schedule delays (Blickstein et al, 2011

  14. Water Determines the Structure and Dynamics of Proteins.

    Science.gov (United States)

    Bellissent-Funel, Marie-Claire; Hassanali, Ali; Havenith, Martina; Henchman, Richard; Pohl, Peter; Sterpone, Fabio; van der Spoel, David; Xu, Yao; Garcia, Angel E

    2016-07-13

    Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.

  15. Three-dimensional structure of poliovirus serotype 1 neutralizing determinants.

    Science.gov (United States)

    Page, G S; Mosser, A G; Hogle, J M; Filman, D J; Rueckert, R R; Chow, M

    1988-01-01

    Antigenic mutants of poliovirus (Sabin strain, serotype 1) were isolated by the resistance of the virus to anti-Sabin neutralizing monoclonal antibodies. The amino acid replacements within the capsid protein sequence causing the altered antigenicity were identified for each of 63 isolates. The mutations cluster into distinct nonoverlapping peptide segments that group into three general immunological phenotypes on the basis of cross-neutralization analyses with 15 neutralizing anti-Sabin monoclonal antibodies. Location of the mutated amino acid residues within the three-dimensional structure of the virion indicates that the majority of these amino acid residues are highly exposed and located within prominent structural features of the viral surface. Those mutated amino acid residues that are less accessible to antibody interaction are often involved in hydrogen bonds or salt bridges that would stabilize the local tertiary structure of the antigenic site. The interactions of the peptide segments that form these neutralizing sites suggest specific models for the generation of neutralization-resistant variants and for the interaction between the viral surface and antibody. Images PMID:2451757

  16. Efficient 2D probe absorption spectrum in nanodiamond nitrogen vacancy centers

    Science.gov (United States)

    Raheli, Ali; Hamedi, H. R.; Sahrai, M.

    2015-09-01

    In this letter, we investigate the 2D probe absorption spectrum in nanodiamond nitrogen vacancy centers under optical excitation. Different cases of the standing waves-matter interaction are considered to study the spatial dependence of probe absorption. It is shown that due to the quantum interference between different quantum paths in this system, various structures of localization as lattice-like, cross-like, circular-like and ‘∞ ’-like patterns can be designed by adjusting the detuning intensities and Zeeman shift.

  17. Advances in RNA Structure Determination | Center for Cancer Research

    Science.gov (United States)

    The recent years have witnessed a revolution in the field of RNA structure and function. Until recently the main contribution of RNA in cellular and disease functions was considered to be a role defined by the central dogma, namely DNA codes for mRNAs, which in turn encode for proteins, a notion facilitated by non-coding ribosomal RNA and tRNA. It was also assumed at the time that less than 2% of DNA in the human genome was used to encode genes, the remainder considered “junk”.

  18. The role of Ar plasma treatment in generating oxygen vacancies in indium tin oxide thin films prepared by the sol-gel process

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Deuk-Kyu [Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seoul, 03722 (Korea, Republic of); Misra, Mirnmoy; Lee, Ye-Eun [Department of BioNano Technology, Gachon University, 1342 Seong-nam dae-ro, Seong-nam si, Gyeonggi-do, 13120 (Korea, Republic of); Baek, Sung-Doo [Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seoul, 03722 (Korea, Republic of); Myoung, Jae-Min, E-mail: jmmyoung@yonsei.ac.kr [Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seoul, 03722 (Korea, Republic of); Lee, Tae Il, E-mail: t2.lee77@gachon.ac.kr [Department of BioNano Technology, Gachon University, 1342 Seong-nam dae-ro, Seong-nam si, Gyeonggi-do, 13120 (Korea, Republic of)

    2017-05-31

    Highlights: • Indium tin oxide thin film with about 41 nm thickness was obtained by the sol-gel process. • Thin film exhibited low resistivity. • Sheet resistance of thin film decreases with Ar plasma treatment time. • Ar plasma treatment on thin film does not alter the crystal structure and optical properties of the ITO thin-film. • There is no significant change in oxygen vacancies after 20 min of plasma treatment. - Abstract: Argon (Ar) plasma treatment was carried out to reduce the sheet resistance of indium tin oxide (ITO) thin films. The Ar plasma treatment did not cause any significant changes to the crystal structure, surface morphology, or optical properties of the ITO thin films. However, an X-ray photoelectron spectroscopy study confirmed that the concentration of oxygen vacancies in the film dramatically increased with the plasma treatment time. Thus, we concluded that the decrease in the sheet resistance was caused by the increase in the oxygen vacancy concentration in the film. Furthermore, to verify how the concentration of oxygen vacancies in the film increased with the Ar plasma treatment time, cumulative and continuous plasma treatments were conducted. The oxygen vacancies were found to be created by surface heating via the outward thermal diffusion of oxygen atoms from inside the film.

  19. Ab initio structure determination of n-diamond

    Science.gov (United States)

    Li, Da; Tian, Fubo; Chu, Binhua; Duan, Defang; Sha, Xiaojing; Lv, Yunzhou; Zhang, Huadi; Lu, Nan; Liu, Bingbing; Cui, Tian

    2015-08-01

    A systematic computational study on the crystal structure of n-diamond has been performed using first-principle methods. A novel carbon allotrope with hexagonal symmetry R32 space group has been predicted. We name it as HR-carbon. HR-carbon composed of lonsdaleite layers and unique C3 isosceles triangle rings, is stable over graphite phase above 14.2 GPa. The simulated x-ray diffraction pattern, Raman, and energy-loss near-edge spectrum can match the experimental results very well, indicating that HR-carbon is a likely candidate structure for n-diamond. HR-carbon has an incompressible atomic arrangement because of unique C3 isosceles triangle rings. The hardness and bulk modulus of HR-carbon are calculated to be 80 GPa and 427 GPa, respectively, which are comparable to those of diamond. C3 isosceles triangle rings are very important for the stability and hardness of HR-carbon.

  20. Some structural determinants of Pavlovian conditioning in artificial neural networks.

    Science.gov (United States)

    Sánchez, José M; Galeazzi, Juan M; Burgos, José E

    2010-05-01

    This paper investigates the possible role of neuroanatomical features in Pavlovian conditioning, via computer simulations with layered, feedforward artificial neural networks. The networks' structure and functioning are described by a strongly bottom-up model that takes into account the roles of hippocampal and dopaminergic systems in conditioning. Neuroanatomical features were simulated as generic structural or architectural features of neural networks. We focused on the number of units per hidden layer and connectivity. The effect of the number of units per hidden layer was investigated through simulations of resistance to extinction in fully connected networks. Large networks were more resistant to extinction than small networks, a stochastic effect of the asynchronous random procedure used in the simulator to update activations and weights. These networks did not simulate second-order conditioning because weight competition prevented conditioning to a stimulus after conditioning to another. Partially connected networks simulated second-order conditioning and devaluation of the second-order stimulus after extinction of a similar first-order stimulus. Similar stimuli were simulated as nonorthogonal input-vectors. Copyright (c) 2009 Elsevier B.V. All rights reserved.

  1. Determinants of the mouse ultrasonic vocal structure and repertoire.

    Science.gov (United States)

    Heckman, Jesse; McGuinness, Brigit; Celikel, Tansu; Englitz, Bernhard

    2016-06-01

    Mouse ultrasonic vocalizations (USV) exhibit a high degree of complexity as demonstrated in recent years. A multitude of factors have been identified to influence USVs on the spectrotemporal as well as structural - e.g. syntactic - level. A synthesis of the various studies that attributes semantics to USV properties or sequences is still lacking. Presently, we address the factors modulating the composition of USVs, specifically age, gender, genetic background (including the targeted FoxP2 mutagenesis), behavioral state and individuality. It emerges that the different factors share a set of common influences, e.g. vocalization rate and frequency range are universally modulated across independent variables described; however, distinct influences exist for sequential structure (different effects for age, behavioral state and genetic background) or vocal repertoire (age). Recently, USV research has seen important advances based on the quantitative maturation of methods on multiple levels of vocalization. Adoption of these methods to address the natural statistics of USV will ultimately benefit several related research areas, e.g. neurolinguistics, neurodevelopmental disorders, multisensory and sensorimotor research. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. A clustering algorithm for determining community structure in complex networks

    Science.gov (United States)

    Jin, Hong; Yu, Wei; Li, ShiJun

    2018-02-01

    Clustering algorithms are attractive for the task of community detection in complex networks. DENCLUE is a representative density based clustering algorithm which has a firm mathematical basis and good clustering properties allowing for arbitrarily shaped clusters in high dimensional datasets. However, this method cannot be directly applied to community discovering due to its inability to deal with network data. Moreover, it requires a careful selection of the density parameter and the noise threshold. To solve these issues, a new community detection method is proposed in this paper. First, we use a spectral analysis technique to map the network data into a low dimensional Euclidean Space which can preserve node structural characteristics. Then, DENCLUE is applied to detect the communities in the network. A mathematical method named Sheather-Jones plug-in is chosen to select the density parameter which can describe the intrinsic clustering structure accurately. Moreover, every node on the network is meaningful so there were no noise nodes as a result the noise threshold can be ignored. We test our algorithm on both benchmark and real-life networks, and the results demonstrate the effectiveness of our algorithm over other popularity density based clustering algorithms adopted to community detection.

  3. Synthesis/literature review for determining structural layer coefficients (SLC) of bases.

    Science.gov (United States)

    2014-12-01

    FDOTs current method of determining a base material structural layer coefficient (SLC) is detailed in the : Materials Manual, Chapter 2.1, Structural Layer Coefficients for Flexible Pavement Base Materials. : Currently, any new base material not a...

  4. Simultaneous modulation of surface composition, oxygen vacancies and assembly in hierarchical Co3O4 mesoporous nanostructures for lithium storage and electrocatalytic oxygen evolution

    DEFF Research Database (Denmark)

    Sun, Hongyu; Zhao, Yanyan; Mølhave, Kristian

    2017-01-01

    in superior electrochemical properties when used as the anode materials for lithium-ion batteries and as an electrocatalyst for the oxygen evolution reaction. The excellent electrochemical performance is attributed to the synergistic effects of novel hierarchical morphology, crystal structure of the active......We developed a facile solution reductive method to simultaneously tune the surface composition, oxygen vacancies and three dimensional assembly in Co3O4 hierarchical nanostructures. The controllable surface composition, oxygen vacancies together with hierarchical micro/nanoarchitectures resulted...... materials, the improvement of intrinsic conductivity and inner surface area induced by the oxygen vacancies. The present strategy not only provides a facile method to assemble novel hierarchical architectures, but also paves a way to control surface structures (chemical composition and crystal defects...

  5. Growth and structural determination of He bubbles in iron/chromium alloys using molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Abhishek, A., E-mail: agraj.abhi@gmail.com [Institute for Plasma Research, BHAT, Gandhinagar, Gujarat 382428 (India); Warrier, M. [Computational Analysis Division, BARC, Visakhapatnam, 530012 (India); Ganesh, R. [Institute for Plasma Research, BHAT, Gandhinagar, Gujarat 382428 (India); Caro, A. [Materials Science and Technology Division, Los Alamos National Laboratory, Los Alamos, NM 87544 (United States)

    2016-04-15

    Helium(He) produced by transmutation process inside structural material due to neutron irradiation plays a vital role in the degradation of material properties. We have carried out Molecular dynamics(MD) simulations to study the growth of He bubble in Iron-Chromium alloy. Simulations are carried out at two different temperatures, viz. 0.1 K and 800 K, upto He bubble radius of 2.5 nm. An equation for variation of volume of He bubbles with the number of He atoms is obtained at both the temperatures. Bubble pressure and potential energy variation is obtained with increasing bubble radius. Dislocations are also found to be emitted after the bubble reaches a critical radius of 0.39 nm at 800 K. Separate MD simulations of He with pre-created voids are also carried out to study the binding energies of He and Vacancy (V) to He{sub m}-V{sub n} cluster. Binding energies are found to be in the range of 1–5.5 eV. - Highlights: • We have obtained the volumetric and radius equation of Helium bubble at 0.1 K and 800 K. • The He bubble pressure variation and per atomic potential energy distribution is obtained at both the temperatures. • Formation and binding energy of He and V to He{sub m} – V{sub n} cluster is obtained in range of 5 < m < 266 & 5 < n < 104 respectively.

  6. Structural Determination of a Transcribing RNA Polymerase II Complex

    Science.gov (United States)

    2000-05-01

    cleft between them Fig. 2. Subunit struc- tures determined pre- viously or rebuilt here A B C fitted to the experi- u197-210 mental pot II electron...and 3 mM DTT). Crystals were cooled to 4*C mental zinc peak (Fig. 2B). The COOH-terminal re- Res. 21, 113 (1993). overnight and maintained at that...detected with the Infrared Space Obser- stituto de Estructura de Ia Materia, Departamento Fisica Molecular, Serrano 121, 28006 Madrid, Spain. vatory

  7. Oxygen vacancies: The origin of n-type conductivity in ZnO

    OpenAIRE

    Liu, Lishu; Mei, Zengxia; Tang, Aihua; Azarov, Alexander; Kuznetsov, Andrej; Xue, Qi-Kun; Du, Xiaolong

    2016-01-01

    Oxygen vacancy (VO) is a common native point defects that plays crucial roles in determining the physical and chemical properties of metal oxides such as ZnO. However, fundamental understanding of VO is still very sparse. Specifically, whether VO is mainly responsible for the n-type conductivity in ZnO has been still unsettled in the past fifty years. Here we report on a study of oxygen self-diffusion by conceiving and growing oxygen-isotope ZnO heterostructures with delicately-controlled che...

  8. Using Dust as Probes to Determine Sheath Extent and Structure

    CERN Document Server

    Douglass, Angela; Qiao, Ke; Matthews, Lorin; Hyde, Truell

    2016-01-01

    Two in-situ experimental methods are presented in which dust particles are used to determine the extent of the sheath and gain information about the time-averaged electric force profile within a RF plasma sheath. These methods are advantageous because they are not only simple and quick to carry out, but they also can be performed using standard dusty plasma experimental equipment. In the first method, dust particles are tracked as they fall through the plasma toward the lower electrode. These trajectories are then used to determine the electric force on the particle as a function of height as well as the extent of the sheath. In the second method, dust particle levitation height is measured across a wide range of RF voltages. Similarities were observed between the two experiments, but in order to understand the underlying physics behind these observations, the same conditions were replicated using a self-consistent fluid model. Through comparison of the fluid model and experimental results, it is shown that t...

  9. Cryo electron microscopy to determine the structure of macromolecular complexes.

    Science.gov (United States)

    Carroni, Marta; Saibil, Helen R

    2016-02-15

    Cryo-electron microscopy (cryo-EM) is a structural molecular and cellular biology technique that has experienced major advances in recent years. Technological developments in image recording as well as in processing software make it possible to obtain three-dimensional reconstructions of macromolecular assemblies at near-atomic resolution that were formerly obtained only by X-ray crystallography or NMR spectroscopy. In parallel, cryo-electron tomography has also benefitted from these technological advances, so that visualization of irregular complexes, organelles or whole cells with their molecular machines in situ has reached subnanometre resolution. Cryo-EM can therefore address a broad range of biological questions. The aim of this review is to provide a brief overview of the principles and current state of the cryo-EM field. Copyright © 2016. Published by Elsevier Inc.

  10. Fast determination of structurally cohesive subgroups in large networks.

    Science.gov (United States)

    Sinkovits, Robert S; Moody, James; Oztan, B Tolga; White, Douglas R

    2016-11-01

    Structurally cohesive subgroups are a powerful and mathematically rigorous way to characterize network robustness. Their strength lies in the ability to detect strong connections among vertices that not only have no neighbors in common, but that may be distantly separated in the graph. Unfortunately, identifying cohesive subgroups is a computationally intensive problem, which has limited empirical assessments of cohesion to relatively small graphs of at most a few thousand vertices. We describe here an approach that exploits the properties of cliques, k-cores and vertex separators to iteratively reduce the complexity of the graph to the point where standard algorithms can be used to complete the analysis. As a proof of principle, we apply our method to the cohesion analysis of a 29,462-vertex biconnected component extracted from a 128,151-vertex co-authorship data set.

  11. Neural Network Enhanced Structure Determination of Osteoporosis, Immune System, and Radiation Repair Proteins Project

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose a dual objective innovation that has valuable NASA applicability and tremendous commercial potential. The first innovation is the structure determination...

  12. Neural Network Enhanced Structure Determination of Osteoporosis, Immune System, and Radiation Repair Proteins Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed innovation will utilize self learning neural network technology to determine the structure of osteoporosis, immune system disease, and excess radiation...

  13. 24 CFR 901.10 - Indicator #1, vacancy rate and unit turnaround time.

    Science.gov (United States)

    2010-04-01

    ... 24 Housing and Urban Development 4 2010-04-01 2010-04-01 false Indicator #1, vacancy rate and unit... HOUSING AND URBAN DEVELOPMENT PUBLIC HOUSING MANAGEMENT ASSESSMENT PROGRAM § 901.10 Indicator #1, vacancy rate and unit turnaround time. This indicator examines the vacancy rate, a PHA's progress in reducing...

  14. 76 FR 76429 - Merchant Marine Personnel Advisory Committee; Vacancies

    Science.gov (United States)

    2011-12-07

    ... SECURITY Coast Guard Merchant Marine Personnel Advisory Committee; Vacancies AGENCY: Coast Guard, DHS... Merchant Marine Personnel Advisory Committee (MERPAC). This Committee advises the Secretary of the Department of Homeland Security on matters related to personnel in the U.S. merchant marine, including but...

  15. 78 FR 1217 - Merchant Marine Personnel Advisory Committee; Vacancies

    Science.gov (United States)

    2013-01-08

    ... SECURITY Coast Guard Merchant Marine Personnel Advisory Committee; Vacancies AGENCY: Coast Guard, DHS... Merchant Marine Personnel Advisory Committee (MERPAC). This Committee advises the Secretary of the Department of Homeland Security on matters related to personnel in the U.S. merchant marine, including but...

  16. 78 FR 54265 - Merchant Marine Personnel Advisory Committee; Vacancies

    Science.gov (United States)

    2013-09-03

    ... SECURITY Coast Guard Merchant Marine Personnel Advisory Committee; Vacancies AGENCY: Coast Guard, DHS... Merchant Marine Personnel Advisory Committee (MERPAC). This Committee advises the Secretary of the Department of Homeland Security on matters related to personnel in the U.S. merchant marine, including but...

  17. Vibrational properties of vacancy in bcc transition metals using ...

    Indian Academy of Sciences (India)

    Embedded atom method; modified embedded atom method; Green's function; force constants; vacancy; phonon dispersion; local density of states; mean square ... employ the modified embedded atom method (MEAM) in which a modified term along with the pair potential and embedding function is added in the total energy.

  18. Growth of metalloid aluminum clusters on graphene vacancies

    Science.gov (United States)

    Alnemrat, Sufian; Mayo, Dennis H.; DeCarlo, Samantha; Hooper, Joseph P.

    2016-01-01

    Ab initio simulations are used to show that graphene vacancy sites may offer a means of templated growth of metalloid aluminum clusters from their monohalide precursors. We present density functional theory and ab initio molecular dynamics simulations of the aluminum halide AlCl interacting with a graphene surface. Unlike a bare Al adatom, AlCl physisorbs weakly on vacancy-free graphene with little charge transfer and no hybridization with carbon orbitals. The barrier for diffusion of AlCl along the surface is negligible. Covalent bonding is seen only with vacancies and results in strong chemisorption and considerable distortion of the nearby lattice. Car-Parrinello molecular dynamics simulations of AlCl liquid around a graphene single vacancy show spontaneous metalloid cluster growth via a process of repeated insertion reactions. This suggests a means of templated cluster nucleation and growth on a carbon substrate and provides some confirmation for the role of a trivalent aluminum species in nucleating a ligated metalloid cluster from AlCl and AlBr solutions.

  19. 75 FR 24961 - Pittsburgh Area Maritime Security Committee; Vacancies

    Science.gov (United States)

    2010-05-06

    ... SECURITY Coast Guard Pittsburgh Area Maritime Security Committee; Vacancies AGENCY: Coast Guard, DHS... the Pittsburgh Area Maritime Security Committee (AMSC) to submit their application for membership, to the Captain of the Port, Pittsburgh, Pennsylvania. DATES: Requests for membership should reach the...

  20. 78 FR 49544 - Great Lakes Pilotage Advisory Committee; Vacancies

    Science.gov (United States)

    2013-08-14

    ... SECURITY Coast Guard Great Lakes Pilotage Advisory Committee; Vacancies AGENCY: Coast Guard, DHS. ACTION: Request for applications. SUMMARY: The Coast Guard seeks applications for membership on the Great Lakes... of Homeland Security and the Coast Guard on matters relating to Great Lakes pilotage, including...

  1. 77 FR 33228 - Great Lakes Pilotage Advisory Committee; Vacancies

    Science.gov (United States)

    2012-06-05

    ... SECURITY Coast Guard Great Lakes Pilotage Advisory Committee; Vacancies AGENCY: Coast Guard, DHS. ACTION: Request for applicants. SUMMARY: The Coast Guard seeks applications for membership on the Great Lakes... of Homeland Security and the Coast Guard on matters relating to Great Lakes pilotage, including...

  2. Triplet states at an O vacancy in alpha-quartz

    DEFF Research Database (Denmark)

    Lægsgaard, Jesper

    2002-01-01

    The energy landscape of an alpha-quartz O vacancy in the lowest triplet state is investigated. Four local minima are identified and geometries, total energies, and electron paramagnetic resonance (EPR) parameters are obtained. On the basis of calculated values for the magnetic dipole interaction...

  3. Vacancy complexes in carbon and boron nitride nanotubes

    CSIR Research Space (South Africa)

    Mashapa, MG

    2012-10-01

    Full Text Available -1 Journal of Nanoscience and Nanotechnology, Vol. 12, 7796-7806, 2012 Vacancy Complexes in Carbon and Boron Nitride Nanotubes M. G. Mashapa1,2, ? N. Chetty1 and S. Sinha Ray2,3 1 Physics Department, University of Pretoria, Pretoria, 0001, South Africa...

  4. 77 FR 15784 - Navigation Safety Advisory Council; Vacancies

    Science.gov (United States)

    2012-03-16

    ... vessel navigation Rules of the Road, aids to maritime navigation, maritime law, vessel safety, port... SECURITY Coast Guard Navigation Safety Advisory Council; Vacancies AGENCY: Coast Guard, DHS. ACTION: Request for applications. SUMMARY: The Coast Guard seeks applications for membership on the Navigation...

  5. 78 FR 42945 - Health Information Technology Policy Committee Vacancy

    Science.gov (United States)

    2013-07-18

    ... OFFICE Health Information Technology Policy Committee Vacancy AGENCY: Government Accountability Office... Reinvestment Act of 2009 (ARRA) established the Health Information Technology Policy Committee (Health IT.... ARRA requires that one member have expertise in health information privacy and security. Due to a...

  6. 77 FR 27774 - Health Information Technology Policy Committee Vacancy

    Science.gov (United States)

    2012-05-11

    ... OFFICE Health Information Technology Policy Committee Vacancy AGENCY: Government Accountability Office... Reinvestment Act of 2009 (ARRA) established the Health Information Technology Policy Committee (Health IT...: [email protected] . GAO: 441 G Street NW., Washington, DC 20548. FOR FURTHER INFORMATION CONTACT: GAO...

  7. DFT Calculations using WIEN2K to determine oxygen defect structure of rare earth doped ceria

    CERN Document Server

    Khalife, Ali Rida

    2014-01-01

    We perform density functional calculations using the program WIEN2K in order to study oxygen vacancies in rare earth doped ceria. The calculation for all rare earth elements were prepared, however only those foe Cadmium and Europium were performed due to lack of time. Also a short description of my stay at CERN was presented

  8. Benzofuranyl Esters: Synthesis, Crystal Structure Determination, Antimicrobial and Antioxidant Activities

    Directory of Open Access Journals (Sweden)

    C. S. Chidan Kumar

    2015-09-01

    Full Text Available A series of five new 2‐(1‐benzofuran‐2‐yl‐2‐oxoethyl 4-(un/substitutedbenzoates 4(a–e, with the general formula of C8H5O(C=OCH2O(C=OC6H4X, X = H, Cl, CH3, OCH3 or NO2, was synthesized in high purity and good yield under mild conditions. The synthesized products 4(a–e were characterized by FTIR, 1H-, 13C- and 1H-13C HMQC NMR spectroscopic analysis and their 3D structures were confirmed by single-crystal X-ray diffraction studies. These compounds were screened for their antimicrobial and antioxidant activities. The tested compounds showed antimicrobial ability in the order of 4b < 4a < 4c < 4d < 4e and the highest potency with minimum inhibition concentration (MIC value of 125 µg/mL was observed for 4e. The results of antioxidant activities revealed the highest activity for compound 4e (32.62% ± 1.34% in diphenyl-2-picrylhydrazyl (DPPH radical scavenging, 4d (31.01% ± 4.35% in ferric reducing antioxidant power (FRAP assay and 4a (27.11% ± 1.06% in metal chelating (MC activity.

  9. HUG and SQUEEZE: using CRYSTALS to incorporate resonant scattering in the SQUEEZE structure-factor contributions to determine absolute structure.

    Science.gov (United States)

    Cooper, Richard I; Flack, Howard D; Watkin, David J

    2017-11-01

    The resonant-scattering contributions to single-crystal X-ray diffraction data enable the absolute structure of crystalline materials to be determined. Crystal structures can be determined even if they contain considerably disordered regions because a correction is available via a discrete Fourier transform of the residual electron density to approximate the X-ray scattering from the disordered region. However, the corrected model cannot normally account for resonant scattering from atoms in the disordered region. Straightforward determination of absolute structure from crystals where the strongly resonantly scattering atoms are not resolved has therefore not been possible. Using an approximate resonant-scattering correction to the X-ray scattering from the disordered regions, we have developed and tested a procedure (HUG) to recover the absolute structure using conventional Flack x refinement or other post-refinement determination methods. Results show that in favourable cases the HUG method works well and the absolute structure can be correctly determined. It offers no useful improvement in cases where the original correction for the disordered region scattering density is problematic, for example, when a large fraction of the scattering density in the crystal is disordered, or when voids are not occupied equally by the disordered species. Crucially, however, if the approach does not work for a given structure, the statistics for the absolute structure measures are not improved, meaning it is unlikely to lead to misassignment of absolute structure.

  10. Structure determination of picolinato copper(II)-amine complexes

    Science.gov (United States)

    Mautner, Franz A.; Massoud, Salah S.

    2007-12-01

    Two series of Cu(II)-picolinato complexes of 1:1 and 3:2 Cu(II)-amine/picolinate namely [Cu(L 1)(pic)]ClO 4 and [Cu 3(L 2) 3(pic) 2(H 2O)](ClO 4) 4· xH 2O or [Cu 3(dpt) 3(pic) 2](ClO 4) 4, where pic = picolinate anion, L 1 = dien (diethylenetriamine), Et 2dien ( N, N-diethyldiethylenetriamine), Medpt (3,3'-diamino- N-methyldipropylamine), L 2 = pmedien ( N, N, N', N″, N″-pentamethyl-diethylenetriamine), TPA (tris(2-pyridylmethyl)amine), and dpt = dipropylenetriamine were synthesized and structurally characterized by electronic and IR spectroscopy. Single crystal X-ray diffraction analysis of the complex [Cu(dien)(pic)]ClO 4 ( 1) reveals its monomeric nature whereas for [Cu 3(pmedien) 3(pic) 2(H 2O)](ClO 4) 4·2H 2O ( 4), it was shown that the complex consists of two subunits of the mononuclear [Cu(pmedien)(pic)] + and the dinuclear [Cu 2(pmedien) 2(pic)(H 2O)] 3+ cations with the perchlorate as counter ions and lattice water molecules. In the mononuclear complexes of 1 and 4 the picolinato anions act as N, O-chelating ligands, whereas N, O, O'-picolinato bridges are observed in the dinuclear [Cu 2(pmedien) 2(pic)(H 2O)] 3+ cations of 4. The aqueous visible spectra of the complexes 1- 6 are consistent with five-coordinate Cu(II) species where distorted square pyramidal geometry (SP) was assigned for complexes 2- 5, trigonal bipyramidal geometry (TBP) for 6 and an intermediate geometry between SP and TBP for 1.

  11. Crystallation, X-Ray Structure Determination and Structure-Based Drug Design for Targeted Malarial Enzymes

    National Research Council Canada - National Science Library

    DeLucas, Lawrence

    1997-01-01

    .... This structure is currently being used for designing lead inhibitors. We have also purified PFPK-DHPS bifunctional enzyme for structure analysis and are presently screening for crystallization conditions...

  12. Mobility and stability of large vacancy and vacancy-copper clusters in iron: An atomistic kinetic Monte Carlo study

    Energy Technology Data Exchange (ETDEWEB)

    Castin, N., E-mail: ncastin@sckcen.be [Studiecentrum voor Kernenergie - Centre d' Etudes de l' energie Nucleaire (SCK-CEN), Nuclear Materials Science Institute, Unit Structural Materials Modelling and Microstructure-Boeretang 200, B2400 Mol (Belgium); Pascuet, M.I., E-mail: pascuet@cnea.gov.ar [Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Av. Rivadavia 1917, C1033AAJ Buenos Aires (Argentina); Malerba, L. [Studiecentrum voor Kernenergie - Centre d' Etudes de l' energie Nucleaire (SCK-CEN), Nuclear Materials Science Institute, Unit Structural Materials Modelling and Microstructure-Boeretang 200, B2400 Mol (Belgium)

    2012-10-15

    The formation of Cu-rich precipitates under irradiation is a major cause for changes in the mechanical response to load of reactor pressure vessel steels. In previous works, it has been shown that the mechanism under which precipitation occurs is governed by diffusion of vacancy-copper (VCu) complexes, also in the absence of irradiation. Coarse-grained computer models (such as object kinetic Monte Carlo) aimed at simulating irradiation processes in model alloys or steels should therefore explicitly include the mobility of Cu precipitates, as a consequence of vacancy hops at their surface. For this purpose, in this work we calculate diffusion coefficients and lifetimes for a large variety of VCu complexes. We use an innovative atomistic model, where vacancy migration energies are calculated with little approximations, taking into account all effects of static relaxation and long-range chemical interaction as predicted by an interatomic potential. Our results show that, contrary to what intuition might suggest, saturation in vacancies tend to slow down the transport of Cu atoms.

  13. Determining the in situ concrete strength of existing structures for assessing their structural safety

    NARCIS (Netherlands)

    Steenbergen, R.D.J.M.; Vervuurt, A.H.J.M.

    2012-01-01

    EN 13791 applies when assessing the in situ compressive strength of structures and precast concrete components. According to the code itself, it may be adopted when doubt arises about the compressive strength of a concrete. For assessing the structural safety of existing structures, however, the

  14. Thermal vacancies and phase separation in bcc mixtures of helium-3 and helium-4

    Energy Technology Data Exchange (ETDEWEB)

    Fraass, Benedick Andrew [Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Physics

    1980-01-01

    Thermal vacancy concentrations in crystals of 3He-4He mixtures have been determined. A new x-ray diffractometer-position sensitive detector system is used to make measurements of the absolute lattice parameter of the helium crystals with an accuracy of 300 ppM, and measurements of changes in lattice parameters to better than 60 ppM. The phase separation of the concentrated3He-4He mixtures has been studied in detail with the x-ray measurements. Vacancy concentrations in crystals with 99%, 51%, 28%, 12%, and 0% 3He have been determined. Phase separation has been studied in mixed crystals with concentrations of 51%, 28%, and 12% 3He and melting pressures between 3.0 and 6.1 MPa. The phase separation temperatures determined in this work are in general agreement with previous work. The pressure dependence of Tc, the phase separation temperature for a 50% mixture, is found to be linear: dTc/dP = -34 mdeg/MPa. The x-ray measurements are used to make several comments on the low temperature phase diagram of the helium mixtures.

  15. Electro-oxidation of water on hematite: Effects of surface termination and oxygen vacancies investigated by first-principles

    DEFF Research Database (Denmark)

    Hellman, Anders; Iandolo, Beniamino; Wickman, Bjorn

    2015-01-01

    The oxygen evolution reaction on hydroxyl- and oxygen-terminated hematite was investigated using first-principle calculations within a theoretical electrochemical framework. Both pristine hematite and hematite containing oxygen vacancies were considered. The onset potential was determined to be 1.......79 V and 2.09 V vs. the reversible hydrogen electrode (RHE) for the pristine hydroxyl- and oxygen-terminated hematite, respectively. The presence of oxygen vacancies in the hematite surface resulted in pronounced shifts of the onset potential to 3.09 V and 1.83 V. respectively. Electrochemical...... oxidation measurements conducted on thin-film hematite anodes, resulted in a measured onset potential of 1.66 V vs. RHE. Furthermore, the threshold potential between the hydroxyl- and oxygen-terminated hematite was determined as a function of pH. The results indicate that electrochemical water oxidation...

  16. Vacancy ordering in γ-Fe 2O 3 nanocrystals observed by 57Fe NMR

    Science.gov (United States)

    Bastow, T. J.; Trinchi, A.; Hill, M. R.; Harris, R.; Muster, T. H.

    2009-09-01

    The identification by 57Fe internal field nuclear magnetic resonance (NMR) of hyperfine fields at four Fe sites in the (average) tetragonal unit cell of vacancy-ordered γ-Fe 2O 3 (maghemite) is reported. The effects of vacancy redistribution due to annealing the partially vacancy-ordered form has been observed in the 57Fe lineshape. In addition, the reduction of the particle size of the vacancy-ordered form has been observed to gradually eliminate the vacancy ordering and then to cause a transition from ferrimagnetism to superparamagnetism.

  17. Structure and partitioning of bacterial DNA: determined by a balance of competion and expansion forces?

    DEFF Research Database (Denmark)

    Woldringh, C. L.; Jensen, Peter Ruhdal; Westerhoff, H. V.

    1995-01-01

    The mechanisms that determine chromosome structure and chromosome partitioning in bacteria are largely unknown. Here we discuss two hypotheses: (i) the structure of the Escherichia coli nucleoid is determined by DNA binding proteins and DNA supercoiling, representing a compaction force on the one...

  18. Mechanochemically induced sulfur doping in ZnO via oxygen vacancy formation.

    Science.gov (United States)

    Daiko, Y; Schmidt, J; Kawamura, G; Romeis, S; Segets, D; Iwamoto, Y; Peukert, W

    2017-05-31

    Surface defects of ZnO nanoparticles were induced via mechanical stressing using a Turbula shaker mixer and a planetary ball mill, and the possibilities for surface modification and functionalization of the ZnO nanoparticles were exemplified by sulfur doping of activated ZnO. Raman spectroscopy reveals that the formation of oxygen vacancies (VO) does not only occur under high stressing conditions in a planetary ball mill but even upon rather 'mild stressing' in the shaker mixer. The temporal evolution of the vacancy concentration in ZnO stressed under different conditions can be described by a model that accounts for stress number and vacancy diffusion with diffusion coefficients of VO of 3.7 × 10-21 m2 s-1 and 2.4 × 10-20 m2 s-1 for stressing in the shaker and the planetary ball mill, respectively. The thickness of the VO layer was estimated to be about 1 nm. Thiourea was mixed with defective ZnO particles, and then heated at various temperatures for sulfur-doping. A linear relationship between the amount of induced VO and the level of sulfur doping was found. Remarkably, mechanical activation is indispensable in order to control the level of sulfur doping quantitatively. High-angle annular dark field scanning transmission electron microscopy (HAADF STEM) observations with energy dispersive X-ray spectroscopy (EDX) analysis clearly revealed that the doped sulfur atoms are concentrated at the particle surface. Thus, ZnO (core)/ZnS (shell) structures are obtained easily via mechanochemical activation and subsequent thermal treatment.

  19. Realizing nanographene activated by a vacancy to solve hydrogen storage problem

    Science.gov (United States)

    Sunnardianto, Gagus Ketut; Maruyama, Isao; Kusakabe, Koichi

    We found a triply hydrogenated vacancy (V111) in nanographene reduces an activation barrier of adsorption-desorption process in both ways in an equal manner from the known values for pristine graphene as well as those of other hydrogenated vacancies of graphene. This finding may give a key to overcome existing problems in the hydrogen uptake and release processes in known hydrogen storage materials, e.g. graphene and organic hydrides (OHs) in near ambient operation temperature. In this study, we used DFT-NEB simulation to estimate the barrier height, which is supported by realized real experiments. We consider a nanographene molecule (VANG) which contains V111 with armchair structure at the periphery. We found interesting feature in comparable values of energy barriers for both hydrogen uptake and release, where hydrogenation process is even a little bit endothermic and dehydrogenation is a little but exothermic nature. Thus, this material structure acts as ``self-catalytic properties'', which has an important role in reducing an energy barrier and as a trapping site for hydrogen serving a new material prevailing other hopeful candidates. The work is supported by JSPS KAKENHI in Science of Atomic Layers\\x9D.

  20. CO2-Induced Defect Engineering: A New Protocol by Doping Vacancies in 2D Heterostructures for Enhanced Visible-Light Photocatalysis

    Science.gov (United States)

    Ren, Yumei; Wang, Chongze; Qi, Yuhang; Chen, Zhimin; Jia, Yu; Xu, Qun

    2017-10-01

    Defect engineering has emerged as an efficient and promising strategy in the field of semiconductor materials, while assembling controllable vacancy defects and two-dimensional (2D) heterostructures into together is a great challenge. In this work, 2D heterostructures of WS2/WO3·H2O doped with oxide vacancies have been synthesized successfully with assistance of supercritical CO2. And the fascinating heterostructures have been evidenced by their significant photocatalysis performance for water splitting. Theoretical calculations demonstrate that the vacancies in the obtained 2D heterostructures can narrow the effective band gap and improve the carrier separation efficiency as well. This wok will provide a positive strategy for fabrication of advanced photocatalyst and a new perspective in understanding the synergistic effect of structural and electronic regulations.

  1. The roles of density-tunable surface oxygen vacancy over bouquet-like Bi2O3 in enhancing photocatalytic activity.

    Science.gov (United States)

    Wu, Yuqi; Lu, Gongxuan

    2014-03-07

    Bouquet-like hierarchical Bi2O3 photocatalyst materials with high-density surface oxygen vacancy are synthesized via a hydrothermal method by the synergetic control of NaOH and a polyvinyl alcohol (PVA) stabilizer. The OH(-) ion addition led to the formation of more relaxed PVA macromolecular clusters, as a result, a thinner PVA film was formed, the species adsorbed on the surface of the produced Bi2O3 crystal nucleus could tune both the surface microstructure size and oxygen vacancy density via controlling the velocity, transfer and reaction of the OH(-) ions. The significant enhancement of photocatalytic performances could be attributed to the high density of the surface oxygen vacancy which was propitious to the charge separation efficiencies, distribution characteristic, and its role in a photo-redox reaction. A turnable-bending self-assembly mechanism was proposed to clarify the formation process of the bouquet-like hierarchical structure.

  2. Long-range ferromagnetic order in LaCoO3 -δ epitaxial films due to the interplay of epitaxial strain and oxygen vacancy ordering

    Science.gov (United States)

    Mehta, V. V.; Biskup, N.; Jenkins, C.; Arenholz, E.; Varela, M.; Suzuki, Y.

    2015-04-01

    We demonstrate that a combination of electronic structure modification and oxygen vacancy ordering can stabilize a long-range ferromagnetic ground state in epitaxial LaCoO3 thin films. Highest saturation magnetization values are found in the thin films in tension on SrTiO3 and (La ,Sr )(Al ,Ta )O3 substrates and the lowest values are found in thin films in compression on LaAlO3. Electron microscopy reveals oxygen vacancy ordering to varying degrees in all samples, although samples with the highest magnetization are the most defective. Element-specific x-ray absorption techniques reveal the presence of high spin Co2 + and Co3 + as well as low spin Co3 + in different proportions depending on the strain state. The interactions among the high spin Co ions and the oxygen vacancy superstructure are correlated with the stabilization of the long-range ferromagnetic order.

  3. Determining the Structure of Oxalate Anion Using Infrared and Raman Spectroscopy Coupled with Gaussian Calculations

    Science.gov (United States)

    Peterson, Karen I.; Pullman, David P.

    2016-01-01

    A laboratory project for the upper-division physical chemistry laboratory is described, and it combines IR and Raman spectroscopies with Gaussian electronic structure calculations to determine the structure of the oxalate anion in solid alkali oxalates and in aqueous solution. The oxalate anion has two limiting structures whose vibrational spectra…

  4. Traditional biomolecular structure determination by NMR spectroscopy allows for major errors

    NARCIS (Netherlands)

    Nabuurs, S.B.; Spronk, C.A.E.M.; Vuister, G.W.; Vriend, G.

    2006-01-01

    One of the major goals of structural genomics projects is to determine the three-dimensional structure of representative members of as many different fold families as possible. Comparative modeling is expected to fill the remaining gaps by providing structural models of homologs of the

  5. Impact of isovalent doping on the trapping of vacancy and interstitial related defects in Si

    Energy Technology Data Exchange (ETDEWEB)

    Sgourou, E. N.; Londos, C. A.; Aliprantis, D. [University of Athens, Solid State Physics Section, Panepistimiopolis Zografos, Athens 157 84 (Greece); Timerkaeva, D. [Laboratoire de Simulation Atomistique (L-Sim), SP2M, INAC, CEA-UJF, 38054 Grenoble Cedex 9 (France); Kazan Federal University, 18 Kremlevskaya St., Kazan, 420018 (Russian Federation); Chroneos, A. [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Materials Engineering, Open University, Milton Keynes MK7 6AA (United Kingdom); Caliste, D.; Pochet, P. [Laboratoire de Simulation Atomistique (L-Sim), SP2M, INAC, CEA-UJF, 38054 Grenoble Cedex 9 (France)

    2013-03-21

    We investigate the impact of isovalent (in particular lead (Pb)) doping on the production and thermal stability of the vacancy-related (VO) and the interstitial-related (C{sub i}O{sub i} and C{sub i}C{sub s}) pairs in 2 MeV electron irradiated Si samples. We compare the Cz-Si samples with high and low carbon concentration, as well as with Pb-C and Ge-C codoped samples. Using Fourier Transform Infrared Spectroscopy (FTIR), we first determine that under the examined conditions the production of VO decreases with the increase of the covalent radius of the prevalent dopant. Moreover, the production of the VO, C{sub i}O{sub i}, and C{sub i}C{sub s} pairs is quite suppressed in Pb-doped Si. In addition, we conclude to an enhanced trapping of both C{sub i} and C{sub s} by Pb impurity under irradiation. The results are further discussed in view of density functional theory calculations. The relative thermodynamic stability of carbon and interstitial related complexes was estimated through the calculations of binding energies of possible defect pairs. This allows to investigate the preferred trapping of vacancies in Pb-doped samples and interstitials in the Ge-doped samples. The different behavior is revealed by considering the analysis of the ratio of vacancy-related to interstitial-related clusters derived from the FTIR measurements. The presence of PbV complexes is confirmed due to the mentioned analysis.

  6. Vacancy complexes induce long-range ferromagnetism in GaN

    KAUST Repository

    Zhang, Zhenkui

    2014-11-14

    By means of density functional theory, we argue that ferromagnetism in GaN can be induced by vacancy complexes. Spin polarization originates from the charge compensation between neutral N and Ga vacancies. Defect formation energy calculations predict that a vacancy complex of two positively charged N vacancies and one doubly negative Ga vacancy is likely to form. This defect complex induces a net moment of 1 μB, which is localized around the negative Ga center and exhibits pronounced in-plane ferromagnetic coupling. In contrast to simple Ga vacancy induced ferromagnetism, the proposed picture is in line with the fact that N vacancies have a low formation energy. Formation energies indicate mutual stabilization of the intrinsic defects in GaN.

  7. Rapid increase of near atomic resolution virus capsid structures determined by cryo-electron microscopy.

    Science.gov (United States)

    Ho, Phuong T; Reddy, Vijay S

    2017-10-27

    The recent technological advances in electron microscopes, detectors, as well as image processing and reconstruction software have brought single particle cryo-electron microscopy (cryo-EM) into prominence for determining structures of bio-molecules at near atomic resolution. This has been particularly true for virus capsids, ribosomes, and other large assemblies, which have been the ideal specimens for structural studies by cryo-EM approaches. An analysis of time series metadata of virus structures on the methods of structure determination, resolution of the structures, and size of the virus particles revealed a rapid increase in the virus structures determined by cryo-EM at near atomic resolution since 2010. In addition, the data highlight the median resolution (∼3.0 Å) and size (∼310.0 Å in diameter) of the virus particles determined by X-ray crystallography while no such limits exist for cryo-EM structures, which have a median diameter of 508 Å. Notably, cryo-EM virus structures in the last four years have a median resolution of 3.9 Å. Taken together with minimal sample requirements, not needing diffraction quality crystals, and being able to achieve similar resolutions of the crystal structures makes cryo-EM the method of choice for current and future virus capsid structure determinations. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Toward a structure determination method for biomineral-associated protein using combined solid- state NMR and computational structure prediction.

    Science.gov (United States)

    Masica, David L; Ash, Jason T; Ndao, Moise; Drobny, Gary P; Gray, Jeffrey J

    2010-12-08

    Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the structure of biomineral-associated proteins cannot be determined by X-ray crystallography or solution nuclear magnetic resonance (NMR). Here we report a method for determining the structure of biomineral-associated proteins. The method combines solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. In addition, the algorithm is able to identify lattice geometries most compatible with ssNMR constraints, representing a quantitative, novel method for investigating crystal-face binding specificity. We use this method to determine most of the structure of human salivary statherin interacting with the mineral phase of tooth enamel. Computation and experiment converge on an ensemble of related structures and identify preferential binding at three crystal surfaces. The work represents a significant advance toward determining structure of biomineral-adsorbed protein using experimentally biased structure prediction. This method is generally applicable to proteins that can be chemically synthesized. Copyright © 2010 Elsevier Ltd. All rights reserved.

  9. The Electronic States of a Double Carbon Vacancy Defect in Pyrene: A Model Study for Graphene

    CERN Document Server

    Machado, Francisco B C; Lischka, Hans

    2016-01-01

    The electronic states occurring in a double vacancy defect for graphene nanoribbons have been calculated in detail based on a pyrene model. Extended ab initio calculations using the MR configuration interaction (MRCI) method have been performed to describe in a balanced way the manifold of electronic states derived from the dangling bonds created by initial removal of two neighboring carbon atoms from the graphene network. In total, this study took into account the characterization of 16 electronic states (eight singlets and eight triplets) considering unrelaxed and relaxed defect structures. The ground state was found to be of 1Ag character with around 50% closed shell character. The geometry optimization process leads to the formation of two five-membered rings in a pentagon octagon pentagon structure. The closed shell character increases thereby to ~70%, the analysis of unpaired density shows only small contributions confirming the chemical stability of that entity. For the unrelaxed structure the first fi...

  10. Orienting oxygen vacancies for fast catalytic reaction

    OpenAIRE

    Jeen, Hyoungjeen; Bi, Zhonghe; Choi, Woo Seok; Chisholm, Matthew F.; Bridges, Craig A.; Paranthaman, M. Parans; Lee, Ho Nyung

    2013-01-01

    Catalysis is indispensable to chemical processes and relevant to many aspects of modern life. Owing to the intriguing electronic structures and good ionic properties, multivalent transition metal oxides have attracted attention as key catalysts for various energy and environmental applications. Here, we demonstrate that brownmillerite strontium cobaltite (SrCoO2.5) can be a good cathode material for sold oxide fuel cells and rechargeable batteries due to the open oxygen frameworks. When the o...

  11. SMEs capital structure determinants during severe economic crisis: The case of Greece

    Directory of Open Access Journals (Sweden)

    D. Balios

    2016-12-01

    Full Text Available The objective of this paper was to explore whether and how the main capital structure determinants of SMEs affected capital structure determination in different ways during the years of economic crisis. We used panel data of 8,052 SMEs operating in Greece during 2009–2012. We found that the effect of capital structure determinants on leverage does not change in an environment of economic crisis; larger SMEs continued to show higher debt ratios, the relationship between profitability and tangibility of assets with leverage continued to be negative, and growth was positively related to leverage.

  12. Strain Control of Oxygen Vacancies in Epitaxial Strontium Cobaltite Films

    Energy Technology Data Exchange (ETDEWEB)

    Petrie, Jonathan R.; Mitra, Chandrima; Jeen, Hyoungjeen; Choi, Woo Seok; Meyer, Tricia L.; Reboredo, Fernando A.; Freeland, John W.; Eres, Gyula; Lee, Ho Nyung

    2016-03-08

    The ability to manipulate oxygen anion defects rather than metal cations in complex oxides can facilitate creating new functionalities critical for emerging energy and device technologies. However, the difficulty in activating oxygen at reduced temperatures hinders the deliberate control of important defects, oxygen vacancies. Here, strontium cobaltite (SrCoOx) is used to demonstrate that epitaxial strain is a powerful tool for manipulating the oxygen vacancy concentration even under highly oxidizing environments and at annealing temperatures as low as 300 degrees C. By applying a small biaxial tensile strain (2%), the oxygen activation energy barrier decreases by approximate to 30%, resulting in a tunable oxygen defi cient steady-state under conditions that would normally fully oxidize unstrained cobaltite. These strain-induced changes in oxygen stoichiometry drive the cobaltite from a ferromagnetic metal towards an antiferromagnetic insulator. The ability to decouple the oxygen vacancy concentration from its typical dependence on the operational environment is useful for effectively designing oxides materials with a specific oxygen stoichiometry.

  13. A vacancy-modulated self-selective resistive switching memory with pronounced nonlinear behavior

    Science.gov (United States)

    Ma, Haili; Feng, Jie; Gao, Tian; Zhu, Xi

    2017-12-01

    In this study, we report a self-selective (nonlinear) resistive switching memory cell, with high on-state half-bias nonlinearity of 650, sub-μA operating current, and high On/Off ratios above 100×. Regarding the cell structure, a thermal oxidized HfO x layer in combination with a sputtered Ta2O5 layer was configured as an active stack, with Pt and Hf as top and bottom electrodes, respectively. The Ta2O5 acts as a selective layer as well as a series resistor, which could make the resistive switching happened in HfO x layer. Through the analysis of the physicochemical properties and electrical conduction mechanisms at each state, a vacancy-modulated resistance switching model was proposed to explain the switching behavior. The conductivity of HfO x layer was changed by polarity-dependent drift of the oxygen vacancy ( V o), resulting in an electron hopping distance change during switching. With the help of Ta2O5 selective layer, high nonlinearity observed in low resistance state. The proposed material stack shows a promising prospect to act as a self-selective cell for 3D vertical RRAM application.

  14. Tensile manipulation of ultrathin gold nanowires at different sizes and atomic vacancies

    Science.gov (United States)

    Wang, Fenying; Fu, Yingqiang; Chi, Baozhu; Dai, Yanfeng; Zhao, Jianwei

    2016-09-01

    The fractures of ultrathin metallic nanowires usually exhibit their uncertainties at small scales. Here, statistics was used to study the uniaxial tension-induced deformation of ultrathin gold nanowires. With the same cross section of gold nanowires (5a × 5a × Ha), different sizes show various deformation mechanisms due to the moving styles of slipped crystalline planes. However, the deformations at different sizes (5a × 5a × 5a) and (5a × 5a × 25a) both show the sensitivity to one atomic vacancy, attributed to the dominant role of the same cross section. The statistical broken position distributions further provide that the deformation fracture is size dependent and sensitive to atomic vacancies, which is explained with the relationship between broken bonds and tensile wave propagation. For the size dependence of mechanical property, the nanowire height (H) of 10a is observed to be a transitional point, when the height is less than 10a, the mechanical strength is unstable, while above this transitional point, mechanical strengths decrease with the nanowire size increasing. Our work provides mechanistic insights into enhancing the reliability of metallic nanostructures by engineering the internal atomic imperfection and structural dimensions.

  15. Fully automated high-quality NMR structure determination of small (2)H-enriched proteins.

    Science.gov (United States)

    Tang, Yuefeng; Schneider, William M; Shen, Yang; Raman, Srivatsan; Inouye, Masayori; Baker, David; Roth, Monica J; Montelione, Gaetano T

    2010-12-01

    Determination of high-quality small protein structures by nuclear magnetic resonance (NMR) methods generally requires acquisition and analysis of an extensive set of structural constraints. The process generally demands extensive backbone and sidechain resonance assignments, and weeks or even months of data collection and interpretation. Here we demonstrate rapid and high-quality protein NMR structure generation using CS-Rosetta with a perdeuterated protein sample made at a significantly reduced cost using new bacterial culture condensation methods. Our strategy provides the basis for a high-throughput approach for routine, rapid, high-quality structure determination of small proteins. As an example, we demonstrate the determination of a high-quality 3D structure of a small 8 kDa protein, E. coli cold shock protein A (CspA), using structure is highly converged and in excellent agreement with the published crystal structure, with a backbone RMSD value of 0.5 Å, an all atom RMSD value of 1.2 Å to the crystal structure for well-defined regions, and RMSD value of 1.1 Å to crystal structure for core, non-solvent exposed sidechain atoms. Cross validation of the structure with (15)N- and (13)C-edited NOESY data obtained with a perdeuterated (15)N, (13)C-enriched (13)CH(3) methyl protonated CspA sample confirms that essentially all of these independently-interpreted NOE-based constraints are already satisfied in each of the 10 CS-Rosetta structures. By these criteria, the CS-Rosetta structure generated by fully automated analysis of data for a perdeuterated sample provides an accurate structure of CspA. This represents a general approach for rapid, automated structure determination of small proteins by NMR.

  16. Identification and quantification of oxygen vacancies in CeO{sub 2} nanocrystals and their role in formation of F-centers

    Energy Technology Data Exchange (ETDEWEB)

    Jaffari, G.Hassnain, E-mail: hassnain@qau.edu.pk [Department of Physics, Quaid-i-Azam University Islamabad (Pakistan); Imran, Ali [Department of Physics, Quaid-i-Azam University Islamabad (Pakistan); Bah, M. [Department of Materials Science and Engineering, University of Delaware, 19716, Newark, DE (United States); Ali, Awais; Bhatti, Arshad S. [Centre for Micro and Nano Devices, Department of Physics, COMSATS Institute of Information Technology, Park Road, Islamabad, 44000 (Pakistan); Qurashi, Umar Saeed [Department of Physics, Quaid-i-Azam University Islamabad (Pakistan); Ismat Shah, S. [Department of Materials Science and Engineering, University of Delaware, 19716, Newark, DE (United States); Department of Physics, University of Delaware, 19716, Newark, DE (United States)

    2017-02-28

    Highlights: • Detail crystal and electronic structural analysis was employed to quantify oxygen vacancies. • The Raman F{sub 2g} mode shifted towards lower wave number, exhibiting mode softening with broader and asymmetric peak. • Observation of absorption edge revealed presence of 4f band within the band gap. • PL emission studies revealed presence of F-centers with corresponding energy level located below 4f band. • Transitions associated by the F-center are mainly associated with 4f{sup 0} to 4f{sup 1}, F{sup ++} to 4f{sup 1} and 4f{sup 0} to F{sup +}. - Abstract: In this work we present synthesis and extensive characterization of Cerium oxide (CeO{sub 2}) nanocrystals. Comparison between the properties of as-prepared and air annealed nanoparticles has been carried out, with a goal to clearly identify the effect of oxygen vacancies on crystal, electronic and band structure. Detail crystal and electronic structural analysis was employed to quantify oxygen vacancies. Structural analysis confirmed that the formation of single phase cubic Fluorite structure for both as-prepared and annealed samples. Crystal and electronic structural studies confirmed that Ce ions exists in two oxidation states, Ce{sup +3} and Ce{sup +4}. Concentration of oxygen vacancies was larger in as-synthesis nanocrystal. A drastic decrease in oxygen vacancy concentration was observed for the sample annealed in air at 550 °C. For the as-prepared sample, the Raman allowed F{sub 2g} mode shifted towards lower wavenumber, exhibiting mode softening with broader and asymmetric peak. Observation of absorption edge revealed presence of 4f band within the band gap. Absorption with different band edge, confirmed different energy position of 4f level for the sample possessing oxygen vacancies. Blue shift of the band edge for as-prepared sample has been discussed in terms of increase in lattice parameter, formation of Ce{sup +3} ions, quantum confinement effect etc. Photoluminescence emission

  17. Modelling the social and structural determinants of tuberculosis: opportunities and challenges

    Science.gov (United States)

    Boccia, D.; Dodd, P. J.; Lönnroth, K.; Dowdy, D. W.; Siroka, A.; Kimerling, M. E.; White, R. G.; Houben, R. M. G. J.

    2017-01-01

    INTRODUCTION: Despite the close link between tuberculosis (TB) and poverty, most mathematical models of TB have not addressed underlying social and structural determinants. OBJECTIVE: To review studies employing mathematical modelling to evaluate the epidemiological impact of the structural determinants of TB. METHODS: We systematically searched PubMed and personal libraries to identify eligible articles. We extracted data on the modelling techniques employed, research question, types of structural determinants modelled and setting. RESULTS: From 232 records identified, we included eight articles published between 2008 and 2015; six employed population-based dynamic TB transmission models and two non-dynamic analytic models. Seven studies focused on proximal TB determinants (four on nutritional status, one on wealth, one on indoor air pollution, and one examined overcrowding, socioeconomic and nutritional status), and one focused on macro-economic influences. CONCLUSIONS: Few modelling studies have attempted to evaluate structural determinants of TB, resulting in key knowledge gaps. Despite the challenges of modelling such a complex system, models must broaden their scope to remain useful for policy making. Given the intersectoral nature of the interrelations between structural determinants and TB outcomes, this work will require multidisciplinary collaborations. A useful starting point would be to focus on developing relatively simple models that can strengthen our knowledge regarding the potential effect of the structural determinants on TB outcomes. PMID:28826444

  18. Oxygen vacancies: The origin of n -type conductivity in ZnO

    Science.gov (United States)

    Liu, Lishu; Mei, Zengxia; Tang, Aihua; Azarov, Alexander; Kuznetsov, Andrej; Xue, Qi-Kun; Du, Xiaolong

    2016-06-01

    Oxygen vacancy (VO) is a common native point defect that plays crucial roles in determining the physical and chemical properties of metal oxides such as ZnO. However, fundamental understanding of VO is still very sparse. Specifically, whether VO is mainly responsible for the n -type conductivity in ZnO has been still unsettled in the past 50 years. Here, we report on a study of oxygen self-diffusion by conceiving and growing oxygen-isotope ZnO heterostructures with delicately controlled chemical potential and Fermi level. The diffusion process is found to be predominantly mediated by VO. We further demonstrate that, in contrast to the general belief of their neutral attribute, the oxygen vacancies in ZnO are actually +2 charged and thus responsible for the unintentional n -type conductivity as well as the nonstoichiometry of ZnO. The methodology can be extended to study oxygen-related point defects and their energetics in other technologically important oxide materials.

  19. Ferromagnetism and half metallicity induced by oxygen vacancies in the double perovskite BaSrNiWO{sub 6}: DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Aharbil, Y. [Laboratoire de Chimie Physique des Matériaux LCPM, Faculté des Sciences Ben M' Sik, Casablanca (Morocco); Labrim, H. [Unité Science de la Matière/DERS/Centre National de l’Energie, des Sciences et des Techniques Nucléaires (CNESTEN), Rabat (Morocco); Benmokhtar, S.; Haddouch, M. Ait [Laboratoire de Chimie Physique des Matériaux LCPM, Faculté des Sciences Ben M' Sik, Casablanca (Morocco); Bahmad, L., E-mail: bahmad@fsr.ac.ma [Mohammed V University in Rabat, Laboratoire de Magnétisme et Physique des Hautes Energies L.M.P.H.E. URAC-12, B.P. 1014, Rabat (Morocco); Belhaj, A. [LIRST, Département de Physique, Faculté Poly-disciplinaire, Université Sultan Moulay Slimane, Béni Mellal (Morocco); Ez-Zahraouy, H.; Benyoussef, A. [Mohammed V University in Rabat, Laboratoire de Magnétisme et Physique des Hautes Energies L.M.P.H.E. URAC-12, B.P. 1014, Rabat (Morocco)

    2016-11-01

    Using the spin polarized density functional theory (DFT) and exploring the Plane-Wave Self-Consistent Field (PWscf) code implemented in Quantum-ESPRESSO package, we investigate the effect of the Oxygen vacancies (V{sub O}) and the Oxygen interstitial (O{sub i}) on the double perovskite BaSrNiWO{sub 6}. This deals with the magnetic ordering and the electronic structure in such a pure sample exhibiting the insulating anti-ferromagnetic (AFM) state. This study shows that the presence of oxygen deficient defects converts the insulating to half metal with ferromagnetic or anti-ferromagnetic states. The magnetic ordering in BaSrNiWO{sub 6−δ} depends on the position of the Oxygen vacancy in the unit cell. However, it has been shown that the Oxygen interstitial preserves the anti-ferromagnetic propriety. We have computed the formation energies of different positions of the Oxygen vacancy (V{sub O}) and the Oxygen interstitial (O{sub i}) in the BaSrNiWO{sub 6} compound. We showed that the formation of V{sub O} is easier and vice versa for the O{sub i} formation. The obtained results reveal(V{sub O}) and the Oxygen interstitial (O{sub i}) that the anti-ferromagnetic can be converted to ferromagnetic in the double perovskite BaSrNiWO{sub 6} induced by Oxygen vacancies V{sub O}. - Highlights: • We have studied the ferromagnetism and Half Metallicity in Double Perovskite BaSrNiWO{sub 6}. • We have applied the Ab-inito calculations using the DFT approach. • We showed the effects induced by Oxygen Vacancies and Oxygen interstitial. • We found that the magnetic ordering in BaSrNiWO{sub 6−δ} depends on the position of the Oxygen vacancy in the unit cell.

  20. Vacancy ordering and superstructure formation in dry and hydrated strontium tantalate perovskites: A TEM perspective

    DEFF Research Database (Denmark)

    Ashok, Anuradha M.; Haavik, Camilla; Norby, Poul

    2014-01-01

    Crystal structures of Sr4(Sr2Ta2)O11 and Sr4(Sr1.92Ta2.08)O11.12, synthesized by solid state reaction technique in dry and hydrated state have been studied mainly using Transmission Electron Microscopy. Due to the lesser ability of X-rays to probe details in oxygen sublattice, the change in crystal...... symmetry due to ordering of oxygen vacancies could be detected better using Transmission Electron Microscopy. After detailed analysis through TEM, it was observed that no major change occurs in the cation sublattice. The TEM observations are compared with XRD data and discussed. The crystal symmetries...... structure. © 2014 Elsevier Ltd....

  1. Processing visual rhetoric in advertisements: Interpretations determined by verbal anchoring and visual structure

    NARCIS (Netherlands)

    Lagerwerf, L.; Hooijdonk, van C.M.J.; Korenberg, A.

    2012-01-01

    This research investigated meaning operation in relation to verbal anchoring and visual structure of visual rhetoric in advertisements. Meaning operation refers to the relation between meaningful visual elements, and determines the number of interpretations of an image. Meaning operation

  2. Determinants of the microbial community structure of eutrophic, hyporheic river sediments polluted with chlorinated aliphatic hydrocarbons

    NARCIS (Netherlands)

    Hamonts, K.; Ryngaert, A.; Smidt, H.; Springael, D.; Dejonghe, W.

    2014-01-01

    Chlorinated aliphatic hydrocarbons (CAHs) often discharge into rivers as contaminated groundwater baseflow. As biotransformation of CAHs in the impacted river sediments might be an effective remediation strategy, we investigated the determinants of the microbial community structure of eutrophic,

  3. Directions for Determining Buffer Zone Distances for Commodity and Structural Fumigation with Methyl Bromide

    Science.gov (United States)

    Buffer zones for commodity and food handling structural applications are distributed across numerous tables. This document provides directions for determining the factors to use to identify the correct table for a given application.

  4. CASD-NMR: critical assessment of automated structure determination by NMR

    NARCIS (Netherlands)

    Rosato, A.; van der Schot, G.; Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238

    2009-01-01

    NMR spectroscopy is currently the only technique for determining the solution structure of biological macromolecules. This typically requires both the assignment of resonances and a labor-intensive analysis of multidimensional nuclear Overhauser effect spectroscopy (NOESY) spectra, in which peaks

  5. Structure determination and analysis of a bacterial chymotrypsin from Cellulomonas bogoriensis.

    Science.gov (United States)

    Shaw, A; Saldajeno, M L; Kolkman, M A B; Jones, B E; Bott, R

    2007-04-01

    The crystal structure of a secreted chymotrypsin from the alkaliphile Cellulomonas bogoriensis has been determined using data to 1.78 A resolution and refined to a crystallographic R factor of 0.167. The crystal structure reveals a large P1 substrate-specificity pocket, as expected for chymotrypsins. The structure is compared with close structural homologues. This comparison does not reveal clear reasons for the alkali tolerance of the enzyme, but the greater compactness of the structure and lowered hydrogen bonding may play a role.

  6. Modelling the social and structural determinants of tuberculosis: opportunities and challenges.

    OpenAIRE

    Pedrazzoli, D; Boccia, D; Dodd, PJ; Lönnroth, K; Dowdy, DW; Siroka, A.; Kimerling, ME; White, RG; Houben, Rmgj

    2017-01-01

    INTRODUCTION: Despite the close link between tuberculosis (TB) and poverty, most mathematical models of TB have not addressed underlying social and structural determinants. OBJECTIVE: To review studies employing mathematical modelling to evaluate the epidemiological impact of the structural determinants of TB. METHODS: We systematically searched PubMed and personal libraries to identify eligible articles. We extracted data on the modelling techniques employed, research question, types of stru...

  7. Determining the velocity fine structure by a laser anemometer with fixed orientation

    Energy Technology Data Exchange (ETDEWEB)

    Kristensen, Leif; Kirkegaard, P.; Mikkelsen, Torben

    2011-02-15

    We have studied the velocity structure functions and spectra which can be determined by a CW-laser anemometer and a (pulsed) lidar anemometer. We have found useful theoretical expressions for both types of anemometers and compared their filtering of the along-beam turbulent velocity. The purpose has been to establish a basis for remote determining of turbulence fine-structure in terms of the rate of dissipation of specific kinetic energy in the atmospheric boundary layer. (Author)

  8. Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins.

    Science.gov (United States)

    Schmidt, Elena; Güntert, Peter

    2013-10-01

    Protein structure determination by NMR can in principle be speeded up both by reducing the measurement time on the NMR spectrometer and by a more efficient analysis of the spectra. Here we study the reliability of protein structure determination based on a single type of spectra, namely nuclear Overhauser effect spectroscopy (NOESY), using a fully automated procedure for the sequence-specific resonance assignment with the recently introduced FLYA algorithm, followed by combined automated NOE distance restraint assignment and structure calculation with CYANA. This NOESY-FLYA method was applied to eight proteins with 63-160 residues for which resonance assignments and solution structures had previously been determined by the Northeast Structural Genomics Consortium (NESG), and unrefined and refined NOESY data sets have been made available for the Critical Assessment of Automated Structure Determination of Proteins by NMR project. Using only peak lists from three-dimensional (13)C- or (15)N-resolved NOESY spectra as input, the FLYA algorithm yielded for the eight proteins 91-98 % correct backbone and side-chain assignments if manually refined peak lists are used, and 64-96 % correct assignments based on raw peak lists. Subsequent structure calculations with CYANA then produced structures with root-mean-square deviation (RMSD) values to the manually determined reference structures of 0.8-2.0 Å if refined peak lists are used. With raw peak lists, calculations for 4 proteins converged resulting in RMSDs to the reference structure of 0.8-2.8 Å, whereas no convergence was obtained for the four other proteins (two of which did already not converge with the correct manual resonance assignments given as input). These results show that, given high-quality experimental NOESY peak lists, the chemical shift assignments can be uncovered, without any recourse to traditional through-bond type assignment experiments, to an extent that is sufficient for calculating accurate three

  9. Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference.

    Science.gov (United States)

    MacCallum, Justin L; Perez, Alberto; Dill, Ken A

    2015-06-02

    More than 100,000 protein structures are now known at atomic detail. However, far more are not yet known, particularly among large or complex proteins. Often, experimental information is only semireliable because it is uncertain, limited, or confusing in important ways. Some experiments give sparse information, some give ambiguous or nonspecific information, and others give uncertain information-where some is right, some is wrong, but we don't know which. We describe a method called Modeling Employing Limited Data (MELD) that can harness such problematic information in a physics-based, Bayesian framework for improved structure determination. We apply MELD to eight proteins of known structure for which such problematic structural data are available, including a sparse NMR dataset, two ambiguous EPR datasets, and four uncertain datasets taken from sequence evolution data. MELD gives excellent structures, indicating its promise for experimental biomolecule structure determination where only semireliable data are available.

  10. Determining Science Student Teachers' Cognitive Structure on the Concept of "Food Chain"

    Science.gov (United States)

    Çinar, Derya

    2015-01-01

    The current study aims to determine science student teachers' cognitive structure on the concept of food chain. Qualitative research method was applied in this study. Fallacies detected in the pre-service teachers' conceptual structures are believed to result in students' developing misconceptions in their future classes and will adversely affect…

  11. Effects of partial La filling and Sb vacancy defects on CoS b3 skutterudites

    Science.gov (United States)

    Hu, Chongze; Zeng, Xiaoyu; Liu, Yufei; Zhou, Menghan; Zhao, Huijuan; Tritt, Terry M.; He, Jian; Jakowski, Jacek; Kent, Paul R. C.; Huang, Jingsong; Sumpter, Bobby G.

    2017-04-01

    Over the past decade, the open frame ("cagey") structure of CoS b3 skutterudite has invited intensive filling studies with various rare-earth elements for delivering state-of-the-art midtemperature thermoelectric performance. To rationalize previously reported experimental results and provide new insight into the underexplored roles of La fillers and Sb vacancies, ab initio density functional theory studies, along with semiclassical Boltzmann transport theory calculations, are performed for pristine CoS b3 of different lattice settings and La-filled CoS b3 with and without Sb's mono- and divacancy defects. The effects of spin-orbit coupling (SOC), partial La filling, Sb vacancy defects, and spin polarization on the electronic and thermoelectric properties are systematically examined. The SOC shows minor effects on the electronic and thermoelectric properties of CoS b3 . The peculiar quasi-Dirac band in the pristine CoS b3 largely survives La filling but not Sb vacancies, which instead introduce dispersive bands in the band gap region. The non-spin-polarized and spin-polarized solutions of La-filled CoS b3 are nearly degenerate. Importantly, the band structure, density of states, and Fermi surface of the latter are significantly spin polarized, giving rise to spin-dependent thermoelectric properties. Seebeck coefficients directly calculated as a function of chemical potential are interpreted in connection with the electronic structures. Temperature-dependent Seebeck coefficients derived for the experimentally studied materials agree well with available experimental data. Seebeck coefficients obtained as a function of charge carrier concentration corroborate the thermoelectrically favorable role at high filling fractions played by the Fermi electron pockets associated with the degenerate valleys in the conduction bands, and also point toward a similar role of the Fermi hole pockets associated with the degenerate hills in the valence bands. These results serve to

  12. Lifetime of Ionic Vacancy Created in Redox Electrode Reaction Measured by Cyclotron MHD Electrode.

    Science.gov (United States)

    Sugiyama, Atsushi; Morimoto, Ryoichi; Osaka, Tetsuya; Mogi, Iwao; Asanuma, Miki; Miura, Makoto; Oshikiri, Yoshinobu; Yamauchi, Yusuke; Aogaki, Ryoichi

    2016-01-21

    The lifetimes of ionic vacancies created in ferricyanide-ferrocyanide redox reaction have been first measured by means of cyclotron magnetohydrodynamic electrode, which is composed of coaxial cylinders partly exposed as electrodes and placed vertically in an electrolytic solution under a vertical magnetic field, so that induced Lorentz force makes ionic vacancies circulate together with the solution along the circumferences. At low magnetic fields, due to low velocities, ionic vacancies once created become extinct on the way of returning, whereas at high magnetic fields, in enhanced velocities, they can come back to their initial birthplaces. Detecting the difference between these two states, we can measure the lifetime of ionic vacancy. As a result, the lifetimes of ionic vacancies created in the oxidation and reduction are the same, and the intrinsic lifetime is 1.25 s, and the formation time of nanobubble from the collision of ionic vacancies is 6.5 ms.

  13. Vacancy dynamic in Ni-Mn-Ga ferromagnetic shape memory alloys

    Energy Technology Data Exchange (ETDEWEB)

    Merida, D., E-mail: david.merida@ehu.es [Fisika Aplikatua II Saila, Euskal Herriko Unibertsitatea UPV/EHU, p.k. 644, 48080 Bilbao (Spain); Elektrizitate eta Elektronika Saila, Euskal Herriko Unibertsitatea UPV/EHU, p.k. 644, 48080 Bilbao (Spain); García, J. A. [Fisika Aplikatua II Saila, Euskal Herriko Unibertsitatea UPV/EHU, p.k. 644, 48080 Bilbao (Spain); BC Materials (Basque Centre for Materials, Application and Nanostructures), 48040 Leioa (Spain); Sánchez-Alarcos, V.; Pérez-Landazábal, J. I.; Recarte, V. [Departamento de Física, Universidad Pública de Navarra, Campus de Arrosadia, 31006 Pamplona (Spain); Plazaola, F. [Elektrizitate eta Elektronika Saila, Euskal Herriko Unibertsitatea UPV/EHU, p.k. 644, 48080 Bilbao (Spain)

    2014-06-09

    Vacancies control any atomic ordering process and consequently most of the order-dependent properties of the martensitic transformation in ferromagnetic shape memory alloys. Positron annihilation spectroscopy demonstrates to be a powerful technique to study vacancies in NiMnGa alloys quenched from different temperatures and subjected to post-quench isothermal annealing treatments. Considering an effective vacancy type the temperature dependence of the vacancy concentration has been evaluated. Samples quenched from 1173 K show a vacancy concentration of 1100 ± 200 ppm. The vacancy migration and formation energies have been estimated to be 0.55 ± 0.05 eV and 0.90 ± 0.07 eV, respectively.

  14. One-dimensional surface damage at grazing projectile incidence: linear vacancy chains on channeled planes

    Science.gov (United States)

    Mazilova, Tatjana I.; Sadanov, Evgenij V.; Ksenofontov, Vjacheslav A.; Mikhailovskij, Igor M.

    2013-11-01

    The onset of erosion pattern formation through exposure of the pristine {211} and {321} tungsten surface with 5 keV He atoms at grazing incidence has been investigated at 21 K by field ion microscopy. We demonstrate that the linear chains of surface vacancies related to irradiation are created in addition to expected individual vacancies and two-dimensional vacancy clusters. The vacancy chains were ideally straight and did not displayed atomic-scale kinks. The asymmetry of the radiation adatom production on the two lateral sides of the vacancy chains was revealed on the W {321} plane. Possible origins for the asymmetry of damage production with respect to the vacancy chains were analyzed in terms of the details of the energy landscape of interatomic interactions on this surface.

  15. Action-derived molecular dynamics simulations for the migration and coalescence of vacancies in graphene and carbon nanotubes.

    Science.gov (United States)

    Lee, Alex Taekyung; Ryu, Byungki; Lee, In-Ho; Chang, K J

    2014-03-19

    We report the results of action-derived molecular dynamics simulations for the migration and coalescence processes of monovacancies in graphene and carbon nanotubes with different chiralities. In carbon nanotubes, the migration pathways and barriers of a monovacancy depend on the tube chirality, while there is no preferential pathway in graphene due to the lattice symmetry and the absence of the curvature effect. The probable pathway changes from the axial to circumferential direction as the chirality varies from armchair to zigzag. The chirality dependence is attributed to the preferential orientation of the reconstructed bond formed around each vacancy site. It is energetically more favourable for two monovacancies to coalesce into a divacancy via alternative movements rather than simultaneous movements. The energy barriers for coalescence are generally determined by the migration barrier for the monovacancy, although there are some variations due to interactions between two diffusing vacancies. In graphene and armchair nanotubes, two monovacancies prefer to migrate along different zigzag atomic chains rather than a single atomic chain connecting these vacancies. On the other hand, in zigzag tubes, the energy barrier for coalescence increases significantly unless monovacancies lie on the same circumference.

  16. Dynamic approach to finite-temperature magnetic phase transitions in the extended J1-J2 model with vacancy order.

    Science.gov (United States)

    Zhou, N J; Zheng, B; Dai, J H

    2013-02-01

    The recently discovered iron-based superconductors A(y)Fe(2-x)Se(2) (A=K, Rb, Cs, Tl) show a long-range antiferromagnetic order with an unexpectedly high transition temperature T(N)~550 K and a unique √5×√5 vacancy order. Taking the extended J(1)-J(2) model as a minimal model, we investigate the finite-temperature magnetic phase transitions in a square lattice with a √5×√5 vacancy superstructure by using large-scale Monte Carlo simulations. By the parallel tempering technique, the block spin checkerboard and stripe antiferromagnetic states are detected to be the ground states for three representative sets of model parameters. The short-time dynamic approach is applied to accurately determine the critical temperature as well as the static and dynamic exponents. Our results indicate that the dramatic enhancement of the critical temperature as observed in experiments should be mainly due to a combination of the vacancy order and the block lattice contraction.

  17. NMR structure determination of protein-ligand complexes by lanthanide labeling.

    Science.gov (United States)

    Pintacuda, Guido; John, Michael; Su, Xun-Cheng; Otting, Gottfried

    2007-03-01

    The paramagnetism of lanthanide ions offers outstanding opportunities for fast determinations of the three-dimensional (3D) structures of protein-ligand complexes by nuclear magnetic resonance (NMR) spectroscopy. It is shown how the combination of pseudocontact shifts (PCSs) induced by a site-specifically bound lanthanide ion and prior knowledge of the 3D structure of the lanthanide-labeled protein can be used to achieve (i) rapid assignments of NMR spectra, (ii) structure determinations of protein-protein complexes, and (iii) identification of the binding mode of low-molecular weight compounds in complexes with proteins. Strategies for site-specific incorporation of lanthanide ions into proteins are summarized.

  18. Analyze the Determinants of Capital Structure for Vietnamese Real Estate Listed Companies

    OpenAIRE

    Nguyen, Nhung Thi Phuong; Nguyen, Lien Phuong; Dang, Hang Thi Thu

    2017-01-01

    This study adopts a two - step system general method of moments (GMM) approach towards investigating the determinants of capital structure for the listed real estate firms on Ho Chi Minh stock exchange (HSX) in Viet Nam from 2010 to 2015. The determinants of capital structure are mixed and different for short-term and long-term indicators. The real estate firms tend to use more debts to finance their investment. Vietnamese real estate firms should focus on balance structure debt due to compli...

  19. Stability of the oxygen vacancy induced conductivity in BaSnO3 thin films on SrTiO3

    Science.gov (United States)

    Jaim, H. M. Iftekhar; Lee, Seunghun; Zhang, Xiaohang; Takeuchi, Ichiro

    2017-10-01

    BaSnO3 (BSO) has emerged as a major candidate for exploration of a variety of functional device applications. In this letter, we report on the role of the oxygen vacancy concentration in the electronic states, the crystal structure, and the transport properties of BSO thin films grown on SrTiO3 substrates by pulsed laser deposition. We fabricated five BSO films systematically reducing the deposition oxygen pressure from 1 × 10-1 Torr to 5 × 10-3 Torr. The BSO films show gradual transition from an insulating one fabricated at 1 × 10-1 Torr to highly conducting ones with decreasing deposition oxygen pressure. X-ray photoelectron spectroscopy measurements show the increasing oxygen vacancy concentration as a function of the decreased deposition oxygen pressure. Films deposited at 5 × 10-3 Torr displayed the lowest room temperature resistivity (1.73 mΩ cm) and the highest concentration of oxygen vacancies. Temperature-dependent resistivity of the samples deposited at low oxygen pressures suggests the presence of shallow states near the conduction band. With decreasing oxygen pressure, the out-of-plane lattice parameter of BSO increases while the in-plane lattice parameter remains nearly the same. Oxygen deficient conducting BSO films with high oxygen vacancies exhibited excellent structural, electronic, and valence state stabilities when they were post-annealed at temperatures up to 760 °C.

  20. Dissociative diffusion mechanism in vacancy-rich materials according to mass action kinetics

    Directory of Open Access Journals (Sweden)

    N. J. Biderman

    2016-05-01

    Full Text Available Two sets of diffusion-reaction numerical simulations using a finite difference method (FDM were conducted to investigate fast impurity diffusion via interstitial sites in vacancy-rich materials such as Cu(In,GaSe2 (CIGS and Cu2ZnSn(S, Se4 (CZTSSe or CZTS via the dissociative diffusion mechanism where the interstitial diffuser ultimately reacts with a vacancy to produce a substitutional. The first set of simulations extends the standard interstitial-limited dissociative diffusion theory to vacancy-rich material conditions where vacancies are annihilated in large amounts, introducing non-equilibrium vacancy concentration profiles. The second simulation set explores the vacancy-limited dissociative diffusion where impurity incorporation increases the equilibrium vacancy concentration. In addition to diffusion profiles of varying concentrations and shapes that were obtained in all simulations, some of the profiles can be fitted with the constant- and limited-source solutions of Fick’s second law despite the non-equilibrium condition induced by the interstitial-vacancy reaction. The first set of simulations reveals that the dissociative diffusion coefficient in vacancy-rich materials is inversely proportional to the initial vacancy concentration. In the second set of numerical simulations, impurity-induced changes in the vacancy concentration lead to distinctive diffusion profile shapes. The simulation results are also compared with published data of impurity diffusion in CIGS. According to the characteristic properties of diffusion profiles from the two set of simulations, experimental detection of the dissociative diffusion mechanism in vacancy-rich materials may be possible.

  1. Suppression of vacancy defects in epitaxial La-doped SrTiO{sub 3} films

    Energy Technology Data Exchange (ETDEWEB)

    Keeble, D. J.; Kanda, G. [Carnegie Laboratory of Physics, SUPA, School of Engineering, Physics, and Mathematics, University of Dundee, Dundee DD1 4HN (United Kingdom); Jalan, B.; Stemmer, S. [Materials Department, University of California, Santa Barbara, California 93106-5050 (United States); Ravelli, L.; Egger, W. [Universitaet Bundeswehr Muenchen, D-85577 Neubiberg (Germany)

    2011-12-05

    Variable energy positron annihilation lifetime spectroscopy of high-mobility La-doped SrTiO{sub 3} grown by molecular beam epitaxy found that the films contained sufficiently low concentrations of Sr vacancies and vacancy cluster defects to allow the observation of positron annihilation events from the perfect lattice. This enabled the concentrations of charged cation vacancies to be estimated, and these were found to be at least an order of magnitude below the La-dopant concentrations.

  2. Charge-Separation Kinetics of Photoexcited Oxygen Vacancies in ZnO Nanowire Field-Effect Transistors

    Science.gov (United States)

    Lu, Ming-Pei; Chen, Chieh-Wei; Lu, Ming-Yen

    2016-11-01

    Photoinduced atomic structural transitions of negative-U defects: neutral oxygen vacancies (VO 0 ), accompanied by lattice relaxation, can form ionized 1 + and 2 + vacancy defects in ZnO materials, giving rise to an optoelectronic phenomenon named "persistent photoconductivity," thereby limiting the applications of ZnO materials in optoelectronic fields. Nevertheless, very little is known about the kinetics of the separation-recombination interactions between an electron and an ionized oxygen vacancy, constituting a photoexcited charge pair, in nanoscale ZnO material systems, especially when considering the effect of electric fields. In this report, we describe the charge-separation kinetics of photoexcited VO 0 defects in ZnO nanowire (NW) field-effect transistor (FET) systems, examined through modulation of the surface electric field of the ZnO NW. We apply oxygen plasma treatment to tailor the doping concentration within the ZnO NWs with the goal of modulating the electric field within their surface space-charge layers. X-ray photoelectron spectroscopy and low-frequency current-noise spectroscopy are applied to identify the change in the density of oxygen-vacancy defects near the NW surface after oxygen plasma treatment. A model describing the initial stage of the photoconductance responses associated with the formation of the photoinduced ionized 1 + state of the oxygen-vacancy defects (VO + ) in the fully depleted ZnO NW FETs in the low-photoconductance regime upon UV excitation is proposed to extract the charge-separation probabilities of the photoexcited electron/VO + pair. Accordingly, the charge-separation probability increases from approximately 0.0012 to 0.042 upon increasing the electric field at the NW surface from approximately 7.5 ×106 to 5.0 ×107 V m-1 . Moreover, we employ modified Braun empirical theory to model the effect of the electric field on the charge-separation behavior of photoexcited electron/VO + pairs in ZnO NWs, obtaining a

  3. The structural determinants that lead to the formation of particular oligomeric structures in the pancreatic-type ribonuclease family.

    Science.gov (United States)

    Benito, A; Laurents, D V; Ribó, M; Vilanova, M

    2008-08-01

    Pancreatic-type ribonucleases are a family of RNA degrading enzymes that share different degrees of sequence identity but a very similar 3D-structure. The prototype of this family is bovine pancreatic ribonuclease or ribonuclease A. This enzyme has been the object of landmark work on the folding, stability, protein chemistry, catalysis, enzyme-substrate interaction and molecular evolution. In the recent years, the interest in the study of pancreatic-type ribonucleases has increased due to the involvement of some members of this family in special biological functions. In addition, dimeric and also higher oligomeric structures can be attained by the members of this family. The oligomers described structurally to date are mainly formed by 3D-domain swapping, a process which consists of the exchange of identical domains (i.e. identical structural elements, usually the N- and C-termini) between the subunits and is considered to be a mechanism for amyloid-type aggregate formation. This review compares the dimeric and oligomeric structures of different members of the pancreatic-type ribonuclease family which are able to acquire these structures, namely, bovine seminal ribonuclease, ribonuclease A and its human counterpart, human pancreatic ribonuclease. A specific focus is placed on what is known about the structural determinants that lead to the acquisition of a particular oligomeric structure and on the proposed mechanism of 3D-swapping.

  4. Structure determination of zeolites and ordered mesoporous materials by electron crystallography.

    Science.gov (United States)

    Sun, Junliang; Zou, Xiaodong

    2010-09-28

    Structure determination of porous materials is important for understanding the materials properties and exploiting their applications. Compared to X-ray diffraction, electron crystallography has two unique advantages. Crystals that are too small to be studied by X-ray diffraction can be studied by electron crystallography. The structure factor phase information, which is lost in diffraction, can be obtained from high resolution transmission electron microscopy (HRTEM) images. Here we will present different techniques and applications of electron crystallography for structure determination of zeolites and ordered mesoporous materials, based on electron diffraction data and/or HRTEM images. Electron crystallography and X-ray diffraction are complementary in many aspects. Their combinations show great potentials for structure determination of complex porous materials.

  5. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2.

    Science.gov (United States)

    Kimanius, Dari; Forsberg, Björn O; Scheres, Sjors Hw; Lindahl, Erik

    2016-11-15

    By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at large computational costs, which has introduced a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated well over two orders-of-magnitude on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.

  6. Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination

    Science.gov (United States)

    Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

    2014-01-01

    The number of macromolecular structures deposited in the Protein Data Bank now approaches 100 000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation. PMID:24034303

  7. Cesium vacancy ordering in phase-separated C sxF e2 -yS e2

    Science.gov (United States)

    Taddei, K. M.; Sturza, M.; Chung, D. Y.; Cao, H. B.; Claus, H.; Kanatzidis, M. G.; Osborn, R.; Rosenkranz, S.; Chmaissem, O.

    2015-09-01

    By simultaneously displaying magnetism and superconductivity in a single phase, the iron-based superconductors provide a model system for the study of magnetism's role in superconductivity. The class of intercalated iron selenide superconductors is unique among these in having the additional property of phase separation and coexistence of two distinct phases—one majority phase with iron vacancy ordering and strong antiferromagnetism, and the other a poorly understood minority microscopic phase with a contested structure. Adding to the intrigue, the majority phase has never been found to show superconductivity on its own while the minority phase has never been successfully synthesized separate from the majority phase. In order to better understand this minority phase, a series of high-quality C sxF e2 -yS e2 single crystals with (0.8 ≤x ≤1 ; 0 ≤y ≤0.3 ) were grown and studied. Neutron and x-ray powder diffraction performed on ground crystals show that the average I 4 /m m m structure of the minority phase is distinctly different from the high-temperature I 4 /m m m parent structure. Moreover, single-crystal diffraction reveals the presence of discrete superlattice reflections that remove the degeneracy of the Cs sites in both the majority and minority phases and reduce their structural symmetries from body centered to primitive. Group theoretical analysis in conjunction with structural modeling shows that the observed superlattice reflections originate from three-dimensional Cs vacancy ordering. This model predicts a 25 % vacancy of the Cs site in the minority phase which is consistent with the site's refined occupancy. Magnetization measurements performed in tandem with neutron single-crystal diffraction provide evidence that the minority phase is the host of superconductivity. Our results also reveal a superconducting dome in which the superconducting transition temperature varies as a function of the nominal valence of iron.

  8. First-principles calculations of the vacancy formation energy in transition and noble metals

    DEFF Research Database (Denmark)

    Korzhavyi, P.A.; Abrikosov, Igor A.; Johansson, Börje

    1999-01-01

    Abstract: The vacancy formation energy and the vacancy formation volume of the 3d, 4d, and 5d transition and noble metals have been calculated within the local-density approximation. The calculations employ the order-N locally self-consistent Green's-function method in conjunction with a supercell...... approach and include electrostatic multipole corrections to the atomic sphere approximation. The results are in excellent agreement with available full-potential calculations and with the vacancy formation energies obtained in positron annihilation measurements. The variation of the vacancy formation...

  9. The interaction between light impurities and vacancies in titanium and aluminum metals: A DFT study

    OpenAIRE

    Kartamyshev, Andrey I.; Vo, Dat Duy; Alexey G. Lipnitskii

    2016-01-01

    In this paper, we present binding energies between hydrogen (H), carbon (C), nitrogen (N) and oxygen (O) atoms and a vacancy in the hexagonal closed-packed (HCP) lattice of titanium (Ti) and the face centered cubic (FCC) lattice of aluminum (Al), calculated using the density functional theory (DFT). We have also investigated the trapping of up to five hydrogen atoms by a vacancy and the reduction of the vacancy formation energy, due to the formation of a hydrogen–vacancy complex. We used the ...

  10. Ab initio study of the oxygen vacancy in SrTiO3

    Science.gov (United States)

    Astala, R.; Bristowe, P. D.

    2001-09-01

    The electrical properties of SrTiO3 are strongly dependent on the oxygen vacancy concentration. We have studied the atomic and electronic properties of a single oxygen vacancy using a local spin density approximation-plane-wave pseudopotential method. The total energies, relaxed geometries, valence charge and spin densities, and densities of electron states are calculated for different charge states of the vacancy. The doubly positively charged state is found to be the most stable. With some charge states, a spin-polarized defect state is observed. Furthermore, we have evaluated the formation energy of the vacancy in the OO→VO + ½O2 process.

  11. Protegrin structure-activity relationships: using homology models of synthetic sequences to determine structural characteristics important for activity.

    Science.gov (United States)

    Ostberg, Nathan; Kaznessis, Yiannis

    2005-02-01

    The protegrin family of antimicrobial peptides is among the shortest in sequence length while remaining very active against a variety of microorganisms. The major goal of this study is to characterize easily calculated molecular properties, which quantitatively show high correlation with antibacterial activity. The peptides studied have high sequence similarity but vary in activity over more than an order of magnitude. Hence, sequence analysis alone cannot be used to predict activity for these peptides. We calculate structural properties of 62 protegrin and protegrin-analogue peptides and correlate them to experimental activities against six microbe species, as well as hemolytic and cytotoxic activities. Natural protegrins structures were compared with synthetic derivatives using homology modeling, and property descriptors were calculated to determine the characteristics that confer their antimicrobial activity. A structure-activity relationship study of all these peptides provides information about the structural properties that affect activity against different microbial species.

  12. Method for providing oxygen ion vacancies in lanthanide oxides

    Science.gov (United States)

    Kay, D. Alan R.; Wilson, William G.

    1989-12-05

    A method for desulfurization of fuel gases resulting from the incomplete combustion of sulfur containing hydrocarbons whereby the gases are treated with lanthanide oxides containing large numbers of oxygen-ion vacancies providing ionic porosity which enhances the ability of the lanthanide oxides to react more rapidly and completely with the sulfur in the fuel gases whereby the sulfur in such gases is reduced to low levels suitable for fuels for firing into boilers of power plants generating electricity with steam turbine driven generators, gas turbines, fuel cells and precursors for liquid fuels such as methanol and the like.

  13. Effects of vacancies on overshooting in nonequilibrium ordering processes

    DEFF Research Database (Denmark)

    Gilhøj, Henriette; Jeppesen, Claus; Mouritsen, Ole G.

    1996-01-01

    The effects of annealed site dilution on the nonequilibrium ordering process in the two-dimensional Ising model with a nonconserved order parameter have been studied using Monte Carlo simulation. It is found that the transient development of a local order that is larger than the equilibrium order...... (overshooting), as recently reported in the pure Ising model [H. Gilhoj, C. Jeppesen, and O. G; Mouritsen, Phys. Rev. Lett. 75, 3305 (1995)], persists in the dilute model and is accompanied by a depletion of the vacancies within the ordered domains....

  14. Metal (Ni, Au)-vacancy complexes in GaN

    Science.gov (United States)

    von Pezold, J.; Bristowe, P. D.

    2006-06-01

    The stability and electronic properties of metal (Ni, Au)-vacancy complexes in GaN were studied using density functional calculations. Two complexes (NiGa-VN and VGa-Aui-VN) were found to exhibit relatively low formation energies in their neutral charge state under p-type conditions and are predicted to act as deep acceptors in GaN. As such they are unlikely to contribute to the hole carrier concentration in p-GaN and are probably not responsible for the low electrical resistance of Au/Ni contacts. They may, however, act as compensation centres in n-GaN.

  15. An approach for de novo structure determination of dynamic molecular assemblies by electron cryomicroscopy.

    Science.gov (United States)

    Sander, Bjoern; Golas, Monika M; Lührmann, Reinhard; Stark, Holger

    2010-06-09

    Single-particle electron cryomicroscopy is a powerful method for three-dimensional (3D) structure determination of macromolecular assemblies. Here we address the challenge of determining a 3D structure in the absence of reference models. The 3D structures are determined by alignment and weighted averaging of densities obtained by native cryo random conical tilt (RCT) reconstructions including consideration of missing data. Our weighted averaging scheme (wRCT) offers advantages for potentially heterogeneous 3D densities of low signal-to-noise ratios. Sets of aligned RCT structures can also be analyzed by multivariate statistical analysis (MSA) to provide insights into snapshots of the assemblies. The approach is used to compute 3D structures of the Escherichia coli 70S ribosome and the human U4/U6.U5 tri-snRNP under vitrified unstained cryo conditions, and to visualize by 3D MSA the L7/L12 stalk of the 70S ribosome and states of tri-snRNP. The approach thus combines de novo 3D structure determination with an analysis of compositional and conformational heterogeneity.

  16. Unexpected positive role of oxygen vacancies in Na-doped ZnO

    Science.gov (United States)

    Yang, X. P.; Lu, J. G.; Zhang, H. H.; Lu, B.; Huang, J. Y.; Ye, C. L.; Ye, Z. Z.

    2012-12-01

    The interaction of Na impurities and O vacancies (VO) in ZnO was studied in theory and experiment. The VO facilitated substitutional Na (NaZn/NaZn-) acceptors with inhibiting interstitial Na (Nai/Nai+) donors, which may benefit the p-type conductivity. The formed (NaZn-VO)+/0 complexes induced the change of band structures of ZnO, with the broadening of gap energies and disappearance of the VO2+-related impurity level, which confirmed by the blue shift of the near-band-edge (NBE) UV emission and the decay of the visible emission in PL spectra. The strong and dominant NBE UV emission suggested acceptable luminescence behaviors of Na-doped ZnO.

  17. Switchable diode effect in oxygen vacancy-modulated SrTiO{sub 3} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Xinqiang; Shuai, Yao; Wu, Chuangui; Luo, Wenbo; Sun, Xiangyu; Zeng, Huizhong; Bai, Xiaoyuan; Gong, Chaoguan; Jian, Ke; Zhang, Wanli [University of Electronic Science and Technology of China, State Key Laboratory of Electronic Thin Films and Integrated Devices, Chengdu (China); Zhang, Lu; Guo, Hongliang [University of Electronic Science and Technology of China, The Center for Robotics, Chengdu (China); Tian, Benlang [26th Institute of China Electronics Technology Group Corporation, Chongqing (China)

    2017-09-15

    SrTiO{sub 3} (STO) single crystal wafer was annealed in vacuum, and co-planar metal-insulator-metal structure of Pt/Ti/STO/Ti/Pt were formed by sputtering Pt/Ti electrodes onto the surface of STO after annealing. The forming-free resistive switching behavior with self-compliance property was observed in the sample. The sample showed switchable diode effect, which is explained by a simple model that redistribution of oxygen vacancies (OVs) under the external electric field results in the formation of n-n{sup +} junction or n{sup +}-n junction (n donated n-type semiconductor; n{sup +} donated heavily doped n-type semiconductor). The self-compliance property is also interpreted by the formation of n-n{sup +}/n{sup +}-n junction caused by the migration of the OVs under the electric field. (orig.)

  18. Quantum Nonlinear Optics with a Germanium-Vacancy Color Center in a Nanoscale Diamond Waveguide

    Science.gov (United States)

    Bhaskar, M. K.; Sukachev, D. D.; Sipahigil, A.; Evans, R. E.; Burek, M. J.; Nguyen, C. T.; Rogers, L. J.; Siyushev, P.; Metsch, M. H.; Park, H.; Jelezko, F.; Lončar, M.; Lukin, M. D.

    2017-06-01

    We demonstrate a quantum nanophotonics platform based on germanium-vacancy (GeV) color centers in fiber-coupled diamond nanophotonic waveguides. We show that GeV optical transitions have a high quantum efficiency and are nearly lifetime broadened in such nanophotonic structures. These properties yield an efficient interface between waveguide photons and a single GeV center without the use of a cavity or slow-light waveguide. As a result, a single GeV center reduces waveguide transmission by 18 ±1 % on resonance in a single pass. We use a nanophotonic interferometer to perform homodyne detection of GeV resonance fluorescence. By probing the photon statistics of the output field, we demonstrate that the GeV-waveguide system is nonlinear at the single-photon level.

  19. Quantum Nonlinear Optics with a Germanium-Vacancy Color Center in a Nanoscale Diamond Waveguide.

    Science.gov (United States)

    Bhaskar, M K; Sukachev, D D; Sipahigil, A; Evans, R E; Burek, M J; Nguyen, C T; Rogers, L J; Siyushev, P; Metsch, M H; Park, H; Jelezko, F; Lončar, M; Lukin, M D

    2017-06-02

    We demonstrate a quantum nanophotonics platform based on germanium-vacancy (GeV) color centers in fiber-coupled diamond nanophotonic waveguides. We show that GeV optical transitions have a high quantum efficiency and are nearly lifetime broadened in such nanophotonic structures. These properties yield an efficient interface between waveguide photons and a single GeV center without the use of a cavity or slow-light waveguide. As a result, a single GeV center reduces waveguide transmission by 18±1% on resonance in a single pass. We use a nanophotonic interferometer to perform homodyne detection of GeV resonance fluorescence. By probing the photon statistics of the output field, we demonstrate that the GeV-waveguide system is nonlinear at the single-photon level.

  20. Properties of nitrogen-vacancy centers in diamond: the group theoretic approach

    Energy Technology Data Exchange (ETDEWEB)

    Maze, J R; Togan, E; Chu, Y; Trifonov, A; Lukin, M D [Department of Physics, Harvard University, Cambridge, MA 02138 (United States); Gali, A [Department of Atomic Physics, Budapest University of Technology and Economics, Budafoki ut 8, H-1111 Budapest (Hungary); Kaxiras, E, E-mail: jmaze@puc.cl, E-mail: agali@eik.bme.hu [Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 (United States)

    2011-02-15

    We present a procedure that makes use of group theory to analyze and predict the main properties of the negatively charged nitrogen-vacancy (NV) center in diamond. We focus on the relatively low temperature limit where both the spin-spin and spin-orbit effects are important to consider. We demonstrate that group theory may be used to clarify several aspects of the NV structure, such as ordering of the singlets in the (e{sup 2}) electronic configuration and the spin-spin and spin-orbit interactions in the (ae) electronic configuration. We also discuss how the optical selection rules and the response of the center to electric field can be used for spin-photon entanglement schemes. Our general formalism is applicable to a broad class of local defects in solids. The present results have important implications for applications in quantum information science and nanomagnetometry.

  1. Trapping of Oxygen Vacancies at Crystallographic Shear Planes in Acceptor-Doped Pb-Based Ferroelectrics.

    Science.gov (United States)

    Batuk, Dmitry; Batuk, Maria; Tsirlin, Alexander A; Hadermann, Joke; Abakumov, Artem M

    2015-12-01

    The defect chemistry of the ferroelectric material PbTiO3 after doping with Fe(III) acceptor ions is reported. Using advanced transmission electron microscopy and powder X-ray and neutron diffraction, we demonstrate that even at concentrations as low as circa 1.7% (material composition approximately ABO2.95), the oxygen vacancies are trapped into extended planar defects, specifically crystallographic shear planes. We investigate the evolution of these defects upon doping and unravel their detailed atomic structure using the formalism of superspace crystallography, thus unveiling their role in nonstoichiometry in the Pb-based perovskites. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Determining Orientational Structure of Diamondoid Thiols Attached to Silver Using Near Edge X-ray Absorption Fine Structure Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Willey, T M; Lee, J I; Fabbri, J D; Wang, D; Nielsen, M; Randel, J C; Schreiner, P R; Fokin, A A; Tkachenko, B A; Fokina, N A; Dahl, J P; Carlson, R K; Terminello, L J; Melosh, N A; van Buuren, T

    2008-10-07

    Near-edge x-ray absorption fine structure spectroscopy (NEXAFS) is a powerful tool for determination of molecular orientation in self-assembled monolayers and other surface-attached molecules. A general framework for using NEXAFS to simultaneously determine molecular tilt and twist of rigid molecules attached to surfaces is presented. This framework is applied to self-assembled monolayers of higher diamondoid, hydrocarbon molecules with cubic-diamond-cage structures. Diamondoid monolayers chemisorbed on metal substrates are known to exhibit interesting electronic and surface properties. This work compares molecular orientation in monolayers prepared on silver substrates using two different thiol positional isomers of [121]tetramantane, and thiols derived from two different pentamantane structural isomers, [1212]pentamantane and [1(2,3)4]pentamantane. The observed differences in monolayer structure demonstrate the utility and limitations of NEXAFS spectroscopy and the framework. The results also demonstrate the ability to control diamondoid assembly, in particular the molecular orientational structure, providing a flexible platform for the modification of surface properties with this exciting new class of nanodiamond materials.

  3. Improved in-cell structure determination of proteins at near-physiological concentration.

    Science.gov (United States)

    Ikeya, Teppei; Hanashima, Tomomi; Hosoya, Saori; Shimazaki, Manato; Ikeda, Shiro; Mishima, Masaki; Güntert, Peter; Ito, Yutaka

    2016-12-02

    Investigating three-dimensional (3D) structures of proteins in living cells by in-cell nuclear magnetic resonance (NMR) spectroscopy opens an avenue towards understanding the structural basis of their functions and physical properties under physiological conditions inside cells. In-cell NMR provides data at atomic resolution non-invasively, and has been used to detect protein-protein interactions, thermodynamics of protein stability, the behavior of intrinsically disordered proteins, etc. in cells. However, so far only a single de novo 3D protein structure could be determined based on data derived only from in-cell NMR. Here we introduce methods that enable in-cell NMR protein structure determination for a larger number of proteins at concentrations that approach physiological ones. The new methods comprise (1) advances in the processing of non-uniformly sampled NMR data, which reduces the measurement time for the intrinsically short-lived in-cell NMR samples, (2) automatic chemical shift assignment for obtaining an optimal resonance assignment, and (3) structure refinement with Bayesian inference, which makes it possible to calculate accurate 3D protein structures from sparse data sets of conformational restraints. As an example application we determined the structure of the B1 domain of protein G at about 250 μM concentration in living E. coli cells.

  4. Structure determination of helical filaments by solid-state NMR spectroscopy

    Science.gov (United States)

    Ahmed, Mumdooh; Spehr, Johannes; König, Renate; Lünsdorf, Heinrich; Rand, Ulfert; Lührs, Thorsten; Ritter, Christiane

    2016-01-01

    The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVSCARD filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers. PMID:26733681

  5. SFG analysis of surface bound proteins: a route towards structure determination.

    Science.gov (United States)

    Weidner, Tobias; Castner, David G

    2013-08-14

    The surface of a material is rapidly covered with proteins once that material is placed in a biological environment. The structure and function of these bound proteins play a key role in the interactions and communications of the material with the biological environment. Thus, it is crucial to gain a molecular level understanding of surface bound protein structure. While X-ray diffraction and solution phase NMR methods are well established for determining the structure of proteins in the crystalline or solution phase, there is not a corresponding single technique that can provide the same level of structural detail about proteins at surfaces or interfaces. However, recent advances in sum frequency generation (SFG) vibrational spectroscopy have significantly increased our ability to obtain structural information about surface bound proteins and peptides. A multi-technique approach of combining SFG with (1) protein engineering methods to selectively introduce mutations and isotopic labels, (2) other experimental methods such as time-of-flight secondary ion mass spectrometry (ToF-SIMS) and near edge X-ray absorption fine structure (NEXAFS) to provide complementary information, and (3) molecular dynamic (MD) simulations to extend the molecular level experimental results is a particularly promising route for structural characterization of surface bound proteins and peptides. By using model peptides and small proteins with well-defined structures, methods have been developed to determine the orientation of both backbone and side chains to the surface.

  6. Study of the relation between oxygen vacancies and ferromagnetism in Fe-doped TiO{sub 2} nano-powders

    Energy Technology Data Exchange (ETDEWEB)

    Mudarra Navarro, Azucena M.; Rodríguez Torres, Claudia E., E-mail: torres@fisica.unlp.edu.ar; Fabiana Cabrera, A. [Departamento de Física – Facultad de Ciencias Exactas, UNLP, Instituto de Física La Plata, CCT-La Plata, CONICET, CC 67, 1900 La Plata (Argentina); Bilovol, Vitaliy [Laboratorio de Sólidos Amorfos, INTECIN-CONICET, Facultad de Ingeniería, UBA, Av. Paseo Colón 850, Buenos Aires C1063ACV (Argentina); Errico, L. A. [Departamento de Física – Facultad de Ciencias Exactas, UNLP, Instituto de Física La Plata, CCT-La Plata, CONICET, CC 67, 1900 La Plata (Argentina); Universidad Nacional del Noroeste de la Pcia. de Buenos Aires (UNNOBA), Monteagudo 2772, Pergamino. CP 2700 Buenos Aires (Argentina); Weissmann, M. [Depto. de Física, Comisión Nacional de Energía Atómica, Av. del Libertador 8250, 1429 Buenos Aires (Argentina)

    2014-06-14

    In this work, we present an experimental and theoretical study of structural and magnetic properties of Fe doped rutile TiO{sub 2} nanopowders. We show that Fe-doping induces the formation of oxygen vacancies in the first-sphere coordination of iron ions, which are in +2 and +3 oxidation states. We found that Fe ions form dimers that share one oxygen vacancy in the case of Fe{sup 3+} and two oxygen vacancies in the case of Fe{sup 2+}. The saturation magnetization is almost independent of iron concentration and slightly increases with the relative fraction of Fe{sup 2+}. Ab initio calculations show that two Fe ions sharing an oxygen vacancy are coupled ferromagnetically, forming a bound magnetic polaron (BMP), but two neighbor BMPs are aligned antiparallel to each other. Extra electron doping plays a fundamental role mediating the magnetic coupling between the ferromagnetic entities: carriers, possibly concentrated at grain boundaries, mediate between the BMP to produce ferromagnetic alignment.

  7. Structure determination of contaminant proteins using the MarathonMR procedure.

    Science.gov (United States)

    Hatti, Kaushik; Biswas, Ansuman; Chaudhary, Santosh; Dadireddy, Venkatareddy; Sekar, Kanagaraj; Srinivasan, Narayanaswamy; Murthy, Mathur R N

    2017-03-01

    In the recent decades, essential steps of protein structure determination such as phasing by multiple isomorphous replacement and multi wave length anomalous dispersion, molecular replacement, refinement of the structure determined and its validation have been fully automated. Several computer program suites that execute all these steps as a pipeline operation have been made available. In spite of these great advances, determination of a protein structure may turn out to be a challenging task for a variety of reasons. It might be difficult to obtain multiple isomorphous replacement or multi wave length anomalous dispersion data or the crystal may have defects such as twinning or pseudo translation. Apart from these usual difficulties, more frequent difficulties have been encountered in recent years because of the large number of projects handled by structural biologists. These new difficulties usually result from contamination of the protein of interest by other proteins or presence of proteins from pathogenic organisms that could withstand the antibiotics used to prevent bacterial contamination. It could also be a result of poor book keeping. Recently, we have developed a procedure called MarathonMR that has the power to resolve some of these problems automatically. In this communication, we describe how the MarathonMR was used to determine four different protein structures that had remained elusive for several years. We describe the plausible reasons for the difficulties encountered in determining these structures and point out that the method presented here could be a validation tool for protein structures deposited in the protein data bank. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei

    Energy Technology Data Exchange (ETDEWEB)

    Begley, Darren W.; Hartley, Robert C.; Davies, Douglas R.; Edwards, Thomas E.; Leonard, Jess T.; Abendroth, Jan; Burris, Courtney A.; Bhandari, Janhavi; Myler, Peter J.; Staker, Bart L.; Stewart, Lance J. (UWASH); (Emerald)

    2011-09-28

    As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification of several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.

  9. Distributions of amino acids suggest that certain residue types more effectively determine protein secondary structure.

    Science.gov (United States)

    Saraswathi, S; Fernández-Martínez, J L; Koliński, A; Jernigan, R L; Kloczkowski, A

    2013-10-01

    Exponential growth in the number of available protein sequences is unmatched by the slower growth in the number of structures. As a result, the development of efficient and fast protein secondary structure prediction methods is essential for the broad comprehension of protein structures. Computational methods that can efficiently determine secondary structure can in turn facilitate protein tertiary structure prediction, since most methods rely initially on secondary structure predictions. Recently, we have developed a fast learning optimized prediction methodology (FLOPRED) for predicting protein secondary structure (Saraswathi et al. in JMM 18:4275, 2012). Data are generated by using knowledge-based potentials combined with structure information from the CATH database. A neural network-based extreme learning machine (ELM) and advanced particle swarm optimization (PSO) are used with this data to obtain better and faster convergence to more accurate secondary structure predicted results. A five-fold cross-validated testing accuracy of 83.8 % and a segment overlap (SOV) score of 78.3 % are obtained in this study. Secondary structure predictions and their accuracy are usually presented for three secondary structure elements: α-helix, β-strand and coil but rarely have the results been analyzed with respect to their constituent amino acids. In this paper, we use the results obtained with FLOPRED to provide detailed behaviors for different amino acid types in the secondary structure prediction. We investigate the influence of the composition, physico-chemical properties and position specific occurrence preferences of amino acids within secondary structure elements. In addition, we identify the correlation between these properties and prediction accuracy. The present detailed results suggest several important ways that secondary structure predictions can be improved in the future that might lead to improved protein design and engineering.

  10. Protein structure determination via an efficient geometric build-up algorithm

    Science.gov (United States)

    2010-01-01

    Background A protein structure can be determined by solving a so-called distance geometry problem whenever a set of inter-atomic distances is available and sufficient. However, the problem is intractable in general and has proved to be a NP hard problem. An updated geometric build-up algorithm (UGB) has been developed recently that controls numerical errors and is efficient in protein structure determination for cases where only sparse exact distance data is available. In this paper, the UGB method has been improved and revised with aims at solving distance geometry problems more efficiently and effectively. Methods An efficient algorithm (called the revised updated geometric build-up algorithm (RUGB)) to build up a protein structure from atomic distance data is presented and provides an effective way of determining a protein structure with sparse exact distance data. In the algorithm, the condition to determine an unpositioned atom iteratively is relaxed (when compared with the UGB algorithm) and data structure techniques are used to make the algorithm more efficient and effective. The algorithm is tested on a set of proteins selected randomly from the Protein Structure Database-PDB. Results We test a set of proteins selected randomly from the Protein Structure Database-PDB. We show that the numerical errors produced by the new RUGB algorithm are smaller when compared with the errors of the UGB algorithm and that the novel RUGB algorithm has a significantly smaller runtime than the UGB algorithm. Conclusions The RUGB algorithm relaxes the condition for updating and incorporates the data structure for accessing neighbours of an atom. The revisions result in an improvement over the UGB algorithm in two important areas: a reduction on the overall runtime and decrease of the numeric error. PMID:20487514

  11. Protein structure determination via an efficient geometric build-up algorithm.

    Science.gov (United States)

    Davis, Robert T; Ernst, Claus; Wu, Di

    2010-05-17

    A protein structure can be determined by solving a so-called distance geometry problem whenever a set of inter-atomic distances is available and sufficient. However, the problem is intractable in general and has proved to be a NP hard problem. An updated geometric build-up algorithm (UGB) has been developed recently that controls numerical errors and is efficient in protein structure determination for cases where only sparse exact distance data is available. In this paper, the UGB method has been improved and revised with aims at solving distance geometry problems more efficiently and effectively. An efficient algorithm (called the revised updated geometric build-up algorithm (RUGB)) to build up a protein structure from atomic distance data is presented and provides an effective way of determining a protein structure with sparse exact distance data. In the algorithm, the condition to determine an unpositioned atom iteratively is relaxed (when compared with the UGB algorithm) and data structure techniques are used to make the algorithm more efficient and effective. The algorithm is tested on a set of proteins selected randomly from the Protein Structure Database-PDB. We test a set of proteins selected randomly from the Protein Structure Database-PDB. We show that the numerical errors produced by the new RUGB algorithm are smaller when compared with the errors of the UGB algorithm and that the novel RUGB algorithm has a significantly smaller runtime than the UGB algorithm. The RUGB algorithm relaxes the condition for updating and incorporates the data structure for accessing neighbours of an atom. The revisions result in an improvement over the UGB algorithm in two important areas: a reduction on the overall runtime and decrease of the numeric error.

  12. Present and future of membrane protein structure determination by electron crystallography

    Science.gov (United States)

    Ubarretxena-Belandia, Iban; Stokes, David L.

    2011-01-01

    Membrane proteins are critical to cell physiology, playing roles in signaling, trafficking, transport, adhesion, and recognition. Despite their relative abundance in the proteome and their prevalence as targets of therapeutic drugs, structural information about membrane proteins is in short supply. This review describes the use of electron crystallography as a tool for determining membrane protein structures. Electron crystallography offers distinct advantages relative to the alternatives of X-ray crystallography and NMR spectroscopy. Namely, membrane proteins are placed in their native membranous environment, which is likely to favor a native conformation and allow changes in conformation in response to physiological ligands. Nevertheless, there are significant logistical challenges in finding appropriate conditions for inducing membrane proteins to form two-dimensional arrays within the membrane and in using electron cryo-microscopy to collect the data required for structure determination. A number of developments are described for high-throughput screening of crystallization trials and for automated imaging of crystals with the electron microscope. These tools are critical for exploring the necessary range of factors governing the crystallization process. There have also been recent software developments to facilitate the process of structure determination. However, further innovations in the algorithms used for processing images and electron diffraction are necessary to improve throughput and to make electron crystallography truly viable as a method for determining atomic structures of membrane proteins. PMID:21115172

  13. Structure determination of an integral membrane protein at room temperature from crystals in situ

    Energy Technology Data Exchange (ETDEWEB)

    Axford, Danny [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Foadi, James [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Hu, Nien-Jen; Choudhury, Hassanul Ghani [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom); Iwata, So [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom); Kyoto University, Kyoto 606-8501 (Japan); Beis, Konstantinos [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Alguel, Yilmaz, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom)

    2015-05-14

    The X-ray structure determination of an integral membrane protein using synchrotron diffraction data measured in situ at room temperature is demonstrated. The structure determination of an integral membrane protein using synchrotron X-ray diffraction data collected at room temperature directly in vapour-diffusion crystallization plates (in situ) is demonstrated. Exposing the crystals in situ eliminates manual sample handling and, since it is performed at room temperature, removes the complication of cryoprotection and potential structural anomalies induced by sample cryocooling. Essential to the method is the ability to limit radiation damage by recording a small amount of data per sample from many samples and subsequently assembling the resulting data sets using specialized software. The validity of this procedure is established by the structure determination of Haemophilus influenza TehA at 2.3 Å resolution. The method presented offers an effective protocol for the fast and efficient determination of membrane-protein structures at room temperature using third-generation synchrotron beamlines.

  14. Structure of Green River oil shale kerogen: determination using solid state /sup 13/C NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Trewhella, M.J.; Poplett, I.J.F.; Grint, A.

    1986-04-01

    A sample of kerogen isolated from a Green River oil shale has been examined using high resolution solid state /sup 13/C NMR spectroscopy. The relative concentrations of carbon types have been determined using a novel peak-synthesis technique applied to the /sup 13/C spectra. This technique has been successfully applied in determining the amount and type of individual carbon atoms in a sample of Green River oil shale kerogen, with sufficient resolution to enable an average structure to be proposed. The kerogen is highly aliphatic and appears to contain substantial quantities of both saturated polycondensed ring structures, and long chain n-alkanes or n-alkyl substituents. 20 references.

  15. DETERMINANTS OF CAPITAL STRUCTURE OF CROATIAN ENTERPRISES BEFORE AND DURING THE FINANCIAL CRISIS

    Directory of Open Access Journals (Sweden)

    Ena Mostarac

    2013-06-01

    Full Text Available This paper analysis capital structure determinants of Croatian enterprises based on a cross-sectional data for pre-recession 2007 and recession 2010 comprising about 10,000 firms. Determinants are selected with reference to the relevant capital structure theories and include asset tangibility, profitability, firm size and business risk. The results indicate highly positive significant impact of tangibility and negative significant impact of profitability on financial leverage in both observed years. Firm size seems to be statistically significant at higher level in crisis period, but at the same time no relationship can be found between business risk and financial leverage that is of economic significance.

  16. Exploration and analysis of the structural and intermediate social determinants of the HIV/AIDS pandemic

    Directory of Open Access Journals (Sweden)

    Yesica Daniela Liscano Pinzón

    2015-08-01

    Full Text Available Understanding distribution, epidemiology and the Social Determinants of Health related with HIV/AIDS are the basis on which we must work to achieve full containment of the epidemic in taking preventive measures such as clinical measures implemented for this purpose. Objective: To analyse intermediate and structural social determinants related to the HIV / AIDS reported in the national and international literature in the period 1993-2013. Material and methods: This research is hermeneutic, was developed in three phases: 1 Literature search and classification results. 2 Revision 3 Analysis of this literature with subsequent preparation of the final report. Results: met inclusion criteria 119 items. Eighty-four were for structural studies of determinants, 33 related to socioeconomic status, gender 25 and 26 with other structural determinants. Thirty-five were for intermediate DDS, 22 related to the conduct and 13 with the material conditions of life. Discussion: the structural determinants (gender and socioeconomic status are those with a high probability of exercising greater constraint on the behaviour of HIV, and therefore require considerable efforts in this field to combat the pandemic. 

  17. Blind testing of routine, fully automated determination of protein structures from NMR data.

    Science.gov (United States)

    Rosato, Antonio; Aramini, James M; Arrowsmith, Cheryl; Bagaria, Anurag; Baker, David; Cavalli, Andrea; Doreleijers, Jurgen F; Eletsky, Alexander; Giachetti, Andrea; Guerry, Paul; Gutmanas, Aleksandras; Güntert, Peter; He, Yunfen; Herrmann, Torsten; Huang, Yuanpeng J; Jaravine, Victor; Jonker, Hendrik R A; Kennedy, Michael A; Lange, Oliver F; Liu, Gaohua; Malliavin, Thérèse E; Mani, Rajeswari; Mao, Binchen; Montelione, Gaetano T; Nilges, Michael; Rossi, Paolo; van der Schot, Gijs; Schwalbe, Harald; Szyperski, Thomas A; Vendruscolo, Michele; Vernon, Robert; Vranken, Wim F; Vries, Sjoerd de; Vuister, Geerten W; Wu, Bin; Yang, Yunhuang; Bonvin, Alexandre M J J

    2012-02-08

    The protocols currently used for protein structure determination by nuclear magnetic resonance (NMR) depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by using a specific computer program. To assess whether it is indeed possible to generate in a fully automated manner NMR structures adequate for deposition in the Protein Data Bank, we gathered 10 experimental data sets with unassigned nuclear Overhauser effect spectroscopy (NOESY) peak lists for various proteins of unknown structure, computed structures for each of them using different, fully automatic programs, and compared the results to each other and to the manually solved reference structures that were not available at the time the data were provided. This constitutes a stringent "blind" assessment similar to the CASP and CAPRI initiatives. This study demonstrates the feasibility of routine, fully automated protein structure determination by NMR. Copyright © 2012 Elsevier Ltd. All rights reserved.

  18. Role of oxygen vacancies for resistive switching in noble metal sandwiched Pr0.67Ca0.33MnO3-δ

    Science.gov (United States)

    Kramer, Thilo; Scherff, Malte; Mierwaldt, Daniel; Hoffmann, Joerg; Jooss, Christian

    2017-06-01

    Non-volatile resistance change under electric stimulation in oxides is a promising path to next generation memory devices. However, the underlying mechanisms are still not fully understood. We report here on the study of switching in Pr0.67Ca0.33MnO3-δ (PCMO) films sandwiched by noble metal Pt electrodes, where electrode oxidation can be excluded. In order to develop an understanding of the switching induced oxygen migration, its initial concentration is modified by post-annealing of the deposited PCMO films. The oxygen distribution is obtained by manganese valence determination using spatially resolved electron energy loss spectroscopy in scanning transmission electron microscopy mode. We observe correlations between virgin state resistance, resistive switching properties, oxygen vacancy distribution, and stress/strain state of the PCMO films and propose a simplified interface resistance model based on the measured valence distribution. It assumes a linear correlation of oxygen vacancy concentration with conductivity and a metal to insulator transition above a critical vacancy concentration threshold. Our results suggest that resistance changes can take place at both interfaces of symmetric devices and only requires small changes in oxygen vacancy concentration.

  19. Direct methods determination of the Si(111)-(6x6)Au surface structure

    DEFF Research Database (Denmark)

    Grozea, D.; Landree, E.; Marks, L.D.

    1998-01-01

    The atomic structure of the Au 6 x 6 on Si(111) phase has been determined using direct methods and surface X-ray diffraction data. This surface structure is very complicated, with 14 independent gold atoms, relaxations in 24 independent silicon sites and three partially occupied gold sites. In one...... the gold structures in the coverage range 0.8-1.5 monolayers as pseudo-glasses with strong short-range order but varying degrees of long-range order. (C) 1998 Elsevier Science B.V. All rights reserved....

  20. Structure determination of isolated metal clusters via far-infrared spectroscopy.

    Science.gov (United States)

    Fielicke, André; Kirilyuk, Andrei; Ratsch, Christian; Behler, Jörg; Scheffler, Matthias; von Helden, Gert; Meijer, Gerard

    2004-07-09

    We present a new method for the size selective structure determination of small isolated metal clusters in the gas phase. The technique is applied to cationic vanadium clusters containing 6 to 23 atoms, whose far infrared absorption spectra are measured in the 140-450 cm(-1) spectral range. The spectra are unique for each cluster size and are true fingerprints of the cluster's structure. By comparing the experimental spectra to spectra obtained from density-functional theory, the geometric cluster structure can be identified.

  1. Ownership and Determinants Capital Structure of Public Listed Companies in Indonesia: a Panel Data Analysis

    Directory of Open Access Journals (Sweden)

    Arief Tri Hardiyanto

    2013-04-01

    Full Text Available Capital structure is a mix of debts and equities used by a company to finance its investment. Debt offers benefit of tax shield from interest expenses that can be deducted in calculating company income tax. Unfortunately, company can not use debts in unlimited amount because it will lead to risk of bankcrupt. Therefore, company needs to establish a target (unobserved capital structure which will optimize the value of the firm. The purpose of this study is to investigate the determinant of capital structure and ownership in public listed companies in Indonesia Stock Exchange using Time-Series CrossSection Regression (TSCSREG and supported with a balanced panel data. Data used are financial statements of 228 public listed companies from group of eight industry sectors. Research finding confirms that tax shield and fixed financial burden are significantly influence the capital structure and state ownership also significantly influence the capital structure of the state owned enterprises.

  2. Determination of crystallographic and macroscopic orientation of planar structures in TEM

    DEFF Research Database (Denmark)

    Huang, X.; Liu, Q.

    1998-01-01

    With the aid of a double-tilt holder in a transmission electron microscope (TEM), simple methods are described for determination of the crystallographic orientation of a planar structure and for calculation of the macroscopic orientation of the planar structure. The correlation between a planar...... structure and a crystallographic plane can be found by comparing the differences in their trace directions on the projection plane and inclination angles with respect to that plane. The angles between the traces of planar structures and the sample axis measured from the TEM micrographs, which have been...... taken at tilted positions, can be transformed to the real macroscopic orientation of the planar structures with estimated error of about +/- 2 degrees. (C) 1998 Elsevier Science B.V. All rights reserved....

  3. Magic angle spinning NMR structure determination of proteins from pseudocontact shifts.

    Science.gov (United States)

    Li, Jianping; Pilla, Kala Bharath; Li, Qingfeng; Zhang, Zhengfeng; Su, Xuncheng; Huber, Thomas; Yang, Jun

    2013-06-05

    Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure.

  4. Internal positron source production with a cyclotron and vacancy study in silicon

    Energy Technology Data Exchange (ETDEWEB)

    Kawasuso, Atsuo; Masuno, Shin-ichi; Okada, Sohei [Japan Atomic Energy Research Inst., Takasaki, Gunma (Japan). Takasaki Radiation Chemistry Research Establishment; Hasegawa, Masayuki; Suezawa, Masashi

    1997-03-01

    In order to detect thermal vacancies in Si, in situ positron annihilation measurement has been performed using an internal source method. An increase (decrease) in S-parameter (W-parameter) was observed above 1200degC. It was explained in terms of the formation of thermal vacancies. (author)

  5. 24 CFR 891.650 - Conditions for receipt of vacancy payments for assisted units.

    Science.gov (United States)

    2010-04-01

    ... HOUSING FOR PERSONS WITH DISABILITIES PROGRAM) SUPPORTIVE HOUSING FOR THE ELDERLY AND PERSONS WITH DISABILITIES Loans for Housing for the Elderly and Persons with Disabilities Section 202 Projects for the... contract, or any applicable law; (2) Notified HUD of the vacancy or prospective vacancy and the reasons for...

  6. 24 CFR 891.445 - Conditions for receipt of vacancy payments for assisted units.

    Science.gov (United States)

    2010-04-01

    ... HOUSING FOR PERSONS WITH DISABILITIES PROGRAM) SUPPORTIVE HOUSING FOR THE ELDERLY AND PERSONS WITH DISABILITIES Project Management § 891.445 Conditions for receipt of vacancy payments for assisted units. (a... cause the vacancy by violating the lease, the PRAC, or any applicable law; (2) Notified HUD of the...

  7. 24 CFR 891.790 - Conditions for receipt of vacancy payments for assisted units.

    Science.gov (United States)

    2010-04-01

    ... HOUSING FOR PERSONS WITH DISABILITIES PROGRAM) SUPPORTIVE HOUSING FOR THE ELDERLY AND PERSONS WITH DISABILITIES Loans for Housing for the Elderly and Persons with Disabilities Section 202 Projects for the... violating the lease, the PAC, or any applicable law; (2) Notified HUD of the vacancy or prospective vacancy...

  8. Ab initio prediction of vacancy properties in concentrated alloys : The case of fcc Cu-Ni

    NARCIS (Netherlands)

    Zhang, X.; Sluiter, M.H.F.

    2015-01-01

    Vacancy properties in concentrated alloys continue to be of great interest because nowadays ab initio supercell simulations reach a scale where even defect properties in disordered alloys appear to be within reach. We show that vacancy properties cannot generally be extracted from supercell total

  9. Nanodiamonds carrying silicon-vacancy quantum emitters with almost lifetime-limited linewidths

    DEFF Research Database (Denmark)

    Jantzen, Uwe; Kurz, Andrea B.; Rudnicki, Daniel S.

    2016-01-01

    the negatively charged silicon vacancy centre, which has recently received considerable attention due to its superb optical properties in bulk diamond. We have measured an ensemble of silicon-vacancy centres across numerous nanodiamonds to have an inhomogeneous distribution of 1.05 nmat 5 K. Individual spectral...

  10. Disentangling the role of small polarons and oxygen vacancies in Ce O2

    Science.gov (United States)

    Sun, Lu; Huang, Xiaowei; Wang, Ligen; Janotti, Anderson

    2017-06-01

    The outstanding performance of cerium oxide (Ce O2) as ion conductor or catalyst strongly depends on the ease of C e4 +↔C e3 + conversion and oxygen vacancy formation. An accurate description of C e3 + and oxygen vacancy is therefore essential to further progress in this area. Using the HSE06 hybrid functional, we investigate the formation and migration of small polarons (C e3 +) and their interaction with oxygen vacancies in Ce O2 , considering the small polaron and vacancy as independent entities. Oxygen vacancies are double donors and can bind up to two small polarons, forming a positively charged or neutral complex. We compute the electron self-trapping energy (i.e., energy gain when forming a small polaron), the small-polaron migration barrier, vacancy formation and migration energies, and vacancy-polaron binding energies. We find that small polarons weakly bind to oxygen vacancies, yet this interaction significantly contributes to the activation energy for hopping electronic conductivity. The results are compared with previous calculations and discussed in the light of available experimental data.

  11. Effect of vacancy on shopping centres'investment returns in Akure ...

    African Journals Online (AJOL)

    The paper examined the effect of vacancy rate on the rental returns of shopping centres in six major retail areas in Akure. Data on rental values and vacancy rates in 35 shopping centres were collected from 17 estate surveying firms in Akure. The shopping centres had a total number of 1,352 rentable spaces with 1,183 ...

  12. Workshop on Measurement Needs for Local-Structure Determination in Inorganic Materials.

    Science.gov (United States)

    Levin, Igor; Vanderah, Terrell

    2008-01-01

    The functional responses (e.g., dielectric, magnetic, catalytic, etc.) of many industrially-relevant materials are controlled by their local structure-a term that refers to the atomic arrangements on a scale ranging from atomic (sub-nanometer) to several nanometers. Thus, accurate knowledge of local structure is central to understanding the properties of nanostructured materials, thereby placing the problem of determining atomic positions on the nanoscale-the so-called "nanostructure problem"-at the center of modern materials development. Today, multiple experimental techniques exist for probing local atomic arrangements; nonetheless, finding accurate comprehensive, and robust structural solutions for the nanostructured materials still remains a formidable challenge because any one of these methods yields only a partial view of the local structure. The primary goal of this 2-day NIST-sponsored workshop was to bring together experts in the key experimental and theoretical areas relevant to local-structure determination to devise a strategy for the collaborative effort required to develop a comprehensive measurement solution on the local scale. The participants unanimously agreed that solving the nanostructure problem-an ultimate frontier in materials characterization-necessitates a coordinated interdisciplinary effort that transcends the existing capabilities of any single institution, including national laboratories, centers, and user facilities. The discussions converged on an institute dedicated to local structure determination as the most viable organizational platform for successfully addressing the nanostructure problem. The proposed "institute" would provide an intellectual infrastructure for local structure determination by (1) developing and maintaining relevant computer software integrated in an open-source global optimization framework (Fig. 2), (2) connecting industrial and academic users with experts in measurement techniques, (3) developing and

  13. Oxygen vacancy and dilute ferromagnetism of ZnGa2O4 doped with Co at the octahedral site

    Directory of Open Access Journals (Sweden)

    Ikuo Nakai

    2016-05-01

    Full Text Available We report magnetism and structure of a diluted magnetic semiconductor Zn[Ga0.97Co0.03]2O4 preferentially doped with Co ions in the octahedral site of zinc gallate ZnGa2O4. Zn[Ga0.97Co0.03]2O4 has a small ferromagnetic component superimposed on a large paramagnetic contribution to the magnetization at room temperature, whereas ZnGa2O4 is diamagnetic. The X-ray powder diffraction confirms that both ZnGa2O4 and Zn[Ga0.97Co0.03]2O4 have a normal spinel structure (space group Fd-3m without any impurity phases. From X-ray absorption fine structure measurements we find the following features in Zn[Ga0.97Co0.03]2O4; all of the Co dopants occupy the octahedral site, about half of which are divalent; around the Co cations there exist the oxygen vacancies and the local distortion of shrink in pair distance, while the local structure around Zn and Ga ions coincides with that expected from the X-ray diffraction. These features suggest that the local disorder including oxygen vacancies and distortions only around Co ions plays an important role in stabilizing the ferromagnetic order between some Co ions in Zn[Ga0.97Co0.03]2O4.

  14. Oxygen vacancy and dilute ferromagnetism of ZnGa2O4 doped with Co at the octahedral site

    Science.gov (United States)

    Nakai, Ikuo; Hisamatsu, Ryouhei; Li, Yingjie; Kurisu, Makio

    2016-05-01

    We report magnetism and structure of a diluted magnetic semiconductor Zn[Ga0.97Co0.03]2O4 preferentially doped with Co ions in the octahedral site of zinc gallate ZnGa2O4. Zn[Ga0.97Co0.03]2O4 has a small ferromagnetic component superimposed on a large paramagnetic contribution to the magnetization at room temperature, whereas ZnGa2O4 is diamagnetic. The X-ray powder diffraction confirms that both ZnGa2O4 and Zn[Ga0.97Co0.03]2O4 have a normal spinel structure (space group Fd-3m) without any impurity phases. From X-ray absorption fine structure measurements we find the following features in Zn[Ga0.97Co0.03]2O4; all of the Co dopants occupy the octahedral site, about half of which are divalent; around the Co cations there exist the oxygen vacancies and the local distortion of shrink in pair distance, while the local structure around Zn and Ga ions coincides with that expected from the X-ray diffraction. These features suggest that the local disorder including oxygen vacancies and distortions only around Co ions plays an important role in stabilizing the ferromagnetic order between some Co ions in Zn[Ga0.97Co0.03]2O4.

  15. Size and edge roughness dependence of thermal conductivity for vacancy-defective graphene ribbons.

    Science.gov (United States)

    Xie, Guofeng; Shen, Yulu

    2015-04-14

    By incorporating the phonon-phonon scattering, phonon-boundary scattering and phonon-vacancy scattering into the linearized Boltzmann transport equation, we theoretically investigate the effects of size and edge roughness on thermal conductivity of single vacancy-defective graphene ribbons. Due to the severe suppression of high-frequency phonons by phonon-vacancy scattering which includes the impacts of missing mass and linkages, as well as the variation of the force constant of bonds associated with vacancies, the low-frequency ballistic phonons have a higher contribution to the thermal conductivity, which results in the stronger length, weaker width and weaker edge roughness dependence on thermal conductivity of vacancy-defective graphene ribbons than that of pristine ones. Our findings are helpful to understand and manipulate thermal conductivity of graphene by phononic engineering.

  16. Doping dependence of self-diffusion in germanium and the charge states of vacancies

    DEFF Research Database (Denmark)

    Südkamp, T.; Bracht, H.; Impellizzeri, G.

    2013-01-01

    Self-diffusion in boron-doped germanium has been studied at temperatures between 526 and 749 °C with secondary ion mass spectrometry. Self-diffusion under acceptor doping is retarded compared to intrinsic conditions. This demonstrates the contribution of charged vacancies in self-diffusion. Taking...... into account the dominance of doubly negatively charged vacancies under donor doping, the doping dependence of self-diffusion is best described with an inverse level ordering for singly and doubly negatively charged vacancies for all doping conditions. The level ordering explains the dominance of doubly...... charged vacancies under donor doping and their decreasing contribution with increasing acceptor doping until neutral vacancies mediate self-diffusion...

  17. Effect of atomic vacancies on ionic polarization of nonstoichiometric strontium titanate ceramics

    Science.gov (United States)

    Sase, Ryuichi; Hoshina, Takuya; Takeda, Hiroaki; Tsurumi, Takaaki

    2017-10-01

    We prepared nonstoichiometric strontium titanate with different Sr/Ti atomic ratios and measured the THz dielectric spectra to discuss the effect of atomic vacancies on the ionic polarization. In the presence of atomic vacancies in strontium titanate, the lattice volume increased and the dielectric permittivity decreased. The expansion of the lattice volume originated from repulsion between oxygen vacancies and cations or between cation vacancies and O ions, causing the reduction in the covalency of the Ti-O bond. In addition, THz dielectric spectra and first-principles calculation revealed that the reduction of permittivity is mainly explained by the hardening of the Slater-type phonon mode. In the presence of oxygen- and titanium-vacancies, the repulsion of the Ti-O bond increased, and then the ionic polarization due to the Slater mode decreased.

  18. Distortion-induced scattering due to vacancies in NbC/sub 0. 72/

    Energy Technology Data Exchange (ETDEWEB)

    Ohshima, K.; Harada, J.; Morinaga, M.; Georgopoulos, P.; Cohen, J.B.

    1988-03-01

    The diffuse X-ray (and electron) scattering from NbC/sub 0.72/, previously thought to be due to vacancy octahedra, is shown to be dominated by the scattering due to mean-square atomic displacements with wave vectors near the Brillouin-zone boundary. The atomic displacements are similar to those produced by an optical phonon. On the basis of the sign and amplitude of the displacement parameters a model for the environment around a carbon vacancy is proposed. The Nb nearest neighbors to a vacancy move away from it, whereas the C neighbors move toward it, and this appears to be due to an enhancement of the strength of the Nb-C bond arising from the presence of vacancies on the C sublattice. There is evidence that these vacancies tend to be correlated along 211 vectors.

  19. Fortuitous structure determination of 'as-isolated' Escherichia coli bacterioferritin in a novel crystal form

    NARCIS (Netherlands)

    van Eerde, Andre; Wolterink-van Loo, Suzanne; van der Oost, John; Dijkstra, Bauke W.

    2006-01-01

    Escherichia coli bacterioferritin was serendipitously crystallized in a novel cubic crystal form and its structure could be determined to 2.5 angstrom resolution despite a high degree of merohedral twinning. This is the first report of crystallographic data on `as-isolated' E. coli bacterioferritin.

  20. The Internal Structure of "Chaos": Letter Category Determines Visual Word Perceptual Units

    Science.gov (United States)

    Chetail, Fabienne; Content, Alain

    2012-01-01

    The processes and the cues determining the orthographic structure of polysyllabic words remain far from clear. In the present study, we investigated the role of letter category (consonant vs. vowels) in the perceptual organization of letter strings. In the syllabic counting task, participants were presented with written words matched for the…

  1. Determinants of Regional Female Labour Market Participation in the Netherlands : A Spatial Structural Equation Modeling Approach

    NARCIS (Netherlands)

    Liu, An; Noback, Inge

    2011-01-01

    The paper analyses the determinants of female labour participation. Structural equation modelling is used to handle theoretical concepts and to solve the typical problem of multicollinearity. The proposed methodology is applied to a dataset for the year 2002 made up of a sample of 278 municipalities

  2. Synthesis and crystal structure determination of YCo1−xFexO3 (x ...

    Indian Academy of Sciences (India)

    Abstract. The results on synthesis, crystal structure determination and calculation of crystallochemical parameters of YCo1−x. FexO3 (x = 0, 0.33, 0.5, 0.67 and 1) perovskites are presented in this work. The com- pounds within this series were synthesized by solution combustion method using two different fuels: urea and.

  3. NMR chemical shift data and ab initio shielding calculations : emerging tools for protein structure determination

    NARCIS (Netherlands)

    Mulder, Frans A. A.; Filatov, Michael

    2010-01-01

    In this tutorial review, we discuss the utilization of chemical shift information as well as ab initio calculations of nuclear shieldings for protein structure determination. Both the empirical and computational aspects of the chemical shift are reviewed and the role of molecular dynamics and the

  4. Structure determination of two metal-organic complexes from high-resolution synchotron powder diffraction dztz

    NARCIS (Netherlands)

    Dova, E.; Goubitz, K.; van Langevelde, A.; Driessen, R.; Mahabiersing, T.; Blaauw, R.; Peschar, R.; Schenk, H.

    2001-01-01

    The crystal structures of [1,2-bis(2,6-diisopropylphenylimino)acenaphthene-N,N′] carbonylchlororhodium(I) (1) and [N,N′-ethylene-nis(3-methylsalicylideneiminato)-O, N, N′, O′](tetrahydrofurfuryl)-cobalt(II) (2) have been determined from high-resolution synchrotron X-ray powder diffraction data.

  5. The determination of the in situ structure by nuclear spin contrast variation

    Energy Technology Data Exchange (ETDEWEB)

    Stuhrmann, H.B. [GKSS Forschungszentrum, Geesthacht (Germany); Nierhaus, K.H. [Max-Planch-Institut fuer Molekulare Genetik, Berlin (Germany)

    1994-12-31

    Polarized neutron scattering from polarized nuclear spins in hydrogenous substances opens a new way of contrast variation. The enhanced contrast due to proton spin polarization was used for the in situ structure determination of tRNA of the functional complex of the E.coli ribosome.

  6. Determining certain geometrical characteristics of metallic engineering structures based on their shift resistance

    Energy Technology Data Exchange (ETDEWEB)

    Kvyatkovskiy, G.I.; Babyuk, I.S.; Bondarev, V.I.; Kirillov, S.A.; Kuzmenko, E.D.

    1983-01-01

    The possibility of determining the depth of submersion in the earth of metallic engineering structures based on their shift resistance is justified. The theoretical curves for real time solution of the problem based on data from field electrical measurements are shown.

  7. Invisible detergents for structure determination of membrane proteins by small-angle neutron scattering

    DEFF Research Database (Denmark)

    Midtgaard, Søren Roi; Darwish, Tamim A.; Pedersen, Martin Cramer

    2018-01-01

    A novel and generally applicable method for determining structures of membrane proteins in solution via small-angle neutron scattering (SANS) is presented. Common detergents for solubilizing membrane proteins were synthesized in isotope-substituted versions for utilizing the intrinsic neutron sca...

  8. Instruction in text-structure as a determinant of senior secondary ...

    African Journals Online (AJOL)

    The study determined the effectiveness of instruction in text-structure on achievement of students in English narrative text. The pretest-posttest control group quasi experimental design was adopted for the study. The participants were 120 students in intact classes from four purposively selected senior secondary schools in ...

  9. Synthesis and crystal structure determination of YCo Fe O 3 (= 0 ...

    Indian Academy of Sciences (India)

    The results on synthesis, crystal structure determination and calculation of crystallochemical parameters of YCo1−FeO3 ( = 0, 0.33, 0.5, 0.67 and 1) perovskites are presented in this work. The compounds within this series were synthesized by solution combustion method using two different fuels: urea and citric acid.

  10. Synthesis and crystal structure determination of Br2SeIBr ...

    Indian Academy of Sciences (India)

    Unknown

    Indian Academy of Sciences. 223. Synthesis and crystal structure determination of Br2SeIBr polyhalogen–chalcogen. A A ALEMI* and E SOLAIMANI†. Department of Inorganic Chemistry, Faculty of Chemistry, University of Tabriz, Iran. †Department of Chemistry, Faculty of Science, University of Shahrood, Shahrood, Iran.

  11. Requirements on paramagnetic relaxation enhancement data for membrane protein structure determination by NMR.

    Science.gov (United States)

    Gottstein, Daniel; Reckel, Sina; Dötsch, Volker; Güntert, Peter

    2012-06-06

    Nuclear magnetic resonance (NMR) structure calculations of the α-helical integral membrane proteins DsbB, GlpG, and halorhodopsin show that distance restraints from paramagnetic relaxation enhancement (PRE) can provide sufficient structural information to determine their structure with an accuracy of about 1.5 Å in the absence of other long-range conformational restraints. Our systematic study with simulated NMR data shows that about one spin label per transmembrane helix is necessary for obtaining enough PRE distance restraints to exclude wrong topologies, such as pseudo mirror images, if only limited other NMR restraints are available. Consequently, an experimentally realistic amount of PRE data enables α-helical membrane protein structure determinations that would not be feasible with the very limited amount of conventional NOESY data normally available for these systems. These findings are in line with our recent first de novo NMR structure determination of a heptahelical integral membrane protein, proteorhodopsin, that relied extensively on PRE data. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

    Science.gov (United States)

    Fernandez-Chamorro, Javier; Lozano, Gloria; Garcia-Martin, Juan Antonio; Ramajo, Jorge; Dotu, Ivan; Clote, Peter; Martinez-Salas, Encarnacion

    2016-04-01

    The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.

  13. Ab initio modeling of vacancies, antisites, and Si dopants in ordered InGaAs

    Science.gov (United States)

    Wang, Jingyang; Lukose, Binit; Thompson, Michael O.; Clancy, Paulette

    2017-01-01

    In0.53Ga0.47As, a III-V compound semiconductor with high electron mobility, is expected to bring better performance than silicon in next-generation n-type MOSFET devices. However, one major challenge to its wide scale adoption is the difficulty of obtaining high enough dopant activation. For Si-doped InGaAs, the best current experimental result, involving 10 min of furnace annealing at temperatures above 700 °C, yields a free electron concentration of 1.4 ×1019 cm-3, a value that still falls short of requirement for practical applications. In this paper, we investigate the origin of low dopant activation in InGaAs by calculating formation energies for a wide variety of single point defects (Si substutionals, Si tetrahedral interstitials, vacancies, and antisites) in Si-doped In0.5Ga0.5As in a CuAu-I type crystal structure. We find that (1) a high electron concentration can only be achieved under In/Ga-poor growth conditions, while As-poor conditions inhibit n-type doping; and (2) in heavily n-doped samples, cation vacancies VIn/Ga-3 contribute the most to the compensation of excess Si donors via the Si III - VIII mechanism (III = In/Ga), thus becoming the limiting factor to higher dopant activation. Under the most favorable growth conditions for n-doping, we find the maximum carrier concentration to be 5.2 ×1018 cm-3 under thermal equilibrium, within an order of magnitude of the best experimental value.

  14. Topochemical Nitridation with Anion Vacancy-Assisted N(3-)/O(2-) Exchange.

    Science.gov (United States)

    Mikita, Riho; Aharen, Tomoko; Yamamoto, Takafumi; Takeiri, Fumitaka; Ya, Tang; Yoshimune, Wataru; Fujita, Koji; Yoshida, Suguru; Tanaka, Katsuhisa; Batuk, Dmitry; Abakumov, Artem M; Brown, Craig M; Kobayashi, Yoji; Kageyama, Hiroshi

    2016-03-09

    We present how the introduction of anion vacancies in oxyhydrides enables a route to access new oxynitrides, by conducting ammonolysis of perovskite oxyhydride EuTiO3-xHx (x ∼ 0.18). At 400 °C, similar to our studies on BaTiO3-xHx, hydride lability enables a low temperature direct ammonolysis of EuTi(3.82+)O2.82H0.18, leading to the N(3-)/H(-)-exchanged product EuTi(4+)O2.82N0.12□0.06. When the ammonolysis temperature was increased up to 800 °C, we observed a further nitridation involving N(3-)/O(2-) exchange, yielding a fully oxidized Eu(3+)Ti(4+)O2N with the GdFeO3-type distortion (Pnma) as a metastable phase, instead of pyrochlore structure. Interestingly, the same reactions using the oxide EuTiO3 proceeded through a 1:1 exchange of N(3-) with O(2-) only above 600 °C and resulted in incomplete nitridation to EuTiO2.25N0.75, indicating that anion vacancies created during the initial nitridation process of EuTiO2.82H0.18 play a crucial role in promoting anion (N(3-)/O(2-)) exchange at high temperatures. Hence, by using (hydride-induced) anion-deficient precursors, we should be able to expand the accessible anion composition of perovskite oxynitrides.

  15. The role of high oxygen vacancy concentration on modification of surface properties and H2S adsorption on the rutile TiO2 (110)

    Science.gov (United States)

    Wei, Shiqian; Wang, Fang; Dan, Meng; Zeng, Kaiyue; Zhou, Ying

    2017-11-01

    In this work, spin-polarized DFT + U method has been employed to investigate adsorption properties of H2S on the rutile TiO2 (110) surface with a high coverage of bridging oxygen vacancies (BOVs). The influence of different BOV coverage (θ-BOVs) on the surface electronic structure is examined. Defected states increase within the band gap with θ-BOVs increasing from 1/8 to 4/8 monolayer (ML). The high defected surface with θ-BOVs = 4/8 ML is determined to have a desired band structure and noticeable visible light response. In addition, H2S adsorption behaviors are noticeably affected by different H2S coverage (θ-H2S). Particularly, it is found molecular adsorption at θ-H2S ≤ 1/8 ML and dissociative adsorption at the higher θ-H2S. The maximization of spontaneous dissociation of H2S can be realized when the BOVs are all covered by H2S molecules. This work gains mechanistic insights into BOVs in tuning the surface properties and provides a guide for the effective utilization of the active surface sites on the rutile TiO2 (110) in the field of H2S splitting.

  16. High-Resolution Macromolecular Structure Determination by MicroED, a cryo-EM Method

    Science.gov (United States)

    Rodriguez, J.A.; Gonen, T.

    2017-01-01

    Microelectron diffraction (MicroED) is a new cryo-electron microscopy (cryo-EM) method capable of determining macromolecular structures at atomic resolution from vanishingly small 3D crystals. MicroED promises to solve atomic resolution structures from even the tiniest of crystals, less than a few hundred nanometers thick. MicroED complements frontier advances in crystallography and represents part of the rebirth of cryo-EM that is making macromolecular structure determination more accessible for all. Here we review the concept and practice of MicroED, for both the electron microscopist and crystallographer. Where other reviews have addressed specific details of the technique (Hattne et al., 2015; Shi et al., 2016; Shi, Nannenga, Iadanza, & Gonen, 2013), we aim to provide context and highlight important features that should be considered when performing a MicroED experiment. PMID:27572734

  17. Determination and structural elucidation of triacylglycerols in krill oil by chromatographic techniques.

    Science.gov (United States)

    Araujo, Pedro; Zhu, Han; Breivik, Joar Fjørtoft; Hjelle, Jan Idar; Zeng, Yingxu

    2014-02-01

    The content of triacylglycerols (TAG) in krill oil is generally omitted from the labels of commercial supplements and unacknowledged in studies aimed at proving its health benefits. The present study demonstrates that TAG compounds, in addition to phospholipids and lysophospholipids, are an important lipid class in pure krill oil. The fatty acid composition of TAG molecules from krill oil and their distribution on the backbone of TAG structures were determined by gas chromatography and liquid chromatography tandem mass spectrometric, respectively. The content of omega 3 polyunsaturated fatty acids (n-3 PUFA) was similar to those reported in the literature for fish oil. It was estimated that 21 % of n-3 PUFA were at the sn-2 position of TAG structures. To our knowledge, this is the first determination and structural characterization of TAG in pure krill oil supplements.

  18. Annihilating vacancies via dynamic reflection and emission of interstitials in nano-crystal tungsten

    Science.gov (United States)

    Li, Xiangyan; Duan, Guohua; Xu, Yichun; Zhang, Yange; Liu, Wei; Liu, C. S.; Liang, Yunfeng; Chen, Jun-Ling; Luo, G.-N.

    2017-11-01

    Radiation damage not only seriously degrades the mechanical properties of tungsten (W) but also enhances hydrogen retention in the material. Introducing a large amount of defect sinks, e.g. grain boundaries (GBs) is an effective method for improving radiation-resistance of W. However, the mechanism by which the vacancies are dynamically annihilated at long timescale in nano-crystal W is still not clear. The dynamic picture for eliminating vacancies with single interstitials and small interstitial-clusters has been investigated by combining molecular dynamics, molecular statics and object Kinetic Monte Carlo methods. On one hand, the annihilation of bulk vacancies was enhanced due to the reflection of an interstitial-cluster of parallel ≤ft crowdions by the GB. The interstitial-cluster was observed to be reflected back into the grain interior when approaching a locally dense GB region. Near this region, the energy landscape for the interstitial was featured by a shoulder, different to the decreasing energy landscape of the interstitial near a locally loose region as indicative of the sink role of the GB. The bulk vacancy on the reflection path was annihilated. On the other hand, the dynamic interstitial emission efficiently anneals bulk vacancies. The single interstitial trapped at the GB firstly moved along the GB quickly and clustered to be the di-interstitial therein, reducing its mobility to a value comparable to that that for bulk vacancy diffusion. Then, the bulk vacancy was recombined via the coupled motion of the di-interstitial along the GB, the diffusion of the vacancy towards the GB and the accompanying interstitial emission. These results suggest that GBs play an efficient role in improving radiation-tolerance of nano-crystal W via reflecting highly-mobile interstitials and interstitial-clusters into the bulk and annihilating bulk vacancies, and via complex coupling of in-boundary interstitial diffusion, clustering of the interstitial and vacancy

  19. Effective Method for Determining Environmental Loads on Supporting Structures for Offshore Wind Turbines

    Directory of Open Access Journals (Sweden)

    Dymarski Paweł

    2016-01-01

    Full Text Available This paper presents a description of an effective method for determining loads due to waves and current acting on the supporting structures of the offshore wind turbines. This method is dedicated to the structures consisting of the cylindrical or conical elements as well as (truncates pyramids of polygon with a large number of sides (8 or more. The presented computational method is based on the Morison equation, which was originally developed only for cylindrically shaped structures. The new algorithm shown here uses the coefficients of inertia and drag forces that were calculated for non-cylindrical shapes. The analysed structure consists of segments which are truncated pyramids on the basis of a hex decagon. The inertia coefficients, CM, and drag coefficients, CD, were determined using RANSE-CFD calculations. The CFD simulations were performed for a specific range of variation of the period, and for a certain range of amplitudes of the velocity. In addition, the analysis of influence of the surface roughness on the inertia and drag coefficients was performed. In the next step, the computations of sea wave, current and wind load on supporting structure for the fifty-year storm were carried out. The simulations were performed in the time domain and as a result the function of forces distribution along the construction elements was obtained. The most unfavourable distribution of forces will be used, to analyse the strength of the structure, as the design load.

  20. GLOBAL EPIDEMIOLOGY OF HIV AMONG FEMALE SEX WORKERS: INFLUENCE OF STRUCTURAL DETERMINANTS

    Science.gov (United States)

    Shannon, K; Strathdee, SA; Goldenberg, SM; Duff, P; Mwangi, P; Rusakova, M; Reza-Paul, S; Lau, J; Deering, K; Pickles, M; Boily, M-C

    2014-01-01

    SUMMARY Female sex workers (FSWs) bear a disproportionately large burden of HIV infection worldwide. Despite decades of research and programme activity, the epidemiology of HIV and the role that structural determinants have in mitigating or potentiating HIV epidemics and access to care for FSWs is poorly understood. We reviewed available published data for HIV prevalence and incidence, condom use, and structural determinants among this group. Only 87 (43%) of 204 unique studies reviewed explicitly examined structural determinants of HIV. Most studies were from Asia, with few from areas with a heavy burden of HIV such as sub-Saharan Africa, Russia, and eastern Europe. To further explore the potential effect of structural determinants on the course of epidemics, we used a deterministic transmission model to simulate potential HIV infections averted through structural changes in regions with concentrated and generalised epidemics, and high HIV prevalence among FSWs. This modelling suggested that elimination of sexual violence alone could avert 17% of HIV infections in Kenya (95% uncertainty interval [UI] 1–31) and 20% in Canada (95% UI 3–39) through its immediate and sustained effect on non-condom use) among FSWs and their clients in the next decade. In Kenya, scaling up of access to antiretroviral therapy among FSWs and their clients to meet WHO eligibility of a CD4 cell count of less than 500 cells per μL could avert 34% (95% UI 25–42) of infections and even modest coverage of sex worker-led outreach could avert 20% (95% UI 8–36) of infections in the next decade. Decriminalisation of sex work would have the greatest effect on the course of HIV epidemics across all settings, averting 33–46% of HIV infections in the next decade. Multipronged structural and community-led interventions are crucial to increase access to prevention and treatment and to promote human rights for FSWs worldwide. PMID:25059947

  1. Global epidemiology of HIV among female sex workers: influence of structural determinants.

    Science.gov (United States)

    Shannon, Kate; Strathdee, Steffanie A; Goldenberg, Shira M; Duff, Putu; Mwangi, Peninah; Rusakova, Maia; Reza-Paul, Sushena; Lau, Joseph; Deering, Kathleen; Pickles, Michael R; Boily, Marie-Claude

    2015-01-03

    Female sex workers (FSWs) bear a disproportionately large burden of HIV infection worldwide. Despite decades of research and programme activity, the epidemiology of HIV and the role that structural determinants have in mitigating or potentiating HIV epidemics and access to care for FSWs is poorly understood. We reviewed available published data for HIV prevalence and incidence, condom use, and structural determinants among this group. Only 87 (43%) of 204 unique studies reviewed explicitly examined structural determinants of HIV. Most studies were from Asia, with few from areas with a heavy burden of HIV such as sub-Saharan Africa, Russia, and eastern Europe. To further explore the potential effect of structural determinants on the course of epidemics, we used a deterministic transmission model to simulate potential HIV infections averted through structural changes in regions with concentrated and generalised epidemics, and high HIV prevalence among FSWs. This modelling suggested that elimination of sexual violence alone could avert 17% of HIV infections in Kenya (95% uncertainty interval [UI] 1-31) and 20% in Canada (95% UI 3-39) through its immediate and sustained effect on non-condom use) among FSWs and their clients in the next decade. In Kenya, scaling up of access to antiretroviral therapy among FSWs and their clients to meet WHO eligibility of a CD4 cell count of less than 500 cells per μL could avert 34% (95% UI 25-42) of infections and even modest coverage of sex worker-led outreach could avert 20% (95% UI 8-36) of infections in the next decade. Decriminalisation of sex work would have the greatest effect on the course of HIV epidemics across all settings, averting 33-46% of HIV infections in the next decade. Multipronged structural and community-led interventions are crucial to increase access to prevention and treatment and to promote human rights for FSWs worldwide. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Integrating NOE and RDC using sum-of-squares relaxation for protein structure determination.

    Science.gov (United States)

    Khoo, Y; Singer, A; Cowburn, D

    2017-07-01

    We revisit the problem of protein structure determination from geometrical restraints from NMR, using convex optimization. It is well-known that the NP-hard distance geometry problem of determining atomic positions from pairwise distance restraints can be relaxed into a convex semidefinite program (SDP). However, often the NOE distance restraints are too imprecise and sparse for accurate structure determination. Residual dipolar coupling (RDC) measurements provide additional geometric information on the angles between atom-pair directions and axes of the principal-axis-frame. The optimization problem involving RDC is highly non-convex and requires a good initialization even within the simulated annealing framework. In this paper, we model the protein backbone as an articulated structure composed of rigid units. Determining the rotation of each rigid unit gives the full protein structure. We propose solving the non-convex optimization problems using the sum-of-squares (SOS) hierarchy, a hierarchy of convex relaxations with increasing complexity and approximation power. Unlike classical global optimization approaches, SOS optimization returns a certificate of optimality if the global optimum is found. Based on the SOS method, we proposed two algorithms-RDC-SOS and RDC-NOE-SOS, that have polynomial time complexity in the number of amino-acid residues and run efficiently on a standard desktop. In many instances, the proposed methods exactly recover the solution to the original non-convex optimization problem. To the best of our knowledge this is the first time SOS relaxation is introduced to solve non-convex optimization problems in structural biology. We further introduce a statistical tool, the Cramér-Rao bound (CRB), to provide an information theoretic bound on the highest resolution one can hope to achieve when determining protein structure from noisy measurements using any unbiased estimator. Our simulation results show that when the RDC measurements are

  3. The Determination of Stress State of Structures Considering Sequence of Construction and Load Application

    Directory of Open Access Journals (Sweden)

    Kuroedov Vladimir

    2016-01-01

    Full Text Available For more accurate calculation of structure it is required to apply loads in the process of its construction instead of load application after structure has taken its final form. This action is necessary in order to observe changes in the stress-strain state of the structure under study. This circumstance is important for the massive hydraulic structures, such as hydroelectric dams. It is required to determine tensions, deformations and displacements in solving the building-up tasks. It is necessary to consider the problem for constructions of linear and nonlinear materials and check the principle of superposition on which the method of solving nonlinear problems is based. Also it is necessary to consider the solution of finite element schemes with the help of various iterative methods, such as the method of additional loads and the method of variable.

  4. Experimental determination of excitonic band structures of single-walled carbon nanotubes using circular dichroism spectra.

    Science.gov (United States)

    Wei, Xiaojun; Tanaka, Takeshi; Yomogida, Yohei; Sato, Naomichi; Saito, Riichiro; Kataura, Hiromichi

    2016-10-05

    Experimental band structure analyses of single-walled carbon nanotubes have not yet been reported, to the best of our knowledge, except for a limited number of reports using scanning tunnelling spectroscopy. Here we demonstrate the experimental determination of the excitonic band structures of single-chirality single-walled carbon nanotubes using their circular dichroism spectra. In this analysis, we use gel column chromatography combining overloading selective adsorption with stepwise elution to separate 12 different single-chirality enantiomers. Our samples show higher circular dichroism intensities than the highest values reported in previous works, indicating their high enantiomeric purity. Excitonic band structure analysis is performed by assigning all observed Eii and Eij optical transitions in the circular dichroism spectra. The results reproduce the asymmetric structures of the valence and conduction bands predicted by density functional theory. Finally, we demonstrate that an extended empirical formula can estimate Eij optical transition energies for any (n,m) species.

  5. Determining the Velocity Fine Structure by a Laser Anemometer in VAD operation

    DEFF Research Database (Denmark)

    Kristensen, Leif; Kirkegaard, Peter; Mikkelsen, Torben

    in one direction and measure a time series of the Doppler wind velocity component along the beam. Applying Taylor’s hypothesis the structure function can be calculated. This technique was discussed by Kristensen et al. (2011). Taylor’s hypothesis cannot, however, be used if there is no mean wind......The theoretical basis for determining the dissipation ε, by measuring the velocity structure function with a CW-laser anemometer has been derived in the case of calm wind conditions. If there is a well defined mean wind speed the structure function can be obtained by having the laser beam pointing....... Then it is necessary to “create” a mean wind by turning the laser beam. Since the instrument is not moved the beam will describe a cone which could be a VAD-scanning. In any case the measured velocity components will not be parallel and this implies that the measured structure function will contain a term which...

  6. The structure of human tripeptidyl peptidase II as determined by a hybrid approach.

    Science.gov (United States)

    Schönegge, Anne-Marie; Villa, Elizabeth; Förster, Friedrich; Hegerl, Reiner; Peters, Jürgen; Baumeister, Wolfgang; Rockel, Beate

    2012-04-04

    Tripeptidyl-peptidase II (TPPII) is a high molecular mass (∼5 MDa) serine protease, which is thought to act downstream of the 26S proteasome, cleaving peptides released by the latter. Here, the structure of human TPPII (HsTPPII) has been determined to subnanometer resolution by cryoelectron microscopy and single-particle analysis. The complex is built from two strands forming a quasihelical structure harboring a complex system of inner cavities. HsTPPII particles exhibit some polymorphism resulting in complexes consisting of nine or of eight dimers per strand. To obtain deeper insights into the architecture and function of HsTPPII, we have created a pseudoatomic structure of the HsTPPII spindle using a comparative model of HsTPPII dimers and molecular dynamics flexible fitting. Analyses of the resulting hybrid structure of the HsTPPII holocomplex provide new insights into the mechanism of maturation and activation. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Improving ION /IOFF and sub-threshold swing in graphene nanoribbon field-effect transistors using single vacancy defects

    Science.gov (United States)

    Nazari, Atefeh; Faez, Rahim; Shamloo, Hassan

    2015-10-01

    Graphene nanoribbon field effect transistors are promising devices for beyond-CMOS nanoelectronics. Graphene is a semiconductor material with zero bandgap and its bandgap must be changed. One of the opening bandgap methods is using graphene nanoribbons. By applying a defect, there is more increase on band gap of monolayer armchair graphene nanoribbon field effect transistor. So, by applying more than one defect, we can reach to much more increase in bandgap of graphene nanoribbon field effect transistors (GNRFET). In this paper, double-gated monolayer armchair graphene nanoribbon field effect transistors (GNRFET) with one single vacancy (1SV) defect (so-called 1SVGNRFET)are simulated and after changing positions of defect in width and length of channel of GNRFET, a structure with three single vacancy (3SVs) defects(so-called 3SVsGNRFET) is offered that this structure has higher ION /IOFF ratio and lower sub-threshold swing than 1SVGNRFET and therefore has better performance. The energy band structure of nanoribbon is obtained by using nearest-neighbour interactions within an approximation tight binding model. Transfer characteristic of the transistor is simulated with solving Poisson-Schrodinger equation self-consistently by using Non- Equilibrium Green Function (NEGF) and in the real space approach.

  8. Oxidation state and interfacial effects on oxygen vacancies in tantalum pentoxide

    Energy Technology Data Exchange (ETDEWEB)

    Bondi, Robert J., E-mail: rjbondi@sandia.gov; Marinella, Matthew J. [Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States)

    2015-02-28

    First-principles density-functional theory calculations are used to study the atomistic structure, structural energetics, and electron density near the O monovacancy (V{sub O}{sup n}; n = 0,1+,2+) in both bulk, amorphous tantalum pentoxide (a-Ta{sub 2}O{sub 5}), and also at vacuum and metallic Ta interfaces. We calculate multivariate vacancy formation energies to evaluate stability as a function of oxidation state, distance from interface plane, and Fermi energy. V{sub O}{sup n} of all oxidation states preferentially segregates at both Ta and vacuum interfaces, where the metallic interface exhibits global formation energy minima. In a-Ta{sub 2}O{sub 5}, V{sub O}{sup 0} is characterized by structural contraction and electron density localization, while V{sub O}{sup 2+} promotes structural expansion and is depleted of electron density. In contrast, interfacial V{sub O}{sup 0} and V{sub O}{sup 2+} show nearly indistinguishable ionic and electronic signatures indicative of a reduced V{sub O} center. Interfacial V{sub O}{sup 2+} extracts electron density from metallic Ta, indicating that V{sub O}{sup 2+} is spontaneously reduced at the expense of the metal. This oxidation/reduction behavior suggests careful selection and processing of both oxide layer and metal electrodes for engineering memristor device operation.

  9. Vacancy-Mediated Magnetism in Pure Copper Oxide Nanoparticles

    Science.gov (United States)

    2010-01-01

    Room temperature ferromagnetism (RTF) is observed in pure copper oxide (CuO) nanoparticles which were prepared by precipitation method with the post-annealing in air without any ferromagnetic dopant. X-ray photoelectron spectroscopy (XPS) result indicates that the mixture valence states of Cu1+ and Cu2+ ions exist at the surface of the particles. Vacuum annealing enhances the ferromagnetism (FM) of CuO nanoparticles, while oxygen atmosphere annealing reduces it. The origin of FM is suggested to the oxygen vacancies at the surface/or interface of the particles. Such a ferromagnet without the presence of any transition metal could be a very good option for a class of spintronics. PMID:20671775

  10. Magnetic field imaging with nitrogen-vacancy ensembles

    Energy Technology Data Exchange (ETDEWEB)

    Pham, L M; Yeung, T K [School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 (United States); Le Sage, D; Stanwix, P L; Glenn, D; Walsworth, R L [Harvard-Smithsonian Center for Astrophysics, Cambridge, MA 02138 (United States); Trifonov, A; Lukin, M D; Park, H; Yacoby, A [Physics Department, Harvard University, Cambridge, MA 02138 (United States); Cappellaro, P [Nuclear Science and Engineering Department, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Hemmer, P R, E-mail: rwalsworth@cfa.harvard.edu [Electrical and Computer Engineering Department, Texas AM University, College Station, TX 77843 (United States)

    2011-04-15

    We demonstrate a method of imaging spatially varying magnetic fields using a thin layer of nitrogen-vacancy (NV) centers at the surface of a diamond chip. Fluorescence emitted by the two-dimensional NV ensemble is detected by a CCD array, from which a vector magnetic field pattern is reconstructed. As a demonstration, ac current is passed through wires placed on the diamond chip surface, and the resulting ac magnetic field patterns are imaged using an echo-based technique with sub-micron resolution over a 140 {mu}mx140 {mu}m field of view, giving single-pixel sensitivity {approx}100 nT/{radical}(Hz). We discuss ongoing efforts to further improve the sensitivity, as well as potential bioimaging applications such as real-time imaging of activity in functional, cultured networks of neurons.

  11. Metal(Ni,Au)-vacancy complexes in GaN

    Energy Technology Data Exchange (ETDEWEB)

    Pezold, J. von; Bristowe, P.D. [Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge CB2 3QZ (United Kingdom)

    2006-06-15

    The stability and electronic properties of metal (Ni, Au)-vacancy complexes in GaN were studied using density functional calculations. Two complexes (Ni{sub Ga}-V{sub N} and V{sub Ga}-Au{sub i}-V{sub N}) were found to exhibit relatively low formation energies in their neutral charge state under p-type conditions and are predicted to act as deep acceptors in GaN. As such they are unlikely to contribute to the hole carrier concentration in p-GaN and are probably not responsible for the low electrical resistance of Au/Ni contacts. They may, however, act as compensation centres in n-GaN. (copyright 2006 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  12. The physics and technology of Nitrogen-vacancy centers

    Science.gov (United States)

    Doherty, Marcus

    The nitrogen-vacancy (NV) center in diamond is a leading platform for the development of quantum microscopy, computing and communication technologies. Its applications stem from its rich optical, spin and charge physics that is becoming well understood. Recently, a number of similar defects in diamond and other materials have been identified. These defects exhibit properties that are potentially superior to the NV center's for specific quantum applications, but are yet to be fully understood. In this presentation, I will briefly review the physics and applications of the NV center before reporting the development of new first principles techniques for modelling its optical, spin and charge dynamics and decoherence processes. These techniques support deeper understanding of the NV center and the design of NV quantum devices, as well as the rapid identification and characterization of emerging defects for quantum technologies. Funding support provided by the ARC (DP120102232 and DP140103862) and the DAAD-Go8 Cooperation Scheme.

  13. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score.

    Science.gov (United States)

    Huang, Yuanpeng Janet; Mao, Binchen; Xu, Fei; Montelione, Gaetano T

    2015-08-01

    ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD-NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases (15)N-(1)H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD-NMR data. These algorithmic improvements include (1) using a global metric of structural accuracy, the discriminating power score, for guiding model selection during the iterative NOE interpretation process, and (2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta.

  14. Images d’un camp de vacances en pays socialiste

    Directory of Open Access Journals (Sweden)

    Ania Szczepanska

    2009-12-01

    Full Text Available En 1976, Marcel Lozinski choisit d’aller filmer un camp de vacances organisé par le mouvement de la jeunesse socialiste dans la région des lacs de Mazurie en Pologne. Le cinéaste décide de filmer le quotidien de ces jeunes familles en vacances, entre quiz politiques, leçons de savoir vivre et concours de la famille modèle. Pour cela, il élabore un protocole de travail singulier : aux vacanciers s’ajoutent des personnes complices du cinéaste dont le rôle sera pour certains de participer activement à la vie collective, pour d’autres de s’y opposer.Tourné en 1976, le documentaire Comment vivre attendra cinq années avant d’être diffusé en salle, en tant que fiction. Pourquoi cette diffusion retardée et surtout, que penser de cette requalification a posteriori ? Outre l’analyse du film lui-même, un entretien mené avec Marcel Lozinski ainsi que des archives consultées à la filmothèque de Varsovie apporteront des éléments d’analyse sur la réception de l’œuvre par les autorités cinématographiques de l’époque, mais également sur le sens produit par les dispositifs mis en place par le cinéaste au cours de ce tournage.

  15. Relationship between Structural and Intermediary Determinants of Health and Preterm Delivery

    Science.gov (United States)

    Dolatian, Mahrokh; Mirabzadeh, Arash; Forouzan, Ameneh Setareh; Sajjadi, Homeira; Alavimajd, Hamid; Mahmoodi, Zohreh; Moafi, Farnoosh

    2014-01-01

    Background Preterm birth is a major health problem that leads to infant morbidity and mortality. The main goal of this study was to find the relationship between social determinants of health and preterm delivery. Methods A prospective longitudinal cohort study was carried out on 500 pregnant women in their 24th to 28th gestational weeks in 2012. The pregnant women filled out a self-report questionnaire on the structural determinant, perceived stress, and perceived social support. The participants were followed up until labor and the data about mother and the newborn were collected after labor. The data were analyzed by SPSS 21 and Lisrel 8.8 software programs using pathway analysis. Results The final path model fit well (CFI=0.96; RMSEA=0.060). Path analysis showed that among structural factors, income had a direct effect (β=0.06) and the factors of income (β=0.00594), number of children (family size) (β=-0.024), as well as mother's education (β=-0.0084) had the greatest overall effect on gestational age at birth respectively. Also, the results showed that among intermediate factors of social determinants of health, stress in the direct path (β=-0.12) and among the overall effects, the perceived stress (β=-0.12) and perceived social support (β=0.0396) affected the gestational age at birth. Conclusion The current study showed that some structural and intermediary determinants such as income and perceived stress had an effect on preterm labor. PMID:24918080

  16. Computational tools for experimental determination and theoretical prediction of protein structure

    Energy Technology Data Exchange (ETDEWEB)

    O`Donoghue, S.; Rost, B.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. The authors intend to review the state of the art in the experimental determination of protein 3D structure (focus on nuclear magnetic resonance), and in the theoretical prediction of protein function and of protein structure in 1D, 2D and 3D from sequence. All the atomic resolution structures determined so far have been derived from either X-ray crystallography (the majority so far) or Nuclear Magnetic Resonance (NMR) Spectroscopy (becoming increasingly more important). The authors briefly describe the physical methods behind both of these techniques; the major computational methods involved will be covered in some detail. They highlight parallels and differences between the methods, and also the current limitations. Special emphasis will be given to techniques which have application to ab initio structure prediction. Large scale sequencing techniques increase the gap between the number of known proteins sequences and that of known protein structures. They describe the scope and principles of methods that contribute successfully to closing that gap. Emphasis will be given on the specification of adequate testing procedures to validate such methods.

  17. Interpopulation variation in contour feather structure is environmentally determined in great tits.

    Science.gov (United States)

    Broggi, Juli; Gamero, Anna; Hohtola, Esa; Orell, Markku; Nilsson, Jan-Åke

    2011-01-01

    The plumage of birds is important for flying, insulation and social communication. Contour feathers cover most of the avian body and among other functions they provide a critical insulation layer against heat loss. Feather structure and composition are known to vary among individuals, which in turn determines variation in the insulation properties of the feather. However, the extent and the proximate mechanisms underlying this variation remain unexplored. We analyzed contour feather structure from two different great tit populations adapted to different winter regimes, one northern population in Oulu (Finland) and one southern population in Lund (Sweden). Great tits from the two populations differed significantly in feather structure. Birds from the northern population had a denser plumage but consisting of shorter feathers with a smaller proportion containing plumulaceous barbs, compared with conspecifics from the southern population. However, differences disappeared when birds originating from the two populations were raised and moulted in identical conditions in a common-garden experiment located in Oulu, under ad libitum nutritional conditions. All birds raised in the aviaries, including adult foster parents moulting in the same captive conditions, developed a similar feather structure. These feathers were different from that of wild birds in Oulu but similar to wild birds in Lund, the latter moulting in more benign conditions than those of Oulu. Wild populations exposed to different conditions develop contour feather differences either due to plastic responses or constraints. Environmental conditions, such as nutrient availability during feather growth play a crucial role in determining such differences in plumage structure among populations.

  18. Interplay Between MEP, Hydraulic Redistribution and Resource Use Efficiency in Determining the Structure of Plant Roots

    Science.gov (United States)

    Quijano, J. C.; Kumar, P.; Drewry, D.

    2010-12-01

    Vegetation roots are structured to provide a variety of functions such as structural stability, and water and nutrient uptake. Can we determine the structure of the vegetation root profile by characterization of the vegetation function from an optimality perspective? We explore this question by examining a variety of optimality functions based on different principles such as thermodynamics (maximum entropy production), resource use efficiency (water use efficiency, nitrogen use efficiency), and ecosystem production (maximum carbon uptake). Furthermore, we examine the role of hydraulic redistribution in determining the root profile structure through these optimality functions. The numerical study is performed using the multi-layer canopy model (MLCan, Drewry et al. 2010) that incorporates hydraulic redistribution. The forcing data is obtained from the Ameriflux Tower located in Blodgett Forest, Sierra Nevada, California. We also consider single species (Ponderosa Pine) and multiple species (Ponderosa Pine, Shrubs) dynamics to assess how the species interaction through hydraulic redistribution influences the optimal results. The results show that the pareto front resulting from the multiobjective framework changes when single or multiple species dynamics are considered because the partition of fluxes in the surface energy balance are different. Also, multi-species model under hydraulic redistribution allows the ecosystem to produce more latent heat which in turn influences the optimal outcomes. Drewry, D.T., P. Kumar, S. Long, C. Bernachi, X Z. Liang, and M. Sivapalan, Ecohydrological Responses of Dense Canopies to Environmental Variability Part 1. Interplay Between Vertical Structure and Photosynthetic Pathway, to appear in Journal of Geophysical Research Biogeosciences 2010.

  19. Structure of a king cobra phospholipase A2 determined from a hemihedrally twinned crystal.

    Science.gov (United States)

    Xu, Sujuan; Gu, Lichuan; Wang, Qiuyan; Shu, Yuyan; Song, Shiying; Lin, Zhengjiong

    2003-09-01

    An acidic PLA(2) (OH APLA(2)-II) from the venom of Ophiophagus hannah (king cobra) shows greater phospholipase A(2) activity and weaker cardiotoxic and myotoxic activity than a homologous acidic PLA(2) from the same venom. The crystal of the enzyme belongs to space group P6(3). The crystals are invariably hemihedrally twinned, exhibiting perfect 622 Laue symmetry. The structure was determined by molecular replacement and refined using a hemihedral twinning program at 2.1 A resolution. The final model has reasonable stereochemistry and a crystallographic R factor of 19.5% (R(free) = 21.5%). The structure reveals the molecular arrangement and the mode of twinning. There are six independent molecules in the asymmetric unit. Owing to the presence of a non-crystallographic twofold parallel to the hemihedral twinning twofold, the molecular packing in the twinned crystal is extremely similar to that in an untwinned crystal for four of the molecules. This unique molecular arrangement may be related to the difficulty in recognizing the twinning. The structure was compared with the previously determined structure of a homologous acidic PLA(2) from the same source. The comparison shows structural changes that might be implicated in the increased catalytic activity and weakened toxicity.

  20. Application of in situ diffraction in high-throughput structure determination platforms.

    Science.gov (United States)

    Aller, Pierre; Sanchez-Weatherby, Juan; Foadi, James; Winter, Graeme; Lobley, Carina M C; Axford, Danny; Ashton, Alun W; Bellini, Domenico; Brandao-Neto, Jose; Culurgioni, Simone; Douangamath, Alice; Duman, Ramona; Evans, Gwyndaf; Fisher, Stuart; Flaig, Ralf; Hall, David R; Lukacik, Petra; Mazzorana, Marco; McAuley, Katherine E; Mykhaylyk, Vitaliy; Owen, Robin L; Paterson, Neil G; Romano, Pierpaolo; Sandy, James; Sorensen, Thomas; von Delft, Frank; Wagner, Armin; Warren, Anna; Williams, Mark; Stuart, David I; Walsh, Martin A

    2015-01-01

    Macromolecular crystallography (MX) is the most powerful technique available to structural biologists to visualize in atomic detail the macromolecular machinery of the cell. Since the emergence of structural genomics initiatives, significant advances have been made in all key steps of the structure determination process. In particular, third-generation synchrotron sources and the application of highly automated approaches to data acquisition and analysis at these facilities have been the major factors in the rate of increase of macromolecular structures determined annually. A plethora of tools are now available to users of synchrotron beamlines to enable rapid and efficient evaluation of samples, collection of the best data, and in favorable cases structure solution in near real time. Here, we provide a short overview of the emerging use of collecting X-ray diffraction data directly from the crystallization experiment. These in situ experiments are now routinely available to users at a number of synchrotron MX beamlines. A practical guide to the use of the method on the MX suite of beamlines at Diamond Light Source is given.