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Sample records for centred local structures

  1. Investigations of the EPR Parameters and Local Lattice Structure for the Rhombic Cu2+ Centre in TZSH Crystal

    NASA Astrophysics Data System (ADS)

    Li, Chao-Ying; Liu, Shi-Fei; Fu, Jin-Xian

    2016-03-01

    The electron paramagnetic resonance (EPR) parameters [i.e. g factors gi (i=x, y, z) and hyperfine structure constants Ai] and the local lattice structure for the Cu2+ centre in Tl2Zn(SO4)2·6H2O (TZSH) crystal were theoretically investigated by utilising the perturbation formulae of these parameters for a 3d9 ion under rhombically elongated octahedra. In the calculations, the admixture of d orbitals in the ground state and the ligand orbital and spin-orbit coupling interactions are taken into account based on the cluster approach. The theoretical EPR parameters show good agreement with the observed values, and the Cu2+-H2O bond lengths are obtained as follows: Rx≈1.98 Å, Ry≈2.09 Å, Rz≈2.32 Å. The results are discussed.

  2. Constructing Learning Spaces? Videoconferencing at Local Learning Centres in Sweden

    ERIC Educational Resources Information Center

    Logdlund, Ulrik

    2010-01-01

    This article explores videoconferencing in the context of local learning centres in Sweden. The practice is described as a "learning space" in which adult learners construct socio-spatial relations. The study goes beyond a sociological apprehension of actors and opposes the idea of the material as neutral, passive and conformed by practice. On the…

  3. Theoretical studies of the EPR parameters and local structures for Cu2+ centres in a (CH3)2NH2Al(SO4)2·6H2O crystal

    NASA Astrophysics Data System (ADS)

    Zhang, Hua-Ming; Xiao, Wen-Bo; Wan, Xiong

    2014-10-01

    Local structure and electron paramagnetic resonance (EPR) parameters (the g factors, gi, and the hyperfine structure constants Ai, i = x, y, z) for the impurity Cu2+ centres in a (CH3)2NH2Al(SO4)2·6H2O (DMAAS) crystal are theoretically investigated by using the high-order perturbation formulas of these parameters for a 3d9 ion in an orthorhombically elongated octahedron. The related molecular orbital coefficients are quantitatively determined from the cluster approach in a uniform way. From the studies, the four planar Cu2+-O2- bond lengths are found to experience the relative variation δR ( ≈0.033 and 0.063 Å) along the X- and Y-axes, while the two parallel bond lengths may undergo relative elongation ΔZ (≈0.058 and 0.052 Å) along the C2 axis for the studied Cu2+ centres I and II, respectively, due to the Jahn-Teller effect. The theoretical EPR parameters based on the above local lattice distortions agree well with the experimental data. The results are discussed.

  4. Type I photosynthetic reaction centres: structure and function.

    PubMed Central

    Heathcote, Peter; Jones, Michael R; Fyfe, Paul K

    2003-01-01

    We review recent advances in the study of the photosystem I reaction centre, following the determination of a spectacular 2.5 A resolution crystal structure for this complex of Synechococcus elongatus. Photosystem I is proving different to type II reaction centres in structure and organization, and the mechanism of transmembrane electron transfer, and is providing insights into the control of function in reaction centres that operate at very low redox potentials. The photosystem I complex of oxygenic organisms has a counterpart in non-oxygenic bacteria, the strictly anaerobic phototrophic green sulphur bacteria and heliobacteria. The most distinctive feature of these type I reaction centres is that they contain two copies of a large core polypeptide (i.e. a homodimer), rather than a heterodimeric arrangement of two related, but different, polypeptides as in the photosystem I complex. To compare the structural organization of the two forms of type I reaction centre, we have modelled the structure of the central region of the reaction centre from green sulphur bacteria, using sequence alignments and the structural coordinates of the S. elongatus Photosystem I complex. The outcome of these modelling studies is described, concentrating on regions of the type I reaction centre where important structure-function relationships have been demonstrated or inferred. PMID:12594931

  5. Measuring the defect structure orientation of a single NV- centre in diamond

    NASA Astrophysics Data System (ADS)

    Doherty, M. W.; Michl, J.; Dolde, F.; Jakobi, I.; Neumann, P.; Manson, N. B.; Wrachtrup, J.

    2014-06-01

    The negatively charged nitrogen-vacancy (NV-) centre in diamond has many exciting applications in quantum nano-metrology, including magnetometry, electrometry, thermometry and piezometry. Indeed, it is possible for a single NV- centre to measure the complete three-dimensional vector of the local electric field or the position of a single fundamental charge in ambient conditions. However, in order to achieve such vector measurements, near complete knowledge of the orientation of the centre's defect structure is required. Here, we demonstrate an optically detected magnetic resonance (ODMR) technique employing rotations of static electric and magnetic fields that precisely determines the orientation of the centre's major and minor trigonal symmetry axes. Thus, our technique is an enabler of the centre's existing vector sensing applications and also motivates new applications in multi-axis rotation sensing, NV growth characterization and diamond crystallography.

  6. From gene to structure: The protein factory of the NBICS Centre of Kurchatov Institute

    SciTech Connect

    Boyko, K. M.; Lipkin, A. V.; Popov, V. O. Kovalchuk, M. V.

    2013-05-15

    The Protein Factory was established at the Centre for Nano, Bio, Info, Cognitive, and Social Sciences and Technologies (NBICS Centre) of the National Research Centre 'Kurchatov Institute' in 2010. The Protein Factory, together with the Centre for Synchrotron Radiation and Nanotechnology, promote research on structural biology. This paper presents the technology platforms developed at the Protein Factory and the facilities available for researchers. The main projects currently being performed at the Protein Factory are briefly described.

  7. Evaluation of a diabetes specialty centre: structure, process and outcome.

    PubMed

    Basa, R P; McLeod, B

    1995-02-01

    The purpose of this study was to evaluate the effectiveness of a diabetes specialty centre in assisting clients with noninsulin-dependent diabetes mellitus to improve their metabolic control and quality of life. A single-subject repeated measures design was used where data was collected on entry to the program, immediately following the 2-day education sessions, and at both 3- and 6-month follow-up visits. Structure and process were taken into consideration, and the main outcome variables measured were knowledge, attitudes, metabolic control (hemoglobin A1c) and perceived quality of life. These variables were chosen in the belief that many factors can influence behaviour and it is the combination of these factors which results in behavioural change and ultimately improvement in metabolic control and quality of life. The main findings were that the facilities and documentation records were adequate, the clients perceived that the primary function of the center was medical management rather than education, and knowledge, metabolic control and quality of life improved significantly after the program. For clients, perceived happiness and quality of life were primary issues. Therefore, improvement in quality of life should be one of the primary goals of diabetes education programs. PMID:7603930

  8. Deformation-induced structural transition in body-centred cubic molybdenum

    PubMed Central

    Wang, S. J.; Wang, H.; Du, K.; Zhang, W.; Sui, M. L.; Mao, S. X.

    2014-01-01

    Molybdenum is a refractory metal that is stable in a body-centred cubic structure at all temperatures before melting. Plastic deformation via structural transitions has never been reported for pure molybdenum, while transformation coupled with plasticity is well known for many alloys and ceramics. Here we demonstrate a structural transformation accompanied by shear deformation from an original <001>-oriented body-centred cubic structure to a <110>-oriented face-centred cubic lattice, captured at crack tips during the straining of molybdenum inside a transmission electron microscope at room temperature. The face-centred cubic domains then revert into <111>-oriented body-centred cubic domains, equivalent to a lattice rotation of 54.7°, and ~15.4% tensile strain is reached. The face-centred cubic structure appears to be a well-defined metastable state, as evidenced by scanning transmission electron microscopy and nanodiffraction, the Nishiyama–Wassermann and Kurdjumov–Sachs relationships between the face-centred cubic and body-centred cubic structures and molecular dynamics simulations. Our findings reveal a deformation mechanism for elemental metals under high-stress deformation conditions. PMID:24603655

  9. Deformation-induced structural transition in body-centred cubic molybdenum.

    PubMed

    Wang, S J; Wang, H; Du, K; Zhang, W; Sui, M L; Mao, S X

    2014-03-07

    Molybdenum is a refractory metal that is stable in a body-centred cubic structure at all temperatures before melting. Plastic deformation via structural transitions has never been reported for pure molybdenum, while transformation coupled with plasticity is well known for many alloys and ceramics. Here we demonstrate a structural transformation accompanied by shear deformation from an original <001>-oriented body-centred cubic structure to a <110>-oriented face-centred cubic lattice, captured at crack tips during the straining of molybdenum inside a transmission electron microscope at room temperature. The face-centred cubic domains then revert into <111>-oriented body-centred cubic domains, equivalent to a lattice rotation of 54.7°, and ~15.4% tensile strain is reached. The face-centred cubic structure appears to be a well-defined metastable state, as evidenced by scanning transmission electron microscopy and nanodiffraction, the Nishiyama-Wassermann and Kurdjumov-Sachs relationships between the face-centred cubic and body-centred cubic structures and molecular dynamics simulations. Our findings reveal a deformation mechanism for elemental metals under high-stress deformation conditions.

  10. Deformation-induced structural transition in body-centred cubic molybdenum.

    PubMed

    Wang, S J; Wang, H; Du, K; Zhang, W; Sui, M L; Mao, S X

    2014-01-01

    Molybdenum is a refractory metal that is stable in a body-centred cubic structure at all temperatures before melting. Plastic deformation via structural transitions has never been reported for pure molybdenum, while transformation coupled with plasticity is well known for many alloys and ceramics. Here we demonstrate a structural transformation accompanied by shear deformation from an original <001>-oriented body-centred cubic structure to a <110>-oriented face-centred cubic lattice, captured at crack tips during the straining of molybdenum inside a transmission electron microscope at room temperature. The face-centred cubic domains then revert into <111>-oriented body-centred cubic domains, equivalent to a lattice rotation of 54.7°, and ~15.4% tensile strain is reached. The face-centred cubic structure appears to be a well-defined metastable state, as evidenced by scanning transmission electron microscopy and nanodiffraction, the Nishiyama-Wassermann and Kurdjumov-Sachs relationships between the face-centred cubic and body-centred cubic structures and molecular dynamics simulations. Our findings reveal a deformation mechanism for elemental metals under high-stress deformation conditions. PMID:24603655

  11. A Study of Self and Task Performance in Childcare Centres as Perceived by Caregivers under Local Administrative Organisations in Thailand

    ERIC Educational Resources Information Center

    Bhulpat, Cheerapan

    2011-01-01

    The purpose of this research was to study the opinions toward self and task performance in childcare centres as perceived by caregivers under the jurisdiction of the Local Administrative Organization. The four areas evaluated were caregiver characteristics, task performance, objectives of caregiving and educating young children and problems and…

  12. The Role and Structure of University Language Centres in Europe.

    ERIC Educational Resources Information Center

    Grauberg, W.

    This report examines both the divergent and common features of university language centers in Europe, focusing primarily on their aims, structures, and methods of operation. Major sections examine the development and types of university language centers. The types include (1) comprehensive centers, (2) centers mainly devoted to the teaching of…

  13. Localized structures in gaseous combustion

    NASA Astrophysics Data System (ADS)

    Knobloch, Edgar; Lo Jacono, David; Bergeon, Alain

    2015-11-01

    We consider a flame between a pair of porous walls at x = +/- 1 that allow fuel and oxidizer to diffuse into the burn region from opposite sides. The burn process is described by a binary one-step process of Arrhenius type. The heat released is redistributed via radiation. Convection is ignored. In 1D the low and high temperature states are connected by an S-shaped branch with a fold at low Damköhler number below which extinction takes place. Various instabilities occur on the upper (flame) branch leading to different time-dependent but 1D flames. In 2D the situation is dramatically modified: near the extinction region the burn front breaks up into structures that are localized in the direction along the front, with multiple branches of such states bifurcating from the fold. These correspond to states with n = 1 , 2 , ⋯ identical and equispaced hotspots. Further bifurcations generate states in which the hotspots are nonidentical and separated by unequal distances. All these states are present in the same parameter interval, implying great sensitivity of the system to initial conditions.

  14. "Bringing Learning Closer to Home": The Value and Impact of the Lisbon Strategy for Strengthening the Role of Local Learning Centres and Partnerships in South-Eastern Europe

    ERIC Educational Resources Information Center

    Zarifis, George K.

    2008-01-01

    This paper presents a comparative examination of four local learning centres that provide learning opportunities throughout life in Bulgaria, Cyprus, Greece and Turkey. The paper aims to assess some of the strengths and weaknesses of different types of local learning centres and partnerships in South-Eastern Europe--in line with the value and…

  15. The model of local mode analysis for structural acoustics of box structures

    NASA Astrophysics Data System (ADS)

    Ngai, King-Wah

    Structure-borne noise is a new noise pollution problem emerging from railway concrete box structures in Hong Kong. Its low frequency noise with intermittent effect can cause considerable nuisance to neighborhoods. The tonal noise peaks in this low frequency range should be one of the important factors in structure-borne noise analysis. In the acoustic field, the deterministic analysis of all the resonant modes of vibration is generally considered as not practical. Many acoustic experts use the statistical energy analysis as the main tool for the noise investigation whereas the application of the experimental modal analysis in the structural acoustic problem is comparatively rare. In the past, most studies mainly focused on the structure-borne noise measurement and analysis. The detail study of the cause of structure-borne noise is lack, especially for the rectangular concrete box structure. In this dissertation, an experimental and analytical approach is adopted to study a typical concrete box model. This thesis aims at confirming the importance of modal analysis in the structure-borne noise study and then at identifying the local vibration modes along the cross-section of box structure. These local modes are responsible for the structure-borne noise radiation. The findings of this study suggest that the web of viaduct cross-section is not as rigid as assumed in the conventional viaduct design and the web face is likely to be more flexible in the vertical displacement of the concrete viaduct. Two types of local vibration modes along the cross-section are identified: the centre mode and the web mode. At the top panel of the viaduct, the centre mode has movement in the middle but not at the edges. The web mode has movement at the edges with the middle fixed. The combined centre and web mode has been found to be important in the structural acoustics of the concrete box structure. In the actual concrete viaduct, the coincidence frequency is especially low (often around

  16. A Foreign Model of Teacher Education and Its Local Appropriation: The English Teachers' Centres in Spain

    ERIC Educational Resources Information Center

    Groves, Tamar

    2015-01-01

    This article explores the implementation of the English model of teachers' centres in the context of 1980s Spain. Originally it was a top-down plan initiated by a national government. However, from the very beginning its fate was dependent on a bottom-up educational project carried out by pedagogical social movements. The first part of the article…

  17. Teaching Reading and Writing in Local Language Using the Child-Centred Pedagogy in Uganda

    ERIC Educational Resources Information Center

    Akello, Dora Lucy; Timmerman, Greetje; Namusisi, Speranza

    2016-01-01

    Uganda introduced the use of mother tongue as medium of instruction in primary schools in 2007. This was meant to promote interaction and participation in the learning process and improve children's proficiency in reading and writing. Drawing elements of interaction and participation from the socio-cultural theory, the child-centred pedagogy was…

  18. Combinatorics of locally optimal RNA secondary structures.

    PubMed

    Fusy, Eric; Clote, Peter

    2014-01-01

    It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is 1.104366∙n-3/2∙2.618034n. Motivated by the kinetics of RNA secondary structure formation, we are interested in determining the asymptotic number of secondary structures that are locally optimal, with respect to a particular energy model. In the Nussinov energy model, where each base pair contributes -1 towards the energy of the structure, locally optimal structures are exactly the saturated structures, for which we have previously shown that asymptotically, there are 1.07427∙n-3/2∙2.35467n many saturated structures for a sequence of length n. In this paper, we consider the base stacking energy model, a mild variant of the Nussinov model, where each stacked base pair contributes -1 toward the energy of the structure. Locally optimal structures with respect to the base stacking energy model are exactly those secondary structures, whose stems cannot be extended. Such structures were first considered by Evers and Giegerich, who described a dynamic programming algorithm to enumerate all locally optimal structures. In this paper, we apply methods from enumerative combinatorics to compute the asymptotic number of such structures. Additionally, we consider analogous combinatorial problems for secondary structures with annotated single-stranded, stacking nucleotides (dangles).

  19. Combinatorics of locally optimal RNA secondary structures.

    PubMed

    Fusy, Eric; Clote, Peter

    2014-01-01

    It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is 1.104366∙n-3/2∙2.618034n. Motivated by the kinetics of RNA secondary structure formation, we are interested in determining the asymptotic number of secondary structures that are locally optimal, with respect to a particular energy model. In the Nussinov energy model, where each base pair contributes -1 towards the energy of the structure, locally optimal structures are exactly the saturated structures, for which we have previously shown that asymptotically, there are 1.07427∙n-3/2∙2.35467n many saturated structures for a sequence of length n. In this paper, we consider the base stacking energy model, a mild variant of the Nussinov model, where each stacked base pair contributes -1 toward the energy of the structure. Locally optimal structures with respect to the base stacking energy model are exactly those secondary structures, whose stems cannot be extended. Such structures were first considered by Evers and Giegerich, who described a dynamic programming algorithm to enumerate all locally optimal structures. In this paper, we apply methods from enumerative combinatorics to compute the asymptotic number of such structures. Additionally, we consider analogous combinatorial problems for secondary structures with annotated single-stranded, stacking nucleotides (dangles). PMID:23263300

  20. Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography

    NASA Astrophysics Data System (ADS)

    Johansson, Linda C.; Arnlund, David; Katona, Gergely; White, Thomas A.; Barty, Anton; Deponte, Daniel P.; Shoeman, Robert L.; Wickstrand, Cecilia; Sharma, Amit; Williams, Garth J.; Aquila, Andrew; Bogan, Michael J.; Caleman, Carl; Davidsson, Jan; Doak, R. Bruce; Frank, Matthias; Fromme, Raimund; Galli, Lorenzo; Grotjohann, Ingo; Hunter, Mark S.; Kassemeyer, Stephan; Kirian, Richard A.; Kupitz, Christopher; Liang, Mengning; Lomb, Lukas; Malmerberg, Erik; Martin, Andrew V.; Messerschmidt, Marc; Nass, Karol; Redecke, Lars; Seibert, M. Marvin; Sjöhamn, Jennie; Steinbrener, Jan; Stellato, Francesco; Wang, Dingjie; Wahlgren, Weixaio Y.; Weierstall, Uwe; Westenhoff, Sebastian; Zatsepin, Nadia A.; Boutet, Sébastien; Spence, John C. H.; Schlichting, Ilme; Chapman, Henry N.; Fromme, Petra; Neutze, Richard

    2013-12-01

    Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 Å resolution and determine its serial femtosecond crystallography structure to 3.5 Å resolution. Although every microcrystal is exposed to a dose of 33 MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure.

  1. Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography

    PubMed Central

    Johansson, Linda C.; Arnlund, David; Katona, Gergely; White, Thomas A.; Barty, Anton; DePonte, Daniel P.; Shoeman, Robert L.; Wickstrand, Cecilia; Sharma, Amit; Williams, Garth J.; Aquila, Andrew; Bogan, Michael J.; Caleman, Carl; Davidsson, Jan; Doak, R Bruce; Frank, Matthias; Fromme, Raimund; Galli, Lorenzo; Grotjohann, Ingo; Hunter, Mark S.; Kassemeyer, Stephan; Kirian, Richard A.; Kupitz, Christopher; Liang, Mengning; Lomb, Lukas; Malmerberg, Erik; Martin, Andrew V.; Messerschmidt, Marc; Nass, Karol; Redecke, Lars; Seibert, M Marvin; Sjöhamn, Jennie; Steinbrener, Jan; Stellato, Francesco; Wang, Dingjie; Wahlgren, Weixaio Y.; Weierstall, Uwe; Westenhoff, Sebastian; Zatsepin, Nadia A.; Boutet, Sébastien; Spence, John C.H.; Schlichting, Ilme; Chapman, Henry N.; Fromme, Petra; Neutze, Richard

    2013-01-01

    Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 Å resolution and determine its serial femtosecond crystallography structure to 3.5 Å resolution. Although every microcrystal is exposed to a dose of 33 MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure. PMID:24352554

  2. Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography.

    PubMed

    Johansson, Linda C; Arnlund, David; Katona, Gergely; White, Thomas A; Barty, Anton; DePonte, Daniel P; Shoeman, Robert L; Wickstrand, Cecilia; Sharma, Amit; Williams, Garth J; Aquila, Andrew; Bogan, Michael J; Caleman, Carl; Davidsson, Jan; Doak, R Bruce; Frank, Matthias; Fromme, Raimund; Galli, Lorenzo; Grotjohann, Ingo; Hunter, Mark S; Kassemeyer, Stephan; Kirian, Richard A; Kupitz, Christopher; Liang, Mengning; Lomb, Lukas; Malmerberg, Erik; Martin, Andrew V; Messerschmidt, Marc; Nass, Karol; Redecke, Lars; Seibert, M Marvin; Sjöhamn, Jennie; Steinbrener, Jan; Stellato, Francesco; Wang, Dingjie; Wahlgren, Weixaio Y; Weierstall, Uwe; Westenhoff, Sebastian; Zatsepin, Nadia A; Boutet, Sébastien; Spence, John C H; Schlichting, Ilme; Chapman, Henry N; Fromme, Petra; Neutze, Richard

    2013-01-01

    Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 Å resolution and determine its serial femtosecond crystallography structure to 3.5 Å resolution. Although every microcrystal is exposed to a dose of 33 MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure.

  3. Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography.

    PubMed

    Johansson, Linda C; Arnlund, David; Katona, Gergely; White, Thomas A; Barty, Anton; DePonte, Daniel P; Shoeman, Robert L; Wickstrand, Cecilia; Sharma, Amit; Williams, Garth J; Aquila, Andrew; Bogan, Michael J; Caleman, Carl; Davidsson, Jan; Doak, R Bruce; Frank, Matthias; Fromme, Raimund; Galli, Lorenzo; Grotjohann, Ingo; Hunter, Mark S; Kassemeyer, Stephan; Kirian, Richard A; Kupitz, Christopher; Liang, Mengning; Lomb, Lukas; Malmerberg, Erik; Martin, Andrew V; Messerschmidt, Marc; Nass, Karol; Redecke, Lars; Seibert, M Marvin; Sjöhamn, Jennie; Steinbrener, Jan; Stellato, Francesco; Wang, Dingjie; Wahlgren, Weixaio Y; Weierstall, Uwe; Westenhoff, Sebastian; Zatsepin, Nadia A; Boutet, Sébastien; Spence, John C H; Schlichting, Ilme; Chapman, Henry N; Fromme, Petra; Neutze, Richard

    2013-01-01

    Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 Å resolution and determine its serial femtosecond crystallography structure to 3.5 Å resolution. Although every microcrystal is exposed to a dose of 33 MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure. PMID:24352554

  4. Deterministic weak localization in periodic structures.

    PubMed

    Tian, C; Larkin, A

    2005-12-01

    In some perfect periodic structures classical motion exhibits deterministic diffusion. For such systems we present the weak localization theory. As a manifestation for the velocity autocorrelation function a universal power law decay is predicted to appear at four Ehrenfest times. This deterministic weak localization is robust against weak quenched disorders, which may be confirmed by coherent backscattering measurements of periodic photonic crystals.

  5. [Local treatment of chronic skin wounds in a Swiss out-patient wound centre 2010].

    PubMed

    Baumgartner, Marc; Tanner, Daniel; Hunziker, Thomas

    2011-03-01

    In Switzerland around 30,000 patients suffer from chronic skin wounds. Appropriate topical wound care along with treatment of the causes of the wounds enables to heal a lot of these patients and to avoid secondary disease such as infections. Thereby, the final goal of wound care is stable reepithelisation. Based on experience with chronic leg ulcers mainly in our out-patient wound centre, we give a survey of the wound dressings we actually use and discuss their wound-phase adapted application. Furthermore, we address the two tissue engineering products reimbursed in Switzerland, Apligraf and EpiDex, as well as the biological matrix product Oasis. The crucial question, which treatment options will be offered in future to the wound patients by our health regulatory and insurance systems, is open to debate.

  6. Structures of two superoxide dismutases from Bacillus anthracis reveal a novel active centre

    SciTech Connect

    Boucher, Ian W.; Kalliomaa, Anne K.; Levdikov, Vladimir M.; Blagova, Elena V.; Fogg, Mark J.; Brannigan, James A. Wilson, Keith S.; Wilkinson, Anthony J.

    2005-07-01

    The crystal structures of two manganese superoxide dismutases from B. anthracis were solved by X-ray crystallography using molecular replacement. The BA4499 and BA5696 genes of Bacillus anthracis encode proteins homologous to manganese superoxide dismutase, suggesting that this organism has an expanded repertoire of antioxidant proteins. Differences in metal specificity and quaternary structure between the dismutases of prokaryotes and higher eukaryotes may be exploited in the development of therapeutic antibacterial compounds. Here, the crystal structure of two Mn superoxide dismutases from B. anthracis solved to high resolution are reported. Comparison of their structures reveals that a highly conserved residue near the active centre is substituted in one of the proteins and that this is a characteristic feature of superoxide dismutases from the B. cereus/B. anthracis/B. thuringiensis group of organisms.

  7. Localizing the VHE γ-ray source at the Galactic Centre

    NASA Astrophysics Data System (ADS)

    Acero, F.; Aharonian, F.; Akhperjanian, A. G.; Anton, G.; Barres de Almeida, U.; Bazer-Bachi, A. R.; Becherini, Y.; Behera, B.; Bernlöhr, K.; Bochow, A.; Boisson, C.; Bolmont, J.; Borrel, V.; Braun, I.; Brucker, J.; Brun, F.; Brun, P.; Bühler, R.; Bulik, T.; Büsching, I.; Boutelier, T.; Chadwick, P. M.; Charbonnier, A.; Chaves, R. C. G.; Cheesebrough, A.; Conrad, J.; Chounet, L.-M.; Clapson, A. C.; Coignet, G.; Dalton, M.; Daniel, M. K.; Davids, I. D.; Degrange, B.; Deil, C.; Dickinson, H. J.; Djannati-Ataï, A.; Domainko, W.; Drury, L. O'c.; Dubois, F.; Dubus, G.; Dyks, J.; Dyrda, M.; Egberts, K.; Eger, P.; Espigat, P.; Fallon, L.; Farnier, C.; Fegan, S.; Feinstein, F.; Fiasson, A.; Förster, A.; Fontaine, G.; Füßling, M.; Gabici, S.; Gallant, Y. A.; Gérard, L.; Gerbig, D.; Giebels, B.; Glicenstein, J. F.; Glück, B.; Goret, P.; Göring, D.; Hauser, M.; Heinz, S.; Heinzelmann, G.; Henri, G.; Hermann, G.; Hinton, J. A.; Hoffmann, A.; Hofmann, W.; Hofverberg, P.; Holleran, M.; Hoppe, S.; Horns, D.; Jacholkowska, A.; de Jager, O. C.; Jahn, C.; Jung, I.; Katarzyński, K.; Katz, U.; Kaufmann, S.; Kerschhaggl, M.; Khangulyan, D.; Khélifi, B.; Keogh, D.; Klochkov, D.; Kluźniak, W.; Kneiske, T.; Komin, Nu.; Kosack, K.; Kossakowski, R.; Lamanna, G.; Lenain, J.-P.; Lohse, T.; Marandon, V.; Martineau-Huynh, O.; Marcowith, A.; Masbou, J.; Maurin, D.; McComb, T. J. L.; Medina, M. C.; Méhault, J.; Moderski, R.; Moulin, E.; Naumann-Godo, M.; de Naurois, M.; Nedbal, D.; Nekrassov, D.; Nicholas, B.; Niemiec, J.; Nolan, S. J.; Ohm, S.; Olive, J.-F.; de Oña Wilhelmi, E.; Orford, K. J.; Ostrowski, M.; Panter, M.; Arribas, M. Paz; Pedaletti, G.; Pelletier, G.; Petrucci, P.-O.; Pita, S.; Pühlhofer, G.; Punch, M.; Quirrenbach, A.; Raubenheimer, B. C.; Raue, M.; Rayner, S. M.; Reimer, O.; Renaud, M.; Rieger, F.; Ripken, J.; Rob, L.; Rosier-Lees, S.; Rowell, G.; Rudak, B.; Rulten, C. B.; Ruppel, J.; Ryde, F.; Sahakian, V.; Santangelo, A.; Schlickeiser, R.; Schöck, F. M.; Schönwald, A.; Schwanke, U.; Schwarzburg, S.; Schwemmer, S.; Shalchi, A.; Sikora, M.; Skilton, J. L.; Sol, H.; Stawarz, Ł.; Steenkamp, R.; Stegmann, C.; Stinzing, F.; Superina, G.; Sushch, I.; Szostek, A.; Tam, P. H.; Tavernet, J.-P.; Terrier, R.; Tibolla, O.; Tluczykont, M.; van Eldik, C.; Vasileiadis, G.; Venter, C.; Venter, L.; Vialle, J. P.; Vincent, P.; Vivier, M.; Völk, H. J.; Volpe, F.; Wagner, S. J.; Ward, M.; Zdziarski, A. A.; Zech, A.; H.E.S.S. Collaboration

    2010-03-01

    The inner 10pc of our Galaxy contains many counterpart candidates of the very high energy (VHE; >100GeV) γ-ray point source HESS J1745-290. Within the point spread function of the H.E.S.S. measurement, at least three objects are capable of accelerating particles to VHE and beyond and of providing the observed γ-ray flux. Previous attempts to address this source confusion were hampered by the fact that the projected distances between these objects were of the order of the error circle radius of the emission centroid (34arcsec, dominated by the pointing uncertainty of the H.E.S.S. instrument). Here we present H.E.S.S. data of the Galactic Centre region, recorded with an improved control of the instrument pointing compared to H.E.S.S. standard pointing procedures. Stars observed during γ-ray observations by optical guiding cameras mounted on each H.E.S.S. telescope are used for off-line pointing calibration, thereby decreasing the systematic pointing uncertainties from 20 to 6arcsec per axis. The position of HESS J1745-290 is obtained by fitting a multi-Gaussian profile to the background-subtracted γ-ray count map. A spatial comparison of the best-fitting position of HESS J1745-290 with the position and morphology of candidate counterparts is performed. The position is, within a total error circle radius of 13arcsec, coincident with the position of the supermassive black hole Sgr A* and the recently discovered pulsar wind nebula candidate G359.95-0.04. It is significantly displaced from the centroid of the supernova remnant Sgr A East, excluding this object with high probability as the dominant source of the VHE γ-ray emission.

  8. Polarization properties of localized structures in VCSELs

    NASA Astrophysics Data System (ADS)

    Averlant, Etienne; Tlidi, Mustapha; Ackemann, Thorsten; Thienpont, Hugo; Panajotov, Krassimir

    2016-04-01

    Broad area Vertical-Cavity Surface-Emitting Lasers (VCSELs) have peculiar polarization properties which are a field of study by itself.1-3 These properties have already been used for localized structure generation, in a simple configuration, where only one polarization component was used.4 Here, we present new experimental and theoretical results on the complex polarization behavior of localized structures generated in an optically-injected broad area VCSEL. A linear stability analysis of the spin-flip VCSEL model is performed for the case of broad area devices, in a restrained and experimentally relevant parameter set. Numerical simulations are performed, in one and two dimensions. They reveal existence of vector localized structures. These structures have a complex polarization state, which is not simply a linear polarization following the one of the optical injection. Experimental results confirm theoretical predictions. Applications of this work can lead to the encoding of small color images in the polarization state of an ensemble of localized structures at the surface of a broad area VCSEL.

  9. Integrated watershed management in Quebec (Canada): a participatory approach centred on local solidarity.

    PubMed

    Baril, P; Maranda, Y; Baudrand, J

    2006-01-01

    The Quebec Water Policy was launched in November 2002 in support of reform of the water governance. One of the government commitments is to gradually implement watershed-based management for 33 major watercourses located primarily in the St. Lawrence plain. At the local and regional levels, watershed organizations are responsible for implementing integrated management, from a sustainable-development perspective, by preparing a master plan for water (MPW), which will include watercourses, lakes, wetlands and aquifers. These watershed organizations rely on public consultation, as well as local and regional expertise, on the responsibilities for water of the municipalities and regional county municipalities of the territory, as well as those of the ministries and other government agencies. They are also required to observe national priorities regarding protection, restoration, and development of water resources and to comply with relevant guidelines, directives, standards, regulations, and legislation. The role of watershed organizations is to act as planning and consultation tables. Government representatives are present, on the initial process, as the facilitator and for scientific and technical support. They do not have, at this moment, any voting or decisional rights. After two years, integrated water management mobilized water stakeholders on watersheds and they are on their way to initiating their first MPW.

  10. Event-horizon-scale structure in the supermassive black hole candidate at the Galactic Centre.

    PubMed

    Doeleman, Sheperd S; Weintroub, Jonathan; Rogers, Alan E E; Plambeck, Richard; Freund, Robert; Tilanus, Remo P J; Friberg, Per; Ziurys, Lucy M; Moran, James M; Corey, Brian; Young, Ken H; Smythe, Daniel L; Titus, Michael; Marrone, Daniel P; Cappallo, Roger J; Bock, Douglas C-J; Bower, Geoffrey C; Chamberlin, Richard; Davis, Gary R; Krichbaum, Thomas P; Lamb, James; Maness, Holly; Niell, Arthur E; Roy, Alan; Strittmatter, Peter; Werthimer, Daniel; Whitney, Alan R; Woody, David

    2008-09-01

    The cores of most galaxies are thought to harbour supermassive black holes, which power galactic nuclei by converting the gravitational energy of accreting matter into radiation. Sagittarius A* (Sgr A*), the compact source of radio, infrared and X-ray emission at the centre of the Milky Way, is the closest example of this phenomenon, with an estimated black hole mass that is 4,000,000 times that of the Sun. A long-standing astronomical goal is to resolve structures in the innermost accretion flow surrounding Sgr A*, where strong gravitational fields will distort the appearance of radiation emitted near the black hole. Radio observations at wavelengths of 3.5 mm and 7 mm have detected intrinsic structure in Sgr A*, but the spatial resolution of observations at these wavelengths is limited by interstellar scattering. Here we report observations at a wavelength of 1.3 mm that set a size of 37(+16)(-10) microarcseconds on the intrinsic diameter of Sgr A*. This is less than the expected apparent size of the event horizon of the presumed black hole, suggesting that the bulk of Sgr A* emission may not be centred on the black hole, but arises in the surrounding accretion flow.

  11. FOLFIRINOX in Locally Advanced and Metastatic Pancreatic Cancer: A Single Centre Cohort Study

    PubMed Central

    Rombouts, SJ; Mungroop, TH; Heilmann, MN; van Laarhoven, HW; Busch, OR; Molenaar, IQ; Besselink, MG; Wilmink, JW

    2016-01-01

    Introduction: FOLFIRINOX is emerging as new standard of care for fit patients with locally advanced pancreatic cancer (LAPC) and metastatic pancreatic cancer (MPC). However, some of the physicians are reluctant to use FOLFIRINOX due to high toxicity rates reported in earlier studies. We reviewed our experience with FOLFIRINOX in LAPC and MPC, focussing on dose adjustments, toxicity and efficacy. Methods: We reviewed all patients with LAPC or MPC treated with FOLFIRINOX in our institution between April 2011 and December 2015. Unresectability (stage III and IV) was determined by the institution's multidisciplinary team for pancreatic cancer. Results: Fifty patients (18 LAPC and 32 MPC) were enrolled, with a median age of 55 years (IQR 49-66) and WHO performance status of 0/1. FOLFIRINOX was given as first-line treatment in 82% of patients. Dose modifications were applied in 90% of patients. The median number of completed cycles was 8 (IQR 5-9). Grade 3-4 toxicity occurred in 52% and grade 5 toxicity in 2%. The response rate was 25% (12% in LAPC, 32% in MPC). Median overall survival and progression-free survival were 14.8 and 10.3 months in LAPC, and 9.0 and 5.9 months in MPC, respectively. Overall 1- and 2-year survival was 65% and 10% in LAPC and 40% and 5% in MPC. Within the LAPC group, 6 patients (33%) underwent local ablative therapy and 1 patient (6%) a resection, leading to a median survival of 21.8 months. Conclusion: FOLFIRINOX treatment with nearly routine dose modification was associated with acceptable toxicity rates, relatively high response rates and an encouraging overall survival.

  12. Detecting structure of haplotypes and local ancestry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We present a two-layer hidden Markov model to detect the structure of haplotypes for unrelated individuals. This allows us to model two scales of linkage disequilibrium (one within a group of haplotypes and one between groups), thereby taking advantage of rich haplotype information to infer local an...

  13. The crystal structure of an oxygen-tolerant hydrogenase uncovers a novel iron-sulphur centre.

    PubMed

    Fritsch, Johannes; Scheerer, Patrick; Frielingsdorf, Stefan; Kroschinsky, Sebastian; Friedrich, Bärbel; Lenz, Oliver; Spahn, Christian M T

    2011-10-16

    Hydrogenases are abundant enzymes that catalyse the reversible interconversion of H(2) into protons and electrons at high rates. Those hydrogenases maintaining their activity in the presence of O(2) are considered to be central to H(2)-based technologies, such as enzymatic fuel cells and for light-driven H(2) production. Despite comprehensive genetic, biochemical, electrochemical and spectroscopic investigations, the molecular background allowing a structural interpretation of how the catalytic centre is protected from irreversible inactivation by O(2) has remained unclear. Here we present the crystal structure of an O(2)-tolerant [NiFe]-hydrogenase from the aerobic H(2) oxidizer Ralstonia eutropha H16 at 1.5 Å resolution. The heterodimeric enzyme consists of a large subunit harbouring the catalytic centre in the H(2)-reduced state and a small subunit containing an electron relay consisting of three different iron-sulphur clusters. The cluster proximal to the active site displays an unprecedented [4Fe-3S] structure and is coordinated by six cysteines. According to the current model, this cofactor operates as an electronic switch depending on the nature of the gas molecule approaching the active site. It serves as an electron acceptor in the course of H(2) oxidation and as an electron-delivering device upon O(2) attack at the active site. This dual function is supported by the capability of the novel iron-sulphur cluster to adopt three redox states at physiological redox potentials. The second structural feature is a network of extended water cavities that may act as a channel facilitating the removal of water produced at the [NiFe] active site. These discoveries will have an impact on the design of biological and chemical H(2)-converting catalysts that are capable of cycling H(2) in air.

  14. Offloading social care responsibilities: recent experiences of local voluntary organisations in a remote urban centre in British Columbia, Canada.

    PubMed

    Hanlon, Neil; Rosenberg, Mark; Clasby, Rachael

    2007-07-01

    Services offered by voluntary organisations are an integral but often overlooked component of health and social care. Of late, there has been a renewed interest in voluntary welfare provision as a viable alternative to state and market. Recent developments in welfare provision in Canada appear to have brought greater social care roles for the voluntary sector at the same time as new and arguably more restrictive funding and accountability mechanisms are being imposed by different arms of the state. To explore these issues more closely, the present paper examines the impressions and experiences of voluntary and formal sector providers of services for senior citizens and people with disabilities in a remote urban centre (population less than 100 000) in the interior of British Columbia, Canada. Two important operational pressures provide the context of the analysis: (1) reform of provincial government funding and regulation of voluntary services; and (2) the restructuring of welfare provision, especially in the areas of health care and social services. The authors found evidence of an escalating incursion of the state into local voluntary sector affairs that needs to be understood in the context of long-standing institutional links between government and 'professional' voluntary welfare provision in British Columbia. The results point to three important directions in contemporary local voluntary provision: (1) an emerging ethos of accountability, efficiency and competition in voluntary provision; (2) increasing pressure to centralise volunteer services; and consequently, (3) the potential erosion of flexibility and personalisation that are seen to characterise the voluntary sector. PMID:17578395

  15. Science Learning Centres Roundup

    ERIC Educational Resources Information Center

    Education in Science, 2010

    2010-01-01

    The national network of Science Learning Centres aims to raise the quality of science teaching from Key Stage 1 through post-16 (ages 5-19). Short courses are provided locally through the regional Science Learning Centres and longer, more intensive programmes are available at the National Science Learning Centre in York. There are a growing number…

  16. Finding local community structure in networks

    NASA Astrophysics Data System (ADS)

    Clauset, Aaron

    2005-08-01

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

  17. Structured Courses as a Strategy for Rural Development: A Case Study of the Kenya Farmer Training Centres.

    ERIC Educational Resources Information Center

    Mulusa, Thomas

    Using library search, structured interviews, mail questionnaires, and personal observations, Kenya's Farmer Training Centre (FTC) Program (a 30-year old experimental rural development strategy) was assessed in terms of its curriculum. How structured courses are utilized within the FTC program should be of interest to administrators, trainers, and…

  18. Guanine quadruplex structures localize to heterochromatin

    PubMed Central

    Hoffmann, Roland F.; Moshkin, Yuri M.; Mouton, Stijn; Grzeschik, Nicola A.; Kalicharan, Ruby D.; Kuipers, Jeroen; Wolters, Anouk H.G.; Nishida, Kazuki; Romashchenko, Aleksander V.; Postberg, Jan; Lipps, Hans; Berezikov, Eugene; Sibon, Ody C.M.; Giepmans, Ben N.G.; Lansdorp, Peter M.

    2016-01-01

    Increasing amounts of data support a role for guanine quadruplex (G4) DNA and RNA structures in various cellular processes. We stained different organisms with monoclonal antibody 1H6 specific for G4 DNA. Strikingly, immuno-electron microscopy showed exquisite specificity for heterochromatin. Polytene chromosomes from Drosophila salivary glands showed bands that co-localized with heterochromatin proteins HP1 and the SNF2 domain-containing protein SUUR. Staining was retained in SUUR knock-out mutants but lost upon overexpression of SUUR. Somatic cells in Macrostomum lignano were strongly labeled, but pluripotent stem cells labeled weakly. Similarly, germline stem cells in Drosophila ovaries were weakly labeled compared to most other cells. The unexpected presence of G4 structures in heterochromatin and the difference in G4 staining between somatic cells and stem cells with germline DNA in ciliates, flatworms, flies and mammals point to a conserved role for G4 structures in nuclear organization and cellular differentiation. PMID:26384414

  19. Gakkel Ridge at 85°E/85°N: Seismicity and Structure of an Ultraslow Spreading Centre

    NASA Astrophysics Data System (ADS)

    Korger, Edith; Schlindwein, Vera

    2014-05-01

    Ultraslow spreading ridges are divergent plate boundaries, which spread apart with less than 20 mm/yr. Their appearance is very rugged, with steep rift flanks, numerous normal faults and discontinuous volcanic activity at discrete volcanic centres - drastically different from ridges which spread faster. Due to the inaccessible area where these ridges are found, much less is know about lithospheric structure than at faster spreading ridges. Gakkel Ridge spans between Greenland and Siberia, crossing through the Arctic Ocean. There, a perennial ice cover inhibits seismic surveys. At 85°E/85°N where the spreading rate is only about 10.2 mm/yr, a volcanic spreading centre is located. It was spectacularly active in 1999, spawning over 250 teleseismically registered earthquakes with body wave magnitudes up to 5.2 and lasting 9 months. At this site, volcanic cones and fresh lava were captured by seafloor imagery in 2007. Making use of the ice cover, three arrays of four seismometers each were deployed in 2007 on ice floes, drifting 16 days over the area and recording more than 300 local events. Due to the drift of the ice floes, the location of the arrays changed with time, resulting in sufficient ray coverage suitable for a local earthquake tomography. We present here the results of this tomography, the first ever done at an ultraslow spreading centre. We compiled a 1D local velocity model from confidently located hypocentres. While incorporating the varying 3D bathymetry and the water layer, we used 124 microearthquakes which had been recorded by at least two arrays for generating a local 3D earthquake tomographic model. At spreading rates below 20 mm/yr it has been proposed that conductive heat loss should increase, leading to a thinner crust. Yet, our results infer a deep Moho at about 7 km beneath seafloor and hypocentres as deep as 16 km (bsf.) which implies an exceptionally thick crust and cold lithosphere. Theoretical thermal models for the axial lithospheric

  20. Localizing Target Structures in Ultrasound Video

    PubMed Central

    Kwitt, R.; Vasconcelos, N.; Razzaque, S.; Aylward, S.

    2013-01-01

    The problem of localizing specific anatomic structures using ultrasound (US) video is considered. This involves automatically determining when an US probe is acquiring images of a previously defined object of interest, during the course of an US examination. Localization using US is motivated by the increased availability of portable, low-cost US probes, which inspire applications where inexperienced personnel and even first-time users acquire US data that is then sent to experts for further assessment. This process is of particular interest for routine examinations in underserved populations as well as for patient triage after natural disasters and large-scale accidents, where experts may be in short supply. The proposed localization approach is motivated by research in the area of dynamic texture analysis and leverages several recent advances in the field of activity recognition. For evaluation, we introduce an annotated and publicly available database of US video, acquired on three phantoms. Several experiments reveal the challenges of applying video analysis approaches to US images and demonstrate that good localization performance is possible with the proposed solution. PMID:23746488

  1. Surgical education at Weill Bugando Medical Centre: supplementing surgical training and investing in local health care providers

    PubMed Central

    Mitchell, Katrina B.; Giiti, Geofrey; Kotecha, Vihar; Chandika, Alphonce; Pryor, Kane O.; Härtl, Roger; Gilyoma, Japhet

    2013-01-01

    Global surgery initiatives increasingly are focused on strengthening education and local health care systems to build surgical capacity. The goal of this education project was to support local health care providers in augmenting the surgical curriculum at a new medical school, thus promoting long-term local goals and involvement. Working with local surgeons, residents, and medical and assistant medical officer students, we identified the most common surgical conditions presenting to Weill Bugando Medical Centre in Mwanza, Tanzania, and the areas of greatest need in surgical education. We developed an 8-week teaching schedule for undergraduate students and an electronic database of clinical surgery topics. In addition, we started teaching basic surgical skills in the operating theatre, bridging to an official and recurring workshop through a supporting international surgery organization. The medical and assistant medical officer students reported increased satisfaction with their clinical surgery rotations and mastery of key educational subjects. The initiation of an Essential Surgical Skills workshop through the Canadian Network for International Surgery showed students had improved comfort with basic surgical techniques. Short-term surgical missions may appear to fill a void in the shortage of health care in the developing world. However, we conclude that global health resources are more appropriately used through projects giving ownership to local providers and promoting education as a foundation of development. This results in better coordination among local and visiting providers and greater impact on education and long-term growth of health care capacity. Les initiatives internationales en ce qui concerne la chirurgie sont de plus en plus axées sur le renforcement des programmes de formation et des systèmes de soins de santé locaux pour consolider les capacités dans ce domaine. L’objectif de ce projet éducatif était d’aider les professionnels de la

  2. New insights into the structure of the reaction centre from Blastochloris viridis: evolution in the laboratory.

    PubMed

    Roszak, Aleksander W; Moulisová, Vladimíra; Reksodipuro, Adhie D P; Gardiner, Alastair T; Fujii, Ritsuko; Hashimoto, Hideki; Isaacs, Neil W; Cogdell, Richard J

    2012-02-15

    Newly determined crystal structures of the photosynthetic RC (reaction centre) from two substrains of the non-sulfur purple bacterium Blastochloris viridis strain DSM 133, together with analysis of their gene sequences, has revealed intraspecies evolutionary changes over a period of 14 years. Over 100 point mutations were identified between these two substrains in the four genes encoding the protein subunits of the RC, of which approximately one-fifth resulted in a total of 16 amino acid changes. The most interesting difference was in the M subunit where the change from a leucine residue to glycine in the carotenoid-binding pocket allowed NS5 (1,2-dihydroneurosporene) to adopt a more sterically favoured conformation, similar to the carotenoid conformation found in other related RCs. The results of the present study, together with a high rate of mutations in laboratory bacterial cultures described recently, suggest that bacteria evolve faster than has been generally recognized. The possibility that amino acid changes occur within protein sequences, without exhibiting any immediately observable phenotype, should be taken into account in studies that involve long-term continuous growth of pure bacterial cultures. The Blc. viridis RC is often studied with sophisticated biophysical techniques and changes such as those described here may well affect their outcome. In other words, there is a danger that laboratory-to-laboratory variation could well be due to different groups not realising that they are actually working with slightly different proteins. A way around this problem is suggested.

  3. Luminescence and ESR studies of relationships between O(-)-centres and structural iron in natural and synthetically hydrated kaolinites.

    PubMed

    Coyne, L M; Costanzo, P M; Theng, B K

    1989-01-01

    Luminescence, induced by dehydration and by wetting with hydrazine and unsymmetrically substituted hydrazine, and related ESR spectra have been observed from several kaolinites, synthetically hydrated kaolinites, and metahalloysites. The amine-wetting luminescence results suggest that intercalation, not a chemiluminescence reaction, is the luminescence trigger. Correlation between hydration-induced luminescence and g = 2 ESR signals associated with O(-)-centres in several natural halloysites, and concurrent diminution of the intensity of both these signal types as a function of aging in two 8.4 angstroms synthetically hydrated, kaolinites, confirm a previously-reported relationship between the luminescence induced by dehydration and in the presence of O(-)-centres (holes, i.e., electron vacancies) in the tetrahedral sheet. Furthermore, the ESR spectra of the 8.4 angstroms hydrate showed a concurrent change in the line shape of the g = 4 signal from a shape usually associated with structural Fe in an ordered kaolinite, to a simpler one typically observed in more disordered kaolinite, halloysite, and montmorillonite. Either structural Fe centres and the O(-)-centres interact, or both are subject to factors previously associated with degree of order. The results question the long-term stability of the 8.4 angstroms hydrate, although XRD does not indicate interlayer collapse over this period. Complex inter-relationships are shown between intercalation, stored energy, structural Fe, and the degree of hydration which may be reflected in catalytic as well as spectroscopic properties of the clays.

  4. Luminescence and ESR studies of relationships between O(-)-centres and structural iron in natural and synthetically hydrated kaolinites

    NASA Technical Reports Server (NTRS)

    Coyne, L. M.; Costanzo, P. M.; Theng, B. K.

    1989-01-01

    Luminescence, induced by dehydration and by wetting with hydrazine and unsymmetrically substituted hydrazine, and related ESR spectra have been observed from several kaolinites, synthetically hydrated kaolinites, and metahalloysites. The amine-wetting luminescence results suggest that intercalation, not a chemiluminescence reaction, is the luminescence trigger. Correlation between hydration-induced luminescence and g = 2 ESR signals associated with O(-)-centres in several natural halloysites, and concurrent diminution of the intensity of both these signal types as a function of aging in two 8.4 angstroms synthetically hydrated, kaolinites, confirm a previously-reported relationship between the luminescence induced by dehydration and in the presence of O(-)-centres (holes, i.e., electron vacancies) in the tetrahedral sheet. Furthermore, the ESR spectra of the 8.4 angstroms hydrate showed a concurrent change in the line shape of the g = 4 signal from a shape usually associated with structural Fe in an ordered kaolinite, to a simpler one typically observed in more disordered kaolinite, halloysite, and montmorillonite. Either structural Fe centres and the O(-)-centres interact, or both are subject to factors previously associated with degree of order. The results question the long-term stability of the 8.4 angstroms hydrate, although XRD does not indicate interlayer collapse over this period. Complex inter-relationships are shown between intercalation, stored energy, structural Fe, and the degree of hydration which may be reflected in catalytic as well as spectroscopic properties of the clays.

  5. [The coordination of care in health centres].

    PubMed

    Ribardière, Olivia

    2016-06-01

    Health centres are structurally designed to facilitate the coordination of care. However, evolutions in society have resulted in forms of consumption of health care which are not necessarily compatible with efficient care coordination. On a local level, teams are nevertheless organising and structuring themselves to offer the right form of care, to the right patient and at the right time.

  6. The structure of locally bounded finite-dimensional representations of connected locally compact groups

    SciTech Connect

    Shtern, A. I.

    2014-04-30

    An analogue of a Lie theorem is obtained for (not necessarily continuous) finite-dimensional representations of soluble finite-dimensional locally compact groups with connected quotient group by the centre. As a corollary, the following automatic continuity proposition is obtained for locally bounded finite-dimensional representations of connected locally compact groups: if G is a connected locally compact group, N is a compact normal subgroup of G such that the quotient group G/N is a Lie group, N{sub 0} is the connected identity component in N, H is the family of elements of G commuting with every element of N{sub 0}, and π is a (not necessarily continuous) locally bounded finite-dimensional representation of G, then π is continuous on the commutator subgroup of H (in the intrinsic topology of the smallest analytic subgroup of G containing this commutator subgroup). Bibliography: 23 titles. (paper)

  7. Effects of closure of an urban level I trauma centre on adjacent hospitals and local injury mortality: a retrospective, observational study

    PubMed Central

    Crandall, Marie; Sharp, Douglas; Wei, Xiong; Nathens, Avery; Hsia, Renee Y

    2016-01-01

    Objective To determine the association of the Martin Luther King Jr Hospital (MLK) closure on the distribution of admissions on adjacent trauma centres, and injury mortality rates in these centres and within the county. Design Observational, retrospective study. Setting Non-public patient-level data from the state of California were obtained for all trauma patients from 1999 to 2009. Geospatial analysis was used to visualise the redistribution of trauma patients to other hospitals after MLK closed. Variance of observed to expected injury mortality using multivariate logistic regression was estimated for the study period. Participants A total of 37 131 trauma patients were admitted to the five major south Los Angeles trauma centres from the MLK service area between 1999 and 2009. Main outcome measures (1) Number and type of trauma admissions to trauma centres in closest proximity to MLK; (2) inhospital injury mortality of trauma patients after the trauma centre closure. Results During and after the MLK closure, trauma admissions increased at three of the four nearby hospitals, particularly admissions for gunshot wounds (GSWs). This redistribution of patient load was accompanied by a dramatic change in the payer mix for surrounding hospitals; one hospital's share of uninsured more than tripled from 12.9% in 1999 to 44.6% by 2009. Overall trauma mortality did not significantly change, but GSW mortality steadily and significantly increased after the closure from 5.0% in 2007 to 7.5% in 2009. Conclusions Though local hospitals experienced a dramatic increase in trauma patient volume, overall mortality for trauma patients did not significantly change after MLK closed. PMID:27165650

  8. A neural-network reinforcement-learning model of domestic chicks that learn to localize the centre of closed arenas.

    PubMed

    Mannella, Francesco; Baldassarre, Gianluca

    2007-03-29

    Previous experiments have shown that when domestic chicks (Gallus gallus) are first trained to locate food elements hidden at the centre of a closed square arena and then are tested in a square arena of double the size, they search for food both at its centre and at a distance from walls similar to the distance of the centre from the walls experienced during training. This paper presents a computational model that successfully reproduces these behaviours. The model is based on a neural-network implementation of the reinforcement-learning actor - critic architecture (in this architecture the 'critic' learns to evaluate perceived states in terms of predicted future rewards, while the 'actor' learns to increase the probability of selecting the actions that lead to higher evaluations). The analysis of the model suggests which type of information and cognitive mechanisms might underlie chicks' behaviours: (i) the tendency to explore the area at a specific distance from walls might be based on the processing of the height of walls' horizontal edges, (ii) the capacity to generalize the search at the centre of square arenas independently of their size might be based on the processing of the relative position of walls' vertical edges on the horizontal plane (equalization of walls' width), and (iii) the whole behaviour exhibited in the large square arena can be reproduced by assuming the existence of an attention process that, at each time, focuses chicks' internal processing on either one of the two previously discussed information sources. The model also produces testable predictions regarding the generalization capabilities that real chicks should exhibit if trained in circular arenas of varying size. The paper also highlights the potentialities of the model to address other experiments on animals' navigation and analyses its strengths and weaknesses in comparison to other models. PMID:17255019

  9. The effect of local symmetry on the energetic position of DX centres in (AlxGa1-x)As and Ga(As1-xPx) alloys

    NASA Astrophysics Data System (ADS)

    Sallese, J. M.; Maude, D. K.; Fille, M. L.; Willke, U.; Gibart, P.; Portal, J. C.

    1992-10-01

    The ionization energy of DX centres in Ga(As,P) is shown to depend upon the chemical nature of the substitutional n-type impurity. Tellurium in Ga(As,P) introduces a DX centre lying at about 100 meV higher than the DX centres associated with other n-type impurities (Si or Sn). A comparative study between Ga(As,P) and (Al,Ga)As alloys confirms that the ionization energy of the tellurium-related DX centre is very sensitive to the local environment of the impurity.

  10. Local conservation laws and the structure of the many-body localized states.

    PubMed

    Serbyn, Maksym; Papić, Z; Abanin, Dmitry A

    2013-09-20

    We construct a complete set of local integrals of motion that characterize the many-body localized (MBL) phase. Our approach relies on the assumption that local perturbations act locally on the eigenstates in the MBL phase, which is supported by numerical simulations of the random-field XXZ spin chain. We describe the structure of the eigenstates in the MBL phase and discuss the implications of local conservation laws for its nonequilibrium quantum dynamics. We argue that the many-body localization can be used to protect coherence in the system by suppressing relaxation between eigenstates with different local integrals of motion.

  11. Invariant current approach to wave propagation in locally symmetric structures

    NASA Astrophysics Data System (ADS)

    Zampetakis, V. E.; Diakonou, M. K.; Morfonios, C. V.; Kalozoumis, P. A.; Diakonos, F. K.; Schmelcher, P.

    2016-05-01

    A theory for wave mechanical systems with local inversion and translation symmetries is developed employing the two-dimensional solution space of the stationary Schrödinger equation. The local symmetries of the potential are encoded into corresponding local basis vectors in terms of symmetry-induced two-point invariant currents which map the basis amplitudes between symmetry-related points. A universal wavefunction structure in locally symmetric potentials is revealed, independently of the physical boundary conditions, by using special local bases which are adapted to the existing local symmetries. The local symmetry bases enable efficient computation of spatially resolved wave amplitudes in systems with arbitrary combinations of local inversion and translation symmetries. The approach opens the perspective of a flexible analysis and control of wave localization in structurally complex systems.

  12. Local and bulk (13)C hyperpolarization in nitrogen-vacancy-centred diamonds at variable fields and orientations.

    PubMed

    Álvarez, Gonzalo A; Bretschneider, Christian O; Fischer, Ran; London, Paz; Kanda, Hisao; Onoda, Shinobu; Isoya, Junichi; Gershoni, David; Frydman, Lucio

    2015-01-01

    Polarizing nuclear spins is of fundamental importance in biology, chemistry and physics. Methods for hyperpolarizing (13)C nuclei from free electrons in bulk usually demand operation at cryogenic temperatures. Room temperature approaches targeting diamonds with nitrogen-vacancy centres could alleviate this need; however, hitherto proposed strategies lack generality as they demand stringent conditions on the strength and/or alignment of the magnetic field. We report here an approach for achieving efficient electron-(13)C spin-alignment transfers, compatible with a broad range of magnetic field strengths and field orientations with respect to the diamond crystal. This versatility results from combining coherent microwave- and incoherent laser-induced transitions between selected energy states of the coupled electron-nuclear spin manifold. (13)C-detected nuclear magnetic resonance experiments demonstrate that this hyperpolarization can be transferred via first-shell or via distant (13)Cs throughout the nuclear bulk ensemble. This method opens new perspectives for applications of diamond nitrogen-vacancy centres in nuclear magnetic resonance, and in quantum information processing. PMID:26404169

  13. Local and bulk 13C hyperpolarization in nitrogen-vacancy-centred diamonds at variable fields and orientations

    PubMed Central

    Álvarez, Gonzalo A.; Bretschneider, Christian O.; Fischer, Ran; London, Paz; Kanda, Hisao; Onoda, Shinobu; Isoya, Junichi; Gershoni, David; Frydman, Lucio

    2015-01-01

    Polarizing nuclear spins is of fundamental importance in biology, chemistry and physics. Methods for hyperpolarizing 13C nuclei from free electrons in bulk usually demand operation at cryogenic temperatures. Room temperature approaches targeting diamonds with nitrogen-vacancy centres could alleviate this need; however, hitherto proposed strategies lack generality as they demand stringent conditions on the strength and/or alignment of the magnetic field. We report here an approach for achieving efficient electron-13C spin-alignment transfers, compatible with a broad range of magnetic field strengths and field orientations with respect to the diamond crystal. This versatility results from combining coherent microwave- and incoherent laser-induced transitions between selected energy states of the coupled electron–nuclear spin manifold. 13C-detected nuclear magnetic resonance experiments demonstrate that this hyperpolarization can be transferred via first-shell or via distant 13Cs throughout the nuclear bulk ensemble. This method opens new perspectives for applications of diamond nitrogen-vacancy centres in nuclear magnetic resonance, and in quantum information processing. PMID:26404169

  14. Structural, magnetic and optical properties of Rh2+ centres in NaCl lattices: An explanation

    NASA Astrophysics Data System (ADS)

    Barriuso, M. T.; Fernandez, P. G.; Aramburu, J. A.; Moreno, M.

    2003-01-01

    A method for exploring Jahn-Teller systems in the framework of Density Functional Theory is described in the present work. Using such a method the properties of the Rh2+ centre in NaCl with remote charge compensation are studied. The calculations support the existence of a strong Jahn-Teller effect and account reasonably for the main features of EPR and optical spectra. The onset of charge transfer excitations is calculated to be at about 3.7 eV a fact which concurs with available experimental data. The elongated geometry is found to be about 200 cm(-1) more stable than the compressed one in agreement with experiments.

  15. Structures of Local Rearrangements in Soft Colloidal Glasses.

    PubMed

    Yang, Xiunan; Liu, Rui; Yang, Mingcheng; Wang, Wei-Hua; Chen, Ke

    2016-06-10

    We image local structural rearrangements in soft colloidal glasses under small periodic perturbations induced by thermal cycling. Local structural entropy S_{2} positively correlates with observed rearrangements in colloidal glasses. The high S_{2} values of the rearranging clusters in glasses indicate that fragile regions in glasses are structurally less correlated, similar to structural defects in crystalline solids. Slow-evolving high S_{2} spots are capable of predicting local rearrangements long before the relaxations occur, while fluctuation-created high S_{2} spots best correlate with local deformations right before the rearrangement events. Local free volumes are also found to correlate with particle rearrangements at extreme values, although the ability to identify relaxation sites is substantially lower than S_{2}. Our experiments provide an efficient structural identifier for the fragile regions in glasses and highlight the important role of structural correlations in the physics of glasses. PMID:27341261

  16. Structural characterization of the melano-macrophage centres (MMC) of goldfish Carassius auratus.

    PubMed

    Herráez, M P; Zapata, A G

    1991-01-01

    In the present work we have studied the organization of melano-macrophage centres (MMCs) in the peripheral lymphoid organs, including spleen, pro- and mesonephros, of the goldfish, Carassius auratus, in an attempt to clarify their cellular composition, origins and functional relationships. Histological analysis demonstrated a similar organization in the three organs on the basis of closely packed phagocytic cells containing abundant pigment. The MMCs of Carassius auratus are found throughout the parenchyma of spleen and kidney and show a close association with the vascular system, i.e. splenic ellipsoids, sinusoids of red pulp and renal blood sinuses. They exhibit distinct degree of development from small groups of actively phagocytic macrophages to large, totally or partially encapsulated centres, where effete phagocytic cells are filled by cell debris. Ultrastructural and histochemical data suggest that the main inclusion observed in the MMCs of Carassius auratus is lipofuscin. Haemosiderin occurs in lesser amounts and melanin is almost restricted to kidney MMCs,--mainly mesonephros--. Our results suggest various non-specific physiological roles for the teleost MMCs, including tissue breakdown and erythrocyte catabolism.

  17. Optimisation of the usage of LHC and local computing resources in a multidisciplinary physics department hosting a WLCG Tier-2 centre

    NASA Astrophysics Data System (ADS)

    Barberis, Stefano; Carminati, Leonardo; Leveraro, Franco; Mazza, Simone Michele; Perini, Laura; Perlz, Francesco; Rebatto, David; Tura, Ruggero; Vaccarossa, Luca; Villaplana, Miguel

    2015-12-01

    We present the approach of the University of Milan Physics Department and the local unit of INFN to allow and encourage the sharing among different research areas of computing, storage and networking resources (the largest ones being those composing the Milan WLCG Tier-2 centre and tailored to the needs of the ATLAS experiment). Computing resources are organised as independent HTCondor pools, with a global master in charge of monitoring them and optimising their usage. The configuration has to provide satisfactory throughput for both serial and parallel (multicore, MPI) jobs. A combination of local, remote and cloud storage options are available. The experience of users from different research areas operating on this shared infrastructure is discussed. The promising direction of improving scientific computing throughput by federating access to distributed computing and storage also seems to fit very well with the objectives listed in the European Horizon 2020 framework for research and development.

  18. Local structure of equality constrained NLP problems

    SciTech Connect

    Mari, J.

    1994-12-31

    We show that locally around a feasible point, the behavior of an equality constrained nonlinear program is described by the gradient and the Hessian of the Lagrangian on the tangent subspace. In particular this holds true for reduced gradient approaches. Applying the same ideas to the control of nonlinear ODE:s, one can device first and second order methods that can be applied also to stiff problems. We finally describe an application of these ideas to the optimization of the production of human growth factor by fed-batch fermentation.

  19. Enhancing community detection by using local structural information

    NASA Astrophysics Data System (ADS)

    Xiang, Ju; Hu, Ke; Zhang, Yan; Bao, Mei-Hua; Tang, Liang; Tang, Yan-Ni; Gao, Yuan-Yuan; Li, Jian-Ming; Chen, Benyan; Hu, Jing-Bo

    2016-03-01

    Many real-world networks, such as gene networks, protein-protein interaction networks and metabolic networks, exhibit community structures, meaning the existence of groups of densely connected vertices in the networks. Many local similarity measures in the networks are closely related to the concept of the community structures, and may have a positive effect on community detection in the networks. Here, various local similarity measures are used to extract local structural information, which is then applied to community detection in the networks by using the edge-reweighting strategy. The effect of the local similarity measures on community detection is carefully investigated and compared in various networks. The experimental results show that the local similarity measures are crucial for the improvement of community detection methods, while the positive effect of the local similarity measures is closely related to the networks under study and applied community detection methods.

  20. Phonon localization in ultrathin layered structures

    NASA Astrophysics Data System (ADS)

    Döring, F.; Eberl, C.; Schlenkrich, S.; Schlenkrich, F.; Hoffmann, S.; Liese, T.; Krebs, H. U.; Pisana, S.; Santos, T.; Schuhmann, H.; Seibt, M.; Mansurova, M.; Ulrichs, H.; Zbarsky, V.; Münzenberg, M.

    2015-04-01

    An efficient way for minimizing phonon thermal conductivity in solids is to nanostructure them by means of reduced phonon mean free path, phonon scattering and phonon reflection at interfaces. A sophisticated approach toward this lies in the fabrication of thin multilayer films of different materials. In this paper, we show by femtosecond-pump-probe reflectivity measurements that in different multilayer systems with varying acoustic mismatch (consisting of metals, semiconductors, oxides and polymers), oscillations due to phonon localization can be observed. For the growth of multilayer films with well-defined layer thicknesses, we used magnetron sputtering, evaporation and pulsed laser deposition. By altering the material combinations and reducing the layer thicknesses down to 3 nm, we observed different mechanisms of phonon blocking, reaching in the frequency regime up to 360 GHz.

  1. Local Structural Alignment of RNA with Affine Gap Model

    NASA Astrophysics Data System (ADS)

    Wong, Thomas K. F.; Cheung, Brenda W. Y.; Lam, T. W.; Yiu, S. M.

    Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps. In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem. Based on a preliminary experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model.

  2. Local gravity and large-scale structure

    NASA Technical Reports Server (NTRS)

    Juszkiewicz, Roman; Vittorio, Nicola; Wyse, Rosemary F. G.

    1990-01-01

    The magnitude and direction of the observed dipole anisotropy of the galaxy distribution can in principle constrain the amount of large-scale power present in the spectrum of primordial density fluctuations. This paper confronts the data, provided by a recent redshift survey of galaxies detected by the IRAS satellite, with the predictions of two cosmological models with very different levels of large-scale power: the biased Cold Dark Matter dominated model (CDM) and a baryon-dominated model (BDM) with isocurvature initial conditions. Model predictions are investigated for the Local Group peculiar velocity, v(R), induced by mass inhomogeneities distributed out to a given radius, R, for R less than about 10,000 km/s. Several convergence measures for v(R) are developed, which can become powerful cosmological tests when deep enough samples become available. For the present data sets, the CDM and BDM predictions are indistinguishable at the 2 sigma level and both are consistent with observations. A promising discriminant between cosmological models is the misalignment angle between v(R) and the apex of the dipole anisotropy of the microwave background.

  3. Local Influence Analysis of Nonlinear Structural Equation Models

    ERIC Educational Resources Information Center

    Lee, Sik-Yum; Tang, Nian-Sheng

    2004-01-01

    By regarding the latent random vectors as hypothetical missing data and based on the conditional expectation of the complete-data log-likelihood function in the EM algorithm, we investigate assessment of local influence of various perturbation schemes in a nonlinear structural equation model. The basic building blocks of local influence analysis…

  4. Automated Localization of Multiple Pelvic Bone Structures on MRI.

    PubMed

    Onal, Sinan; Lai-Yuen, Susana; Bao, Paul; Weitzenfeld, Alfredo; Hart, Stuart

    2016-01-01

    In this paper, we present a fully automated localization method for multiple pelvic bone structures on magnetic resonance images (MRI). Pelvic bone structures are at present identified manually on MRI to locate reference points for measurement and evaluation of pelvic organ prolapse (POP). Given that this is a time-consuming and subjective procedure, there is a need to localize pelvic bone structures automatically. However, bone structures are not easily differentiable from soft tissue on MRI as their pixel intensities tend to be very similar. In this paper, we present a model that combines support vector machines and nonlinear regression capturing global and local information to automatically identify the bounding boxes of bone structures on MRI. The model identifies the location of the pelvic bone structures by establishing the association between their relative locations and using local information such as texture features. Results show that the proposed method is able to locate the bone structures of interest accurately (dice similarity index >0.75) in 87-91% of the images. This research aims to enable accurate, consistent, and fully automated localization of bone structures on MRI to facilitate and improve the diagnosis of health conditions such as female POP.

  5. Charge distribution as a tool to investigate structural details. III. Extension to description in terms of anion-centred polyhedra.

    PubMed

    Eon, Jean-Guillaume; Nespolo, Massimo

    2015-02-01

    The charge distribution (CHARDI) method is a self-consistent generalization of Pauling's concept of bond strength which does not make use of empirical parameters but exploits the experimental geometry of the coordination polyhedra building a crystal structure. In the two previous articles of this series [Nespolo et al. (1999). Acta Cryst. B55, 902-916; Nespolo et al. (2001). Acta Cryst. B57, 652-664], we have presented the features and advantages of this approach and its extension to distorted and heterovalent polyhedra and to hydrogen bonds. In this third article we generalize CHARDI to structures based on anion-centred polyhedra, which have drawn attention in recent years, and we show that computations based on both descriptions can be useful to obtain a deeper insight into the structural details, in particular for mixed-valence compounds where CHARDI is able to give precise indications on the statistical distribution of atoms with different oxidation number. A graph-theoretical description of the structures rationalizes and gives further support to the conclusions obtained via the CHARDI approach.

  6. Deriving quantum theory from its local structure and reversibility.

    PubMed

    de la Torre, Gonzalo; Masanes, Lluís; Short, Anthony J; Müller, Markus P

    2012-08-31

    We investigate the class of physical theories with the same local structure as quantum theory but potentially different global structure. It has previously been shown that any bipartite correlations generated by such a theory can be simulated in quantum theory but that this does not hold for tripartite correlations. Here we explore whether imposing an additional constraint on this space of theories-that of dynamical reversibility-will allow us to recover the global quantum structure. In the particular case in which the local systems are identical qubits, we show that any theory admitting at least one continuous reversible interaction must be identical to quantum theory.

  7. Structure of local interactions in complex financial dynamics

    PubMed Central

    Jiang, X. F.; Chen, T. T.; Zheng, B.

    2014-01-01

    With the network methods and random matrix theory, we investigate the interaction structure of communities in financial markets. In particular, based on the random matrix decomposition, we clarify that the local interactions between the business sectors (subsectors) are mainly contained in the sector mode. In the sector mode, the average correlation inside the sectors is positive, while that between the sectors is negative. Further, we explore the time evolution of the interaction structure of the business sectors, and observe that the local interaction structure changes dramatically during a financial bubble or crisis. PMID:24936906

  8. An online substructure identification method for local structural health monitoring

    NASA Astrophysics Data System (ADS)

    Hou, Jilin; Jankowski, Łukasz; Ou, Jinping

    2013-09-01

    This paper proposes a substructure isolation method, which uses time series of measured local response for online monitoring of substructures. The proposed monitoring process consists of two key steps: construction of the isolated substructure, and its identification. The isolated substructure is an independent virtual structure, which is numerically isolated from the global structure by placing virtual supports on the interface. First, the isolated substructure is constructed by a specific linear combination of time series of its measured local responses. Then, the isolated substructure is identified using its local natural frequencies extracted from the combined responses. The substructure is assumed to be linear; the outside part of the global structure can have any characteristics. The method has no requirements on the initial state of the structure, and so the process can be carried out repetitively for online monitoring. Online isolation and monitoring is illustrated in a numerical example with a frame model, and then verified in a cantilever beam experiment.

  9. Reconstruction of biofilm images: combining local and global structural parameters

    SciTech Connect

    Resat, Haluk; Renslow, Ryan S.; Beyenal, Haluk

    2014-11-07

    Digitized images can be used for quantitative comparison of biofilms grown under different conditions. Using biofilm image reconstruction, it was previously found that biofilms with a completely different look can have nearly identical structural parameters and that the most commonly utilized global structural parameters were not sufficient to uniquely define these biofilms. Here, additional local and global parameters are introduced to show that these parameters considerably increase the reliability of the image reconstruction process. Assessment using human evaluators indicated that the correct identification rate of the reconstructed images increased from 50% to 72% with the introduction of the new parameters into the reconstruction procedure. An expanded set of parameters especially improved the identification of biofilm structures with internal orientational features and of structures in which colony sizes and spatial locations varied. Hence, the newly introduced structural parameter sets helped to better classify the biofilms by incorporating finer local structural details into the reconstruction process.

  10. Effects of Temperature on Structure and Mobility of the <100> Edge Dislocation in Body-Centred Cubic Iron

    SciTech Connect

    Terentyev, Dmitry; Osetskiy, Yury N; Bacon, David J

    2010-01-01

    Dislocation segments with Burgers vector b = <1 0 0> are formed during deformation of body-centred-cubic (bcc) metals by the interaction between dislocations with b = 1/2<1 1 1>. Such segments are also created by reactions between dislocations and dislocation loops in irradiated bcc metals. The obstacle resistance produced by these segments on gliding dislocations is controlled by their mobility, which is determined in turn by the atomic structure of their cores. The core structure of a straight <1 0 0> edge dislocation is investigated here by atomic-scale computer simulation for {alpha}-iron using three different interatomic potentials. At low temperature the dislocation has a non-planar core consisting of two 1/2<1 1 1> fractional dislocations with atomic disregistry spread on planes inclined to the main glide plane. Increasing temperature modifies this core structure and so reduces the critical applied shear stress for glide of the <1 0 0> dislocation. It is concluded that the response of the <1 0 0> edge dislocation to temperature or applied stress determines specific reaction pathways occurring between a moving dislocation and 1/2<1 1 1> dislocation loops. The implications of this for plastic flow in unirradiated and irradiated ferritic materials are discussed and demonstrated by examples.

  11. Vision ergonomics at recycling centres.

    PubMed

    Hemphälä, Hillevi; Kihlstedt, Annika; Eklund, Jörgen

    2010-05-01

    All municipalities in Sweden offer their inhabitants a service for disposing of large-size and hazardous waste at local recycling centres. Opening hours at these centres include hours of darkness. The aims of this study were to 1) describe user and employee experiences of lighting and signs at Swedish recycling centres, 2) measure and assess the lighting system at the two recently built recycling centres in Linköping and to assess the legibility and visibility of the signs used and 3) propose recommendations regarding lighting and signs for recycling centres. Interviews and questionnaires were used to assess experiences of employees and users, and light measurements were performed. By observing users, activities with different visual demands at different areas within the recycling centres were identified. Based on the literature, standards and stakeholder experiences, recommendations regarding lighting systems and sign design, illuminance, luminance and uniformity are proposed for recycling centres.

  12. Periodic colour-centre structure formed under filamentation of mid-IR femtosecond laser radiation in a LiF crystal

    NASA Astrophysics Data System (ADS)

    Kuznetsov, A. V.; Kompanets, V. O.; Dormidonov, A. E.; Chekalin, S. V.; Shlenov, S. A.; Kandidov, V. P.

    2016-04-01

    A colour-centre structure formed in a LiF crystal under filamentation of a femtosecond mid-IR laser pulse with a power slightly exceeding the critical power for self-focusing has been experimentally and theoretically investigated. Strictly periodic oscillations have been detected for the first time for the density of the colour centres induced in an isotropic LiF crystal under filamentation of a laser beam with a wavelength tuned in the range from 2600 to 3350 nm. The structure period is found to be about 30 μm. With an increase in the laser radiation wavelength, the period of the oscillations decreases and their amplitude increases. The maximum colour centre density, observed under filamentation of a 3100-nm beam, is related to the increased contribution of the direct generation of colour centres as a result of the absorption of an integer number of photons by the exciton band. It is numerically shown that the formation of a periodic colour-centre structure in LiF is due to the periodic change in the light field amplitude in the light bullet (1.5 optical periods long) formed under filamentation.

  13. Structural and functional coupling of Hsp90- and Sgt1-centred multi-protein complexes.

    PubMed

    Zhang, Minghao; Botër, Marta; Li, Kuoyu; Kadota, Yasuhiro; Panaretou, Barry; Prodromou, Chrisostomos; Shirasu, Ken; Pearl, Laurence H

    2008-10-22

    Sgt1 is an adaptor protein implicated in a variety of processes, including formation of the kinetochore complex in yeast, and regulation of innate immunity systems in plants and animals. Sgt1 has been found to associate with SCF E3 ubiquitin ligases, the CBF3 kinetochore complex, plant R proteins and related animal Nod-like receptors, and with the Hsp90 molecular chaperone. We have determined the crystal structure of the core Hsp90-Sgt1 complex, revealing a distinct site of interaction on the Hsp90 N-terminal domain. Using the structure, we developed mutations in Sgt1 interfacial residues, which specifically abrogate interaction with Hsp90, and disrupt Sgt1-dependent functions in vivo, in plants and yeast. We show that Sgt1 bridges the Hsp90 molecular chaperone system to the substrate-specific arm of SCF ubiquitin ligase complexes, suggesting a role in SCF assembly and regulation, and providing multiple complementary routes for ubiquitination of Hsp90 client proteins. PMID:18818696

  14. Implementing Responsibility Centre Budgeting

    ERIC Educational Resources Information Center

    Vonasek, Joseph

    2011-01-01

    Recently, institutes of higher education (universities) have shown a renewed interest in organisational structures and operating methodologies that generate productivity and innovation; responsibility centre budgeting (RCB) is one such process. This paper describes the underlying principles constituting RCB, its origin and structural elements, and…

  15. Local flow structures defined by kinematic events in isotropic turbulence

    NASA Technical Reports Server (NTRS)

    Adrian, R. J.; Ditter, J. L.

    1988-01-01

    The spatial structure of turbulent motion in incompressible isotropic turbulence is investigated using a conditional average in which the conditional event specifies the local deformation tensor in addition to the local velocity vector. This average gives the best estimate of the flow field around a fixed point x given the kinematic state at x. Estimates are calculated for various kinematic states in isotropic turbulence, including pure translation, pure shear, plane strain, axisymmetric strain, and pure rotation. It is demonstrated that the large-scale motion is dominated by a vortex ring structure associated with the translational component, except at critical points of the velocity vector field.

  16. Our Milky Way structure in the context of local galaxies

    NASA Astrophysics Data System (ADS)

    Shen, Juntai

    2015-08-01

    The Milky Way is the closest galaxy to us, and has been studied extensively due to its proximity. Understanding its structure and dynamics will help us understand spiral galaxies in general. I will review the latest research progress in the structure, kinematics, and dynamics of the Milky Way in the context of local galaxies. I will cover most structural components (the bulge/bar, disk, and spiral structures) and discuss the implications of some new results on the formation history of our home galaxy.

  17. A novel method to compare protein structures using local descriptors

    PubMed Central

    2011-01-01

    Background Protein structure comparison is one of the most widely performed tasks in bioinformatics. However, currently used methods have problems with the so-called "difficult similarities", including considerable shifts and distortions of structure, sequential swaps and circular permutations. There is a demand for efficient and automated systems capable of overcoming these difficulties, which may lead to the discovery of previously unknown structural relationships. Results We present a novel method for protein structure comparison based on the formalism of local descriptors of protein structure - DEscriptor Defined Alignment (DEDAL). Local similarities identified by pairs of similar descriptors are extended into global structural alignments. We demonstrate the method's capability by aligning structures in difficult benchmark sets: curated alignments in the SISYPHUS database, as well as SISY and RIPC sets, including non-sequential and non-rigid-body alignments. On the most difficult RIPC set of sequence alignment pairs the method achieves an accuracy of 77% (the second best method tested achieves 60% accuracy). Conclusions DEDAL is fast enough to be used in whole proteome applications, and by lowering the threshold of detectable structure similarity it may shed additional light on molecular evolution processes. It is well suited to improving automatic classification of structure domains, helping analyze protein fold space, or to improving protein classification schemes. DEDAL is available online at http://bioexploratorium.pl/EP/DEDAL. PMID:21849047

  18. Cosmic Flows and the Structure of the Local Universe

    NASA Astrophysics Data System (ADS)

    Steinmetz, Matthias

    2016-03-01

    The Local Volume is the area of the cosmos we can analyze in most detail with respect to the properties of its galaxy population, their abundance, their inner structure, their distribution, and their formation. Indeed, many challenges of the cosmological concordance model such as the substructure crisis or the surprising occurrence of vast planes of satellite galaxies are intimately linked to observations of the local galaxy population. However, owing to the peculiar environment of our Milky Way system and its cosmic neighborhood, the Local Volume may also be severely biased. Cosmography, i.e. the reconstruction of the local cosmic web from cosmic flows, and constrained simulations of structure formation as a tool to produce simulated local group analogues provide a powerful method to analyze and quantify these biases. Possible applications include the analysis of the local distribution of dwarf galaxies around luminous galaxies and the characterization of the mass accretion history of these objects. Thanks to the extension of galaxy velocity data out to distances in excess of 200Mpc, we are now capable to reconstruct the 3D matter distribution out to these distances, thus constraining the formation history of object such as the Virgo Cluster.

  19. One Single Static Measurement Predicts Wave Localization in Complex Structures

    NASA Astrophysics Data System (ADS)

    Lefebvre, Gautier; Gondel, Alexane; Dubois, Marc; Atlan, Michael; Feppon, Florian; Labbé, Aimé; Gillot, Camille; Garelli, Alix; Ernoult, Maxence; Mayboroda, Svitlana; Filoche, Marcel; Sebbah, Patrick

    2016-08-01

    A recent theoretical breakthrough has brought a new tool, called the localization landscape, for predicting the localization regions of vibration modes in complex or disordered systems. Here, we report on the first experiment which measures the localization landscape and demonstrates its predictive power. Holographic measurement of the static deformation under uniform load of a thin plate with complex geometry provides direct access to the landscape function. When put in vibration, this system shows modes precisely confined within the subregions delineated by the landscape function. Also the maxima of this function match the measured eigenfrequencies, while the minima of the valley network gives the frequencies at which modes become extended. This approach fully characterizes the low frequency spectrum of a complex structure from a single static measurement. It paves the way for controlling and engineering eigenmodes in any vibratory system, especially where a structural or microscopic description is not accessible.

  20. One Single Static Measurement Predicts Wave Localization in Complex Structures.

    PubMed

    Lefebvre, Gautier; Gondel, Alexane; Dubois, Marc; Atlan, Michael; Feppon, Florian; Labbé, Aimé; Gillot, Camille; Garelli, Alix; Ernoult, Maxence; Mayboroda, Svitlana; Filoche, Marcel; Sebbah, Patrick

    2016-08-12

    A recent theoretical breakthrough has brought a new tool, called the localization landscape, for predicting the localization regions of vibration modes in complex or disordered systems. Here, we report on the first experiment which measures the localization landscape and demonstrates its predictive power. Holographic measurement of the static deformation under uniform load of a thin plate with complex geometry provides direct access to the landscape function. When put in vibration, this system shows modes precisely confined within the subregions delineated by the landscape function. Also the maxima of this function match the measured eigenfrequencies, while the minima of the valley network gives the frequencies at which modes become extended. This approach fully characterizes the low frequency spectrum of a complex structure from a single static measurement. It paves the way for controlling and engineering eigenmodes in any vibratory system, especially where a structural or microscopic description is not accessible. PMID:27563967

  1. The Changing Market Structure of Local Television News.

    ERIC Educational Resources Information Center

    Powers, Angela

    The growth in competition for revenues, along with the advent of cable, independent television and video cassette recorders (VCR), may signify a change in the market structure of local television news. To explain if and how this change may be occurring, an explanation of economic theory as well as evidence from "Broadcast and Cable Yearbook" and…

  2. Structures of Participation in the "University of Local Knowledge"

    ERIC Educational Resources Information Center

    Evans, Penny; Irish, Sharon

    2013-01-01

    "Structures of Participation" concerns a recent media arts project, the University of Local Knowledge (ULK). ULK is simultaneously a critique of established academic institutions and disciplines and a system for self-organized learning among the residents of Knowle West, an area of south Bristol (UK). Beginning in 2009, the Knowle West…

  3. Local structure of numerically generated worm hole spacetime.

    NASA Astrophysics Data System (ADS)

    Siino, M.

    The author investigates the evolution of the apparent horizons in a numerically gererated worm hole spacetime. The behavior of the apparent horizons is affected by the dynamics of the matter field. By using the local mass of the system, he interprets the evolution of the worm hole structure.

  4. Local Structure of CuIn3Se5

    SciTech Connect

    Chang, C. H.; Wei, S. H.; Leyarovska, N.; Johnson, J. W.; Zhang, S. B.; Stanbery, B. J.; Anderson, T. J.

    2000-01-01

    The results of a detailed EXAFS study of the Cu-K, In-K, and Se-K edges CuIn3Se5 are reported. The Cu and In first nearest neighbor local structures were found to be almost identical to those in CuInSe2.

  5. Localization of acoustic modes in periodic porous silicon structures

    PubMed Central

    2014-01-01

    The propagation of longitudinal acoustic waves in multilayer structures based on porous silicon and the experimental measurement of acoustic transmission for the structures in the gigahertz range are reported and studied theoretically. The considered structures exhibit band gaps in the transmission spectrum and these are localized modes inside the band gap, coming from defect layers introduced in periodic systems. The frequency at which the acoustic resonances appear can be tuned by changing the porosity and/or thickness of the defect layer. PMID:25206317

  6. Viscoplastic response of structures for intense local heating

    NASA Technical Reports Server (NTRS)

    Thornton, Earl A.; Kolenski, J. D.

    1994-01-01

    A thermoviscoplastic finite element method employing the Bodner-Partom constitutve model is used to investigate the response of simplified thermal-structural models to intense local heating. The computational method formulates the problem in rate and advances the solution in time by numerical integration. The thermoviscoplastic response of simplified structures with prescribed temperatures is investigated. With rapid rises of temperature, the nickel alloy structures display initially higher yield stresses due to strain rate effects. As temperatures approach elevated values, yield stress and stiffness degrade rapidly and pronounced plastic deformation occurs.

  7. Neural networks for local structure detection in polymorphic systems.

    PubMed

    Geiger, Philipp; Dellago, Christoph

    2013-10-28

    The accurate identification and classification of local ordered and disordered structures is an important task in atomistic computer simulations. Here, we demonstrate that properly trained artificial neural networks can be used for this purpose. Based on a neural network approach recently developed for the calculation of energies and forces, the proposed method recognizes local atomic arrangements from a set of symmetry functions that characterize the environment around a given atom. The algorithm is simple and flexible and it does not rely on the definition of a reference frame. Using the Lennard-Jones system as well as liquid water and ice as illustrative examples, we show that the neural networks developed here detect amorphous and crystalline structures with high accuracy even in the case of complex atomic arrangements, for which conventional structure detection approaches are unreliable.

  8. Local magnetic structure determination using polarized neutron holography

    SciTech Connect

    Szakál, Alex Markó, Márton Cser, László

    2015-05-07

    A unique and important property of the neutron is that it possesses magnetic moment. This property is widely used for determination of magnetic structure of crystalline samples observing the magnetic components of the diffraction peaks. Investigations of diffraction patterns give information only about the averaged structure of a crystal but for discovering of local spin arrangement around a specific (e.g., impurity) nucleus remains still a challenging problem. Neutron holography is a useful tool to investigate the local structure around a specific nucleus embedded in a crystal lattice. The method has been successfully applied experimentally in several cases using non-magnetic short range interaction of the neutron and the nucleus. A mathematical model of the hologram using interaction between magnetic moment of the atom and the neutron spin for polarized neutron holography is provided. Validity of a polarized neutron holographic experiment is demonstrated by applying the proposed method on model systems.

  9. Topological framework for local structure analysis in condensed matter

    PubMed Central

    Lazar, Emanuel A.; Han, Jian; Srolovitz, David J.

    2015-01-01

    Physical systems are frequently modeled as sets of points in space, each representing the position of an atom, molecule, or mesoscale particle. As many properties of such systems depend on the underlying ordering of their constituent particles, understanding that structure is a primary objective of condensed matter research. Although perfect crystals are fully described by a set of translation and basis vectors, real-world materials are never perfect, as thermal vibrations and defects introduce significant deviation from ideal order. Meanwhile, liquids and glasses present yet more complexity. A complete understanding of structure thus remains a central, open problem. Here we propose a unified mathematical framework, based on the topology of the Voronoi cell of a particle, for classifying local structure in ordered and disordered systems that is powerful and practical. We explain the underlying reason why this topological description of local structure is better suited for structural analysis than continuous descriptions. We demonstrate the connection of this approach to the behavior of physical systems and explore how crystalline structure is compromised at elevated temperatures. We also illustrate potential applications to identifying defects in plastically deformed polycrystals at high temperatures, automating analysis of complex structures, and characterizing general disordered systems. PMID:26460045

  10. Tracking Coherent Structures and Source Localization in Geophysical Flows

    NASA Astrophysics Data System (ADS)

    Forgoston, Eric; Hsieh, Ani; Schwartz, Ira; Yecko, Philip

    There has been a steady increase in the deployment of autonomous underwater and surface vehicles for applications such as ocean monitoring, tracking of marine processes, and forecasting contaminant transport. The underwater environment poses unique challenges since robots must operate in a communication and localization-limited environment where their dynamics are tightly coupled with the environmental dynamics. This work presents current efforts in understanding the impact of geophysical fluid dynamics on underwater vehicle control and autonomy. The focus of the talk is on the use of collaborative vehicles to track Lagrangian coherent structures and to localize contaminant spills. Research supported by the National Science Foundation and the Office of Naval Research.

  11. A local average distance descriptor for flexible protein structure comparison

    PubMed Central

    2014-01-01

    Background Protein structures are flexible and often show conformational changes upon binding to other molecules to exert biological functions. As protein structures correlate with characteristic functions, structure comparison allows classification and prediction of proteins of undefined functions. However, most comparison methods treat proteins as rigid bodies and cannot retrieve similarities of proteins with large conformational changes effectively. Results In this paper, we propose a novel descriptor, local average distance (LAD), based on either the geodesic distances (GDs) or Euclidean distances (EDs) for pairwise flexible protein structure comparison. The proposed method was compared with 7 structural alignment methods and 7 shape descriptors on two datasets comprising hinge bending motions from the MolMovDB, and the results have shown that our method outperformed all other methods regarding retrieving similar structures in terms of precision-recall curve, retrieval success rate, R-precision, mean average precision and F1-measure. Conclusions Both ED- and GD-based LAD descriptors are effective to search deformed structures and overcome the problems of self-connection caused by a large bending motion. We have also demonstrated that the ED-based LAD is more robust than the GD-based descriptor. The proposed algorithm provides an alternative approach for blasting structure database, discovering previously unknown conformational relationships, and reorganizing protein structure classification. PMID:24694083

  12. Wycheproof Education Centre.

    ERIC Educational Resources Information Center

    Sweetnam and Godfrey, Melbourne (Australia).

    The Wycheproof township in New South Wales (Australia) is the regional center for a grain farming community. The Wycheproof Education Centre was formed by the merger of a separate primary and secondary school (on one site with existing buildings), into a single governing body that is educationally structured into junior, middle, and senior…

  13. Theoretical investigations on the defect structures and spin Hamiltonian parameters for various orthorhombic Rh2+ centres in KTiOPO4 and KTiOAsO4

    NASA Astrophysics Data System (ADS)

    Ding, Chang-Chun; Wu, Shao-Yi; Zhang, Li-Juan; Li, Guo-Liang; Zhang, Zhi-Hong

    2015-12-01

    The defect structures and spin Hamiltonian parameters (SHPs) for three Rh2+ centres (denoted C1 in KTiOAsO4 and C2 and C3 in KTiOPO4) are theoretically investigated by utilising the perturbation formulae for a 4d7 ion under orthorhombically (D2h) elongated octahedra. The defect structures are characterized by the axial elongation ratios of 4.91%, 4.93% and 4.90% along the Z axis and the planar bond length variation ratios of 0.05%, 0.01% and 0.04% for centres C1, C2 and C3, respectively, owing to the Jahn-Teller effect. The nearly identical moderate axial elongation ratios and the slightly different tiny planar bond length variation ratios may suitably account for the comparable moderate axial g anisotropies ∆g (≈0.6087, 0.6124 and 0.6067) and the slightly dissimilar tiny perpendicular g anisotropies δg (≈0.0649, 0.0097 and 0.0509) of the three centres, respectively. All centres demonstrate similar strong crystal-field interactions and moderate covalence arising from the comparable short impurity-ligand distances.

  14. Earth Structure, Ice Mass Changes, and the Local Dynamic Geoid

    NASA Astrophysics Data System (ADS)

    Harig, C.; Simons, F. J.

    2014-12-01

    Spherical Slepian localization functions are a useful method for studying regional mass changes observed by satellite gravimetry. By projecting data onto a sparse basis set, the local field can be estimated more easily than with the full spherical harmonic basis. We have used this method previously to estimate the ice mass change in Greenland from GRACE data, and it can also be applied to other planetary problems such as global magnetic fields. Earth's static geoid, in contrast to the time-variable field, is in large part related to the internal density and rheological structure of the Earth. Past studies have used dynamic geoid kernels to relate this density structure and the internal deformation it induces to the surface geopotential at large scales. These now classical studies of the eighties and nineties were able to estimate the mantle's radial rheological profile, placing constraints on the ratio between upper and lower mantle viscosity. By combining these two methods, spherical Slepian localization and dynamic geoid kernels, we have created local dynamic geoid kernels which are sensitive only to density variations within an area of interest. With these kernels we can estimate the approximate local radial rheological structure that best explains the locally observed geoid on a regional basis. First-order differences of the regional mantle viscosity structure are accessible to this technique. In this contribution we present our latest, as yet unpublished results on the geographical and temporal pattern of ice mass changes in Antarctica over the past decade, and we introduce a new approach to extract regional information about the internal structure of the Earth from the static global gravity field. Both sets of results are linked in terms of the relevant physics, but also in being developed from the marriage of Slepian functions and geoid kernels. We make predictions on the utility of our approach to derive fully three-dimensional rheological Earth models, to

  15. Local structure co-occurrence pattern for image retrieval

    NASA Astrophysics Data System (ADS)

    Zhang, Ke; Zhang, Fan; Lu, Jia; Lu, Yinghua; Kong, Jun; Zhang, Ming

    2016-03-01

    Image description and annotation is an active research topic in content-based image retrieval. How to utilize human visual perception is a key approach to intelligent image feature extraction and representation. This paper has proposed an image feature descriptor called the local structure co-occurrence pattern (LSCP). LSCP extracts the whole visual perception for an image by building a local binary structure, and it is represented by a color-shape co-occurrence matrix which explores the relationship of multivisual feature spaces according to visual attention mechanism. As a result, LSCP not only describes low-level visual features integrated with texture feature, color feature, and shape feature but also bridges high-level semantic comprehension. Extensive experimental results on an image retrieval task on the benchmark datasets, corel-10,000, MIT VisTex, and INRIA Holidays, have demonstrated the usefulness, effectiveness, and robustness of the proposed LSCP.

  16. Local density maxima - Progenitors of structure. [of galaxies

    NASA Technical Reports Server (NTRS)

    Hoffman, Y.; Shaham, J.

    1985-01-01

    Beginning with a short review of the observational data and of some previous theoretical ideas and numerical simulations, the question is addressed of how the large-scale structure that emerges around local density maxima depends on the nature of the primordial density perturbations field. The density contrast profile around local maxima is given, to a good approximation, by the primordial two-point correlation function. The mean number density of objects of a given core mass is calculated as a function of the primordial power spectrum, p(k). In an open universe, rich clusters should have halos steeper than galactic haloes. The observed structure is found to be consistent with omega-sub-zero less than 1.0 and n = -1.

  17. Dynamics of Localized Structures in Systems with Broken Parity Symmetry

    NASA Astrophysics Data System (ADS)

    Javaloyes, J.; Camelin, P.; Marconi, M.; Giudici, M.

    2016-04-01

    A great variety of nonlinear dissipative systems are known to host structures having a correlation range much shorter than the size of the system. The dynamics of these localized structures (LSs) has been investigated so far in situations featuring parity symmetry. In this Letter we extend this analysis to systems lacking this property. We show that the LS drifting speed in a parameter varying landscape is not simply proportional to the parameter gradient, as found in parity preserving situations. The symmetry breaking implies a new contribution to the velocity field which is a function of the parameter value, thus leading to a new paradigm for LSs manipulation. We illustrate this general concept by studying the trajectories of the LSs found in a passively mode-locked laser operated in the localization regime. Moreover, the lack of parity affects significantly LSs interactions which are governed by asymmetrical repulsive forces.

  18. The local spiral structure of the Milky Way

    PubMed Central

    Xu, Ye; Reid, Mark; Dame, Thomas; Menten, Karl; Sakai, Nobuyuki; Li, Jingjing; Brunthaler, Andreas; Moscadelli, Luca; Zhang, Bo; Zheng, Xingwu

    2016-01-01

    The nature of the spiral structure of the Milky Way has long been debated. Only in the last decade have astronomers been able to accurately measure distances to a substantial number of high-mass star-forming regions, the classic tracers of spiral structure in galaxies. We report distance measurements at radio wavelengths using the Very Long Baseline Array for eight regions of massive star formation near the Local spiral arm of the Milky Way. Combined with previous measurements, these observations reveal that the Local Arm is larger than previously thought, and both its pitch angle and star formation rate are comparable to those of the Galaxy’s major spiral arms, such as Sagittarius and Perseus. Toward the constellation Cygnus, sources in the Local Arm extend for a great distance along our line of sight and roughly along the solar orbit. Because of this orientation, these sources cluster both on the sky and in velocity to form the complex and long enigmatic Cygnus X region. We also identify a spur that branches between the Local and Sagittarius spiral arms. PMID:27704048

  19. Seismic structure of ultra-slow spreading crust formed at the Mid-Cayman Spreading Centre, Caribbean Sea

    NASA Astrophysics Data System (ADS)

    Grevemeyer, I.; Merz, M.; Dannowski, A.; Papenberg, C. A.; Hayman, N. W.; Van Avendonk, H. J.; Peirce, C.

    2015-12-01

    About 57% of the Earth's surface is covered by oceanic crust and new ocean floor is continuously created along the ~60.000 km long mid-ocean ridge (MOR) system. About 25% of the MOR spread at an ultra-slow spreading rate of <20 mm/yr. At ultra-slow spreading rates the melt supply to the ridge is thought to dramatically decrease and crustal thickness decreases to a thickness of <6 km. However, we know little about the processes shaping crust at reduced spreading rates. A formation of crust from a magma chamber would suggest the creation of a well stratified crust, with an extrusive upper crust (layer 2) and a lower gabbroic crust (lower 3) and a well-defined crust-mantle boundary and hence a seismic Moho. In contrast, decompressional melting without formation of a magma chamber would support a crustal structure where seismic velocities change gradually from values typical of crustal rocks to mantle rocks. Here, we report initial results from a survey from the ultra-slow spreading Cayman Spreading Centre in the Caribbean Sea, sampling mature crust along a flowline from both conjugated ridge flanks. The seismic refraction and wide-angle survey was conducted using ocean-bottom-seismometers from Germany, the UK, and Texas and a 5500 cubic-inch airgun-array source towed by the German research vessel METEOR in April 2015. Typical crustal velocities support a thin crust of 3 to 5 km thickness. However, a well-defined Moho boundary was not observed. Thus, velocities change gradually from crustal-type velocities (<7.2 km/s) to values of 7.6-7.8 km/s, supporting mantle rocks. We suggest that reduced mantle velocities indicate gabbroic intrusions within the mantle rather than indicating serpentinization.

  20. Towards accurate structural characterization of metal centres in protein crystals: the structures of Ni and Cu T{sub 6} bovine insulin derivatives

    SciTech Connect

    Frankaer, Christian Grundahl; Mossin, Susanne; Ståhl, Kenny; Harris, Pernille

    2014-01-01

    The level of structural detail around the metal sites in Ni{sup 2+} and Cu{sup 2+} T{sub 6} insulin derivatives was significantly improved by using a combination of single-crystal X-ray crystallography and X-ray absorption spectroscopy. Photoreduction and subsequent radiation damage of the Cu{sup 2+} sites in Cu insulin was followed by XANES spectroscopy. Using synchrotron radiation (SR), the crystal structures of T{sub 6} bovine insulin complexed with Ni{sup 2+} and Cu{sup 2+} were solved to 1.50 and 1.45 Å resolution, respectively. The level of detail around the metal centres in these structures was highly limited, and the coordination of water in Cu site II of the copper insulin derivative was deteriorated as a consequence of radiation damage. To provide more detail, X-ray absorption spectroscopy (XAS) was used to improve the information level about metal coordination in each derivative. The nickel derivative contains hexacoordinated Ni{sup 2+} with trigonal symmetry, whereas the copper derivative contains tetragonally distorted hexacoordinated Cu{sup 2+} as a result of the Jahn–Teller effect, with a significantly longer coordination distance for one of the three water molecules in the coordination sphere. That the copper centre is of type II was further confirmed by electron paramagnetic resonance (EPR). The coordination distances were refined from EXAFS with standard deviations within 0.01 Å. The insulin derivative containing Cu{sup 2+} is sensitive towards photoreduction when exposed to SR. During the reduction of Cu{sup 2+} to Cu{sup +}, the coordination geometry of copper changes towards lower coordination numbers. Primary damage, i.e. photoreduction, was followed directly by XANES as a function of radiation dose, while secondary damage in the form of structural changes around the Cu atoms after exposure to different radiation doses was studied by crystallography using a laboratory diffractometer. Protection against photoreduction and subsequent

  1. Assessing the local identifiability of probabilistic knowledge structures.

    PubMed

    Stefanutti, Luca; Heller, Jürgen; Anselmi, Pasquale; Robusto, Egidio

    2012-12-01

    Given a collection Q of problems, in knowledge space theory Doignon & Falmagne, (International Journal of Man-Machine Studies 23:175-196, 1985) the knowledge state of a student is the collection K ⊆ Q of all problems that this student is capable of solving. A knowledge structure is a pair (Q, ), where is a collection of knowledge states that contains at least the empty set and Q. A probabilistic knowledge structure (PKS) is a knowledge structure (Q, , π), where π is a probability distribution on the knowledge states. The PKS that has received the most attention is the basic local independence model BLIM; Falmagne & Doignon, (British Journal of Mathematical and Statistical Psychology 41:1-23, 1988a, Journal of Mathematical Psychology 32:232-258, 1988b). To the best of our knowledge, systematic investigations in the literature concerning the identifiability of the BLIM are totally missing. Based on the theoretical work of Bamber and van Santen (Journal of Mathematical Psychology 29:443-473, 1985), the present article is aimed to present a method and a corresponding computerized procedure for assessing the local identifiability of the BLIM, which is applicable to any finite knowledge structure of moderate size. PMID:22588988

  2. Local Structure of Cerium in Aluminophosphate and Silicophosphate Glasses

    SciTech Connect

    Rygel, Jennifer L.; Chen, Yongsheng; Pantano, Carlo G.; Shibata, Tomohiro; Du, Jincheng; Kokou, Leopold; Woodman, Robert; Belcher, James

    2011-09-20

    The local structure of cerium in two systematic compositional series of glasses, nominally CeP{sub 3}O{sub 9}-AlP{sub 3}O{sub 9} and CeP{sub 3}O{sub 9}-SiP{sub 2}O{sub 7}, was interrogated using X-ray photoelectron spectroscopy (XPS) and X-ray absorption fine structure (XAFS) spectroscopy. XPS revealed that, for glasses melted in air, {>=}95% of cerium ions are Ce{sup 3+}. This was independently confirmed using X-ray absorption near edge spectroscopy (XANES). Ce K-edge extended X-ray absorption fine structure (EXAFS) has been used to determine the local structure of Ce{sup 3+}. Near the metaphosphate composition, cerium was found to have an average cerium coordination number of {approx}7.0 and an average cerium-oxygen bond length of 2.41 {angstrom}. The average cerium coordination number and average cerium-oxygen bond distance were found to increase with decreasing cerium concentration in both compositional series. Rare-earth clustering is suggested based on numerical calculations for glasses containing {>=}14 and {>=}15 mol% Ce{sub 2}O{sub 3} for the aluminophosphate and silicophosphate series, respectively.

  3. Probing local structure in glass by the application of shear

    NASA Astrophysics Data System (ADS)

    Weingartner, Nicholas B.; Nussinov, Zohar

    2016-09-01

    The glass transition remains one of the great unsolved mysteries of contemporary condensed matter physics. When crystallization is bypassed by rapid cooling, a supercooled liquid, retaining amorphous particle arrangement, results. The physical phenomenology of supercooled liquids is as vast as it is interesting. Most significant, the viscosity of the supercooled liquid displays an incredible increase over a narrow temperature range. Eventually, the supercooled liquid ceases to flow, becomes a glass, and gains rigidity and solid-like behaviors. Understanding what underpins the monumental growth of viscosity, and how rigidity results without long range order is a long-sought goal. Furthermore, discerning what role local structure plays in the kinetics of supercooled liquids remains an open question. Many theories of the glassy slowdown require the growth of static lengthscale related to structure with lowering of the temperature and provide a link between slowdown and propagation of ‘amorphous order’. In light of this, we examine the recently proposed shear penetration depth in the context of other length scales and its relation to local structure. We provide numerical data, based on the simulations of NiZr2, illustrating that this length scale exhibits dramatic growth upon approach to the glass transition and further discuss this in relation to percolating structural connectivity in similar glassforming systems.

  4. Comparative population genetic structures and local adaptation of two mutualists.

    PubMed

    Anderson, Bruce; Olivieri, Isabelle; Lourmas, Mathieu; Stewart, Barbara A

    2004-08-01

    Similar patterns of dispersal and gene flow between closely associated organisms may promote local adaptation and coevolutionary processes. We compare the genetic structures of the two species of a plant genus (Roridula gorgonias and R. dentata) and their respective obligately associated hemipteran mutualists (Pameridea roridulae and P. marlothi) using allozymes. In addition, we determine whether genetic structure is related to differences in host choice by Pameridea. Allozyme variation was found to be very structured among plant populations but less so among hemipteran populations. Strong genetic structuring among hemipteran populations was only evident when large distances isolated the plant populations on which they live. Although genetic distances among plant populations were correlated with genetic distances among hemipteran populations, genetic distances of both plants and hemipterans were better correlated with geographic distance. Because Roridula and Pameridea have different scales of gene flow, adaptation at the local population level is unlikely. However, the restricted gene flow of both plants and hemipterans could enable adaptation to occur at a regional level. In choice experiments, the hemipteran (Pameridea) has a strong preference for its carnivorous host plant (Roridula) above unrelated host plants. Pameridea also prefers its host species to its closely related sister species. Specialization at the specific level is likely to reinforce cospeciation processes in this mutualism. However, Pameridea does not exhibit intraspecific preferences toward plants from their natal populations above plants from isolated, non-natal populations. PMID:15446426

  5. A phenomenological theory of spatially structured local synaptic connectivity.

    PubMed

    Amirikian, Bagrat

    2005-06-01

    The structure of local synaptic circuits is the key to understanding cortical function and how neuronal functional modules such as cortical columns are formed. The central problem in deciphering cortical microcircuits is the quantification of synaptic connectivity between neuron pairs. I present a theoretical model that accounts for the axon and dendrite morphologies of pre- and postsynaptic cells and provides the average number of synaptic contacts formed between them as a function of their relative locations in three-dimensional space. An important aspect of the current approach is the representation of a complex structure of an axonal/dendritic arbor as a superposition of basic structures-synaptic clouds. Each cloud has three structural parameters that can be directly estimated from two-dimensional drawings of the underlying arbor. Using empirical data available in literature, I applied this theory to three morphologically different types of cell pairs. I found that, within a wide range of cell separations, the theory is in very good agreement with empirical data on (i) axonal-dendritic contacts of pyramidal cells and (ii) somatic synapses formed by the axons of inhibitory interneurons. Since for many types of neurons plane arborization drawings are available from literature, this theory can provide a practical means for quantitatively deriving local synaptic circuits based on the actual observed densities of specific types of neurons and their morphologies. It can also have significant implications for computational models of cortical networks by making it possible to wire up simulated neural networks in a realistic fashion.

  6. Electronic Structure, Localization and 5f Occupancy in Pu Materials

    SciTech Connect

    Joyce, John J.; Beaux, Miles F.; Durakiewicz, Tomasz; Graham, Kevin S.; Bauer, Eric D.; Mitchell, Jeremy N.; Tobash, Paul H.; Richmond, Scott

    2012-05-03

    The electronic structure of delta plutonium ({delta}-Pu) and plutonium compounds is investigated using photoelectron spectroscopy (PES). Results for {delta}-Pu show a small component of the valence electronic structure which might reasonably be associated with a 5f{sup 6} configuration. PES results for PuTe are used as an indication for the 5f{sup 6} configuration due to the presence of atomic multiplet structure. Temperature dependent PES data on {delta}-Pu indicate a narrow peak centered 20 meV below the Fermi energy and 100 meV wide. The first PES data for PuCoIn5 indicate a 5f electronic structure more localized than the 5fs in the closely related PuCoGa{sub 5}. There is support from the PES data for a description of Pu materials with an electronic configuration of 5f{sup 5} with some admixture of 5f{sup 6} as well as a localized/delocalized 5f{sup 5} description.

  7. Comparative population genetic structures and local adaptation of two mutualists.

    PubMed

    Anderson, Bruce; Olivieri, Isabelle; Lourmas, Mathieu; Stewart, Barbara A

    2004-08-01

    Similar patterns of dispersal and gene flow between closely associated organisms may promote local adaptation and coevolutionary processes. We compare the genetic structures of the two species of a plant genus (Roridula gorgonias and R. dentata) and their respective obligately associated hemipteran mutualists (Pameridea roridulae and P. marlothi) using allozymes. In addition, we determine whether genetic structure is related to differences in host choice by Pameridea. Allozyme variation was found to be very structured among plant populations but less so among hemipteran populations. Strong genetic structuring among hemipteran populations was only evident when large distances isolated the plant populations on which they live. Although genetic distances among plant populations were correlated with genetic distances among hemipteran populations, genetic distances of both plants and hemipterans were better correlated with geographic distance. Because Roridula and Pameridea have different scales of gene flow, adaptation at the local population level is unlikely. However, the restricted gene flow of both plants and hemipterans could enable adaptation to occur at a regional level. In choice experiments, the hemipteran (Pameridea) has a strong preference for its carnivorous host plant (Roridula) above unrelated host plants. Pameridea also prefers its host species to its closely related sister species. Specialization at the specific level is likely to reinforce cospeciation processes in this mutualism. However, Pameridea does not exhibit intraspecific preferences toward plants from their natal populations above plants from isolated, non-natal populations.

  8. Role of nonlinear localized structures and turbulence in magnetized plasma

    NASA Astrophysics Data System (ADS)

    Pathak, Neha; Yadav, Nitin; Uma, R.; Sharma, R. P.

    2016-09-01

    In the present study, we have analyzed the field localization of kinetic Alfvén wave (KAW) due to the presence of background density perturbation, which are assumed to be originated by the three dimensionally propagating low frequency KAW. These localized structures play an important role for energy transportation at smaller scales in the dispersion range of magnetic power spectrum. For the present model, governing dynamic equations of high frequency pump KAW and low frequency KAW has been derived by considering ponderomotive nonlinearity. Further, these coupled equations have been numerically solved to analyze the resulting localized structures of pump KAW and magnetic power spectrum in the magnetopause regime. Numerically calculated spectrum exhibits inertial range having spectral index of -3/2 followed by steeper scaling; this steepening in the turbulent spectrum is a signature of energy transportation from larger to smaller scales. In this way, the proposed mechanism, which is based on nonlinear wave-wave interaction, may be useful for understanding the particle acceleration and turbulence in magnetopause.

  9. Local Interfacial Structure in Downward Two-Phase Bubbly Flow

    SciTech Connect

    Hiroshi Goda; Seungjin Kim; Paranjape, Sidharth S.; Finch, Joshua P.; Mamoru Ishii; Uhle, Jennifer

    2002-07-01

    The local interfacial structure for vertical air-water co-current downward two-phase flow was investigated under adiabatic conditions. A multi-sensor conductivity probe was utilized in order to acquire the local two-phase flow parameters. The present experimental loop consisted of 25.4 mm and 50.8 mm ID round tubes as test sections. The measurement was performed at three axial locations: L/D = 13, 68 and 133 for the 25.4 mm ID loop and L/D 7, 34, 67 for the 50.8 mm ID loop, in order to study the axial development of the flow. A total of 7 and 10 local measurement points along the tube radius were chosen for the 25.4 mm ID loop and the 50.8 mm ID loop, respectively. The experimental flow conditions were determined within bubbly flow regime. The acquired local parameters included the void fraction, interfacial area concentration, bubble interface frequency, bubble Sauter mean diameter, and interfacial velocity. (authors)

  10. Protein structure prediction with local adjust tabu search algorithm

    PubMed Central

    2014-01-01

    Background Protein folding structure prediction is one of the most challenging problems in the bioinformatics domain. Because of the complexity of the realistic protein structure, the simplified structure model and the computational method should be adopted in the research. The AB off-lattice model is one of the simplification models, which only considers two classes of amino acids, hydrophobic (A) residues and hydrophilic (B) residues. Results The main work of this paper is to discuss how to optimize the lowest energy configurations in 2D off-lattice model and 3D off-lattice model by using Fibonacci sequences and real protein sequences. In order to avoid falling into local minimum and faster convergence to the global minimum, we introduce a novel method (SATS) to the protein structure problem, which combines simulated annealing algorithm and tabu search algorithm. Various strategies, such as the new encoding strategy, the adaptive neighborhood generation strategy and the local adjustment strategy, are adopted successfully for high-speed searching the optimal conformation corresponds to the lowest energy of the protein sequences. Experimental results show that some of the results obtained by the improved SATS are better than those reported in previous literatures, and we can sure that the lowest energy folding state for short Fibonacci sequences have been found. Conclusions Although the off-lattice models is not very realistic, they can reflect some important characteristics of the realistic protein. It can be found that 3D off-lattice model is more like native folding structure of the realistic protein than 2D off-lattice model. In addition, compared with some previous researches, the proposed hybrid algorithm can more effectively and more quickly search the spatial folding structure of a protein chain. PMID:25474708

  11. Measuring capital market efficiency: Global and local correlations structure

    NASA Astrophysics Data System (ADS)

    Kristoufek, Ladislav; Vosvrda, Miloslav

    2013-01-01

    We introduce a new measure for capital market efficiency. The measure takes into consideration the correlation structure of the returns (long-term and short-term memory) and local herding behavior (fractal dimension). The efficiency measure is taken as a distance from an ideal efficient market situation. The proposed methodology is applied to a portfolio of 41 stock indices. We find that the Japanese NIKKEI is the most efficient market. From a geographical point of view, the more efficient markets are dominated by the European stock indices and the less efficient markets cover mainly Latin America, Asia and Oceania. The inefficiency is mainly driven by a local herding, i.e. a low fractal dimension.

  12. Point-to-set lengths, local structure, and glassiness

    NASA Astrophysics Data System (ADS)

    Yaida, Sho; Berthier, Ludovic; Charbonneau, Patrick; Tarjus, Gilles

    2016-09-01

    The growing sluggishness of glass-forming liquids is thought to be accompanied by growing structural order. The nature of such order, however, remains hotly debated. A decade ago, point-to-set (PTS) correlation lengths were proposed as measures of amorphous order in glass formers, but recent results raise doubts as to their generality. Here, we extend the definition of PTS correlations to agnostically capture any type of growing order in liquids, be it local or amorphous. This advance enables the formulation of a clear distinction between slowing down due to conventional critical ordering and that due to glassiness, and provides a unified framework to assess the relative importance of specific local order and generic amorphous order in glass formation.

  13. The effects of local blowing perturbations on thermal turbulent structures

    NASA Astrophysics Data System (ADS)

    Liu, Can; Araya, Guillermo; Leonardi, Stefano; Castillo, Luciano

    2013-11-01

    Blowing is an active flow control technique with several industrial applications, particularly in film cooling of turbine blades. In the past, the effects of localized blowing have been mostly analyzed on the velocity field and its influence of the flow parameters and turbulence structures (Krogstad and Kourakine, 2000). However, little literature can be found on the effects of blowing on the coherent thermal structures. In the present study, an incompressible turbulent channel flow with given steady blowing at the wall is simulated via DNS by means of five spanwise holes. The Reynolds number based on the friction velocity and half channel height is approximately Re = 394 and the molecular Prandtl number is Pr = 0.71. Temperature is considered a passive scalar with isothermal conditions at the wall. Different blowing amplitudes and perturbing angles (with respect to the streamwise direction) are applied to find out their effects on the turbulent thermal structures by means of a two-point correlation analysis. In addition, local reduction and increase of drag are connected to vorticity. The corresponding influence of perturbing amplitudes and angles on the energy budget of thermal fluctuations and turbulent Prandtl numbers are also shown and discussed.

  14. Localized structural health monitoring via transmission zero invariance

    NASA Astrophysics Data System (ADS)

    Reich, Gregory William

    2000-11-01

    This thesis presents a method of localized health monitoring based on an invariance property of transmission zeros of substructural frequency response functions. The proposed method has several desirable characteristics which make it attractive for use in damage detection applications. These are the independence from initial parameter estimates, the determination of a unique damage location, and the fact that the method is particularly suited for structural continuum applications where other methods perform poorly. The proposed method is based on a substructuring technique for structural mechanics. The structural equations of motion are cast in a variational framework and are mathematically decomposed into substructures using Lagrange multipliers as boundary constraints. The global dynamics of the system are then written in terms of the independent dynamics of each substructure plus the inter-element dynamics. The frequency response functions of the localized form represent the energy transfer between unique input forces which are derived from the total global force input and output variables which exist independently on a substructure. Because transmission zeros are highly dependent on the input and output of the system under consideration, they exhibit different characteristics in the local form versus the global form. If damage is limited to a change in flexibility, then it can be shown that the transmission zeros of a partition of the full transfer function matrix corresponding to a damaged substructure are invariant to the damage. Transmission zeros of partitions of the transfer function matrix corresponding to healthy substructures likewise can be shown to vary with the damage. Identification of the substructure whose zeros exhibit the least amount of variation between tests results in identification of the damage location. Analytical and experimental examples are used to demonstrate the theory and abilities of the proposed method. In each example, the system

  15. Localized Epidermal Drug Delivery Induced by Supramolecular Solvent Structuring.

    PubMed

    Benaouda, F; Jones, S A; Martin, G P; Brown, M B

    2016-01-01

    The preferential localization of drug molecules in the epidermis of human skin is considered advantageous for a number of agents, but achieving such a delivery profile can be problematic. The aim of the present study was to assess if the manipulation of solvent supramolecular structuring in the skin could be used to promote drug residence in the epidermal tissue. Skin deposition studies showed that a 175-fold increase in the epidermal loading of a model drug diclofenac (138.65 ± 11.67 μg·cm(-2)), compared to a control (0.81 ± 0.13 μg·cm(-2)), could be achieved by colocalizing the drug with a high concentration of propylene glycol (PG) in the tissue. For such a system at 1 h postdose application, the PG flux into the skin was 9.3 mg·cm(2)·h(-1) and the PG-water ratio in the epidermis was 76:24 (v/v). At this solvent ratio infrared spectroscopy indicated that PG rich supramolecular structures, which displayed a relatively strong physical affinity for the drug, were formed. Encouraging the production of the PG-rich supermolecular structures in the epidermis by applying diclofenac to the skin using a high PG loading dose (240 μg·cm(-2)) produced an epidermal-transdermal drug distribution of 6.8:1. However, generating water-rich solvent supermolecular structures in the epidermis by applying diclofenac using a low PG loading dose (2.2 μg·cm(-2)) led to a loss of preferential epidermal localization of diclofenac in the tissue (0.7:1 epidermal-transdermal drug distribution). This change in diclofenac skin deposition profile in response to PG variations and the accompanying FTIR data supported the notion that supramolecular solvent structures could control drug accumulation in the human epidermis. PMID:26593153

  16. Localized structures in dissipative media: from optics to plant ecology

    PubMed Central

    Tlidi, M.; Staliunas, K.; Panajotov, K.; Vladimirov, A. G.; Clerc, M. G.

    2014-01-01

    Localized structures (LSs) in dissipative media appear in various fields of natural science such as biology, chemistry, plant ecology, optics and laser physics. The proposal for this Theme Issue was to gather specialists from various fields of nonlinear science towards a cross-fertilization among active areas of research. This is a cross-disciplinary area of research dominated by nonlinear optics due to potential applications for all-optical control of light, optical storage and information processing. This Theme Issue contains contributions from 18 active groups involved in the LS field and have all made significant contributions in recent years. PMID:25246688

  17. Localization-Based Super-Resolution Imaging of Cellular Structures

    PubMed Central

    Kanchanawong, Pakorn; Waterman, Clare M.

    2013-01-01

    Fluorescence microscopy allows direct visualization of fluorescently tagged proteins within cells. However, the spatial resolution of conventional fluorescence microscopes is limited by diffraction to ~250 nm, prompting the development of super-resolution microscopy which offers resolution approaching the scale of single proteins, i.e., ~20 nm. Here, we describe protocols for single molecule localization-based super-resolution imaging, using focal adhesion proteins as an example and employing either photoswitchable fluorophores or photoactivatable fluorescent proteins. These protocols should also be easily adaptable to imaging a broad array of macromolecular assemblies in cells whose components can be fluorescently tagged and assemble into high density structures. PMID:23868582

  18. Locally Biased Galaxy Formation and Large-Scale Structure

    NASA Astrophysics Data System (ADS)

    Narayanan, Vijay K.; Berlind, Andreas A.; Weinberg, David H.

    2000-01-01

    We examine the influence of the morphology-density relation and a wide range of simple models for biased galaxy formation on statistical measures of large-scale structure. We contrast the behavior of local biasing models, in which the efficiency of galaxy formation is determined by the density, geometry, or velocity dispersion of the local mass distribution, with that of nonlocal biasing models, in which galaxy formation is modulated coherently over scales larger than the galaxy correlation length. If morphological segregation of galaxies is governed by a local morphology-density relation, then the correlation function of E/S0 galaxies should be steeper and stronger than that of spiral galaxies on small scales, as observed, while on large scales the E/S0 and spiral galaxies should have correlation functions with the same shape but different amplitudes. Similarly, all of our local bias models produce scale-independent amplification of the correlation function and power spectrum in the linear and mildly nonlinear regimes; only a nonlocal biasing mechanism can alter the shape of the power spectrum on large scales. Moments of the biased galaxy distribution retain the hierarchical pattern of the mass moments, but biasing alters the values and scale dependence of the hierarchical amplitudes S3 and S4. Pair-weighted moments of the galaxy velocity distribution are sensitive to the details of the bias prescription even if galaxies have the same local velocity distribution as the underlying dark matter. The nonlinearity of the relation between galaxy density and mass density depends on the biasing prescription and the smoothing scale, and the scatter in this relation is a useful diagnostic of the physical parameters that determine the bias. While the assumption that galaxy formation is governed by local physics leads to some important simplifications on large scales, even local biasing is a multifaceted phenomenon whose impact cannot be described by a single parameter or

  19. Global functions in global-local finite-element analysis of localized stresses in prismatic structures

    NASA Technical Reports Server (NTRS)

    Dong, Stanley B.

    1989-01-01

    An important consideration in the global local finite-element method (GLFEM) is the availability of global functions for the given problem. The role and mathematical requirements of these global functions in a GLFEM analysis of localized stress states in prismatic structures are discussed. A method is described for determining these global functions. Underlying this method are theorems due to Toupin and Knowles on strain energy decay rates, which are related to a quantitative expression of Saint-Venant's principle. It is mentioned that a mathematically complete set of global functions can be generated, so that any arbitrary interface condition between the finite element and global subregions can be represented. Convergence to the true behavior can be achieved with increasing global functions and finite-element degrees of freedom. Specific attention is devoted to mathematically two-dimensional and three-dimensional prismatic structures. Comments are offered on the GLFEM analysis of NASA flat panel with a discontinuous stiffener. Methods for determining global functions for other effects are also indicated, such as steady-state dynamics and bodies under initial stress.

  20. Optical spectrum and local lattice structure for ruby

    NASA Astrophysics Data System (ADS)

    Wang, H.; Kuang, X.-Y.; Mao, A.-J.; Huang, X.-F.

    2007-01-01

    By diagonalizing the 120×120 complete energy matrices for d3 ion in trigonal crystal field, which contains the electrostatic interaction, the trigonal field as well as the spin-orbit interaction, the unified calculation of the whole optical and EPR spectra for ruby are made. And matrix elements of the Zeeman energy with the magnetic field parallel or perpendicular to the trigonal axis are introduced into the complete energy matrices for obtaining the g factors of the energy levels. It is concluded that zero-field splitting and optical spectra as well as g factors are in good agreement with the experimental data and the distorted local lattice structure is determined firstly results from a stretching of the O2- ions along the C3 axis. The pressure-induced shifts of energy levels, g factors and local lattice structure are also discussed. In particular, all the calculations are carried out successfully within the framework of the crystal-field model which is consistent with the opinion of Macfarlane and Sturge that if all terms within the d3 configuration are included, one need not go outside conventional crystal-field theory.

  1. Mechanochemically synthesized fluorides: local structures and ion transport.

    PubMed

    Preishuber-Pflügl, Florian; Wilkening, Martin

    2016-06-01

    The performance of new sensors or advanced electrochemical energy storage devices strongly depends on the active materials chosen to realize such systems. In particular, their morphology may greatly influence their overall macroscopic properties. Frequently, limitations in classical ways of chemical preparation routes hamper the development of materials with tailored properties. Fortunately, such hurdles can be overcome by mechanochemical synthesis. The versatility of mechanosynthesis allows the provision of compounds that are not available through common synthesis routes. The mechanical treatment of two or three starting materials in high-energy ball mills enables the synthesis not only of new compounds but also of nanocrystalline materials with unusual properties such as enhanced ion dynamics. Fast ion transport is of crucial importance in electrochemical energy storage. It is worth noting that mechanosynthesis also provides access to metastable phases that cannot be synthesized by conventional solid state synthesis. Ceramic synthesis routes often yield the thermally, i.e., thermodynamically, stable products rather than metastable compounds. In this perspective we report the mechanochemical synthesis of nanocrystalline fluorine ion conductors that serve as model substances to understand the relationship between local structures and ion dynamics. While ion transport properties were complementarily probed via conductivity spectroscopy and nuclear magnetic relaxation, local structures of the phases prepared were investigated by high-resolution (19)F NMR spectroscopy carried out by fast magic angle spinning. The combination of nuclear and non-nuclear techniques also helped us to shed light on the mechanisms controlling mechanochemical reactions in general. PMID:27172256

  2. Mechanochemically synthesized fluorides: local structures and ion transport.

    PubMed

    Preishuber-Pflügl, Florian; Wilkening, Martin

    2016-06-01

    The performance of new sensors or advanced electrochemical energy storage devices strongly depends on the active materials chosen to realize such systems. In particular, their morphology may greatly influence their overall macroscopic properties. Frequently, limitations in classical ways of chemical preparation routes hamper the development of materials with tailored properties. Fortunately, such hurdles can be overcome by mechanochemical synthesis. The versatility of mechanosynthesis allows the provision of compounds that are not available through common synthesis routes. The mechanical treatment of two or three starting materials in high-energy ball mills enables the synthesis not only of new compounds but also of nanocrystalline materials with unusual properties such as enhanced ion dynamics. Fast ion transport is of crucial importance in electrochemical energy storage. It is worth noting that mechanosynthesis also provides access to metastable phases that cannot be synthesized by conventional solid state synthesis. Ceramic synthesis routes often yield the thermally, i.e., thermodynamically, stable products rather than metastable compounds. In this perspective we report the mechanochemical synthesis of nanocrystalline fluorine ion conductors that serve as model substances to understand the relationship between local structures and ion dynamics. While ion transport properties were complementarily probed via conductivity spectroscopy and nuclear magnetic relaxation, local structures of the phases prepared were investigated by high-resolution (19)F NMR spectroscopy carried out by fast magic angle spinning. The combination of nuclear and non-nuclear techniques also helped us to shed light on the mechanisms controlling mechanochemical reactions in general.

  3. Embrittlement and Flow Localization in Reactor Structural Materials

    SciTech Connect

    Xianglin Wu; Xiao Pan; James Stubbins

    2006-10-06

    Many reactor components and structural members are made from metal alloys due, in large part, to their strength and ability to resist brittle fracture by plastic deformation. However, brittle fracture can occur when structural material cannot undergo extensive, or even limited, plastic deformation due to irradiation exposure. Certain irradiation conditions lead to the development of a damage microstructure where plastic flow is limited to very small volumes or regions of material, as opposed to the general plastic flow in unexposed materials. This process is referred to as flow localization or plastic instability. The true stress at the onset of necking is a constant regardless of the irradiation level. It is called 'critical stress' and this critical stress has strong temperature dependence. Interrupted tensile testes of 316L SS have been performed to investigate the microstructure evolution and competing mechanism between mechanic twinning and planar slip which are believed to be the controlling mechanism for flow localization. Deformation twinning is the major contribution of strain hardening and good ductility for low temperatures, and the activation of twinning system is determined by the critical twinning stress. Phases transform and texture analyses are also discussed in this study. Finite element analysis is carried out to complement the microstructural analysis and for the prediction of materaials performance with and without stress concentration and irradiation.

  4. Structure-dependent interatomic dispersion coefficients in oxides with maximally localized Wannier functions

    NASA Astrophysics Data System (ADS)

    Sukhomlinov, Sergey V.; Smirnov, Konstantin S.

    2012-11-01

    The interatomic C6 dispersion coefficients in crystalline and amorphous SiO2 and ZrO2 structures were obtained with the approach proposed by Silvestrelli (2008 Phys. Rev. Lett. 100 053002) and based on the use of maximally localized Wannier functions (MLWFs) for partitioning the electron density. Localization of Wannier functions close to the nuclei in oxide systems makes it possible to assign the MLWFs to the atoms in an unambiguous way and then to compute the C6 coefficients in an atom pairwise manner. A modification of the method is suggested in which the MLWFs are condensed to effective orbitals centred on the atoms and parameters of these effective orbitals are used for computing the interatomic dispersion coefficients. The obtained values of the dispersion coefficients were found to vary not only from one oxide to another, but also between different modifications of the same compound. The oxygen-oxygen coefficient {C}_{6}^{{OO}} reveals the largest variation and its value in ZrO2 structures is twice as large as that in SiO2 ones. Atomic characteristics obtained in the frame of the effective orbital method, such as the self-atom dispersion coefficient, and the oxide ion polarizability were found to correlate with the metal-oxygen bond length and the oxygen coordination number in the systems. This behaviour is attributed to the confinement of electrons by the electrostatic potential. The values of the coefficient and of the polarizability were related to charges of the oxygen atoms. In all studied systems the oxygen atoms having larger absolute values of charge were found to be less polarizable because of a stronger confinement effect. The obtained results can be used in the development of polarizable force fields for the atomistic modelling of oxide materials.

  5. Structure-dependent interatomic dispersion coefficients in oxides with maximally localized Wannier functions.

    PubMed

    Sukhomlinov, Sergey V; Smirnov, Konstantin S

    2012-11-28

    The interatomic C(6) dispersion coefficients in crystalline and amorphous SiO(2) and ZrO(2) structures were obtained with the approach proposed by Silvestrelli (2008 Phys. Rev. Lett. 100 053002) and based on the use of maximally localized Wannier functions (MLWFs) for partitioning the electron density. Localization of Wannier functions close to the nuclei in oxide systems makes it possible to assign the MLWFs to the atoms in an unambiguous way and then to compute the C(6) coefficients in an atom pairwise manner. A modification of the method is suggested in which the MLWFs are condensed to effective orbitals centred on the atoms and parameters of these effective orbitals are used for computing the interatomic dispersion coefficients. The obtained values of the dispersion coefficients were found to vary not only from one oxide to another, but also between different modifications of the same compound. The oxygen-oxygen coefficient C6(OO) reveals the largest variation and its value in ZrO(2) structures is twice as large as that in SiO(2) ones. Atomic characteristics obtained in the frame of the effective orbital method, such as the self-atom dispersion coefficient, and the oxide ion polarizability were found to correlate with the metal-oxygen bond length and the oxygen coordination number in the systems. This behaviour is attributed to the confinement of electrons by the electrostatic potential. The values of the coefficient and of the polarizability were related to charges of the oxygen atoms. In all studied systems the oxygen atoms having larger absolute values of charge were found to be less polarizable because of a stronger confinement effect. The obtained results can be used in the development of polarizable force fields for the atomistic modelling of oxide materials.

  6. Segmentation of knee MRI using structure enhanced local phase filtering

    NASA Astrophysics Data System (ADS)

    Lim, Mikhiel; Hacihaliloglu, Ilker

    2016-03-01

    The segmentation of bone surfaces from magnetic resonance imaging (MRI) data has applications in the quanti- tative measurement of knee osteoarthritis, surgery planning for patient specific total knee arthroplasty and its subsequent fabrication of artificial implants. However, due to the problems associated with MRI imaging such as low contrast between bone and surrounding tissues, noise, bias fields, and the partial volume effect, segmentation of bone surfaces continues to be a challenging operation. In this paper, a new framework is presented for the enhancement of knee MRI scans prior to segmentation in order to obtain high contrast bone images. During the first stage, a new contrast enhanced relative total variation (RTV) regularization method is used in order to remove textural noise from the bone structures and surrounding soft tissue interface. This salient bone edge information is further enhanced using a sparse gradient counting method based on L0 gradient minimization, which globally controls how many non-zero gradients are resulted in order to approximate prominent bone structures in a structure-sparsity-management manner. The last stage of the framework involves incorporation of local phase bone boundary information in order to provide an intensity invariant enhancement of contrast between the bone and surrounding soft tissue. The enhanced images are segmented using a fast random walker algorithm. Validation against expert segmentation was performed on 10 clinical knee MRI images, and achieved a mean dice similarity coefficient (DSC) of 0.975.

  7. Local structure of solid Rb at megabar pressures

    SciTech Connect

    De Panfilis, S.; Gorelli, F.; Santoro, M.; Ulivi, L.; Gregoryanz, E.; Irifune, T.; Shinmei, T.; Kantor, I.; Mathon, O.; Pascarelli, S.

    2015-06-07

    We have investigated the local and electronic structure of solid rubidium by means of x-ray absorption spectroscopy up to 101.0 GPa, thus doubling the maximum investigated experimental pressure. This study confirms the predicted stability of phase VI and was completed by the combination of two pivotal instrumental solutions. On one side, we made use of nanocrystalline diamond anvils, which, contrary to the more commonly used single crystal diamond anvils, do not generate sharp Bragg peaks (glitches) at specific energies that spoil the weak fine structure oscillations in the x-ray absorption cross section. Second, we exploited the performance of a state-of-the-art x-ray focussing device yielding a beam spot size of 5 × 5 μm{sup 2}, spatially stable over the entire energy scan. An advanced data analysis protocol was implemented to extract the pressure dependence of the structural parameters in phase VI of solid Rb from 51.2 GPa up to the highest pressure. A continuous reduction of the nearest neighbour distances was observed, reaching about 6% over the probed pressure range. We also discuss a phenomenological model based on the Einstein approximation to describe the pressure behaviour of the mean-square relative displacement. Within this simplified scheme, we estimate the Grüneisen parameter for this high pressure Rb phase to be in the 1.3–1.5 interval.

  8. Evaluating the Importance of Local Environment on Tree Structural Allometries

    NASA Astrophysics Data System (ADS)

    Duncanson, L.; Cook, B. D.; Rourke, O.; Hurtt, G. C.; Dubayah, R.

    2013-12-01

    Allometric relationships relating various forest structural properties such as DBH, tree height and aboveground biomass have been developed through detailed field data collection both in the United States, and globally. However, there has been limited attention to explaining observed variability in these relationships. Often, a single relationship is developed for a single species, and is applied irrespective of environment. In this research, we attempt to explain allometry as a function of environment by focusing on the relationship between DBH, crown radius and tree height. Two primary datasets are used to conduct this research. First, the Forest Inventory Analysis (FIA) dataset, including tree DBH and height information for the United States, are used to investigate variability in the relationship between DBH and tree height. Second, high-resolution airborne lidar datasets were collected from areas across the US, Canada and Costa Rica and are applied to investigate variability in the relationship between crown radius and height. The lidar datasets are run through a generalized canopy delineation algorithm to produce multilayered estimates of individual tree location, height, and crown radius. Power law functions are fit to the relationships between DBH and tree height, and crown radius and tree height. The mean and standard deviation of the power law exponents are compared to environmental attributes including precipitation, temperature, topography, and age since disturbance. This research demonstrates that although universal tendencies are observed in average power law exponents, considerable local variability exists that can be partially attributed to local environment. Therefore local environment, as well as tree species, should be accounted for in the development and application of allometric equations for forest studies.

  9. Balancing Newtonian gravity and spin to create localized structures

    NASA Astrophysics Data System (ADS)

    Bush, Michael; Lindner, John

    2015-03-01

    Using geometry and Newtonian physics, we design localized structures that do not require electromagnetic or other forces to resist implosion or explosion. In two-dimensional Euclidean space, we find an equilibrium configuration of a rotating ring of massive dust whose inward gravity is the centripetal force that spins it. We find similar solutions in three-dimensional Euclidean and hyperbolic spaces, but only in the limit of vanishing mass. Finally, in three-dimensional Euclidean space, we generalize the two-dimensional result by finding an equilibrium configuration of a spherical shell of massive dust that supports itself against gravitational collapse by spinning isoclinically in four dimensions so its three-dimensional acceleration is everywhere inward. These Newtonian ``atoms'' illuminate classical physics and geometry.

  10. Optical fingerprint recognition based on local minutiae structure coding.

    PubMed

    Yi, Yao; Cao, Liangcai; Guo, Wei; Luo, Yaping; Feng, Jianjiang; He, Qingsheng; Jin, Guofan

    2013-07-15

    A parallel volume holographic optical fingerprint recognition system robust to fingerprint translation, rotation and nonlinear distortion is proposed. The optical fingerprint recognition measures the similarity by using the optical filters of multiplexed holograms recorded in the holographic media. A fingerprint is encoded into multiple template data pages based on the local minutiae structure coding method after it is adapted for the optical data channel. An improved filter recording time schedule and a post-filtering calibration technology are combined to suppress the calculating error from the large variations in data page filling ratio. Experimental results tested on FVC2002 DB1 and a forensic database comprising 270,216 fingerprints demonstrate the robustness and feasibility of the system.

  11. Prospective multi-centre Voxel Based Morphometry study employing scanner specific segmentations: Procedure development using CaliBrain structural MRI data

    PubMed Central

    2009-01-01

    Background Structural Magnetic Resonance Imaging (sMRI) of the brain is employed in the assessment of a wide range of neuropsychiatric disorders. In order to improve statistical power in such studies it is desirable to pool scanning resources from multiple centres. The CaliBrain project was designed to provide for an assessment of scanner differences at three centres in Scotland, and to assess the practicality of pooling scans from multiple-centres. Methods We scanned healthy subjects twice on each of the 3 scanners in the CaliBrain project with T1-weighted sequences. The tissue classifier supplied within the Statistical Parametric Mapping (SPM5) application was used to map the grey and white tissue for each scan. We were thus able to assess within scanner variability and between scanner differences. We have sought to correct for between scanner differences by adjusting the probability mappings of tissue occupancy (tissue priors) used in SPM5 for tissue classification. The adjustment procedure resulted in separate sets of tissue priors being developed for each scanner and we refer to these as scanner specific priors. Results Voxel Based Morphometry (VBM) analyses and metric tests indicated that the use of scanner specific priors reduced tissue classification differences between scanners. However, the metric results also demonstrated that the between scanner differences were not reduced to the level of within scanner variability, the ideal for scanner harmonisation. Conclusion Our results indicate the development of scanner specific priors for SPM can assist in pooling of scan resources from different research centres. This can facilitate improvements in the statistical power of quantitative brain imaging studies. PMID:19445668

  12. Studies of local magnetism and local structure in La(2-x)Sr(x)CuO4

    NASA Technical Reports Server (NTRS)

    Budnick, J. I.; Tan, Z.; Filipkowski, M.

    1991-01-01

    The muon spin rotation (MUSR) study of local magnetism of Sr-doped La2CrO4 is reviewed. Emphasis is placed on magnetic order as detected by local and bulk probes with local atomic environments studies by x ray absorption fine structure (XAFS). Correlations between the MUSR study of local magnetic ordering and the bulk magnetization study are presented along with a discussion of the dependence upon oxygen stoichiometry. Results are presented for both superconducting phases and magnetic phases. Recent data which reveals the existence of local magnetic ordering in the hydrogen-doped YBa2Cu3O7 system are also discussed.

  13. Local structures of copper-doped ZnO films

    SciTech Connect

    Ma, Q.; Buchholz, D.B.; Chang, R.P.H.

    2009-01-05

    We report the local structures of a series of copper-doped zinc oxide films using polarization-dependent x-ray-absorption spectroscopy. The films were grown by pulsed-laser ablation under various conditions. The results show that films where copper exists solely as clusters are not ferromagnetic. The results also show that some of the copper-doped zinc oxide films are not ferromagnetic despite the fact that the copper substitution for zinc in the ZnO lattice is in the Cu{sup 2+} state, which provides the necessary unpaired spins for ferromagnetism. Therefore, Cu{sup 2+}/Zn{sup 2+} substitution is not the only imperative condition for ferromagnetism to occur. We present characteristics unique to the electronic and atomic structure of ferromagnetic films and argue that the increased covalence of the Cu{sub Zn}-O bond found in these films is a prerequisite for the spin alignments in a substitutionally copper-doped zinc oxide film.

  14. Identification of ligand templates using local structure alignment for structure-based drug design.

    PubMed

    Lee, Hui Sun; Im, Wonpil

    2012-10-22

    With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. On the basis of the fact that the structurally similar binding sites share information about their ligands, we have developed a local structure alignment tool, G-LoSA (graph-based local structure alignment). The known protein-ligand binding-site structure library is searched by G-LoSA to detect binding-site structures with similar geometry and physicochemical properties to a query binding-site structure regardless of sequence continuity and protein fold. Then, the ligands in the identified complexes are used as templates (i.e., template ligands) to predict/design a ligand for the target protein. The performance of G-LoSA is validated against 76 benchmark targets from the Astex diverse set. Using the currently available protein-ligand structure library, G-LoSA is able to identify a single template ligand (from a nonhomologous protein complex) that is highly similar to the target ligand in more than half of the benchmark targets. In addition, our benchmark analyses show that an assembly of structural fragments from multiple template ligands with partial similarity to the target ligand can be used to design novel ligand structures specific to the target protein. This study clearly indicates that a template-based ligand modeling has potential for de novo ligand design and can be a complementary approach to the receptor structure based methods.

  15. Recent Advances in Plant NLR Structure, Function, Localization, and Signaling

    PubMed Central

    Qi, Dong; Innes, Roger W.

    2013-01-01

    Nucleotide-binding domain leucine-rich repeat (NLR) proteins play a central role in the innate immune systems of plants and vertebrates. In plants, NLR proteins function as intracellular receptors that detect pathogen effector proteins directly, or indirectly by recognizing effector-induced modifications to other host proteins. NLR activation triggers a suite of defense responses associated with programed cell death (PCD). The molecular mechanisms underlying NLR activation, and how activation is translated into defense responses, have been particularly challenging to elucidate in plants. Recent reports, however, are beginning to shed some light. It is becoming clear that plant NLR proteins are targeted to diverse sub-cellular locations, likely depending on the locations where the effectors are detected. These reports also indicate that some NLRs re-localize following effector detection, while others do not, and such relocalization may reflect differences in signaling pathways. There have also been recent advances in understanding the structure of plant NLR proteins, with crystal structures now available for the N-terminal domains of two well-studied NLRs, a coiled-coil (CC) domain and a Toll-interleukin Receptor (TIR). Significant improvements in molecular modeling have enabled more informed structure-function studies, illuminating roles of intra- and inter-molecular interactions in NLR activation regulation. Several independent studies also suggest that intracellular trafficking is involved in NLR-mediated resistance. Lastly, progress is being made on identifying transcriptional regulatory complexes activated by NLRs. Current models for how plant NLR proteins are activated and how they induce defenses are discussed, with an emphasis on what remains to be determined. PMID:24155748

  16. Seismic Structure of Villarrica Volcano obtained through Local Tomography

    NASA Astrophysics Data System (ADS)

    Mora-Stock, Cindy; Thorwart, Martin; Rabbel, Wolfgang

    2016-04-01

    We present a first model of the inner structure of the Villarrica volcano (Southern Chile) derived from P-wave arrival time inversion from local volcano tectonic (VT) events. A total set of 75 DSS-Cube stations was installed at the volcano surroundings between March 1st and 14th, 2012, with 50 of them at the crater, flanks and around the volcano. Volcano tectonic earthquakes located inside the network describe a NS-trending structure between 2 and 7 km below sea level at a transition zone between low and high P-wave velocity zones. The location and trend of the volume is consistent with a branch of the Liquiñe - Ofqui Fault Zone, a long lived arc-parallel 1000 km long strike-slip fault at the Chilean subduction zone. Values for P-wave velocity (Vp) averaged 4.5 km/s, and Vp/Vs ratios gave values of 1.6 to 1.7. The maximum variation of Vp is of the order of ±20%. Checkerboard test and Bootstrap method were applied. Bootstrap method shows that the standard deviation of the tomographic solutions is of the order of ±9%. Resolution given by Checkerboard test is of the order of 2-3 km. We observed three low velocity zones (LVZs) located between 1 and 5 km depth that can be associated with magma and/or other fluids. One main LVZ at 1-2 km towards NNW from the locus of seismicity; and two conduit-like LVZ s reaching from the locus of seismicity towards the surface features of the Los Nevados and Challupén pyroclastic flows (ENE and S of the crater, respectively). These two LVZs are thought to be remnant conduits of these previous eruptions. High velocity zones are observed to the east and below the crater, and can be interpreted as consolidated crustal rocks and volcanic products from previously collapsed caldera.

  17. GraphClust: alignment-free structural clustering of local RNA secondary structures

    PubMed Central

    Rose, Dominic; Backofen, Rolf

    2012-01-01

    Motivation: Clustering according to sequence–structure similarity has now become a generally accepted scheme for ncRNA annotation. Its application to complete genomic sequences as well as whole transcriptomes is therefore desirable but hindered by extremely high computational costs. Results: We present a novel linear-time, alignment-free method for comparing and clustering RNAs according to sequence and structure. The approach scales to datasets of hundreds of thousands of sequences. The quality of the retrieved clusters has been benchmarked against known ncRNA datasets and is comparable to state-of-the-art sequence–structure methods although achieving speedups of several orders of magnitude. A selection of applications aiming at the detection of novel structural ncRNAs are presented. Exemplarily, we predicted local structural elements specific to lincRNAs likely functionally associating involved transcripts to vital processes of the human nervous system. In total, we predicted 349 local structural RNA elements. Availability: The GraphClust pipeline is available on request. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22689765

  18. Local genetic structure in a white-bearded manakin population.

    PubMed

    Höglund, Jacob; Shorey, Lisa

    2003-09-01

    Local genetic structure was studied in lekking white-bearded manakins in a study area on northern Trinidad, West Indies. The study population consisted of nine leks, at which a total of 238 birds were caught. By genotyping the individuals at eight polymorphic microsatellite loci we inferred some males on leks to be related (r = 0.25) as we found an average number of 14.8 half-sib relationships and two full-sib relationships per lek. We found that the sampled birds belonged to one genetic population that was slightly inbred (FIS and FIT = 0.02). Kinship coefficients decreased with increasing geographical distance, indicating that related birds displayed at the same or nearby leks. However, leks did not consist of only one family group because the average genetic distance (aij) between males within leks was higher than when comparing males on leks within close proximity. These patterns suggest limited male dispersal, that some type of kin recognition process between individuals may exist in this species and that males on leks may be more likely to establish themselves as territory-holding birds if a relative is already present. PMID:12919483

  19. Historic timber skeleton structures and the local seismic culture

    NASA Astrophysics Data System (ADS)

    Bostenaru, M.

    2009-04-01

    This presentation deals with the employment of timber skeleton structure and the local seismic culture. After the 1755 earthquake in the reconstruction of Lisbon a type of building with timber skeleton and masonry infill called "gaiola pombalina" was promoted, since this was designed to better resists earthquakes. "Gaiola" means cage, and it was also named after the Marques de Pombal who introduced it in the reconstruction following the earthquake. The „gaiola pombalina" presents a timber skeleton with Saint Andrew crosses in the interior walls with masonry infill and thick masonry load bearing walls loosing in thickness to the upper floors in the exterior walls. The masonry can fall out during earthquakes but the building remains staying given the interior timber skeleton. The type of buildings with timber structure and (masonry) infill behaved well in earthquakes in various parts of the earth, like Nepal (the dhaji dewary type), Pakistan, Turkey (the himiş type after the 1999 earthquake) [both latter types were researched by Langenbach, www.conservationtech.com and www.traditional-is-modern.net] and also in Germany after the 1356 earthquake (the Southern German subtype of Fachwerk). Also in Italy a subtype called "casa baraccata" was promoted in a construction code to a similar time (following the 1783 earthquake in Southern Italy, see Tobriner 1983) as that of the "gaiola pombalina", the time of the Baroque, when town planning acquired another status. Unlike at the "gaiola pombalina" the "casa baraccata" the timber skeleton is at the exterior walls. For this reason this type of buildings is considered to be an expression of the local seismic culture. However, this type of buildings is common also for areas where seismic risk is not an issue, like half-timbered in England and the northern subtype of Fachwerk in Northern Germany, and in some high seismic risk regions with mountains and timber resources like Romania is not spread. Given these premises the author

  20. Centre-embedded structures are a by-product of associative learning and working memory constraints: evidence from baboons (Papio Papio).

    PubMed

    Rey, Arnaud; Perruchet, Pierre; Fagot, Joël

    2012-04-01

    Influential theories have claimed that the ability for recursion forms the computational core of human language faculty distinguishing our communication system from that of other animals (Hauser, Chomsky, & Fitch, 2002). In the present study, we consider an alternative view on recursion by studying the contribution of associative and working memory processes. After an intensive paired-associate training with visual shapes, we observed that baboons spontaneously ordered their responses in keeping with a recursive, centre-embedded structure. This result suggests that the human ability for recursion might partly if not entirely originate from fundamental processing constraints already present in nonhuman primates and that the critical distinction between animal communication and human language should more likely be found in working memory capacities than in an ability to produce recursive structures per se.

  1. Enhancement of initial equivalency for protein structure alignment based on encoded local structures.

    PubMed

    Hung, Kenneth; Wang, Jui-Chih; Chen, Cheng-Wei; Chuang, Cheng-Long; Tsai, Kun-Nan; Chen, Chung-Ming

    2012-11-01

    Most alignment algorithms find an initial equivalent residue pair followed by an iterative optimization process to explore better near-optimal alignments in the surrounding solution space of the initial alignment. It plays a decisive role in determining the alignment quality since a poor initial alignment may make the final alignment trapped in an undesirable local optimum even with an iterative optimization. We proposed a vector-based alignment algorithm with a new initial alignment approach accounting for local structure features called MIRAGE-align. The new idea is to enhance the quality of the initial alignment based on encoded local structural alphabets to identify the protein structure pair whose sequence identity falls in or below twilight zone. The statistical analysis of alignment quality based on Match Index (MI) and computation time demonstrated that MIRAGE-align algorithm outperformed four previously published algorithms, i.e., the residue-based algorithm (CE), the vector-based algorithm (SSM), TM-align, and Fr-TM-align. MIRAGE-align yields a better estimate of initial solution to enhance the quality of initial alignment and enable the employment of a non-iterative optimization process to achieve a better alignment. PMID:22717522

  2. Structural anisotropy quantification improves the final superresolution image of localization microscopy

    NASA Astrophysics Data System (ADS)

    Wang, Yina; Huang, Zhen-li

    2016-07-01

    Superresolution localization microscopy initially produces a dataset of fluorophore coordinates instead of a conventional digital image. Therefore, superresolution localization microscopy requires additional data analysis to present a final superresolution image. However, methods of employing the structural information within the localization dataset to improve the data analysis performance remain poorly developed. Here, we quantify the structural information in a localization dataset using structural anisotropy, and propose to use it as a figure of merit for localization event filtering. With simulated as well as experimental data of a biological specimen, we demonstrate that exploring structural anisotropy has allowed us to obtain superresolution images with a much cleaner background.

  3. Analysis of pan-African Centres of excellence in health innovation highlights opportunities and challenges for local innovation and financing in the continent

    PubMed Central

    2012-01-01

    A pool of 38 pan-African Centres of Excellence (CoEs) in health innovation has been selected and recognized by the African Network for Drugs and Diagnostics Innovation (ANDI), through a competitive criteria based process. The process identified a number of opportunities and challenges for health R&D and innovation in the continent: i) it provides a direct evidence for the existence of innovation capability that can be leveraged to fill specific gaps in the continent; ii) it revealed a research and financing pattern that is largely fragmented and uncoordinated, and iii) it highlights the most frequent funders of health research in the continent. The CoEs are envisioned as an innovative network of public and private institutions with a critical mass of expertise and resources to support projects and a variety of activities for capacity building and scientific exchange, including hosting fellows, trainees, scientists on sabbaticals and exchange with other African and non-African institutions. PMID:22838941

  4. Perceptual centres in speech - an acoustic analysis

    NASA Astrophysics Data System (ADS)

    Scott, Sophie Kerttu

    Perceptual centres, or P-centres, represent the perceptual moments of occurrence of acoustic signals - the 'beat' of a sound. P-centres underlie the perception and production of rhythm in perceptually regular speech sequences. P-centres have been modelled both in speech and non speech (music) domains. The three aims of this thesis were toatest out current P-centre models to determine which best accounted for the experimental data bto identify a candidate parameter to map P-centres onto (a local approach) as opposed to the previous global models which rely upon the whole signal to determine the P-centre the final aim was to develop a model of P-centre location which could be applied to speech and non speech signals. The first aim was investigated by a series of experiments in which a) speech from different speakers was investigated to determine whether different models could account for variation between speakers b) whether rendering the amplitude time plot of a speech signal affects the P-centre of the signal c) whether increasing the amplitude at the offset of a speech signal alters P-centres in the production and perception of speech. The second aim was carried out by a) manipulating the rise time of different speech signals to determine whether the P-centre was affected, and whether the type of speech sound ramped affected the P-centre shift b) manipulating the rise time and decay time of a synthetic vowel to determine whether the onset alteration was had more affect on P-centre than the offset manipulation c) and whether the duration of a vowel affected the P-centre, if other attributes (amplitude, spectral contents) were held constant. The third aim - modelling P-centres - was based on these results. The Frequency dependent Amplitude Increase Model of P-centre location (FAIM) was developed using a modelling protocol, the APU GammaTone Filterbank and the speech from different speakers. The P-centres of the stimuli corpus were highly predicted by attributes of

  5. Titanium local structure in tektite probed by X-ray absorption fine structure spectroscopy.

    PubMed

    Wang, Ling; Yoshiasa, Akira; Okube, Maki; Takeda, Takashi

    2011-11-01

    The local structure of titanium in tektites from six strewn fields was studied by Ti K-edge X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) in order to provide quantitative data on Ti-O distance and Ti coordination number. The titanium in tektites possessed different coordination environment types. XANES spectra patterns revealed resemblance to high-temperature TiO(2)-SiO(2) glass and TiO(2) anatase. All samples showed that the valence of Ti is 4+. Based on the Ti-O distances, coordination numbers and radial distribution function determined by EXAFS analyses, the tektites were classified into three types: type I, Ti occupies a four-coordinated tetrahedral site with Ti-O distances of 1.84-1.79 Å; type II, Ti occupies a five-coordinated trigonal bipyramidal or tetragonal pyramidal site with Ti-O distances of 1.92-1.89 Å; type III, Ti occupies a six-coordinated octahedral site with Ti-O distances of 2.00-1.96 Å. Although Ti occupies the TiO(6) octahedral site in most titanium minerals under ambient conditions, some tektites have four- and five-coordinated Ti. This study indicated that the local structure of Ti might change in impact events and the following stages.

  6. A special kind of local structure in the CMB intensity maps: duel peak structure

    NASA Astrophysics Data System (ADS)

    Liu, Hao; Li, Ti-Pei

    2009-03-01

    We study the local structure of Cosmic Microwave Background (CMB) temperature maps released by the Wilkinson Microwave Anisotropy Probe (WMAP) team, and find a new kind of structure, which can be described as follows: a peak (or valley) of average temperature is often followed by a peak of temperature fluctuation that is 4° away. This structure is important for the following reasons: both the well known cold spot detected by Cruz et al. and the hot spot detected by Vielva et al. with the same technology (the third spot in their article) have such structure; more spots that are similar to them can be found on CMB maps and they also tend to be significant cold/hot spots; if we change the 4° characteristic into an artificial one, such as 3° or 5°, there will be less 'similar spots', and the temperature peaks or valleys will be less significant. The presented 'similar spots' have passed a strict consistency test which requires them to be significant on at least three different CMB temperature maps. We hope that this article could arouse some interest in the relationship of average temperature with temperature fluctuation in local areas; meanwhile, we are also trying to find an explanation for it which might be important to CMB observation and theory.

  7. Titanium local structure in tektite probed by X-ray absorption fine structure spectroscopy.

    PubMed

    Wang, Ling; Yoshiasa, Akira; Okube, Maki; Takeda, Takashi

    2011-11-01

    The local structure of titanium in tektites from six strewn fields was studied by Ti K-edge X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) in order to provide quantitative data on Ti-O distance and Ti coordination number. The titanium in tektites possessed different coordination environment types. XANES spectra patterns revealed resemblance to high-temperature TiO(2)-SiO(2) glass and TiO(2) anatase. All samples showed that the valence of Ti is 4+. Based on the Ti-O distances, coordination numbers and radial distribution function determined by EXAFS analyses, the tektites were classified into three types: type I, Ti occupies a four-coordinated tetrahedral site with Ti-O distances of 1.84-1.79 Å; type II, Ti occupies a five-coordinated trigonal bipyramidal or tetragonal pyramidal site with Ti-O distances of 1.92-1.89 Å; type III, Ti occupies a six-coordinated octahedral site with Ti-O distances of 2.00-1.96 Å. Although Ti occupies the TiO(6) octahedral site in most titanium minerals under ambient conditions, some tektites have four- and five-coordinated Ti. This study indicated that the local structure of Ti might change in impact events and the following stages. PMID:21997913

  8. Organizational Structure and Behaviour in Day Care: Differences between Non-Profit and For-Profit Centres.

    ERIC Educational Resources Information Center

    Canning, Patricia M.; Lyon, Mary E.; Kienapple, Kim; Young, Jeffrey

    2002-01-01

    Examined how Canadian day care centers are operated and managed, to identify differences in organizational structure and behavior between non-profit and for-profit centers and characteristics of structure and management linked with high quality care. Found that non-profit centers were more complex, more formalized, and less centralized than…

  9. AWSEM-MD: Protein Structure Prediction Using Coarse-grained Physical Potentials and Bioinformatically Based Local Structure Biasing

    PubMed Central

    Davtyan, Aram; Schafer, Nicholas P.; Zheng, Weihua; Clementi, Cecilia; Wolynes, Peter G.; Papoian, Garegin A.

    2012-01-01

    The Associative memory, Water mediated, Structure and Energy Model (AWSEM) is a coarse-grained protein force field. AWSEM contains physically motivated terms, such as hydrogen bonding, as well as a bioinformatically based local structure biasing term, which efficiently takes into account many-body effects that are modulated by the local sequence. When combined with appropriate local or global alignments to choose memories, AWSEM can be used to perform de novo protein structure prediction. Herein we present structure prediction results for a particular choice of local sequence alignment method based on short residue sequences called fragments. We demonstrate the model’s structure prediction capabilities for three levels of global homology between the target sequence and those proteins used for local structure biasing, all of which assume that the structure of the target sequence is not known. When there are no homologs in the database of structures used for local structure biasing, AWSEM calculations produce structural predictions that are somewhat improved compared with prior works using related approaches. The inclusion of a small number of structures from homologous sequences improves structure prediction only marginally but when the fragment search is restricted to only homologous sequences, AWSEM can perform high resolution structure prediction and can be used for kinetics and dynamics studies. PMID:22545654

  10. Comparison of perceived quality amongst migrant and local patients using primary health care delivered by community health centres in Shenzhen, China

    PubMed Central

    2014-01-01

    Background Providing good quality primary health care to all inhabitants is one of the Chinese Government’s health care objectives. However, information is scarce regarding the difference in quality of primary health care delivered to migrants and local residents respectively. This study aimed to compare patients’ perceptions of quality of primary health care between migrants and local patients, and their willingness to use and recommend primary health care to others. Methods A cross-sectional survey was conducted. 787 patients in total were chosen from four randomly drawn Community Health Centers (CHCs) for interviews. Results Local residents scored higher than migrants in terms of their satisfaction with types of drugs available (3.62 vs. 3.45, p = 0.035), attitude of health workers (4.41 vs. 4.14, p = 0.042) and waiting time (4.30 vs. 3.86, p < 0.001). Even though there was no significant difference in overall satisfaction between local residents and migrants (4.16 vs. 3.91, p = 0.159), migrants were more likely to utilize primary health care as the first choice for their usual health problems (94.1% vs. 87.1%, p = 0.032), while local residents were more inclined to recommend Traditional Chinese Medicine to others (65.6% vs. 56.6%, p = 0.026). Conclusions Quality of primary health care given to migrants is less satisfactory than to local residents in terms of attitude of health workers and waiting time. Our study suggests quality of care could be improved through extending opening hours of CHCs and strengthening professional ethics education. Considering CHCs as the first choice by migrants might be due to their health insurance scheme, while locals’ recommendations for traditional Chinese medicine were possibly because of cultural differences. PMID:24779564

  11. Local Large-Scale Structure and the Assumption of Homogeneity

    NASA Astrophysics Data System (ADS)

    Keenan, Ryan C.; Barger, Amy J.; Cowie, Lennox L.

    2016-10-01

    Our recent estimates of galaxy counts and the luminosity density in the near-infrared (Keenan et al. 2010, 2012) indicated that the local universe may be under-dense on radial scales of several hundred megaparsecs. Such a large-scale local under-density could introduce significant biases in the measurement and interpretation of cosmological observables, such as the inferred effects of dark energy on the rate of expansion. In Keenan et al. (2013), we measured the K-band luminosity density as a function of distance from us to test for such a local under-density. We made this measurement over the redshift range 0.01 < z < 0.2 (radial distances D ~ 50 - 800 h 70 -1 Mpc). We found that the shape of the K-band luminosity function is relatively constant as a function of distance and environment. We derive a local (z < 0.07, D < 300 h 70 -1 Mpc) K-band luminosity density that agrees well with previously published studies. At z > 0.07, we measure an increasing luminosity density that by z ~ 0.1 rises to a value of ~ 1.5 times higher than that measured locally. This implies that the stellar mass density follows a similar trend. Assuming that the underlying dark matter distribution is traced by this luminous matter, this suggests that the local mass density may be lower than the global mass density of the universe at an amplitude and on a scale that is sufficient to introduce significant biases into the measurement of basic cosmological observables. At least one study has shown that an under-density of roughly this amplitude and scale could resolve the apparent tension between direct local measurements of the Hubble constant and those inferred by Planck team. Other theoretical studies have concluded that such an under-density could account for what looks like an accelerating expansion, even when no dark energy is present.

  12. Local structure of Titanium in natural glasses probed by X-ray absorption fine structure

    NASA Astrophysics Data System (ADS)

    Wang, L.; Yoshiasa, A.; Okube, M.; Nakatani, T.; Hayasaka, Y.; Isobe, H.

    2013-04-01

    Synchrotron radiation has been used to collect titanium K-edge absorption spectra of a suite of natural glasses (tektites, impact glasses, fault rocks and volcanic glasses). XANES and XAFS analysis provided the qualitative and quantitative information of Ti oxidation state, Ti-O distance and site geometry. Tektites possess four-, five-, six-coordinated Ti, whereas fault rock-pseudotachylite, volcanic glasses and impact glass only presented five- and six-coordinated Ti. This study indicated that different petrogenesis of natural glasses has different local structures of titanium.

  13. Geometrical regularization of nonrigid registration using local anisotropic structure and joint saliency map

    NASA Astrophysics Data System (ADS)

    Zhou, Jiawei; Qin, Binjie

    2011-06-01

    Nonrigid image registration is a crucial task to study local structural/volumetric change in many applications. The presence and resection of brain tumor in pre- and intra-operative brain images will greatly distort local anatomical structure and introduce non-corresponding outlier features. This can cause serious conflicts in achieving a smoothly varying deformation field in nonrigid registration. In this paper, a novel regularizing scheme, which is based on local anisotropic structure and Joint Saliency Map weighted regularization, is introduced in registration to aim at handling local complex deformation and outliers. The sparse displacement is regularized to adapt its smoothness as well as orientation according to the local anisotropic structure. Moreover, the Joint Saliency Map guides the assignment of data certainty so that the reliable corresponding structural voxels are emphasized in regularization. The results show that our method is sufficiently accurate and effective to both local large deformation and outliers while maintaining an overall smooth deformation field.

  14. Hen egg-white lysozyme crystallisation: protein stacking and structure stability enhanced by a Tellurium(VI)-centred polyoxotungstate.

    PubMed

    Bijelic, Aleksandar; Molitor, Christian; Mauracher, Stephan G; Al-Oweini, Rami; Kortz, Ulrich; Rompel, Annette

    2015-01-19

    As synchrotron radiation becomes more intense, detectors become faster and structure-solving software becomes more elaborate, obtaining single crystals suitable for data collection is now the bottleneck in macromolecular crystallography. Hence, there is a need for novel and advanced crystallisation agents with the ability to crystallise proteins that are otherwise challenging. Here, an Anderson-Evans-type polyoxometalate (POM), specifically Na6 [TeW6 O24 ]⋅22 H2 O (TEW), is employed as a crystallisation additive. Its effects on protein crystallisation are demonstrated with hen egg-white lysozyme (HEWL), which co-crystallises with TEW in the vicinity (or within) the liquid-liquid phase separation (LLPS) region. The X-ray structure (PDB ID: 4PHI) determination revealed that TEW molecules are part of the crystal lattice, thus demonstrating specific binding to HEWL with electrostatic interactions and hydrogen bonds. The negatively charged TEW polyoxotungstate binds to sites with a positive electrostatic potential located between two (or more) symmetry-related protein chains. Thus, TEW facilitates the formation of protein-protein interfaces of otherwise repulsive surfaces, and thereby the realisation of a stable crystal lattice. In addition to retaining the isomorphicity of the protein structure, the anomalous scattering of the POMs was used for macromolecular phasing. The results suggest that hexatungstotellurate(VI) has great potential as a crystallisation additive to promote both protein crystallisation and structure elucidation. PMID:25521080

  15. Local Structures in Adult Education: A Discussion Paper.

    ERIC Educational Resources Information Center

    Irish National Association of Adult Education, Dublin.

    In January 2002, Ireland's minister of state announced the establishment of the National Adult Learning Council to take effect in March 2002. One of the council's priorities will be to establish local adult learning boards (LALBs) to oversee development and delivery of adult education. An Irish government white paper recommended that LALBs'…

  16. Global/local methods research using a common structural analysis framework

    NASA Technical Reports Server (NTRS)

    Knight, Norman F., Jr.; Ransom, Jonathan B.; Griffin, O. H., Jr.; Thompson, Danniella M.

    1991-01-01

    Methodologies for global/local stress analysis are described including both two- and three-dimensional analysis methods. These methods are being developed within a common structural analysis framework. Representative structural analysis problems are presented to demonstrate the global/local methodologies being developed.

  17. Structural Biomechanics Modulate Intramuscular Distribution of Locally Delivered Drugs

    PubMed Central

    Wu, Peter I-Kung; Edelman, Elazer R.

    2008-01-01

    As local drug delivery continues to emerge as a clinical force, so does understanding of its potentially narrow therapeutic window. Classic molecular transport studies are of value but do not typically account for the local nature of drug transport or the regional dynamic function in target tissues like muscle that may undergo cyclical and variable mechanical motion and loading. We examine the impact of dynamic architecture on intramuscular drug distribution. We designed a tissue mounting technique and mechanical loading system that uniquely enables pharmacokinetics investigations in association with control of muscle biomechanics while preserving physiologic tissue architecture. The system was validated and used to elucidate the influence of architecture and controlled cyclic strain on intramuscular drug distribution. Rat soleus muscles underwent controlled deformations within a drug delivery chamber that preserved in vivo physiology. Penetration of 1 mM 20 kDa FITC-dextran at planar surfaces of the soleus increased significantly from 0.52 ± 0.09 mm under 80 min of static (0%) strain to 0.81 ± 0.09 mm under cyclic (3 Hz, 0–20% peak-to-peak) strain, demonstrating the driving effect of cyclic loading on transport. Penetration at curved margins was 1.57- and 2.53-fold greater than at planar surfaces under static and cyclic strain, respectively, and was enhanced 1.6-fold more by cyclic strain, revealing architecturally dictated spatial heterogeneity in transport and modulation of motion dynamics. Architectural geometry and dynamics modulate the impact of mechanical loading on local drug penetration and intramuscular distribution. Future work will use the biomechanical test system to investigate mechanisms underlying transport effects of specific loading regimens. It is hoped that this work will initiate a broader understanding of intramuscular pharmacokinetics and guide local drug delivery strategies. PMID:18706562

  18. The role of local structure in dynamical arrest

    NASA Astrophysics Data System (ADS)

    Royall, C. Patrick; Williams, Stephen R.

    2015-02-01

    Amorphous solids, or glasses, are distinguished from crystalline solids by their lack of long-range structural order. At the level of two-body structural correlations, glassformers show no qualitative change upon vitrifying from a supercooled liquid. Nonetheless the dynamical properties of a glass are so much slower that it appears to take on the properties of a solid. While many theories of the glass transition focus on dynamical quantities, a solid's resistance to flow is often viewed as a consequence of its structure. Here we address the viewpoint that this remains the case for a glass. Recent developments using higher-order measures show a clear emergence of structure upon dynamical arrest in a variety of glass formers and offer the tantalising hope of a structural mechanism for arrest. However a rigorous fundamental identification of such a causal link between structure and arrest remains elusive. We undertake a critical survey of this work in experiments, computer simulation and theory and discuss what might strengthen the link between structure and dynamical arrest. We move on to highlight the relationship between crystallisation and glass-forming ability made possible by this deeper understanding of the structure of the liquid state, and emphasise the potential to design materials with optimal glassforming and crystallisation ability, for applications such as phase-change memory. We then consider aspects of the phenomenology of glassy systems where structural measures have yet to make a large impact, such as polyamorphism (the existence of multiple liquid states), ageing (the time-evolution of non-equilibrium materials below their glass transition) and the response of glassy materials to external fields such as shear.

  19. GP clinic and community health centre approach to after hours and the role of Medicare Locals in educating and raising awareness.

    PubMed

    Rinehart, Natalie E; Smorgon, Samantha; Holman, Jessica

    2014-01-01

    This article reviews a Quality Improvement Project concerning how GP clinics approach after hours (AH) primary care information for themselves and their patients. Medicare Locals have been given the responsibility of coordinating AH services in their catchments and supporting health systems and patients in accessing care appropriate to their needs. The AH project conducted by Inner North West Melbourne Medicare Local (INWMML) sought to explore how a range of GP clinics approached AH information before an educational forum, evaluation of its developed resources for increasing awareness of AH options and how clinics would choose to change their approach to AH following this process. The findings suggested that 46 participating clinic staff had a strong focus on hospitals and locum services as the main AH options despite telephone advice line options being available. Additionally, there was a lack of awareness for some clinic staff concerning services for mental health, dental health and residential aged care. The educational forum and the AH resources developed (i.e. brochures, posters and service directory) by INWMML were rated as valuable and would be used and shared with other health care providers and patients. Confidence that patients would be able to find appropriate care in the AH period after clinics had finished implementing planned changes, rose significantly in key areas after participating in the AH project.

  20. GP clinic and community health centre approach to after hours and the role of Medicare Locals in educating and raising awareness.

    PubMed

    Rinehart, Natalie E; Smorgon, Samantha; Holman, Jessica

    2014-01-01

    This article reviews a Quality Improvement Project concerning how GP clinics approach after hours (AH) primary care information for themselves and their patients. Medicare Locals have been given the responsibility of coordinating AH services in their catchments and supporting health systems and patients in accessing care appropriate to their needs. The AH project conducted by Inner North West Melbourne Medicare Local (INWMML) sought to explore how a range of GP clinics approached AH information before an educational forum, evaluation of its developed resources for increasing awareness of AH options and how clinics would choose to change their approach to AH following this process. The findings suggested that 46 participating clinic staff had a strong focus on hospitals and locum services as the main AH options despite telephone advice line options being available. Additionally, there was a lack of awareness for some clinic staff concerning services for mental health, dental health and residential aged care. The educational forum and the AH resources developed (i.e. brochures, posters and service directory) by INWMML were rated as valuable and would be used and shared with other health care providers and patients. Confidence that patients would be able to find appropriate care in the AH period after clinics had finished implementing planned changes, rose significantly in key areas after participating in the AH project. PMID:23480857

  1. Local x-ray diffraction analysis of the structure of dendrites in single-crystal nickel-base superalloys

    SciTech Connect

    Brueckner, U.; Epishin, A.; Link, T.

    1997-12-01

    The structure of the dendrites in the single-crystal nickel-base superalloys SC16, SRR99 and CMSX4 with different refractory element levels (Mo + Ta + W + Re) has been investigated by local X-ray diffraction. A special technique was used to improve the spatial resolution of the X-ray diffraction and to enable the precise control of the X-ray spot position within the dendritic structure. A significant change of the {gamma}/{gamma}{prime}-lattice misfit was found within the dendrite in the superalloys with higher refractory element levels SRR99 and CMSX4. The observed misfit change is based on the change of the {gamma}-lattice parameter due to segregation of W and Re. The intensity of the X-ray beam reflected from the dendrite periphery was found to be weaker than that from the dendrite centre because of the mosaicity. Therefore misfit measurements without knowledge of the X-ray spot position in the dendritic structure lead to values that correspond more to the dendrite core.

  2. Optical Activity Governed by Local Chiral Structures in Two-Dimensional Curved Metallic Nanostructures.

    PubMed

    Narushima, Tetsuya; Hashiyada, Shun; Okamoto, Hiromi

    2016-07-01

    Chiral nanostructures show macroscopic optical activity. Local optical activity and its handedness are not uniform in the nanostructure, and are spatially distributed depending on the shape of the nanostructure. In this study we fabricated curved chain nanostructures made of gold by connecting linearly two or more arc structures in a two-dimensional plane. Spatial features of local optical activity in the chain structures were evaluated with near-field circular dichroism (CD) imaging, and analyzed with the aid of classical electromagnetic simulation. The electromagnetic simulation predicted that local optical activity appears at inflection points where arc structures are connected. The handedness of the local optical activity was dependent on the handedness of the local chirality at the inflection point. Chiral chain structures have odd inflection points and the local optical activity distributed symmetrically with respect to structural centers. In contrast, achiral chain structures have even inflection points and showed antisymmetric distribution. In the near-field CD images of fabricated chain nanostructures, the symmetric and antisymmetric distributions of local CD were observed for chiral and achiral chain structures, respectively, consistent with the simulated results. The handedness of the local optical activity was found to be determined by the handedness of the inflection point, for the fabricated chain structures having two or more inflection points. The local optical activity was thus governed primarily by the local chirality of the inflection points for the gold chain structures. The total effect of all the inflection points in the chain structure is considered to be a predominant factor that determines the macroscopic optical activity. Chirality 28:540-544, 2016. © 2016 Wiley Periodicals, Inc.

  3. Spatial variation in the population structure and reproductive biology of Rimicaris hybisae (Caridea: Alvinocarididae) at hydrothermal vents on the Mid-Cayman Spreading Centre.

    PubMed

    Nye, Verity; Copley, Jonathan T; Tyler, Paul A

    2013-01-01

    The dynamics and microdistribution of faunal assemblages at hydrothermal vents often reflect the fine-scale spatial and temporal heterogeneity of the vent environment. This study examined the reproductive development and population structure of the caridean shrimp Rimicaris hybisae at the Beebe and Von Damm Vent Fields (Mid-Cayman Spreading Centre, Caribbean) using spatially discrete samples collected in January 2012. Rimicaris hybisae is gonochoric and exhibits iteroparous reproduction. Oocyte size-frequency distributions (21-823 µm feret diameters) varied significantly among samples. Embryo development was asynchronous among females, which may result in asynchronous larval release for the populations. Specimens of R. hybisae from the Von Damm Vent Field (2294 m) were significantly larger than specimens from the Beebe Vent Field. Brooding females at Von Damm exhibited greater size-specific fecundity, possibly as a consequence of a non-linear relationship between fecundity and body size that was consistent across both vent fields. Samples collected from several locations at the Beebe Vent Field (4944-4972 m) revealed spatial variability in the sex ratios, population structure, size, and development of oocytes and embryos of this mobile species. Samples from the Von Damm Vent Field and sample J2-613-24 from Beebe Woods exhibited the highest frequencies of ovigerous females and significantly female-biased sex ratios. Environmental variables within shrimp aggregations may influence the distribution of ovigerous females, resulting in a spatially heterogeneous pattern of reproductive development in R. hybisae, as found in other vent taxa.

  4. Localization of wood floor structure by infrared thermography

    NASA Astrophysics Data System (ADS)

    Cochior Plescanu, C.; Klein, M.; Ibarra-Castanedo, C.; Bendada, A.; Maldague, X.

    2008-03-01

    One of our industrial partners, Assek Technologie, is interested in developing a technique that would improve the drying process of wood floor in basements after flooding. In order to optimize the procedure, the floor structure and the damaged (wet) area extent must first be determined with minimum intrusion (minimum or no dismantling). The present study presents the use of infrared thermography to reveal the structure of (flooded) wood floors. The procedure involves opening holes in the floor. Injecting some hot air through those holes reveals the framing structure even if the floor is covered by vinyl or ceramic tiles. This study indicates that thermal imaging can also be used as a tool to validate the decontamination process after drying. Thermal images were obtained on small-scale models and in a demonstration room.

  5. Local Crystalline Structure in an Amorphous Protein Dense Phase

    PubMed Central

    Greene, Daniel G.; Modla, Shannon; Wagner, Norman J.; Sandler, Stanley I.; Lenhoff, Abraham M.

    2015-01-01

    Proteins exhibit a variety of dense phases ranging from gels, aggregates, and precipitates to crystalline phases and dense liquids. Although the structure of the crystalline phase is known in atomistic detail, little attention has been paid to noncrystalline protein dense phases, and in many cases the structures of these phases are assumed to be fully amorphous. In this work, we used small-angle neutron scattering, electron microscopy, and electron tomography to measure the structure of ovalbumin precipitate particles salted out with ammonium sulfate. We found that the ovalbumin phase-separates into core-shell particles with a core radius of ∼2 μm and shell thickness of ∼0.5 μm. Within this shell region, nanostructures comprised of crystallites of ovalbumin self-assemble into a well-defined bicontinuous network with branches ∼12 nm thick. These results demonstrate that the protein gel is comprised in part of nanocrystalline protein. PMID:26488663

  6. Identification of local variations within secondary structures of proteins.

    PubMed

    Kumar, Prasun; Bansal, Manju

    2015-05-01

    Secondary-structure elements (SSEs) play an important role in the folding of proteins. Identification of SSEs in proteins is a common problem in structural biology. A new method, ASSP (Assignment of Secondary Structure in Proteins), using only the path traversed by the C(α) atoms has been developed. The algorithm is based on the premise that the protein structure can be divided into continuous or uniform stretches, which can be defined in terms of helical parameters, and depending on their values the stretches can be classified into different SSEs, namely α-helices, 310-helices, π-helices, extended β-strands and polyproline II (PPII) and other left-handed helices. The methodology was validated using an unbiased clustering of these parameters for a protein data set consisting of 1008 protein chains, which suggested that there are seven well defined clusters associated with different SSEs. Apart from α-helices and extended β-strands, 310-helices and π-helices were also found to occur in substantial numbers. ASSP was able to discriminate non-α-helical segments from flanking α-helices, which were often identified as part of α-helices by other algorithms. ASSP can also lead to the identification of novel SSEs. It is believed that ASSP could provide a better understanding of the finer nuances of protein secondary structure and could make an important contribution to the better understanding of comparatively less frequently occurring structural motifs. At the same time, it can contribute to the identification of novel SSEs. A standalone version of the program for the Linux as well as the Windows operating systems is freely downloadable and a web-server version is also available at http://nucleix.mbu.iisc.ernet.in/assp/index.php.

  7. Identification of local variations within secondary structures of proteins.

    PubMed

    Kumar, Prasun; Bansal, Manju

    2015-05-01

    Secondary-structure elements (SSEs) play an important role in the folding of proteins. Identification of SSEs in proteins is a common problem in structural biology. A new method, ASSP (Assignment of Secondary Structure in Proteins), using only the path traversed by the C(α) atoms has been developed. The algorithm is based on the premise that the protein structure can be divided into continuous or uniform stretches, which can be defined in terms of helical parameters, and depending on their values the stretches can be classified into different SSEs, namely α-helices, 310-helices, π-helices, extended β-strands and polyproline II (PPII) and other left-handed helices. The methodology was validated using an unbiased clustering of these parameters for a protein data set consisting of 1008 protein chains, which suggested that there are seven well defined clusters associated with different SSEs. Apart from α-helices and extended β-strands, 310-helices and π-helices were also found to occur in substantial numbers. ASSP was able to discriminate non-α-helical segments from flanking α-helices, which were often identified as part of α-helices by other algorithms. ASSP can also lead to the identification of novel SSEs. It is believed that ASSP could provide a better understanding of the finer nuances of protein secondary structure and could make an important contribution to the better understanding of comparatively less frequently occurring structural motifs. At the same time, it can contribute to the identification of novel SSEs. A standalone version of the program for the Linux as well as the Windows operating systems is freely downloadable and a web-server version is also available at http://nucleix.mbu.iisc.ernet.in/assp/index.php. PMID:25945573

  8. The Local Job Bank Program: Performance, Structure, and Direction.

    ERIC Educational Resources Information Center

    Ullman, Joseph C.; Huber, George P.

    The book represents an effort to assess the performance, structure, and direction of the Job Bank Program of the Public Employment Service, a program meant to improve the functioning of the labor market information system in the United States. The research had three goals: to assess the relative goal achievement of job banks; to determine its…

  9. Improving hybrid statistical and physical forcefields through local structure enumeration.

    PubMed

    Conway, Patrick; DiMaio, Frank

    2016-08-01

    Forcefields used in biomolecular simulations are comprised of energetic terms that are physical in nature, based on parameter fitting to quantum mechanical simulation or experimental data, or statistical, drawing off high-resolution structural data to describe distributions of molecular features. Combining the two in a single forcefield is challenging, since physical terms describe some, but not all, of the observed statistics, leading to double counting. In this manuscript, we develop a general scheme for correcting statistical potentials used in combination with physical terms. We apply these corrections to the sidechain torsional potential used in the Rosetta all-atom forcefield. We show the approach identifies instances of double-counted interactions, including electrostatic interactions between sidechain and nearby backbone, and steric interactions between neighboring Cβ atoms within secondary structural elements. Moreover, this scheme allows for the inclusion of intraresidue physical terms, previously turned off to avoid overlap with the statistical potential. Combined, these corrections lead to a forcefield with improved performance on several structure prediction tasks, including rotamer prediction and native structure discrimination. PMID:27239808

  10. Improving hybrid statistical and physical forcefields through local structure enumeration.

    PubMed

    Conway, Patrick; DiMaio, Frank

    2016-08-01

    Forcefields used in biomolecular simulations are comprised of energetic terms that are physical in nature, based on parameter fitting to quantum mechanical simulation or experimental data, or statistical, drawing off high-resolution structural data to describe distributions of molecular features. Combining the two in a single forcefield is challenging, since physical terms describe some, but not all, of the observed statistics, leading to double counting. In this manuscript, we develop a general scheme for correcting statistical potentials used in combination with physical terms. We apply these corrections to the sidechain torsional potential used in the Rosetta all-atom forcefield. We show the approach identifies instances of double-counted interactions, including electrostatic interactions between sidechain and nearby backbone, and steric interactions between neighboring Cβ atoms within secondary structural elements. Moreover, this scheme allows for the inclusion of intraresidue physical terms, previously turned off to avoid overlap with the statistical potential. Combined, these corrections lead to a forcefield with improved performance on several structure prediction tasks, including rotamer prediction and native structure discrimination.

  11. Localizing Age-Related Individual Differences in a Hierarchical Structure

    ERIC Educational Resources Information Center

    Salthouse, Timothy A.

    2004-01-01

    Data from 33 separate studies were combined to create an aggregate data set consisting of 16 cognitive variables and 6832 different individuals who ranged between 18 and 95 years of age. Analyses were conducted to determine where in a hierarchical structure of cognitive abilities individual differences associated with age, gender, education, and…

  12. HPV Prevalence and Prognostic Value in a Prospective Cohort of 255 Patients with Locally Advanced HNSCC: A Single-Centre Experience

    PubMed Central

    Thibaudeau, E.; Fortin, B.; Coutlée, F.; Nguyen-Tan, P.; Weng, X.; Audet, M.-L.; Abboud, O.; Guertin, L.; Christopoulos, A.; Tabet, J.; Soulières, D.

    2013-01-01

    Background. HPV is a positive prognostic factor in HNSCC. We studied the prevalence and prognostic impact of HPV on survival parameters and treatment toxicity in patients with locally advanced HNSCC treated with concomitant chemoradiation therapy. Methods. Data on efficacy and toxicity were available for 560 patients. HPV was detected by PCR. Analysis was performed using Kaplan-Meier survival curves, Fisher's test for categorical data, and log-rank statistics for failure times. Results. Median follow-up was 4.7 years. DNA extraction was successful in 255 cases. HPV prevalence was 68.6%, and 53.3% for HPV 16. For HPV+ and HPV−, median LRC was 8.9 and 2.2 years (P = 0.0002), median DFS was 8.9 and 2.1 years (P = 0.0014), and median OS was 8.9 and 3.1 years (P = 0.0002). Survival was different based on HPV genotype, stage, treatment period, and chemotherapy regimen. COX adjusted analysis for T, N, age, and treatment remained significant (P = 0.004). Conclusions. Oropharyngeal cancer is increasingly linked to HPV. This study confirms that HPV status is associated with improved prognosis among H&N cancer patients receiving CRT and should be a stratification factor for clinical trials including H&N cases. Toxicity of CRT is not modified for the HPV population. PMID:23710185

  13. Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm.

    PubMed

    Lehtonen, J V; Denessiouk, K; May, A C; Johnson, M S

    1999-02-15

    We have developed a generic tool for the automatic identification of regions of local structural similarity in unrelated proteins having different folds, as well as for defining more global similarities that result from homologous protein structures. The computer program GENFIT has evolved from the genetic algorithm-based three-dimensional protein structure comparison program GA_FIT. GENFIT, however, can locate and superimpose regions of local structural homology regardless of their position in a pair of structures, the fold topology, or the chain direction. Furthermore, it is possible to restrict the search to a volume centered about a region of interest (e.g., catalytic site, ligand-binding site) in two protein structures. We present a number of examples to illustrate the function of the program, which is a parallel processing implementation designed for distribution to multiple machines over a local network or to run on a single multiprocessor computer.

  14. Local genetic structure in a clonal dioecious angiosperm.

    PubMed

    Ruggiero, M V; Reusch, T B H; Procaccini, G

    2005-04-01

    We used seven microsatellite loci to characterize genetic structure and clonal architecture at three different spatial scales (from meters to centimetres) of a Cymodocea nodosa population. C. nodosa exhibits both sexual reproduction and vegetative propagation by rhizome elongation. Seeds remain buried in the sediment nearby the mother plant in a dormant stage until germination. Seed dispersal potential is therefore expected to be extremely restricted. High clonal diversity (up to 67% of distinct genotypes) and a highly intermingled configuration of genets at different spatial scales were found. No significant differences in genetic structure were found among the three spatial scales, indicating that genetic diversity is evenly distributed along the meadow. Autocorrelation analyses of kinship estimates confirmed the absence of spatial clumping of genets at small spatial scale and the expectations of a very restricted seed dispersal (observed dispersal range 1-21 m) in this species. PMID:15773928

  15. Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. A response to the letter by the Cambridge Crystallographic Data Centre.

    PubMed

    Baldi, Pierre

    2011-12-27

    A response is presented to sentiments expressed in "Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response from The Cambridge Crystallographic Data Centre", recently published in the Journal of Chemical Information and Modeling, (1) which may give readers a misleading impression regarding significant impediments to scientific research posed by the CCDC.

  16. Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. A response to the letter by the Cambridge Crystallographic Data Centre.

    PubMed

    Baldi, Pierre

    2011-12-27

    A response is presented to sentiments expressed in "Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response from The Cambridge Crystallographic Data Centre", recently published in the Journal of Chemical Information and Modeling, (1) which may give readers a misleading impression regarding significant impediments to scientific research posed by the CCDC. PMID:22107601

  17. Transcription inactivation through local refolding of the RNA polymerase structure

    SciTech Connect

    Belogurov, Georgiy A.; Vassylyeva, Marina N.; Sevostyanova, Anastasiya; Appleman, James R.; Xiang, Alan X.; Lira, Ricardo; Webber, Stephen E.; Klyuyev, Sergiy; Nudler, Evgeny; Artsimovitch, Irina; Vassylyev, Dmitry G.

    2009-02-12

    Structural studies of antibiotics not only provide a shortcut to medicine allowing for rational structure-based drug design, but may also capture snapshots of dynamic intermediates that become 'frozen' after inhibitor binding. Myxopyronin inhibits bacterial RNA polymerase (RNAP) by an unknown mechanism. Here we report the structure of dMyx - a desmethyl derivative of myxopyronin B - complexed with a Thermus thermophilus RNAP holoenzyme. The antibiotic binds to a pocket deep inside the RNAP clamp head domain, which interacts with the DNA template in the transcription bubble. Notably, binding of dMyx stabilizes refolding of the {beta}'-subunit switch-2 segment, resulting in a configuration that might indirectly compromise binding to, or directly clash with, the melted template DNA strand. Consistently, footprinting data show that the antibiotic binding does not prevent nucleation of the promoter DNA melting but instead blocks its propagation towards the active site. Myxopyronins are thus, to our knowledge, a first structurally characterized class of antibiotics that target formation of the pre-catalytic transcription initiation complex - the decisive step in gene expression control. Notably, mutations designed in switch-2 mimic the dMyx effects on promoter complexes in the absence of antibiotic. Overall, our results indicate a plausible mechanism of the dMyx action and a stepwise pathway of open complex formation in which core enzyme mediates the final stage of DNA melting near the transcription start site, and that switch-2 might act as a molecular checkpoint for DNA loading in response to regulatory signals or antibiotics. The universally conserved switch-2 may have the same role in all multisubunit RNAPs.

  18. Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure

    DOE PAGESBeta

    Timoshenko, J.; Shivhare, A.; Scott, R. W.; Lu, D.; Frenkel, A. I.

    2016-06-30

    We adopted ab-initio X-ray Absorption Near Edge Structure (XANES) modelling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modelling, where the candidate structures are known, and the inverse modelling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by following the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

  19. Study of local structure and magnetism in high-T(sub c) copper oxide superconductors

    NASA Technical Reports Server (NTRS)

    Budnick, J. I.; Tan, Z.; Filipkowski, M.; Niedermayer, CH.; Glueckler, H.; Simon, R.; Golnik, A.; Rauer, M.; Recknagel, E.; Weidinger, A.

    1990-01-01

    The muon spin rotation (MUSR) study of local magnetism of Sr-doped La2CuO4 is reviewed. Emphasis is placed on magnetic order as detected by local and bulk probes with local atomic environments studied by x ray absorption fine structure (XAFS). Correlations between the MUSR study of local magnetic ordering and the bulk magnetization study are presented along with a discussion of the dependence upon oxygen stoichiometry. Results are presented for both superconducting phases and magnetic phases. Recent data which reveals the existence of local magnetic ordering in the hydrogen-doped YBa2Cu3O7 system are also discussed.

  20. The Effects of a Locally Developed mHealth Intervention on Delivery and Postnatal Care Utilization; A Prospective Controlled Evaluation among Health Centres in Ethiopia

    PubMed Central

    Shiferaw, Solomon; Spigt, Mark; Tekie, Michael; Abdullah, Muna; Fantahun, Mesganaw; Dinant, Geert-Jan

    2016-01-01

    Background Although there are studies showing that mobile phone solutions can improve health service delivery outcomes in the developed world, there is little empirical evidence that demonstrates the impact of mHealth interventions on key maternal health outcomes in low income settings. Methods A non-randomized controlled study was conducted in the Amhara region, Ethiopia in 10 health facilities (5 intervention, 5 control) together serving around 250,000 people. Health workers in the intervention group received an android phone (3 phones per facility) loaded with an application that sends reminders for scheduled visits during antenatal care (ANC), delivery and postnatal care (PNC), and educational messages on dangers signs and common complaints during pregnancy. The intervention was developed at Addis Ababa University in Ethiopia. Primary outcomes were the percentage of women who had at least 4 ANC visits, institutional delivery and PNC visits at the health center after 12 months of implementation of the intervention. Findings Overall 933 and 1037 women were included in the cross-sectional surveys at baseline and at follow-up respectively. In addition, the medical records of 1224 women who had at least one antenatal care visit were followed in the longitudinal study. Women who had their ANC visit in the intervention health centers were significantly more likely to deliver their baby in the same health center compared to the control group (43.1% versus 28.4%; Adjusted Odds Ratio (AOR): 1.98 (95%CI 1.53–2.55)). A significantly higher percentage of women who had ANC in the intervention group had PNC in the same health center compared to the control health centers (41.2% versus 21.1%: AOR: 2.77 (95%CI 2.12–3.61)). Conclusions Our findings demonstrated that a locally customized mHealth application during ANC can significantly improve delivery and postnatal care service utilization possibly through positively influencing the behavior of health workers and their

  1. Dynamics of galaxy structures in the Local Volume

    NASA Astrophysics Data System (ADS)

    Karachentsev, I. D.

    2016-10-01

    I consider a sample of `Updated Nearby Galaxy Catalog' that contains eight hundred objects within 11 Mpc. Environment of each galaxy is characterized by a tidal index Θ1 depending on separation and mass of the galaxy Main Disturber (=MD). The UNGC galaxies with a common MD are ascribed to its `suite' and ranked according to their Θ1. Fifteen the most populated suites contain more than half of the UNGC sample. The fraction of MDs among the brightest galaxies is almost 100% and drops to 50% at M_B = -18 mag. The observational properties of galaxies accumulated in UNGC are used to derive orbital masses of giant galaxies via motions of their satellites. The average orbital-to-stellar mass ratio for them is M orb M* ~= 30, corresponding to the mean local density of matter Ωm ~= 0.09, i.e 1/3 of the global cosmic one. The dark-to-stellar mass ratio for the Milky Way and M31 is typical for other neighboring giant galaxies.

  2. Gene structure and chromosomal localization of plasma kallikrein

    SciTech Connect

    Beaubien, G.; Mbikay, M.; Chretien, M.; Seidah, N.G. ); Rosinski-Chupin, I. ); Mattei, M.G. )

    1991-02-12

    Plasma kallikrein (Fletcher factor) is a hepatic serine proteinase that participates in the early phase of blood coagulation. From two genomic libraries, the authors succeeded to isolate four overlapping clones representing the entire rat plasma kallikrein gene. Using selective DNA sequencing, polymerase chain reactions, and restriction mapping, the authors demonstrated that the gene for rat plasma kallikrein was 22 kb in length. Similar to human factor XI the authors also found that the plasma kallikrein gene is composed of 15 exons and 14 introns. A potential transcription initiation step was determined by a novel application of the polymerase chain reaction technique. Computer analysis of the 5{prime}-promoter region of this gene revealed some putative control elements that might regulate the rat plasma kallikrein gene expression. These data and the results of chromosomal localization reported in the present study for mouse (chromosome 8) and human (chromosome 4) plasma kallikrein genes strongly corroborate a genic duplication event from a common ancestor to both plasma kallikrein and factor XI.

  3. Local structure analysis of some Cu(II) theophylline complexes

    NASA Astrophysics Data System (ADS)

    David, L.; Cozar, O.; Forizs, E.; Cr ăciun, C.; Ristoiu, D.; B ălan, C.

    1999-10-01

    The CuT 2L 2·2H 2O complexes [T=Theophylline (1,3-dimethylxanthine); L=NH 3, n-propylamine (npa), 2-aminoethanol (ae)] were prepared and investigated by ESR spectroscopy. Powder ESR spectrum of CuT 2(NH 3) 2·2H 2O is axial ( g||=2.255, g⊥=2.059). ESR spectrum of CuT 2(npa) 2·2H 2O with ( g||=2.299, g⊥=2.081) is a superposition of one axial ( g||=2.299, g⊥=2.073) and one isotropic component ( g0≈2.089), in the same amount. The axial spectra of the former complexes are due to a static Jahn-Teller effect ( EJT≈2880 cm -1). ESR spectrum of CuT 2(ae) 2·2H 2O is orthorhombic ( g1c=2.199, g2c=2.095, g3c=2.037). The local symmetries around the Cu(II) ions remain unchanged by DMF solvating, by adsorbing these solutions on NaY zeolite or by lowering the temperature.

  4. Local structure and electrical switching in chalcogenide glasses

    NASA Astrophysics Data System (ADS)

    Murugavel, S.; Asokan, S.

    1998-08-01

    Bulk AlxAs40Te60-x and AlxAs40-xTe60 glasses (5<=x<=20) are found to exhibit memory and threshold switching. 27Al solid-state NMR measurements reveal that in both series of glasses, Al resides in tetrahedrally (fourfold) as well as octahedrally (sixfold) coordinated environments, with the fraction of fourfold coordinated Al atoms in the glasses decreasing with Al content. Fourfold coordinated Al atoms provide structural flexibility, and promote memory switching at low Al content (x<15). At higher Al content, the growth in the fraction of sixfold coordinated atoms leads to increased network connectivity, which promotes threshold switching.

  5. Input clustering and the microscale structure of local circuits

    PubMed Central

    DeBello, William M.; McBride, Thomas J.; Nichols, Grant S.; Pannoni, Katy E.; Sanculi, Daniel; Totten, Douglas J.

    2014-01-01

    The recent development of powerful tools for high-throughput mapping of synaptic networks promises major advances in understanding brain function. One open question is how circuits integrate and store information. Competing models based on random vs. structured connectivity make distinct predictions regarding the dendritic addressing of synaptic inputs. In this article we review recent experimental tests of one of these models, the input clustering hypothesis. Across circuits, brain regions and species, there is growing evidence of a link between synaptic co-activation and dendritic location, although this finding is not universal. The functional implications of input clustering and future challenges are discussed. PMID:25309336

  6. Global/local stress analysis of composite structures. M.S. Thesis

    NASA Technical Reports Server (NTRS)

    Ransom, Jonathan B.

    1989-01-01

    A method for performing a global/local stress analysis is described and its capabilities are demonstrated. The method employs spline interpolation functions which satisfy the linear plate bending equation to determine displacements and rotations from a global model which are used as boundary conditions for the local model. Then, the local model is analyzed independent of the global model of the structure. This approach can be used to determine local, detailed stress states for specific structural regions using independent, refined local models which exploit information from less-refined global models. The method presented is not restricted to having a priori knowledge of the location of the regions requiring local detailed stress analysis. This approach also reduces the computational effort necessary to obtain the detailed stress state. Criteria for applying the method are developed. The effectiveness of the method is demonstrated using a classical stress concentration problem and a graphite-epoxy blade-stiffened panel with a discontinuous stiffener.

  7. Theoretical model for assessing properties of local structures in metalloprotein

    NASA Astrophysics Data System (ADS)

    Koyimatu, M.; Shimahara, H.; Iwayama, M.; Sugimori, K.; Kawaguchi, K.; Saito, H.; Nagao, H.

    2013-02-01

    For model structures containing two aromatic rings such as the indole of Trp5 and the imidazole of His64 in human carbonic anhydrase (hCAII), the location and orientation of the rings with regard to each other contribute to the magnitude of the entire interaction energy. Here the energetic contribution of the indole ring of Trp5 on the imidazole ring of the "out" conformation of His64 were calculated to compare with that of the alternative "in" conformation of His64 by using the MP2/6-311++G(d,p)//B3LYP/6-31G(d,p) method. We suggest that 1) Trp5 and the "out" conformation of His64 are predicted to form a stack of planar parallel rings via π-stacking interaction and 2) the energy is 1.73-1.83 kcal/mol to stabilize the "out" conformation, compared with the "in" conformation.

  8. The effects of local spatial structure on epidemiological invasions.

    PubMed Central

    Keeling, M J

    1999-01-01

    Predicting the likely success of invasions is vitally important in ecology and especially epidemiology. Whether an organism can successfully invade and persist in the short-term is highly dependent on the spatial correlations that develop in the early stages of invasion. By modelling the correlations between individuals, we are able to understand the role of spatial heterogeneity in invasion dynamics without the need for large-scale computer simulations. Here, a natural methodology is developed for modelling the behaviour of individuals in a fixed network. This formulation is applied to the spread of a disease through a structured network to determine invasion thresholds and some statistical properties of a single epidemic. PMID:10343409

  9. Interplay between microscopic diffusion and local structure of liquid water.

    PubMed

    Cunsolo, Alessandro; Orecchini, Andrea; Petrillo, Caterina; Sacchetti, Francesco

    2010-12-23

    We present a quasielastic neutron scattering (QENS) study of single-particle dynamics in pure water, measured at temperatures between 256 and 293 K along an isobaric path at 200 MPa. A thorough analysis of the spectral line shapes reveals a departure from simple models of continuous or jump diffusion, with such an effect becoming stronger at lower temperatures. We show that such a diverging trend of dynamical quantities upon cooling closely resembles the divergent (anomalous) compressibility observed in water by small-angle diffraction. Such an analogy suggests an interesting interplay between single-particle diffusion and structural arrangements in liquid water, both bearing witness of the well-known water anomalies. In particular, a fit of dynamical parameters by a Vogel-Tammann-Fulcher law provides a critical temperature of about 220 K, interestingly close to the hypothesized position of the second critical point of water and to the so-called Widom line. PMID:21114328

  10. Twin Masks of Spiral Structure? A Local Perspective

    NASA Astrophysics Data System (ADS)

    Steiman-Cameron, Thomas Y.

    We examine models for the spiral structure of the Milky Way proposed over the past half century. Many approaches have been pursued to decipher the geometry of the Galaxy's spiral arms, often with conflicting results. While a general consensus exists that a global pattern exists, considerable disagreement remains in the details. Arm geometries, orientations, and even the number of arms are still debated. Close examination of the literature reveals a clear division between four- and two-arm spiral arms. Four-arm models follow naturally from observations of classical tracers of spiral arms - enhanced gas densities and associated star formation - while two-arm models primarily flow from observations linked to the distribution of cool evolved stars. We examine the dichotomy between two-arm and four-arm models and discuss its implications.

  11. Regional and local geologic structure of the Momotombo field, Nicaragua

    SciTech Connect

    Goldsmith, L.H.

    1980-09-01

    The regional geologic-tectonic setting of northwestern Nicaragua is the result of subduction. Differential plate margin movement and segmentation formed a deep rift paralleling the Middle American Trench. Deep-seated shear faults provided access to sublithospheric magmas to create the Nicaraguan volcanic chain. Volcan Momotombo is the southernmost volcano of the Marabios Range of northern Nicaragua. It hosts a proven geothermal resource known as the Momotombo field, located within a small graben structure and measuring less than one square kilometer. This geothermally productive area appears not to be a geothermal reservoir, but rather part of a thermal convection system. Wells in the central and eastern part of the field have diminished in output and temperature. The presence of a temperature inversion zone, clearly distinguishable in the eastern end of the field, indicates that no conductive heating of the productive zone is taking place.

  12. Myanmar: The Community Learning Centre Experience.

    ERIC Educational Resources Information Center

    Middelborg, Jorn; Duvieusart, Baudouin, Ed.

    A community learning centre (CLC) is a local educational institution outside the formal education system, usually set up and managed by local people. CLCs were first introduced in Myanmar in 1994, and by 2001 there were 71 CLCs in 11 townships. The townships are characterized by remoteness, landlessness, unemployment, dependency on one cash crop,…

  13. Local atomic structure modulations activate metal oxide as electrocatalyst for hydrogen evolution in acidic water.

    PubMed

    Li, Yu Hang; Liu, Peng Fei; Pan, Lin Feng; Wang, Hai Feng; Yang, Zhen Zhong; Zheng, Li Rong; Hu, P; Zhao, Hui Jun; Gu, Lin; Yang, Hua Gui

    2015-08-19

    Modifications of local structure at atomic level could precisely and effectively tune the capacity of materials, enabling enhancement in the catalytic activity. Here we modulate the local atomic structure of a classical but inert transition metal oxide, tungsten trioxide, to be an efficient electrocatalyst for hydrogen evolution in acidic water, which has shown promise as an alternative to platinum. Structural analyses and theoretical calculations together indicate that the origin of the enhanced activity could be attributed to the tailored electronic structure by means of the local atomic structure modulations. We anticipate that suitable structure modulations might be applied on other transition metal oxides to meet the optimal thermodynamic and kinetic requirements, which may pave the way to unlock the potential of other promising candidates as cost-effective electrocatalysts for hydrogen evolution in industry.

  14. Local atomic structure modulations activate metal oxide as electrocatalyst for hydrogen evolution in acidic water

    PubMed Central

    Li, Yu Hang; Liu, Peng Fei; Pan, Lin Feng; Wang, Hai Feng; Yang, Zhen Zhong; Zheng, Li Rong; Hu, P.; Zhao, Hui Jun; Gu, Lin; Yang, Hua Gui

    2015-01-01

    Modifications of local structure at atomic level could precisely and effectively tune the capacity of materials, enabling enhancement in the catalytic activity. Here we modulate the local atomic structure of a classical but inert transition metal oxide, tungsten trioxide, to be an efficient electrocatalyst for hydrogen evolution in acidic water, which has shown promise as an alternative to platinum. Structural analyses and theoretical calculations together indicate that the origin of the enhanced activity could be attributed to the tailored electronic structure by means of the local atomic structure modulations. We anticipate that suitable structure modulations might be applied on other transition metal oxides to meet the optimal thermodynamic and kinetic requirements, which may pave the way to unlock the potential of other promising candidates as cost-effective electrocatalysts for hydrogen evolution in industry. PMID:26286479

  15. From local structure to a global framework: recognition of protein folds

    PubMed Central

    Joseph, Agnel Praveen; de Brevern, Alexandre G.

    2014-01-01

    Protein folding has been a major area of research for many years. Nonetheless, the mechanisms leading to the formation of an active biological fold are still not fully apprehended. The huge amount of available sequence and structural information provides hints to identify the putative fold for a given sequence. Indeed, protein structures prefer a limited number of local backbone conformations, some being characterized by preferences for certain amino acids. These preferences largely depend on the local structural environment. The prediction of local backbone conformations has become an important factor to correctly identifying the global protein fold. Here, we review the developments in the field of local structure prediction and especially their implication in protein fold recognition. PMID:24740960

  16. Global-Local Visual Processing in High Functioning Children with Autism: Structural vs. Implicit Task Biases

    ERIC Educational Resources Information Center

    Iarocci, Grace; Burack, Jacob A.; Shore, David I.; Mottron, Laurent; Enns, James T.

    2006-01-01

    Global-local processing was examined in high-functioning children with autism and in groups of typically developing children. In experiment 1, the effects of structural bias were tested by comparing visual search that favored access to either local or global targets. The children with autism were not unusually sensitive to either level of visual…

  17. Application of Local Linear Embedding to Nonlinear Exploratory Latent Structure Analysis

    ERIC Educational Resources Information Center

    Wang, Haonan; Iyer, Hari

    2007-01-01

    In this paper we discuss the use of a recent dimension reduction technique called Locally Linear Embedding, introduced by Roweis and Saul, for performing an exploratory latent structure analysis. The coordinate variables from the locally linear embedding describing the manifold on which the data reside serve as the latent variable scores. We…

  18. Austromegabalanus psittacus barnacle shell structure and proteoglycan localization and functionality.

    PubMed

    Fernández, M S; Arias, J I; Neira-Carrillo, A; Arias, J L

    2015-09-01

    Comparative analyzes of biomineralization models have being crucial for the understanding of the functional properties of biominerals and the elucidation of the processes through which biomacromolecules control the synthesis and structural organization of inorganic mineral-based biomaterials. Among calcium carbonate-containing bioceramics, egg, mollusk and echinoderm shells, and crustacean carapaces, have being fairly well characterized. However, Thoraceca barnacles, although being crustacea, showing molting cycle, build a quite stable and heavily mineralized shell that completely surround the animal, which is for life firmly cemented to the substratum. This makes barnacles an interesting model for studying processes of biomineralization. Here we studied the main microstructural and ultrastructural features of Austromegabalanus psittacus barnacle shell, characterize the occurrence of specific proteoglycans (keratan-, dermatan- and chondroitin-6-sulfate proteoglycans) in different soluble and insoluble organic fractions extracted from the shell, and tested them for their ability to crystallize calcium carbonate in vitro. Our results indicate that, in the barnacle model, proteoglycans are good candidates for the modification of the calcite crystal morphology, although the cooperative effect of some additional proteins in the shell could not be excluded.

  19. Austromegabalanus psittacus barnacle shell structure and proteoglycan localization and functionality.

    PubMed

    Fernández, M S; Arias, J I; Neira-Carrillo, A; Arias, J L

    2015-09-01

    Comparative analyzes of biomineralization models have being crucial for the understanding of the functional properties of biominerals and the elucidation of the processes through which biomacromolecules control the synthesis and structural organization of inorganic mineral-based biomaterials. Among calcium carbonate-containing bioceramics, egg, mollusk and echinoderm shells, and crustacean carapaces, have being fairly well characterized. However, Thoraceca barnacles, although being crustacea, showing molting cycle, build a quite stable and heavily mineralized shell that completely surround the animal, which is for life firmly cemented to the substratum. This makes barnacles an interesting model for studying processes of biomineralization. Here we studied the main microstructural and ultrastructural features of Austromegabalanus psittacus barnacle shell, characterize the occurrence of specific proteoglycans (keratan-, dermatan- and chondroitin-6-sulfate proteoglycans) in different soluble and insoluble organic fractions extracted from the shell, and tested them for their ability to crystallize calcium carbonate in vitro. Our results indicate that, in the barnacle model, proteoglycans are good candidates for the modification of the calcite crystal morphology, although the cooperative effect of some additional proteins in the shell could not be excluded. PMID:26276577

  20. Local structures of high-entropy alloys (HEAs) on atomic scales: An overview

    DOE PAGESBeta

    Diao, Haoyan; Santodonato, Louis J.; Tang, Zhi; Egami, Takeshi; Liaw, Peter K.

    2015-01-01

    The high-entropy alloys, containing several elements mixed in equimolar or near-equimolar ratios, have shown exceptional engineering properties. Local structures on the atomic level are essential to understand the mechanical behaviors and related mechanisms. This article covers the local structure and stress on the atomic level are reviewed by the pair-distribution function of neutron-diffraction data, ab-initio molecular dynamics simulations, and the atomic probe microscopy.

  1. Unique local structures of Ca, Ti, Fe and Zr in natural glasses formed by meteorite impact

    NASA Astrophysics Data System (ADS)

    Yoshiasa, Akira; Tobase, Tsubasa; Okube, Maki; Wang, Ling; Isobe, Hiroshi; Mashimo, Tsutomu; Graduate School of Science; Technology Collaboration; Materials; Structures Laboratory, Tokyo Institute of Technology Collaboration

    2015-06-01

    The local structures of cation in tektite from six strewn fields, impact-related glass, and non-impact-related glass were studied by Ca, Ti, Fe and Zr K-edge X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS). Shock compression also causes local structural changes of gest and minor elements as well as transition of host structures. How to be left a record is peculiar by each element. The XAFS measurements were performed at the beam lines BL-NW10A and BL-9C, KEK, Japan. The comparison of XANES spectra and bonding distances between crystalline reference minerals and natural glasses was done. Based on the different valence states of iron, the degrees of oxidation states were estimated. The local structures of Ca, Ti and Zr ions are useful probe for physical conditions and formation process of glasses. Tektites experienced high quenching rates and a reduced atmospheric environment when they were ejected into outer space. Other impact-related glass, which was remained close to the crater, experienced a more complicated environment. The local structural changes of cation in the impact-related glass are rich in a variety. Analysis of local structure is help to compare their formation process and distinguish them.

  2. Deciphering the shape and deformation of secondary structures through local conformation analysis

    PubMed Central

    2011-01-01

    Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons. PMID:21284872

  3. MolLoc: a web tool for the local structural alignment of molecular surfaces.

    PubMed

    Angaran, Stefano; Bock, Mary Ellen; Garutti, Claudio; Guerra, Concettina

    2009-07-01

    MolLoc stands for Molecular Local surface comparison, and is a web server for the structural comparison of molecular surfaces. Given two structures in PDB format, the user can compare their binding sites, cavities or any arbitrary residue selection. Moreover, the web server allows the comparison of a query structure with a list of structures. Each comparison produces a structural alignment that maximizes the extension of the superimposition of the surfaces, and returns the pairs of atoms with similar physicochemical properties that are close in space after the superimposition. Based on this subset of atoms sharing similar physicochemical properties a new rototranslation is derived that best superimposes them. MolLoc approach is both local and surface-oriented, and therefore it can be particularly useful when testing if molecules with different sequences and folds share any local surface similarity. The MolLoc web server is available at http://bcb.dei.unipd.it/MolLoc.

  4. Local anesthetics structure-dependently interact with anionic phospholipid membranes to modify the fluidity.

    PubMed

    Tsuchiya, Hironori; Ueno, Takahiro; Mizogami, Maki; Takakura, Ko

    2010-01-01

    While bupivacaine is more cardiotoxic than other local anesthetics, the mechanistic background for different toxic effects remains unclear. Several cardiotoxic compounds act on lipid bilayers to change the physicochemical properties of membranes. We comparatively studied the interaction of local anesthetics with lipid membranous systems which might be related to their structure-selective cardiotoxicity. Amide local anesthetics (10-300 microM) were reacted with unilamellar vesicles which were prepared with different phospholipids and cholesterol of varying lipid compositions. They were compared on the potencies to modify membrane fluidity by measuring fluorescence polarization. Local anesthetics interacted with liposomal membranes to increase the fluidity. Increasing anionic phospholipids in membranes enhanced the membrane-fluidizing effects of local anesthetics with the potency being cardiolipin>phosphatidic acid>phosphatidylglycerol>phosphatidylserine. Cardiolipin was most effective on bupivacaine, followed by ropivacaine. Local anesthetics interacted differently with biomimetic membranes consisting of 10mol% cardiolipin, 50mol% other phospholipids and 40mol% cholesterol with the potency being bupivacaine>ropivacaine>lidocaine>prilocaine, which agreed with the rank order of cardiotoxicity. Bupivacaine significantly fluidized 2.5-12.5mol% cardiolipin-containing membranes at cardiotoxicologically relevant concentrations. Bupivacaine is considered to affect lipid bilayers by interacting electrostatically with negatively charged cardiolipin head groups and hydrophobically with phospholipid acyl chains. The structure-dependent interaction with lipid membranes containing cardiolipin, which is preferentially localized in cardiomyocyte mitochondrial membranes, may be a mechanistic clue to explain the structure-selective cardiotoxicity of local anesthetics.

  5. How localized is ``local?'' Efficiency vs. accuracy of O(N) domain decomposition in local orbital based all-electron electronic structure theory

    NASA Astrophysics Data System (ADS)

    Havu, Vile; Blum, Volker; Scheffler, Matthias

    2007-03-01

    Numeric atom-centered local orbitals (NAO) are efficient basis sets for all-electron electronic structure theory. The locality of NAO's can be exploited to render (in principle) all operations of the self-consistency cycle O(N). This is straightforward for 3D integrals using domain decomposition into spatially close subsets of integration points, enabling critical computational savings that are effective from ˜tens of atoms (no significant overhead for smaller systems) and make large systems (100s of atoms) computationally feasible. Using a new all-electron NAO-based code,^1 we investigate the quantitative impact of exploiting this locality on two distinct classes of systems: Large light-element molecules [Alanine-based polypeptide chains (Ala)n], and compact transition metal clusters. Strict NAO locality is achieved by imposing a cutoff potential with an onset radius rc, and exploited by appropriately shaped integration domains (subsets of integration points). Conventional tight rc<= 3å have no measurable accuracy impact in (Ala)n, but introduce inaccuracies of 20-30 meV/atom in Cun. The domain shape impacts the computational effort by only 10-20 % for reasonable rc. ^1 V. Blum, R. Gehrke, P. Havu, V. Havu, M. Scheffler, The FHI Ab Initio Molecular Simulations (aims) Project, Fritz-Haber-Institut, Berlin (2006).

  6. Workshop on Measurement Needs for Local-Structure Determination in Inorganic Materials

    PubMed Central

    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

  7. Incorporation of local structure into kriging models for the prediction of atomistic properties in the water decamer.

    PubMed

    Davie, Stuart J; Di Pasquale, Nicodemo; Popelier, Paul L A

    2016-10-15

    Machine learning algorithms have been demonstrated to predict atomistic properties approaching the accuracy of quantum chemical calculations at significantly less computational cost. Difficulties arise, however, when attempting to apply these techniques to large systems, or systems possessing excessive conformational freedom. In this article, the machine learning method kriging is applied to predict both the intra-atomic and interatomic energies, as well as the electrostatic multipole moments, of the atoms of a water molecule at the center of a 10 water molecule (decamer) cluster. Unlike previous work, where the properties of small water clusters were predicted using a molecular local frame, and where training set inputs (features) were based on atomic index, a variety of feature definitions and coordinate frames are considered here to increase prediction accuracy. It is shown that, for a water molecule at the center of a decamer, no single method of defining features or coordinate schemes is optimal for every property. However, explicitly accounting for the structure of the first solvation shell in the definition of the features of the kriging training set, and centring the coordinate frame on the atom-of-interest will, in general, return better predictions than models that apply the standard methods of feature definition, or a molecular coordinate frame. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  8. Incorporation of local structure into kriging models for the prediction of atomistic properties in the water decamer.

    PubMed

    Davie, Stuart J; Di Pasquale, Nicodemo; Popelier, Paul L A

    2016-10-15

    Machine learning algorithms have been demonstrated to predict atomistic properties approaching the accuracy of quantum chemical calculations at significantly less computational cost. Difficulties arise, however, when attempting to apply these techniques to large systems, or systems possessing excessive conformational freedom. In this article, the machine learning method kriging is applied to predict both the intra-atomic and interatomic energies, as well as the electrostatic multipole moments, of the atoms of a water molecule at the center of a 10 water molecule (decamer) cluster. Unlike previous work, where the properties of small water clusters were predicted using a molecular local frame, and where training set inputs (features) were based on atomic index, a variety of feature definitions and coordinate frames are considered here to increase prediction accuracy. It is shown that, for a water molecule at the center of a decamer, no single method of defining features or coordinate schemes is optimal for every property. However, explicitly accounting for the structure of the first solvation shell in the definition of the features of the kriging training set, and centring the coordinate frame on the atom-of-interest will, in general, return better predictions than models that apply the standard methods of feature definition, or a molecular coordinate frame. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27535711

  9. Incorporation of local structure into kriging models for the prediction of atomistic properties in the water decamer

    PubMed Central

    Davie, Stuart J; Di Pasquale, Nicodemo

    2016-01-01

    Machine learning algorithms have been demonstrated to predict atomistic properties approaching the accuracy of quantum chemical calculations at significantly less computational cost. Difficulties arise, however, when attempting to apply these techniques to large systems, or systems possessing excessive conformational freedom. In this article, the machine learning method kriging is applied to predict both the intra‐atomic and interatomic energies, as well as the electrostatic multipole moments, of the atoms of a water molecule at the center of a 10 water molecule (decamer) cluster. Unlike previous work, where the properties of small water clusters were predicted using a molecular local frame, and where training set inputs (features) were based on atomic index, a variety of feature definitions and coordinate frames are considered here to increase prediction accuracy. It is shown that, for a water molecule at the center of a decamer, no single method of defining features or coordinate schemes is optimal for every property. However, explicitly accounting for the structure of the first solvation shell in the definition of the features of the kriging training set, and centring the coordinate frame on the atom‐of‐interest will, in general, return better predictions than models that apply the standard methods of feature definition, or a molecular coordinate frame. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27535711

  10. Local structure information by EXAFS analysis using two algorithms for Fourier transform calculation

    NASA Astrophysics Data System (ADS)

    Aldea, N.; Pintea, S.; Rednic, V.; Matei, F.; Tiandou, Hu; Yaning, Xie

    2009-08-01

    The present work is a comparison study between different algorithms of Fourier transform for obtaining very accurate local structure results using Extended X-ray Absorption Fine Structure technique. In this paper we focus on the local structural characteristics of supported nickel catalysts and Fe3O4 core-shell nanocomposites. The radial distribution function could be efficiently calculated by the fast Fourier transform when the coordination shells are well separated while the Filon quadrature gave remarkable results for close-shell coordination.

  11. Pretoria Centre Reaches Out

    NASA Astrophysics Data System (ADS)

    Bosman, Olivier

    2014-08-01

    On 5 July 2014 six members of the Pretoria Centre of ASSA braved the light pollution of one of the shopping malls in Centurion to reach out to shoppers a la John Dobson and to show them the moon, Mars and Saturn. Although the centre hosts regular monthly public observing evenings, it was felt that we should take astronomy to the people rather than wait for the people to come to us.

  12. The analysis of space time structure in QCD vacuum, I: localization vs global behavior in local observables and Dirac eigenmodes

    NASA Astrophysics Data System (ADS)

    Horváth, Ivan

    2005-03-01

    The structure of QCD vacuum can be studied from first principles using lattice-regularized theory. This line of research entered a qualitatively new phase recently, wherein the space-time structure (at least for some quantities) can be directly observed in configurations dominating the QCD path integral, i.e., without any subjective processing of typical configurations. This approach to QCD vacuum structure does not rely on any proposed picture of QCD vacuum but rather attempts to characterize this structure in a model-independent manner, so that a coherent physical picture of the vacuum can emerge when such unbiased numerical information accumulates to a sufficient degree. An important part of this program is to develop a set of suitable quantitative characteristics describing the space-time structure in a meaningful and physically relevant manner. One of the basic pertinent issues here is whether QCD vacuum dynamics can be understood in terms of localized vacuum objects, or whether such objects behave as inherently global entities. The first direct studies of vacuum structure strongly support the latter. In this paper, we develop a formal framework which allows to answer this question in a quantitative manner. We discuss in detail how to apply this approach to Dirac eigenmodes and to basic scalar and pseudoscalar composites of gauge fields (action density and topological charge density). The approach is illustrated numerically on overlap Dirac zero modes and near-zero modes. This illustrative data provides direct quantitative evidence supporting our earlier arguments for the global nature of QCD Dirac eigenmodes.

  13. Protein Classification Based on Analysis of Local Sequence-Structure Correspondence

    SciTech Connect

    Zemla, A T

    2006-02-13

    The goal of this project was to develop an algorithm to detect and calculate common structural motifs in compared structures, and define a set of numerical criteria to be used for fully automated motif based protein structure classification. The Protein Data Bank (PDB) contains more than 33,000 experimentally solved protein structures, and the Structural Classification of Proteins (SCOP) database, a manual classification of these structures, cannot keep pace with the rapid growth of the PDB. In our approach called STRALCP (STRucture Alignment based Clustering of Proteins), we generate detailed information about global and local similarities between given set of structures, identify similar fragments that are conserved within analyzed proteins, and use these conserved regions (detected structural motifs) to classify proteins.

  14. Local structure studies of Fe2TeO6 using x-ray absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Singh, Harishchandra; Yadav, A. K.

    2016-05-01

    In the present study, we have performed EXAFS measurements on powder samples of Fe2TeO6 (FTO) to probe the local structure surrounding at the Fe site. The structural parameters (atomic coordination and lattice parameters) of FTO used for simulation of theoretical EXAFS spectra of the samples have been obtained from Rietveld refined structure on synchrotron X-ray Diffraction (SXRD) data. Quite similar and satisfactory structural parameters have been obtained from both the study, indicating goodness of synchrotron structural analysis over EXAFS analysis. SXRD and EXAFS results shows absence of any secondary phase proves current synthesis superior over reported techniques.

  15. Density Functional Modeling of the Local Structure of Kaolinite Subjected to Thermal Dehydroxylation

    SciTech Connect

    White, Claire E.; Provis, John L.; Proffen, Thomas; Riley, Daniel P.; van Deventer, Jannie S.J.

    2010-11-19

    Understanding the atomic-level changes that occur as kaolinite is converted (thermally dehydroxylated) to metakaolin is critical to the optimization of this large-scale industrial process. Metakaolin is X-ray amorphous; therefore, conventional crystallographic techniques do not reveal the changes in local structure during its formation. Local structure-based experimental techniques are useful in understanding the atomic structure but do not provide the thermodynamic information which is necessary to ensure plausibility of refined structures. Here, kaolinite dehydroxylation is modeled using density functional theory, and a stepwise methodology, where several water molecules are removed from the structure, geometry optimization is carried out, and then the process is repeated. Hence, the structure remains in an energetically and thermodynamically feasible state while transitioning from kaolinite to metakaolin. The structures generated during the dehydroxylation process are validated by comparison with X-ray and neutron pair distribution function data. Thus, this study illustrates one possible route by which dehydroxylation of kaolinite can take place, revealing a chemically, energetically, and experimentally plausible structure of metakaolin. This methodology of density functional modeling of the stepwise changes in a material is not limited in application to kaolinite or other aluminosilicates and provides an accurate representation of the local structural changes occurring in materials used in industrially important processes.

  16. Structural information content of networks: graph entropy based on local vertex functionals.

    PubMed

    Dehmer, Matthias; Emmert-Streib, Frank

    2008-04-01

    In this paper we define the structural information content of graphs as their corresponding graph entropy. This definition is based on local vertex functionals obtained by calculating j-spheres via the algorithm of Dijkstra. We prove that the graph entropy and, hence, the local vertex functionals can be computed with polynomial time complexity enabling the application of our measure for large graphs. In this paper we present numerical results for the graph entropy of chemical graphs and discuss resulting properties. PMID:18243802

  17. Local formation of a Heusler structure in CoFe-Al alloys

    NASA Astrophysics Data System (ADS)

    Wurmehl, S.; Jacobs, P. J.; Kohlhepp, J. T.; Swagten, H. J. M.; Koopmans, B.; Maat, S.; Carey, M. J.; Childress, J. R.

    2011-01-01

    We systematically study the changes in the local atomic environments of Co in CoFe-Al alloys as a function of Al content by means of nuclear magnetic resonance. We find that a Co2FeAl Heusler type structure is formed on a local scale. The observed formation of a highly spin-polarized Heusler compound may explain the improved magnetotransport properties in CoFe-Al based current-perpendicular-to-the-plane spin-valves.

  18. Local and global structural drivers for the photoactivation of the orange carotenoid protein.

    PubMed

    Gupta, Sayan; Guttman, Miklos; Leverenz, Ryan L; Zhumadilova, Kulyash; Pawlowski, Emily G; Petzold, Christopher J; Lee, Kelly K; Ralston, Corie Y; Kerfeld, Cheryl A

    2015-10-13

    Photoprotective mechanisms are of fundamental importance for the survival of photosynthetic organisms. In cyanobacteria, the orange carotenoid protein (OCP), when activated by intense blue light, binds to the light-harvesting antenna and triggers the dissipation of excess captured light energy. Using a combination of small angle X-ray scattering (SAXS), X-ray hydroxyl radical footprinting, circular dichroism, and H/D exchange mass spectrometry, we identified both the local and global structural changes in the OCP upon photoactivation. SAXS and H/D exchange data showed that global tertiary structural changes, including complete domain dissociation, occur upon photoactivation, but with alteration of secondary structure confined to only the N terminus of the OCP. Microsecond radiolytic labeling identified rearrangement of the H-bonding network associated with conserved residues and structural water molecules. Collectively, these data provide experimental evidence for an ensemble of local and global structural changes, upon activation of the OCP, that are essential for photoprotection.

  19. Local and global structural drivers for the photoactivation of the orange carotenoid protein

    PubMed Central

    Gupta, Sayan; Guttman, Miklos; Leverenz, Ryan L.; Zhumadilova, Kulyash; Pawlowski, Emily G.; Petzold, Christopher J.; Lee, Kelly K.; Ralston, Corie Y.; Kerfeld, Cheryl A.

    2015-01-01

    Photoprotective mechanisms are of fundamental importance for the survival of photosynthetic organisms. In cyanobacteria, the orange carotenoid protein (OCP), when activated by intense blue light, binds to the light-harvesting antenna and triggers the dissipation of excess captured light energy. Using a combination of small angle X-ray scattering (SAXS), X-ray hydroxyl radical footprinting, circular dichroism, and H/D exchange mass spectrometry, we identified both the local and global structural changes in the OCP upon photoactivation. SAXS and H/D exchange data showed that global tertiary structural changes, including complete domain dissociation, occur upon photoactivation, but with alteration of secondary structure confined to only the N terminus of the OCP. Microsecond radiolytic labeling identified rearrangement of the H-bonding network associated with conserved residues and structural water molecules. Collectively, these data provide experimental evidence for an ensemble of local and global structural changes, upon activation of the OCP, that are essential for photoprotection. PMID:26385969

  20. Identification, characterization and evolution of non-local quasi-Lagrangian structures in turbulence

    NASA Astrophysics Data System (ADS)

    Yang, Yue

    2016-06-01

    The recent progress on non-local Lagrangian and quasi-Lagrangian structures in turbulence is reviewed. The quasi-Lagrangian structures, e.g., vortex surfaces in viscous flow, gas-liquid interfaces in multi-phase flow, and flame fronts in premixed combustion, can show essential Lagrangian following properties, but they are able to have topological changes in the temporal evolution. In addition, they can represent or influence the turbulent flow field. The challenges for the investigation of the non-local structures include their identification, characterization, and evolution. The improving understanding of the quasi-Lagrangian structures is expected to be helpful to elucidate crucial dynamics and develop structure-based predictive models in turbulence.

  1. Localization microscopy study of FtsZ structures in E. coli cells during SOS-response

    NASA Astrophysics Data System (ADS)

    Vedyaykin, A. D.; Sabantsev, A. V.; Vishnyakov, I. E.; Borchsenius, S. N.; Fedorova, Y. V.; Melnikov, A. S.; Serdobintsev, P. Yu; Khodorkovskii, M. A.

    2014-10-01

    Localization microscopy allows visualization of biological structures with resolution well below the diffraction limit. This is achieved by temporal separation of single fluorophore molecules emission and subsequent localization of them with the precision of few tens of nanometers. This method was previously successfully used to obtain images of FtsZ structures in Escherichia coli cells using FtsZ fusion with fluorescent protein mEos2. In this work we obtained superresolution images of FtsZ structures in fixed E. coli cells using immunocytochemical labeling. Comparison of superresolution FtsZ structures in cells undergoing SOS-response and "healthy" cells shows that FtsZ structures are partially disassembled during SOS-response, but still retain some periodicity.

  2. Correlation between locally deformed structure and oxide film properties in austenitic stainless steel irradiated with neutrons

    NASA Astrophysics Data System (ADS)

    Chimi, Yasuhiro; Kitsunai, Yuji; Kasahara, Shigeki; Chatani, Kazuhiro; Koshiishi, Masato; Nishiyama, Yutaka

    2016-07-01

    To elucidate the mechanism of irradiation-assisted stress corrosion cracking (IASCC) in high-temperature water for neutron-irradiated austenitic stainless steels (SSs), the locally deformed structures, the oxide films formed on the deformed areas, and their correlation were investigated. Tensile specimens made of irradiated 316L SSs were strained 0.1%-2% at room temperature or at 563 K, and the surface structures and crystal misorientation among grains were evaluated. The strained specimens were immersed in high-temperature water, and the microstructures of the oxide films on the locally deformed areas were observed. The appearance of visible step structures on the specimens' surface depended on the neutron dose and the applied strain. The surface oxides were observed to be prone to increase in thickness around grain boundaries (GBs) with increasing neutron dose and increasing local strain at the GBs. No penetrative oxidation was observed along GBs or along surface steps.

  3. Distinct local electronic structure and magnetism for Mn in amorphous Si and Ge

    SciTech Connect

    Zeng, Li; Cao, J. X.; Helgren, E.; Karel, J.; Arenholz, E.; Ouyang, Lu; Smith, David J.; Wu, R. Q.; Hellman, F.

    2010-06-01

    Transition metals such as Mn generally have large local moments in covalent semiconductors due to their partially filled d shells. However, Mn magnetization in group-IV semiconductors is more complicated than often recognized. Here we report a striking crossover from a quenched Mn moment (<0.1 {mu}{sub B}) in amorphous Si (a-Si) to a large distinct local Mn moment ({ge}3{mu}{sub B}) in amorphous Ge (a-Ge) over a wide range of Mn concentrations (0.005-0.20). Corresponding differences are observed in d-shell electronic structure and the sign of the Hall effect. Density-functional-theory calculations show distinct local structures, consistent with different atomic density measured for a-Si and a-Ge, respectively, and the Mn coordination number N{sub c} is found to be the key factor. Despite the amorphous structure, Mn in a-Si is in a relatively well-defined high coordination interstitial type site with broadened d bands, low moment, and electron (n-type) carriers, while Mn in a-Ge is in a low coordination substitutional type site with large local moment and holes (p-type) carriers. Moreover, the correlation between N{sub c} and the magnitude of the local moment is essentially independent of the matrix; the local Mn moments approach zero when N{sub c} > 7 for both a-Si and a-Ge.

  4. Doubly periodic structure for the study of inhomogeneous bulk fermion matter with spatial localizations

    SciTech Connect

    Vantournhout, Klaas; Jachowicz, Natalie; Ryckebusch, Jan

    2011-09-15

    We present a method that offers perspectives to perform fully antisymmetrized simulations for inhomogeneous bulk fermion matter. The technique bears resemblance to classical periodic boundary conditions, using localized single-particle states. Such localized states are an ideal tool to discuss phenomena where spatial localization plays an important role. The antisymmetrization is obtained introducing a doubly periodic structure in the many-body fermion wave functions. This results in circulant matrices for the evaluation of expectation values, leading to a computationally tractable formalism to study fully antisymmetrized bulk fermion matter. We show that the proposed technique is able to reproduce essential fermion features in an elegant and computationally advantageous manner.

  5. Local structure in BaTi O3-BiSc O3 dipole glasses

    NASA Astrophysics Data System (ADS)

    Levin, I.; Krayzman, V.; Woicik, J. C.; Bridges, F.; Sterbinsky, G. E.; Usher, T.-M.; Jones, J. L.; Torrejon, D.

    2016-03-01

    Local structures in cubic perovskite-type (B a0.6B i0.4) (T i0.6S c0.4) O3 solid solutions that exhibit reentrant dipole glass behavior have been studied with variable-temperature x-ray/neutron total scattering, extended x-ray absorption fine structure, and electron diffraction methods. Simultaneous fitting of these data using a reverse Monte Carlo algorithm provided instantaneous atomic configurations, which have been used to extract local displacements of the constituent species. The smaller Bi and Ti atoms exhibit probability density distributions that consist of 14 and 8 split sites, respectively. In contrast, Ba and Sc feature single-site distributions. The multisite distributions arise from large and strongly anisotropic off-center displacements of Bi and Ti. The cation displacements are correlated over a short range, with a correlation length limited by chemical disorder. The magnitudes of these displacements and their anisotropy, which are largely determined by local chemistry, change relatively insignificantly on cooling from room temperature. The structure features a nonrandom distribution of local polarization with low-dimensional polar clusters that are several unit cells in size. In situ measurements of atomic pair-distribution function under applied electric field were used to study field-induced changes in the local structure; however, no significant effects besides lattice expansion in the direction of the field could be observed up to electric-field values of 4 kV m m-1 .

  6. Local Atomic Structure of Semiconductor Alloys Using Pair Distribution Function Analysis

    SciTech Connect

    Billinge, S.J.L.; Thorpe, M.F.

    2002-06-24

    We have been taking advantage of recent experimental developments, which involve utilizing diffraction data from x-rays or neutrons out to very large wave-vectors, to obtain a detailed structural characterization of semiconductor alloys. This approach allows an accurate Pair Distribution Function (PDF) to be obtained to 20A and beyond and reveals the local structure of the alloy directly. These data can be modeled explicitly to learn about local correlations and short-range order in materials. We are combining theory, modeling and experiments to study a range of materials from semiconductors to thermoelectrics and proton conductors.

  7. Local structure of multiferroic RMn 2O 5: Important role of the R site

    NASA Astrophysics Data System (ADS)

    Tyson, T. A.; Chen, Z.; DeLeon, M. A.; Yoong, S.; Cheong, S.-W.

    2009-06-01

    The temperature and magnetic field dependent local structure of RMn 2O 5 systems was examined. While no significant displacements of the Mn ions are observed, it is found that the R-O distribution exhibits changes at low temperature which are possibly related to the changes in the electric polarization. Density functional computations are used to explore the system dynamics and to link the local structural measurements with anomalous changes in the infrared absorption spectra. The anomalous R-O distribution and observed coupling to magnetic fields point to the need to properly treat the 4f electrons on the R sites in these systems.

  8. The Comparative Structural Study of Vitreous Matrices P{sub 2}O{sub 5}centre dotMeO [MeO ident to Li{sub 2}O (M{sub 1}) or CaO (M{sub 2})] Systems and {sub x}Fe{sub 2}O{sub 3}(100-x)[P{sub 2}O{sub 5}centre dotMeO] Glasses by Raman Spectroscopy

    SciTech Connect

    Andronache, C.

    2010-01-21

    For getting information about the way in which the structural units presented in glass matrices P{sub 2}O{sub 5}centre dotLi{sub 2}O (M{sub 1}) and P{sub 2}O{sub 5}centre dotCaO (M{sub 2}) are modifying with the substitutions Li{sub 2}O with CaO, these glasses where investigated by Raman spectroscopies. The absorption bands obtained and their assignments for each those two matrices are summarized. The influence of Fe{sub 2}O{sub 3} content on the structure of M1 and M2 matrices was followed.

  9. Correlations Between Amino Acids at Different Sites in Local Sequences of Protein Fragments with Given Structural Patterns

    NASA Astrophysics Data System (ADS)

    Lu, Wen; Liu, Hai-yan

    2007-02-01

    Ample evidence suggests that the local structures of peptide fragments in native proteins are to some extent encoded by their local sequences. Detecting such local correlations is important but it is still an open question what would be the most appropriate method. This is partly because conventional sequence analyses treat amino acid preferences at each site of a protein sequence independently, while it is often the inter-site interactions that bring about local sequence-structure correlations. Here a new scheme is introduced to capture the correlation between amino acid preferences at different sites for different local structure types. A library of nine-residue fragments is constructed, and the fragments are divided into clusters based on their local structures. For each local structure cluster or type, chi-square tests are used to identify correlated preferences of amino acid combinations at pairs of sites. A score function is constructed including both the single site amino acid preferences and the dual-site amino acid combination preferences, which can be used to identify whether a sequence fragment would have a strong tendency to form a particular local structure in native proteins. The results show that, given a local structure pattern, dual-site amino acid combinations contain different information from single site amino acid preferences. Representative examples show that many of the statistically identified correlations agree with previously-proposed heuristic rules about local sequence-structure correlations, or are consistent with physical-chemical interactions required to stabilize particular local structures. Results also show that such dual-site correlations in the score function significantly improves the Z-score matching a sequence fragment to its native local structure relative to non-native local structures, and certain local structure types are highly predictable from the local sequence alone if inter-site correlations are considered.

  10. Structure based classification of μ-CT images of human trabecular bone using local Minkowski Functionals

    NASA Astrophysics Data System (ADS)

    Monetti, Roberto A.; Bauer, Jan; Sidorenko, Irina; Müller, Dirk; Rummeny, Ernst; Matsuura, Maiko; Eckstein, Felix; Lochmueller, Eva-Maria; Zysset, Philippe; Räth, Christoph

    2011-03-01

    We analyse μ-CT tomographic images of human trabecular bone in vitro. We consider a sample consisting of 201 bone specimens harvested from six different skeletal sites within a narrow range of bone fraction values. Using the characterization of the trabecular bone network given by local Minkowski Functionals, we apply classification algorithms in order to reveal structural similarities in the sample. Clusters show some interesting specific structural features, like compact, porous, and fragmented structures. The contribution of the different skeletal sites to these clusters indicate some variability due to intrinsic structural differences of the specific skeletal site.

  11. Discussions on equivalent solutions and localized structures via the mapping method based on Riccati equation

    NASA Astrophysics Data System (ADS)

    Xu, Ling; Cheng, Xuan; Dai, Chao-Qing

    2015-12-01

    Although the mapping method based on Riccati equation was proposed to obtain variable separation solutions many years ago, two important problems have not been studied: i) the equivalence of variable separation solutions by means of the mapping method based on Riccati equation with the radical sign combined ansatz; and ii) lack of physical meanings for some localized structures constructed by variable separation solutions. In this paper, we re-study the (2+1)-dimensional Boiti-Leon-Pempinelli equation via the mapping method based on Riccati equation and prove that nine types of variable separation solutions are actually equivalent to each other. Moreover, we also re-study localized structures constructed by variable separation solutions. Results indicate that some localized structures reported in the literature are lacking real values due to the appearance of the divergent and un-physical phenomenon for the initial field. Therefore, we must be careful with the initial field to avoid the appearance of some un-physical or even divergent structures in it when we construct localized structures for the potential field.

  12. Modular localization and the holistic structure of causal quantum theory, a historical perspective

    NASA Astrophysics Data System (ADS)

    Schroer, Bert

    2015-02-01

    Recent insights into the conceptual structure of localization in QFT (modular localization) led to clarifications of old unsolved problems. The oldest one is the Einstein-Jordan conundrum which led Jordan in 1925 to the discovery of quantum field theory. This comparison of fluctuations in subsystems of heat bath systems (Einstein) with those resulting from the restriction of the QFT vacuum state to an open subvolume (Jordan) leads to a perfect analogy; the globally pure vacuum state becomes upon local restriction a strongly impure KMS state. This phenomenon of localization-caused thermal behavior as well as the vacuum-polarization clouds at the causal boundary of the localization region places localization in QFT into a sharp contrast with quantum mechanics and justifies the attribute "holstic". In fact it positions the E-J Gedankenexperiment into the same conceptual category as the cosmological constant problem and the Unruh Gedankenexperiment. The holistic structure of QFT resulting from "modular localization" also leads to a revision of the conceptual origin of the crucial crossing property which entered particle theory at the time of the bootstrap S-matrix approach but suffered from incorrect use in the S-matrix settings of the dual model and string theory. The new holistic point of view, which strengthens the autonomous aspect of QFT, also comes with new messages for gauge theory by exposing the clash between Hilbert space structure and localization and presenting alternative solutions based on the use of stringlocal fields in Hilbert space. Among other things this leads to a reformulation of the Englert-Higgs symmetry breaking mechanism.

  13. Evolution of local atomic structure during solidification of Al2Au liquid: An ab initio study

    SciTech Connect

    Xiong, L H; Lou, H B; Wang, X D; Debela, T T; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z

    2014-04-01

    The local atomic structure evolution in Al2Au alloy during solidification from 2000 K to 400 K was studied by ab initio molecular dynamics simulations and analyzed using the structure factor, pair correlation functions, bond angle distributions, the Honeycutt-Anderson (HA) index and Voronoi tessellation methods. It was found that the icosahedral-like clusters are negligible in the Al2Au stable liquid and supercooled liquid states, and the most abundant clusters are those having HA indices of 131 and 120 or Voronoi indices of < 0,4,4,0 >, < 0,3, 6,0 > and < 0,4,4,2 > with coordination numbers of 8, 9 and 10, respectively. These clusters are similar to the local atomic structures in the CaF2-type Al2Au crystal, revealing the existence of structure heredity between liquid and crystalline phase in Al2Au alloy. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  14. XAFS study on Ca local structure in natural glasses and tektite

    NASA Astrophysics Data System (ADS)

    Tobase, T.; Wang, L.; Yoshiasa, A.; Okube, M.; Nakatani, T.; Hayasaka, Y.; Isobe, H.

    2013-04-01

    The local structures of tektite and natural glasses were studied by Ca K-edge X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) in order to provide quantitative data on bonding distances and coordination numbers. The pre-edge peak intensities of tektites are 10.7-11.7%, and those of peudotachylite, Kirauea volcanic glass, impactite, pitchstone and perlite are 6.7-10.9%. The main peak shoulder intensities of tektites are 68.3-70.7%, and other natural glasses are 63.0-63.9%. XAFS analysis indicated all tektites possess 7-coordinated Ca, but natural glasses possess 6-, 7- and 8- coordinated Ca. This study indicated that different petrogenesis of natural glasses gives different local structures of calcium.

  15. Lidar Calibration Centre

    NASA Astrophysics Data System (ADS)

    Pappalardo, Gelsomina; Freudenthaler, Volker; Nicolae, Doina; Mona, Lucia; Belegante, Livio; D'Amico, Giuseppe

    2016-06-01

    This paper presents the newly established Lidar Calibration Centre, a distributed infrastructure in Europe, whose goal is to offer services for complete characterization and calibration of lidars and ceilometers. Mobile reference lidars, laboratories for testing and characterization of optics and electronics, facilities for inspection and debugging of instruments, as well as for training in good practices are open to users from the scientific community, operational services and private sector. The Lidar Calibration Centre offers support for trans-national access through the EC HORIZON2020 project ACTRIS-2.

  16. In the Field: The Canadian Ecology Centre.

    ERIC Educational Resources Information Center

    Magee, Clare

    2000-01-01

    The Canadian Ecology Centre (Ontario) offers year-round residential and day programs in outdoor and environmental education for secondary students, field placement and internship opportunities for college students, and ecotourism programs, while providing employment and tax revenues to the local community. Dubbed consensus environmentalism, the…

  17. Structural Heterogeneity in the Localized Excited States of Poly(3-hexylthiophene).

    PubMed

    Yu, Wenjian; Magnanelli, Timothy J; Zhou, Jiawang; Bragg, Arthur E

    2016-06-01

    Transient hole-burning and resonantly enhanced Raman spectroscopies are used to probe heterogeneities among localized singlet excitons of poly(3-hexylthiophene) in solution. Transient hole-burning spectroscopy facilitated by population dumping through wavelength-selective stimulated emission exposes inhomogeneous broadening of the exciton absorption band in the near-infrared, as reflected by correlations between stimulated emission and excited-state absorption transition energies. Dump-induced spectral diffusion of the exciton absorption band reflects structural fluctuations in the locally excited polymer. This diffusion is observed to occur slightly faster or slower than the nonequilibrium relaxation that follows direct excitation of the polymer (8-9 ps), with the time scale for diffusion varying with subpopulation: dumping across small vs large band gaps results in diffusion over 5 vs 35 ps, respectively. Furthermore, incomplete spectral relaxation of transient holes reflects that subsets of locally excited structural motifs prepared through photoexcitation cannot interchange through structural fluctuations that occur over the singlet-exciton lifetime. Raman spectra of the C═C/C-C stretching region collected in resonance at energies across the exciton absorption band exhibit frequency and intensity trends (Raman "dispersion") ascribed to variation in the local effective conjugation length. Together, results explicitly reveal heterogeneities among excitonic states associated with variations and fluctuations in local conformational order. PMID:27167593

  18. Introducing anisotropic Minkowski functionals and quantitative anisotropy measures for local structure analysis in biomedical imaging

    NASA Astrophysics Data System (ADS)

    Wismüller, Axel; De, Titas; Lochmüller, Eva; Eckstein, Felix; Nagarajan, Mahesh B.

    2013-03-01

    The ability of Minkowski Functionals to characterize local structure in different biological tissue types has been demonstrated in a variety of medical image processing tasks. We introduce anisotropic Minkowski Functionals (AMFs) as a novel variant that captures the inherent anisotropy of the underlying gray-level structures. To quantify the anisotropy characterized by our approach, we further introduce a method to compute a quantitative measure motivated by a technique utilized in MR diffusion tensor imaging, namely fractional anisotropy. We showcase the applicability of our method in the research context of characterizing the local structure properties of trabecular bone micro-architecture in the proximal femur as visualized on multi-detector CT. To this end, AMFs were computed locally for each pixel of ROIs extracted from the head, neck and trochanter regions. Fractional anisotropy was then used to quantify the local anisotropy of the trabecular structures found in these ROIs and to compare its distribution in different anatomical regions. Our results suggest a significantly greater concentration of anisotropic trabecular structures in the head and neck regions when compared to the trochanter region (p < 10-4). We also evaluated the ability of such AMFs to predict bone strength in the femoral head of proximal femur specimens obtained from 50 donors. Our results suggest that such AMFs, when used in conjunction with multi-regression models, can outperform more conventional features such as BMD in predicting failure load. We conclude that such anisotropic Minkowski Functionals can capture valuable information regarding directional attributes of local structure, which may be useful in a wide scope of biomedical imaging applications.

  19. Tuning LDA+U for electron localization and structure at oxygen vacancies in ceria.

    PubMed

    Castleton, C W M; Kullgren, J; Hermansson, K

    2007-12-28

    We examine the real space structure and the electronic structure (particularly Ce4f electron localization) of oxygen vacancies in CeO(2) (ceria) as a function of U in density functional theory studies with the rotationally invariant forms of the LDA+U and GGA+U functionals. The four nearest neighbor Ce ions always relax outwards, with those not carrying localized Ce4f charge moving furthest. Several quantification schemes show that the charge starts to become localized at U approximately 3 eV and that the degree of localization reaches a maximum at approximately 6 eV for LDA+U or at approximately 5.5 eV for GGA+U. For higher U it decreases rapidly as charge is transferred onto second neighbor O ions and beyond. The localization is never into atomic corelike states; at maximum localization about 80-90% of the Ce4f charge is located on the two nearest neighboring Ce ions. However, if we look at the total atomic charge we find that the two ions only make a net gain of (0.2-0.4)e each, so localization is actually very incomplete, with localization of Ce4f electrons coming at the expense of moving other electrons off the Ce ions. We have also revisited some properties of defect-free ceria and find that with LDA+U the crystal structure is actually best described with U=3-4 eV, while the experimental band structure is obtained with U=7-8 eV. (For GGA+U the lattice parameters worsen for U>0 eV, but the band structure is similar to LDA+U.) The best overall choice is U approximately 6 eV with LDA+U and approximately 5.5 eV for GGA+U, since the localization is most important, but a consistent choice for both CeO(2) and Ce(2)O(3), with and without vacancies, is hard to find.

  20. Hybrid local FEM/global LISA modeling of damped guided wave propagation in complex composite structures

    NASA Astrophysics Data System (ADS)

    Shen, Yanfeng; Cesnik, Carlos E. S.

    2016-09-01

    This paper presents a new hybrid modeling technique for the efficient simulation of guided wave generation, propagation, and interaction with damage in complex composite structures. A local finite element model is deployed to capture the piezoelectric effects and actuation dynamics of the transmitter, while the global domain wave propagation and interaction with structural complexity (structure features and damage) are solved utilizing a local interaction simulation approach (LISA). This hybrid approach allows the accurate modeling of the local dynamics of the transducers and keeping the LISA formulation in an explicit format, which facilitates its readiness for parallel computing. The global LISA framework was extended through the 3D Kelvin-Voigt viscoelasticity theory to include anisotropic damping effects for composite structures, as an improvement over the existing LISA formulation. The global LISA framework was implemented using the compute unified device architecture running on graphic processing units. A commercial preprocessor is integrated seamlessly with the computational framework for grid generation and material property allocation to handle complex structures. The excitability and damping effects are successfully captured by this hybrid model, with experimental validation using the scanning laser doppler vibrometry. To demonstrate the capability of our hybrid approach for complex structures, guided wave propagation and interaction with a delamination in a composite panel with stiffeners is presented.

  1. Hybrid local FEM/global LISA modeling of damped guided wave propagation in complex composite structures

    NASA Astrophysics Data System (ADS)

    Shen, Yanfeng; Cesnik, Carlos E. S.

    2016-09-01

    This paper presents a new hybrid modeling technique for the efficient simulation of guided wave generation, propagation, and interaction with damage in complex composite structures. A local finite element model is deployed to capture the piezoelectric effects and actuation dynamics of the transmitter, while the global domain wave propagation and interaction with structural complexity (structure features and damage) are solved utilizing a local interaction simulation approach (LISA). This hybrid approach allows the accurate modeling of the local dynamics of the transducers and keeping the LISA formulation in an explicit format, which facilitates its readiness for parallel computing. The global LISA framework was extended through the 3D Kelvin–Voigt viscoelasticity theory to include anisotropic damping effects for composite structures, as an improvement over the existing LISA formulation. The global LISA framework was implemented using the compute unified device architecture running on graphic processing units. A commercial preprocessor is integrated seamlessly with the computational framework for grid generation and material property allocation to handle complex structures. The excitability and damping effects are successfully captured by this hybrid model, with experimental validation using the scanning laser doppler vibrometry. To demonstrate the capability of our hybrid approach for complex structures, guided wave propagation and interaction with a delamination in a composite panel with stiffeners is presented.

  2. Local Structural Analysis of Half-Metallic Ferromagnet CrO2

    NASA Astrophysics Data System (ADS)

    Kodama, Katsuaki; Ikeda, Kazutaka; Isobe, Masahiko; Takeda, Hikaru; Itoh, Masayuki; Ueda, Yutaka; Shamoto, Shin-ichi; Otomo, Toshiya

    2016-09-01

    We have performed powder neutron diffraction on the half-metallic ferromagnet CrO2 which has a rutile-type crystal structure with a tetragonal unit cell. Although the powder diffraction pattern can be fitted by the reported crystal structure including a single Cr site, the atomic pair distribution function (PDF) can be fitted by the structural model with an orthorhombic unit cell including two kinds of inequivalent Cr sites. The difference between the valences of the two inequivalent Cr sites, δ of Cr+4±δ, estimated from the local structural parameters is about 0.06. The shapes of the two CrO6 octahedra are slightly different, suggesting the short-range orbital ordering of the Cr 3d orbitals. The lattice distortion and the improvement of the fitting to the PDF obtained using the locally distorted structure model are apparent in the region below about 10 Å, suggesting that the domain size or correlation length of the locally distorted structure is about 10 Å, roughly corresponding to the size of two unit cells.

  3. Local structure and spin transition in Fe2O3 hematite at high pressure

    NASA Astrophysics Data System (ADS)

    Sanson, Andrea; Kantor, Innokenty; Cerantola, Valerio; Irifune, Tetsuo; Carnera, Alberto; Pascarelli, Sakura

    2016-07-01

    The pressure evolution of the local structure of Fe2O3 hematite has been determined by extended x-ray absorption fine structure up to ˜79 GPa. Below the phase-transition pressure at ˜50 GPa, no increasing of FeO6 octahedra distortion is observed as pressure is applied. Above the phase transition, an abrupt decrease of the nearest-neighbor Fe-O distance is observed concomitantly with a strong reduction in the FeO6 distortion. This information on the local structure, used as a test-bench for the different high-pressure forms proposed in the literature, suggests that the orthorhombic structure with space group A b a 2 , recently proposed by Bykova et al. [Nat. Commun. 7, 10661 (2016), 10.1038/ncomms10661], is the most probable, but puts into question the presence of the P 21 /n form in the pressure range 54-67 GPa. Finally, the crossover from Fe high-spin to low-spin states with pressure increase has been monitored from the pre-edge region of the Fe K -edge absorption spectra. Its "simultaneous" comparison with the local structural changes allows us to conclude that it is the electronic transition that drives the structural transition and not vice versa.

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

    NASA Astrophysics Data System (ADS)

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

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

  5. Local Laser Strengthening of Steel Sheets for Load Adapted Component Design in Car Body Structures

    NASA Astrophysics Data System (ADS)

    Jahn, Axel; Heitmanek, Marco; Standfuss, Jens; Brenner, Berndt; Wunderlich, Gerd; Donat, Bernd

    The current trend in car body construction concerning light weight design and car safety improvement increasingly requires an adaption of the local material properties on the component load. Martensitic hardenable steels, which are typically used in car body components, show a significant hardening effect, for instance in laser welded seams. This effect can be purposefully used as a local strengthening method. For several steel grades the local strengthening, resulting from a laser remelting process was investigated. The strength in the treated zone was determined at crash relevant strain rates. A load adapted design of complex reinforcement structures was developed for compression and bending loaded tube samples, using numerical simulation of the deformation behavior. Especially for bending loaded parts, the crash energy absorption can be increased significantly by local laser strengthening.

  6. Local temperature redistribution and structural transition during joule-heating-driven conductance switching in VO2.

    PubMed

    Kumar, Suhas; Pickett, Matthew D; Strachan, John Paul; Gibson, Gary; Nishi, Yoshio; Williams, R Stanley

    2013-11-13

    Joule-heating induced conductance-switching is studied in VO2 , a Mott insulator. Complementary in situ techniques including optical characterization, blackbody microscopy, scanning transmission X-ray microscopy (STXM) and numerical simulations are used. Abrupt redistribution in local temperature is shown to occur upon conductance-switching along with a structural phase transition, at the same current.

  7. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures

    NASA Astrophysics Data System (ADS)

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-05-01

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous–crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature.

  8. Local structures of Ca, Ti and Fe in meteorite fusion crusts

    NASA Astrophysics Data System (ADS)

    Tobase, T.; Yoshiasa, A.; Hiratoko, T.; Hongu, H.; Isobe, H.; Nakatsuka, A.; Arima, H.; Sugiyama, K.

    2016-05-01

    The local structures of meteorite fusion crusts were studied by Ca, Ti and Fe K-edge XANES and EXAFS spectroscopy. The surface of meteorites were melted and volatilized with extreme high temperature and large temperature gradient when meteorites were rushed into atmosphere. This study indicated that meteorite fusion crusts have unique local structures. The local structures of fusion crusts differ from tektites especially in intensity of the shoulder in the rising flank of the edge in Ca XANES spectra. It is consistent with chemical composition change by the volatilization of Si at fusion during atmospheric entry. The high estimated Fe3+/ (Fe2++Fe3+) ratio in meteorite fusion crusts indicates that meteorite fusion crusts are formed into atmospheric oxidation condition. The Ca-O distances in meteorite fusion crusts are 2.612.66 A and are extremely longer than in other natural glasses. The fusion crusts have unique local structure since they experienced extremely high temperature and short quenching time. The XAFS method is effective in distinction of meteorite fusion crusts and classification of natural glass.

  9. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures

    PubMed Central

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-01-01

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous–crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature. PMID:27220411

  10. On the robustness of the localized spatiotemporal structures in electron-positron-ion plasmas

    SciTech Connect

    Mahajan, S.M.; Berezhiani, V.I. |; Miklaszewski, R.

    1998-04-01

    It is shown that, in an electron-positron plasma with a small fraction of ions, large-amplitude localized spatiotemporal structures (light bullets) can be readily generated and sustained. These light bullets are found to be exceptionally robust: they can emerge from a large variety of initial field distributions and are remarkably stable.

  11. Spaghetti Politics: Local Electoral Systems and Alliance Structure in Italy, 1984-2001

    ERIC Educational Resources Information Center

    Parigi, Paolo; Bearman, Peter S.

    2008-01-01

    This article describes the impact of the Italian electoral reforms of 1993 on the structure of local political alliances. The reform, which moved Italy from a purely proportional representation system to a mixed, largely majoritarian system, was designed to increase transparency, reduce corruption, limit the number of political parties, and create…

  12. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures.

    PubMed

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-05-25

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous-crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature.

  13. Impacts of Information Subsidies and Community Structure on Local Press Coverage of Environmental Contamination.

    ERIC Educational Resources Information Center

    Griffin, Robert J.; Dunwoody, Sharon

    1995-01-01

    Finds that a press kit sent by an environmental group to midwestern newspapers influenced them to delegate local staff to cover the story. Indicates that the press's function to report or raise issues concerning industrial toxic releases and related health risks is tempered by community structure and particularly by community reliance on…

  14. Characterization of local complex structures in a recurrence plot to improve nonlinear dynamic discriminant analysis

    NASA Astrophysics Data System (ADS)

    Ding, Hang

    2014-01-01

    Structures in recurrence plots (RPs), preserving the rich information of nonlinear invariants and trajectory characteristics, have been increasingly analyzed in dynamic discrimination studies. The conventional analysis of RPs is mainly focused on quantifying the overall diagonal and vertical line structures through a method, called recurrence quantification analysis (RQA). This study extensively explores the information in RPs by quantifying local complex RP structures. To do this, an approach was developed to analyze the combination of three major RQA variables: determinism, laminarity, and recurrence rate (DLR) in a metawindow moving over a RP. It was then evaluated in two experiments discriminating (1) ideal nonlinear dynamic series emulated from the Lorenz system with different control parameters and (2) data sets of human heart rate regulations with normal sinus rhythms (n = 18) and congestive heart failure (n = 29). Finally, the DLR was compared with seven major RQA variables in terms of discriminatory power, measured by standardized mean difference (DSMD). In the two experiments, DLR resulted in the highest discriminatory power with DSMD = 2.53 and 0.98, respectively, which were 7.41 and 2.09 times the best performance from RQA. The study also revealed that the optimal RP structures for the discriminations were neither typical diagonal structures nor vertical structures. These findings indicate that local complex RP structures contain some rich information unexploited by RQA. Therefore, future research to extensively analyze complex RP structures would potentially improve the effectiveness of the RP analysis in dynamic discrimination studies.

  15. Local Fine Structural Insight into Mechanism of Electrochemical Passivation of Titanium.

    PubMed

    Wang, Lu; Yu, Hongying; Wang, Ke; Xu, Haisong; Wang, Shaoyang; Sun, Dongbai

    2016-07-20

    Electrochemically formed passive film on titanium in 1.0 M H2SO4 solution and its thickness, composition, chemical state, and local fine structure are examined by Auger electron spectroscopy (AES), X-ray photoelectron spectroscopy (XPS), and X-ray absorption fine structure. AES analysis reveals that the thickness and composition of oxide film are proportional to the reciprocal of current density in potentiodynamic polarization. XPS depth profiles of the chemical states of titanium exhibit the coexistence of various valences cations in the surface. Quantitative X-ray absorption near edge structure analysis of the local electronic structure of the topmost surface (∼5.0 nm) shows that the ratio of [TiO2]/[Ti2O3] is consistent with that of passivation/dissolution of electrochemical activity. Theoretical calculation and analysis of extended X-ray absorption fine structure spectra at Ti K-edge indicate that both the structures of passivation and dissolution are distorted caused by the appearance of two different sites of Ti-O and Ti-Ti. And the bound water in the topmost surface plays a vital role in structural disorder confirmed by XPS. Overall, the increase of average Ti-O coordination causes the electrochemical passivation, and the dissolution is due to the decrease of average Ti-Ti coordination. The structural variations of passivation in coordination number and interatomic distance are in good agreement with the prediction of point defect model. PMID:27355902

  16. Advances in Structural Integrity Analysis Methods for Aging Metallic Airframe Structures with Local Damage

    NASA Technical Reports Server (NTRS)

    Starnes, James H., Jr.; Newman, James C., Jr.; Harris, Charles E.; Piascik, Robert S.; Young, Richard D.; Rose, Cheryl A.

    2003-01-01

    Analysis methodologies for predicting fatigue-crack growth from rivet holes in panels subjected to cyclic loads and for predicting the residual strength of aluminum fuselage structures with cracks and subjected to combined internal pressure and mechanical loads are described. The fatigue-crack growth analysis methodology is based on small-crack theory and a plasticity induced crack-closure model, and the effect of a corrosive environment on crack-growth rate is included. The residual strength analysis methodology is based on the critical crack-tip-opening-angle fracture criterion that characterizes the fracture behavior of a material of interest, and a geometric and material nonlinear finite element shell analysis code that performs the structural analysis of the fuselage structure of interest. The methodologies have been verified experimentally for structures ranging from laboratory coupons to full-scale structural components. Analytical and experimental results based on these methodologies are described and compared for laboratory coupons and flat panels, small-scale pressurized shells, and full-scale curved stiffened panels. The residual strength analysis methodology is sufficiently general to include the effects of multiple-site damage on structural behavior.

  17. Crystallographic Data Centre Services and Publications.

    ERIC Educational Resources Information Center

    Cambridge Univ. (England). Chemical Lab.

    The Cambridge Crystallographic Data Centre is concerned with the retrieval, evaluation, synthesis, and dissemination of structural data based on diffraction methods. The source of input is almost entirely primary journals. Bibliographic information and numeric data on crystal and molecular structures are on magnetic tapes. The bibliographic file…

  18. The GSO Data Centre

    NASA Astrophysics Data System (ADS)

    Paletou, F.; Glorian, J.-M.; Génot, V.; Rouillard, A.; Petit, P.; Palacios, A.; Caux, E.; Wakelam, V.

    2015-12-01

    Hereafter we describe the activities of the Grand Sud-Ouest Data Centre operated for INSU (CNRS) by the OMP--IRAP and the Université Paul Sabatier in Toulouse, in a collaboration with the OASU--LAB in Bordeaux and OREME--LUPM in Montpellier.

  19. Discovering a Discovery Centre

    ERIC Educational Resources Information Center

    McCullagh, John; Stewart, James; Greenwood, Julian

    2007-01-01

    There has recently been a growth in the popularity of "science centres" and this development provides an excellent opportunity to support the primary science curriculum. Their use is therefore well worth including within initial teacher education courses. Hence, undergraduate student teachers at Stranmillis University College Belfast may now…

  20. The Iranian Documentation Centre.

    ERIC Educational Resources Information Center

    Harvey, John F.

    The purpose of the Iranian Documentation Centr (Irandoc) was to collect that portion of the world's literature which was pertinent to Iran's research interests, to organize that material, and to promote its use by Iranian researchers. Stated more succinctly, Irandoc's purpose was to obtain ready access to the world's scientific literature in order…

  1. Maple Leaf Outdoor Centre.

    ERIC Educational Resources Information Center

    Maguire, Molly; Gunton, Ric

    2000-01-01

    Maple Leaf Outdoor Centre (Ontario) has added year-round outdoor education facilities and programs to help support its summer camp for disadvantaged children. Schools, youth centers, religious groups, and athletic teams conduct their own programs, collaborate with staff, or use staff-developed programs emphasizing adventure education and personal…

  2. Local orderings in long-range-disordered bismuth-layered intergrowth structure

    SciTech Connect

    Zhang, Faqiang; Li, Yongxiang; Gu, Hui; Gao, Xiang

    2014-04-01

    A series of intergrowth bismuth-layered (Bi{sub 3}TiNbO{sub 9}){sub 2}(Bi{sub 4}Ti{sub 3}O{sub 12}) (2{sub 2}3) ceramics were prepared by conventional solid-state reaction to study the characteristics of the local orderings in long-range-disordered intergrowth structures. High-resolution high-angle annular dark-field (HAADF) imaging reveals the intergrowth structure composed of mixtures of -23-, -223-, -2223- and -22- sequences, while the -223- structure is the thermodynamic stable state of this intergrowth system. It was confirmed by the crystals of recurrent -223- structure prepared by self-flux method and the nature of the local ordering was discussed from their differences in repeating units. The statistics show that when repeating units reach 4 or higher, the independent -223- intergrowth ordering emerges clearly among the competing associated orderings. We infer it is the kinetic factor that induces local compositional variance to result in long-range disordered intergrowth structures. - Graphical abstract: The long-range-disordered intergrowth structure in a (Bi{sub 3}TiNbO{sub 9}){sub 2}(Bi{sub 4}Ti{sub 3}O{sub 12}) (2{sub 2}3) grain, which is composed of various types of local orderings, such as -22-, -23- and -223-. - Highlights: • The characteristic of the long-range-disordered (Bi{sub 3}TiNbO{sub 9}){sub 2}(Bi{sub 4}Ti{sub 3}O{sub 12}) (2{sub 2}3) structure was statistically analyzed, and the ordered -223- structure was speculated to be the thermodynamic stable state of the system. • The crystals of the -223- structure were successfully prepared for the first time by self-melt method. • The lower limit of the repeating units (L) to uniquely determine an independent intergrowth structure was speculated to be L=4. • The analysis inferred that the kinetic process is the controlling factor to limit the structural continuity and induce the long-range-disordered intergrowth structure.

  3. A multilevel approach for minimum weight structural design including local and system buckling constraints

    NASA Technical Reports Server (NTRS)

    Schmit, L. A., Jr.; Ramanathan, R. K.

    1977-01-01

    A rational multilevel approach for minimum weight structural design of truss and wing structures including local and system buckling constraints is presented. Overall proportioning of the structure is achieved at the system level subject to strength, displacement and system buckling constraints, while the detailed component designs are carried out separately at the component level satisfying local buckling constraints. Total structural weight is taken to be the objective function at the system level while employing the change in the equivalent system stiffness of the component as the component level objective function. Finite element analysis is used to predict static response while system buckling behavior is handled by incorporating a geometric stiffness matrix capability. Buckling load factors and the corresponding mode shapes are obtained by solving the eigenvalue problem associated with the assembled elastic stiffness and geometric stiffness matrices for the structural system. At the component level various local buckling failure modes are guarded against using semi-empirical formulas. Mathematical programming techniques are employed at both the system and component level.

  4. Connecting the dots: how local structure affects global integration in infants.

    PubMed

    Palomares, Melanie; Pettet, Mark; Vildavski, Vladimir; Hou, Chuan; Norcia, Anthony

    2010-07-01

    Glass patterns are moirés created from a sparse random-dot field paired with its spatially shifted copy. Because discrimination of these patterns is not based on local features, they have been used extensively to study global integration processes. Here, we investigated whether 4- to 5.5-month-old infants are sensitive to the global structure of Glass patterns by measuring visual-evoked potentials. Although we found strong responses to the appearance of the constituent dots, we found sensitivity to the global structure of the Glass patterns in the infants only over a very limited range of spatial separation. In contrast, we observed robust responses in the infants when we connected the dot pairs of the Glass pattern with lines. Moreover, both infants and adults showed differential responses to exchanges between line patterns portraying different global structures. A control study varying luminance contrast in adults suggests that infant sensitivity to global structure is not primarily limited by reduced element visibility. Together our results suggest that the insensitivity to structure in conventional Glass patterns is due to inefficiencies in extracting the local orientation cues generated by the dot pairs. Once the local orientations are made unambiguous or when the interpolation span is small, infants can integrate these signals over the image.

  5. New Approach for 3D Local Structure Refinement Using Non-Muffin-Tin XANES Analysis

    SciTech Connect

    Smolentsev, Grigory; Soldatov, Alexander V.; Feiters, Martin C.

    2007-02-02

    A new technique of 3D local structure refinement using full-potential X-ray absorption near edge structure (XANES) analysis is proposed and demonstrated in application to metalloorganic complexes of Ni. It can be applied to determine local structure in those cases where the muffin-tin approximation used in most full multiple scattering schemes fails. The method is based on the fitting of experimental XANES data using multidimensional interpolation of spectra as a function of structural parameters, recently proposed by us, and ab-initio full potential calculations of XANES using finite difference method. The small number of required ab-initio calculations is the main advantage of the approach, which allows one to use computationally time-expensive non-muffin-tin finite-difference method. The possibility to extract information on bond angles in addition to bond-lengths accessible to standard EXAFS is demonstrated and it opens new perspectives of quantitative XANES analysis as a 3D local structure probe.

  6. Polydisperse hard spheres: crystallization kinetics in small systems and role of local structure

    NASA Astrophysics Data System (ADS)

    Campo, Matteo; Speck, Thomas

    2016-08-01

    We study numerically the crystallization of a hard-sphere mixture with 8% polydispersity. Although often used as a model glass former, for small system sizes we observe crystallization in molecular dynamics simulations. This opens the possibility to study the competition between crystallization and structural relaxation of the melt, which typically is out of reach due to the disparate timescales. We quantify the dependence of relaxation and crystallization times on density and system size. For one density and system size we perform a detailed committor analysis to investigate the suitability of local structures as order parameters to describe the crystallization process. We find that local structures are strongly correlated with generic bond order and add little information to the reaction coordinate.

  7. Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD.

    PubMed

    Feig, Michael

    2016-07-25

    A method for the local refinement of protein structures that targets improvements in local stereochemistry while preserving the overall fold is presented. The method uses force field-based minimization and sampling via molecular dynamics simulations with a modified force field to bring bonds, angles, and torsion angles into an acceptable range for high-resolution protein structures. The method is implemented in the locPREFMD web server and was tested on computational models submitted to CASP11. Using MolProbity scores as the main assessment criterion, the locPREFMD method significantly improves the stereochemical quality of given input models close to the quality expected for experimental structures while maintaining the Cα coordinates of the initial model.

  8. Site-specific local structure of Mn in artificial manganese ferrite films

    SciTech Connect

    Kravtsov, E.; Haskel, D.; Cady, A.; Yang, A.; Vittoria, C.; Harris, V. G.; Zuo, X.

    2006-09-01

    Diffraction anomalous fine structure (DAFS) spectroscopy has been applied to resolve site-specific Mn local structure in manganese ferrite films grown under nonequilibrium conditions. The DAFS spectra were measured at a number of Bragg reflections in the vicinity of the Mn absorption K edge. The DAFS data analysis done with an iterative Kramers-Kroenig algorithm made it possible to solve separately the local structure around crystallographically inequivalent Mn sites in the unit cell with nominal octahedral and tetrahedral coordination. The strong preference for Mn to be tetrahedrally coordinated in this compound is not only manifested in the relative site occupancies but also in a strong reduction in coordination number for Mn ions at nominal octahedral sites.

  9. Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD.

    PubMed

    Feig, Michael

    2016-07-25

    A method for the local refinement of protein structures that targets improvements in local stereochemistry while preserving the overall fold is presented. The method uses force field-based minimization and sampling via molecular dynamics simulations with a modified force field to bring bonds, angles, and torsion angles into an acceptable range for high-resolution protein structures. The method is implemented in the locPREFMD web server and was tested on computational models submitted to CASP11. Using MolProbity scores as the main assessment criterion, the locPREFMD method significantly improves the stereochemical quality of given input models close to the quality expected for experimental structures while maintaining the Cα coordinates of the initial model. PMID:27380201

  10. Applying local Green's functions to study the influence of the crustal structure on hydrological loading displacements

    NASA Astrophysics Data System (ADS)

    Dill, Robert; Klemann, Volker

    2015-04-01

    The influence of the elastic Earth properties on seasonal or shorter periodic surface mass loads due to atmospheric surface pressure and terrestrial water storage variations is usually modeled by applying a local isostatic model like a homogeneous half-space model, or by a one dimensional spherical Earth model like PREM from which a unique set of elastic load Love numbers, or alternatively, elastic Green's functions are derived. The drawbacks of these strategies are that, in the first case, the response according to the local Earth structure is valid only if load and observer almost coincide, or that, in the second case, only the response of an average Earth structure is considered. However, for surface loads with horizontal scales less than 2500 km2, as for instance, for strong localized hydrological signals associated with heavy precipitation events and river floods, the Earth elastic response becomes very sensitive to inhomogeneities in the Earth crustal structure. We derive a set of local Green's functions defined for every global 1°× 1° gridcell for the 3-layer crustal structure TEA12. Local Green's functions show standard deviations of ±12% in the vertical and ±21% in the horizontal directions for distances in the range from 0.1° to 0.5°. The application of local Green's functions introduces a variability of 0.5 - 1.0 mm into the hydrological loading displacements, both in vertical and in horizontal directions. Maximum changes due to the local crustal structures are from -25% to +26% in the vertical and -91% to +55% in the horizontal displacements. In addition, the horizontal displacement changes its direction significantly, even to the opposite. The modeling of a site-dependent crustal response to surface loads provides an alternative way to probe the density and elastic structure of the Earth's crust and mantle by means of observed surface deformations caused by mass re-distributions. In addition, realistic loading models allow the monitoring of mass

  11. Strain properties analysis and wireless collection system of PVDF for structural local health monitoring of civil engineering structures

    NASA Astrophysics Data System (ADS)

    Yu, Yan; Wang, Yang; Dong, Weijie; Jin, Yajing; Ou, Jinping

    2009-07-01

    For large civil engineering structures and base establishments, for example, bridges, super-high buildings, long-span space structures, offshore platforms and pipe systems of water & gas supply, their lives are up to a few decades or centuries. Damaged by environmental loads, fatigue effects, corrosion effects and material aging, these structures experience inevitably such side effects as damage accumulation, resistance reduction and even accidents. The traditional civil structure is a kind of passive one, whose performance and status are unpredictable to a great extent, but the informatics' introduction breaks a new path to obtain the status of the structure, thus it is an important research direction to evaluate and improve reliability of civil structures by the use of monitoring and health diagnosis technique, and this also assures the security of service for civil engineering structures. Smart material structure, originated from the aerospace sector, has been a research hotspot in civil engineering, medicine, shipping, and so on. For structural health monitoring of civil engineering, the research about high-performance sensing unit of smart material structure is very important, and this will possibly push further the development and application of monitoring and health diagnosis techniques. At present, piezoelectric materials are one of the most widely used sensing materials among the research of smart material structures. As one of the piezoelectric materials, PVDF(Polyvinylidene Fluoride)film is widely considered for the advantages of low cost, good mechanical ability, high sensibility, the ability of being easily placed and resistance of corrosion. However, only a few studies exit about building a mature monitoring system using PVDF. In this paper, for the sake of using PVDF for sensing unit for structural local monitoring of civil engineering, the strain sensing properties of PVDF are studied in detail. Firstly, the operating mechanism of PVDF is analyzed

  12. Structural and Contextual Dimensions of Iranian Primary Health Care System at Local Level

    PubMed Central

    Zanganeh Baygi, Mehdi; Seyedin, Hesam; Salehi, Masoud; Jafari Sirizi, Mehdi

    2014-01-01

    Background: In recent years, family physician plan was established as the main strategy of health system in Iran, while organizational structure of the primary health care system has remained the same as thirty years ago. Objectives: This study was performed to illustrate structural and contextual dimensions of organizational structure and relationship between them in Iranian primary health care system at local level. Materials and Methods: A cross-sectional quantitative study was conducted from January to June 2013, during which 121 questionnaires were distributed among senior and junior managers of city health centers at Medical Sciences universities in Iran. Validity of the questionnaire was confirmed by experts (CVI = 0.089 and CVR more than 0.85) and Cronbach α was utilized for reliability (α = 0.904). We used multistage sampling method in this study and analysis of the data was performed by SPSS software using different tests. Results: Local level of primary health care system in Iran had mechanical structure, but in contextual dimensions the results showed different types. There was a significant relationship between structural and contextual dimensions (r = 0.642, P value < 0.001). Goals and culture dimensions had strongest effects on structural dimensions. Conclusions: Because of the changes in goals and strategies of Iranian health system in recent years, it is urgently recommended to reform the current structure to increase efficiency and effectiveness of the system. PMID:25763257

  13. Electric-field-induced local and mesoscale structural changes in polycrystalline dielectrics and ferroelectrics

    SciTech Connect

    Usher, Tedi -Marie; Levin, Igor; Daniels, John E.; Jones, Jacob L.

    2015-10-01

    In this study, the atomic-scale response of dielectrics/ferroelectrics to electric fields is central to their functionality. Here we introduce an in situ characterization method that reveals changes in the local atomic structure in polycrystalline materials under fields. The method employs atomic pair distribution functions (PDFs), determined from X-ray total scattering that depends on orientation relative to the applied field, to probe structural changes over length scales from sub-Ångstrom to several nanometres. The PDF is sensitive to local ionic displacements and their short-range order, a key uniqueness relative to other techniques. The method is applied to representative ferroelectrics, BaTiO3 and Na½Bi½TiO3, and dielectric SrTiO3. For Na½Bi½TiO3, the results reveal an abrupt field-induced monoclinic to rhombohedral phase transition, accompanied by ordering of the local Bi displacements and reorientation of the nanoscale ferroelectric domains. For BaTiO3 and SrTiO3, the local/nanoscale structural changes observed in the PDFs are dominated by piezoelectric lattice strain and ionic polarizability, respectively.

  14. Electric-field-induced local and mesoscale structural changes in polycrystalline dielectrics and ferroelectrics

    DOE PAGESBeta

    Usher, Tedi -Marie; Levin, Igor; Daniels, John E.; Jones, Jacob L.

    2015-10-01

    In this study, the atomic-scale response of dielectrics/ferroelectrics to electric fields is central to their functionality. Here we introduce an in situ characterization method that reveals changes in the local atomic structure in polycrystalline materials under fields. The method employs atomic pair distribution functions (PDFs), determined from X-ray total scattering that depends on orientation relative to the applied field, to probe structural changes over length scales from sub-Ångstrom to several nanometres. The PDF is sensitive to local ionic displacements and their short-range order, a key uniqueness relative to other techniques. The method is applied to representative ferroelectrics, BaTiO3 and Na½Bi½TiO3,more » and dielectric SrTiO3. For Na½Bi½TiO3, the results reveal an abrupt field-induced monoclinic to rhombohedral phase transition, accompanied by ordering of the local Bi displacements and reorientation of the nanoscale ferroelectric domains. For BaTiO3 and SrTiO3, the local/nanoscale structural changes observed in the PDFs are dominated by piezoelectric lattice strain and ionic polarizability, respectively.« less

  15. Electric-field-induced local and mesoscale structural changes in polycrystalline dielectrics and ferroelectrics.

    PubMed

    Usher, Tedi-Marie; Levin, Igor; Daniels, John E; Jones, Jacob L

    2015-01-01

    The atomic-scale response of dielectrics/ferroelectrics to electric fields is central to their functionality. Here we introduce an in situ characterization method that reveals changes in the local atomic structure in polycrystalline materials under fields. The method employs atomic pair distribution functions (PDFs), determined from X-ray total scattering that depends on orientation relative to the applied field, to probe structural changes over length scales from sub-Ångstrom to several nanometres. The PDF is sensitive to local ionic displacements and their short-range order, a key uniqueness relative to other techniques. The method is applied to representative ferroelectrics, BaTiO3 and Na½Bi½TiO3, and dielectric SrTiO3. For Na½Bi½TiO3, the results reveal an abrupt field-induced monoclinic to rhombohedral phase transition, accompanied by ordering of the local Bi displacements and reorientation of the nanoscale ferroelectric domains. For BaTiO3 and SrTiO3, the local/nanoscale structural changes observed in the PDFs are dominated by piezoelectric lattice strain and ionic polarizability, respectively. PMID:26424360

  16. Local Structure in Ab Initio Liquid Water: Signatures of Amorphous Phases

    NASA Astrophysics Data System (ADS)

    Santra, Biswajit; Distasio, Robert A., Jr.; Martelli, Fausto; Car, Roberto

    Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyze the local structure in such highly accurate ab initio liquid water. At ambient conditions, the LSI probability distribution, P(I), was unimodal with most water molecules characterized by more disordered high-density-like local environments. With thermal excitations removed, the resultant bimodal P(I) in the inherent potential energy surface (IPES) exhibited a 3:1 ratio between high- and low-density-like molecules, with the latter forming small connected clusters amid the predominant population. By considering the spatial correlations and hydrogen bond network topologies among water molecules with the same LSI identities, we demonstrate that the signatures of the experimentally observed low- and high-density amorphous phases of ice are present in the IPES of ambient liquid water This work was supported by the DOE: DE-SC0008626, DE-SC0005180.

  17. Functional and structural basis of the nuclear localization signal in the ZIC3 zinc finger domain

    PubMed Central

    Hatayama, Minoru; Tomizawa, Tadashi; Sakai-Kato, Kumiko; Bouvagnet, Patrice; Kose, Shingo; Imamoto, Naoko; Yokoyama, Shigeyuki; Utsunomiya-Tate, Naoko; Mikoshiba, Katsuhiko; Kigawa, Takanori; Aruga, Jun

    2008-01-01

    Disruptions in ZIC3 cause heterotaxy, a congenital anomaly of the left–right axis. ZIC3 encodes a nuclear protein with a zinc finger (ZF) domain that contains five tandem C2H2 ZF motifs. Missense mutations in the first ZF motif (ZF1) result in defective nuclear localization, which may underlie the pathogenesis of heterotaxy. Here we revealed the structural and functional basis of the nuclear localization signal (NLS) of ZIC3 and investigated its relationship to the defect caused by ZF1 mutation. The ZIC3 NLS was located in the ZF2 and ZF3 regions, rather than ZF1. Several basic residues interspersed throughout these regions were responsible for the nuclear localization, but R320, K337 and R350 were particularly important. NMR structure analysis revealed that ZF1–4 had a similar structure to GLI ZF, and the basic side chains of the NLS clustered together in two regions on the protein surface, similar to classical bipartite NLSs. Among the residues for the ZF1 mutations, C253 and H286 were positioned for the metal chelation, whereas W255 was positioned in the hydrophobic core formed by ZF1 and ZF2. Tryptophan 255 was a highly conserved inter-finger connector and formed part of a structural motif (tandem CXW-C-H-H) that is shared with GLI, Glis and some fungal ZF proteins. Furthermore, we found that knockdown of Karyopherin α1/α6 impaired ZIC3 nuclear localization, and physical interactions between the NLS and the nuclear import adapter proteins were disturbed by mutations in the NLS but not by W255G. These results indicate that ZIC3 is imported into the cell nucleus by the Karyopherin (Importin) system and that the impaired nuclear localization by the ZF1 mutation is not due to a direct influence on the NLS. PMID:18716025

  18. Self-Sustained Localized Structures in a Boundary-Layer Flow

    NASA Astrophysics Data System (ADS)

    Duguet, Yohann; Schlatter, Philipp; Henningson, Dan S.; Eckhardt, Bruno

    2012-01-01

    When a boundary layer starts to develop spatially over a flat plate, only disturbances of sufficiently large amplitude survive and trigger turbulence subcritically. Direct numerical simulation of the Blasius boundary-layer flow is carried out to track the dynamics in the region of phase space separating transitional from relaminarizing trajectories. In this intermediate regime, the corresponding disturbance is fully localized and spreads slowly in space. This structure is dominated by a robust pair of low-speed streaks, whose convective instabilities spawn hairpin vortices evolving downstream into transient disturbances. A quasicyclic mechanism for the generation of offspring is unfolded using dynamical rescaling with the local boundary-layer thickness.

  19. Possible healthcare-associated transmission as a cause of secondary infection and population structure of Staphylococcus aureus isolates from two wound treatment centres in Ghana.

    PubMed

    Kpeli, G; Darko Otchere, I; Lamelas, A; Buultjens, A L; Bulach, D; Baines, S L; Seemann, T; Giulieri, S; Nakobu, Z; Aboagye, S Y; Owusu-Mireku, E; Pluschke, G; Stinear, T P; Yeboah-Manu, D

    2016-09-01

    We have previously shown that secondary infections of Buruli ulcer wounds were frequently caused by Staphylococcus aureus. To gain understanding into possible routes of secondary infection, we characterized S. aureus isolates from patient lesions and surrounding environments across two Ghanaian health centres. One hundred and one S. aureus isolates were isolated from wounds (n = 93, 92.1%) and the hospital environment (n = 8, 7.9%) and characterized by the spa gene, mecA and the Panton-Valentine leucocidin toxin followed by spa sequencing and whole genome sequencing of a subset of 49 isolates. Spa typing and sequencing of the spa gene from 91 isolates identified 29 different spa types with t355 (ST152), t186 (ST88), and t346 dominating. Although many distinct strains were isolated from both health centres, genotype clustering was identified within centres. In addition, we identified a cluster consisting of isolates from a healthcare worker, patients dressed that same day and forceps used for dressing, pointing to possible healthcare-associated transmission. These clusters were confirmed by phylogenomic analysis. Twenty-four (22.8%) isolates were identified as methicillin-resistant S. aureus and lukFS genes encoding Panton-Valentine leucocidin were identified in 67 (63.8%) of the isolates. Phenotype screening showed widespread resistance to tetracycline, erythromycin, rifampicin, amikacin and streptomycin. Genomics confirmed the widespread presence of antibiotic resistance genes to β-lactams, chloramphenicol, trimethoprim, quinolone, streptomycin and tetracycline. Our findings indicate that the healthcare environment probably contributes to the superinfection of Buruli ulcer wounds and calls for improved training in wound management and infection control techniques. PMID:27547406

  20. Turbulence Suppression in a coherent structure of localized current and vorticity

    NASA Astrophysics Data System (ADS)

    Kim, Juhyung; Terry, Paul W.

    2010-11-01

    As a prelude to studying momentum transport in the RFP we examine the quasi-single helicity state of RFX as a transport barrier. Using analytic and numerical approaches we investigate turbulence suppression by a coherent structure of localized current and vorticity with a reduced MHD model. Previously, suppression was investigated inside a localized vortex structure in 2D Navier-Stokes turbulenceootnotetextP. W. Terry, D. E. Newman, and N. Mattor. Phys. Fluids A, 40 (5):927--937, 1992. and a localized current structure in kinetic Alfvén wave turbulence.ootnotetextP. W. Terry and K. W. Smith. Astrophys. J., 6650 (1):402--415, 2007. Following the previous works, the time scales of coherent structures with a flow shear and magnetic field shear and ambient turbulence are assumed to be separated and a variant of eddy-damped quasinormal Markovian (EDQNM) closure is applied to the turbulence. Qualitative criteria will be estimated for flow shear dominated, and magnetic field shear dominated suppression of turbulence. Numerical calculations will be given for comparison with the analytical estimates.

  1. Local structure of temperature and pH-sensitive colloidal microgels

    NASA Astrophysics Data System (ADS)

    Nigro, Valentina; Angelini, Roberta; Bertoldo, Monica; Bruni, Fabio; Castelvetro, Valter; Ricci, Maria Antonietta; Rogers, Sarah; Ruzicka, Barbara

    2015-09-01

    The temperature dependence of the local intra-particle structure of colloidal microgel particles, composed of interpenetrated polymer networks, has been investigated by small-angle neutron scattering at different pH and concentrations, in the range (299÷315) K, where a volume phase transition from a swollen to a shrunken state takes place. Data are well described by a theoretical model that takes into account the presence of both interpenetrated polymer networks and cross-linkers. Two different behaviors are found across the volume phase transition. At neutral pH and T ≈ 307 K, a sharp change of the local structure from a water rich open inhomogeneous interpenetrated polymer network to a homogeneous porous solid-like structure after expelling water is observed. Differently, at acidic pH, the local structure changes almost continuously. These findings demonstrate that a fine control of the pH of the system allows to tune the sharpness of the volume-phase transition.

  2. Rearrangement dynamics in colloidal particle packings identified through local structure and machine-learning

    NASA Astrophysics Data System (ADS)

    Davidson, Zoey S.; Still, Tim; Gratale, Matthew D.; Ma, Xiaoguang; Schoenholz, Samuel S.; Sussman, Daniel M.; Liu, A. J.; Yodh, A. G.

    We explore the connection between measures of local structure and particle rearrangements in soft thermal quasi-two-dimensional colloidal systems employing a machine learning approach. Local structure is characterized by two and three point structure functions that measure radial and angular distributions of particles, and rearrangements are identified by a measure of change in average colloidal particle position. By generating labeled training data, we can extract the features of these functions that contribute to the likelihood of a rearrangement. In particular, we use a machine-learning algorithm to construct a decision function in the form of a scalar field we call softness that with high accuracy labels regions of particles more likely to rearrange. Thus, we can predict dynamic rearrangements from the instantaneous local structure. The softness field remains a good predictor when we vary the packing fraction between training and test data sets. In glassy samples, the softness field can identify aging as particles become less likely to undergo cage rearrangements. We gratefully acknowledge financial support through NSF DMR12-05463, MRSEC DMR11-20901, NASA NNX08AO0G, and DE-FG02-05ER46199.

  3. Molecular dynamics simulations of the local structures and transport coefficients of molten alkali chlorides.

    PubMed

    Wang, Jia; Sun, Ze; Lu, Guimin; Yu, Jianguo

    2014-08-28

    Systematic results from molecular dynamics simulations of molten alkali chlorides (ACl) serials are presented in detail in this paper. The effects of temperature and cationic size on the structures and transport properties of molten salts have been investigated and analyzed. The local structures of molten ACl have been studied via the analysis of radial distribution functions and angular distribution functions. The coordination number of ACl decreases when ACl melts from solid and increases as cationic radius increases. Molten LiCl takes a distorted tetrahedral complex as the microconfiguration, while other melts have the tendency to keep the original local structure of the corresponding crystal. Temperature has no significant effect on the local structures of molten ACls. The results also show that the Tosi-Fumi potential predicts positive temperature dependences for self-diffusion coefficients and ionic conductivity, and negative temperature dependences for both viscosity and thermal conductivity of molten ACls. Ionic diffusivity decreases as cationic radius increases from LiCl to CsCl. The simulation results are in agreement with the experimental data available in the literature.

  4. Local structure of temperature and pH-sensitive colloidal microgels

    SciTech Connect

    Nigro, Valentina Bruni, Fabio; Ricci, Maria Antonietta; Angelini, Roberta; Ruzicka, Barbara; Bertoldo, Monica; Castelvetro, Valter; Rogers, Sarah

    2015-09-21

    The temperature dependence of the local intra-particle structure of colloidal microgel particles, composed of interpenetrated polymer networks, has been investigated by small-angle neutron scattering at different pH and concentrations, in the range (299÷315) K, where a volume phase transition from a swollen to a shrunken state takes place. Data are well described by a theoretical model that takes into account the presence of both interpenetrated polymer networks and cross-linkers. Two different behaviors are found across the volume phase transition. At neutral pH and T ≈ 307 K, a sharp change of the local structure from a water rich open inhomogeneous interpenetrated polymer network to a homogeneous porous solid-like structure after expelling water is observed. Differently, at acidic pH, the local structure changes almost continuously. These findings demonstrate that a fine control of the pH of the system allows to tune the sharpness of the volume-phase transition.

  5. Local atomic structure inheritance in Ag{sub 50}Sn{sub 50} melt

    SciTech Connect

    Bai, Yanwen; Bian, Xiufang Qin, Jingyu; Hu, Lina; Yang, Jianfei; Zhang, Kai; Zhao, Xiaolin; Yang, Chuncheng; Zhang, Shuo; Huang, Yuying

    2014-01-28

    Local structure inheritance signatures were observed during the alloying process of the Ag{sub 50}Sn{sub 50} melt, using high-temperature X-ray diffraction and ab initio molecular dynamics simulations. The coordination number N{sub m} around Ag atom is similar in the alloy and in pure Ag melts (N{sub m} ∼ 10), while, during the alloying process, the local structure around Sn atoms rearranges. Sn-Sn covalent bonds were substituted by Ag-Sn chemical bonds, and the total coordination number around Sn increases by about 70% as compared with those in the pure Sn melt. Changes in the electronic structure of the alloy have been studied by Ag and Sn K-edge X-ray absorption spectroscopy, as well as by calculations of the partial density of states. We propose that a leading mechanism for local structure inheritance in Ag{sub 50}Sn{sub 50} is due to s-p dehybridization of Sn and to the interplay between Sn-s and Ag-d electrons.

  6. Protein subcellular localization prediction based on compartment-specific features and structure conservation

    PubMed Central

    Su, Emily Chia-Yu; Chiu, Hua-Sheng; Lo, Allan; Hwang, Jenn-Kang; Sung, Ting-Yi; Hsu, Wen-Lian

    2007-01-01

    Background Protein subcellular localization is crucial for genome annotation, protein function prediction, and drug discovery. Determination of subcellular localization using experimental approaches is time-consuming; thus, computational approaches become highly desirable. Extensive studies of localization prediction have led to the development of several methods including composition-based and homology-based methods. However, their performance might be significantly degraded if homologous sequences are not detected. Moreover, methods that integrate various features could suffer from the problem of low coverage in high-throughput proteomic analyses due to the lack of information to characterize unknown proteins. Results We propose a hybrid prediction method for Gram-negative bacteria that combines a one-versus-one support vector machines (SVM) model and a structural homology approach. The SVM model comprises a number of binary classifiers, in which biological features derived from Gram-negative bacteria translocation pathways are incorporated. In the structural homology approach, we employ secondary structure alignment for structural similarity comparison and assign the known localization of the top-ranked protein as the predicted localization of a query protein. The hybrid method achieves overall accuracy of 93.7% and 93.2% using ten-fold cross-validation on the benchmark data sets. In the assessment of the evaluation data sets, our method also attains accurate prediction accuracy of 84.0%, especially when testing on sequences with a low level of homology to the training data. A three-way data split procedure is also incorporated to prevent overestimation of the predictive performance. In addition, we show that the prediction accuracy should be approximately 85% for non-redundant data sets of sequence identity less than 30%. Conclusion Our results demonstrate that biological features derived from Gram-negative bacteria translocation pathways yield a significant

  7. DAFS study of site-specific local structure of Mn in manganese ferrite films.

    SciTech Connect

    Kravtsov, E.; Haskel, D.; Cady, A.; Yang, A.; Vittoria, C.; Zuo, X.; Harris, V. G.; X-Ray Science Division; Inst. of Metal Physics; Northeastern Univ.; Nankai Univ.

    2006-01-01

    Manganese ferrite (MnFe{sub 2}O{sub 4}) is a well-known magnetic material widely used in electronics for many years. It is well established that its magnetic behavior is strongly influenced by local structural properties of Mn ions, which are distributed between crystallographically inequivalent tetrahedral and octahedral sites in the unit cell. In order to understand and be able to tune properties of these structures, it is necessary to have detailed site-specific structural information on the system. Here we report on the application of diffraction-anomalous fine structure (DAFS) spectroscopy to resolve site-specific Mn local structures in manganese ferrite films. The DAFS measurements were done at undulator beamline 4-ID-D of the Advanced Photon Source at Argonne National Laboratory. The DAFS spectra (Fig. 1) were measured at several Bragg reflections in the vicinity of the Mn absorption K-edge, having probed separately contributions from tetrahedrally and octahedrally coordinated Mn sites. The DAFS data analysis done with an iterative Kramers-Kroenig algorithm made it possible to solve separately the local structure around different inequivalent Mn sites in the unit cell. The reliability of the data treatment was checked carefully, and it was showed that the site-specific structural parameters obtained with DAFS allow us to describe fluorescence EXAFS spectrum measured independently. Fig. 2 shows individual site contributions to the imaginary part of the resonant scattering amplitude obtained from the treatment of the data of Fig. 1. The analysis of the refined site-specific absorption spectra was done using EXAFS methods based on theoretical standards. We provided direct evidence for the tetrahedral Mn-O bond distance being increased relative to the corresponding Fe-O distance in bulk manganese ferrites. The first coordination shell number was found to be reduced significantly for Mn atoms at these sites. This finding is consistent with the well-known tendency

  8. Local structure, composition, and crystallization mechanism of a model two-phase "composite nanoglass"

    NASA Astrophysics Data System (ADS)

    Chattopadhyay, Soma; Kelly, S. D.; Shibata, Tomohiro; Balasubramanian, M.; Srinivasan, S. G.; Du, Jincheng; Banerjee, Rajarshi; Ayyub, Pushan

    2016-02-01

    We report a detailed study of the local composition and structure of a model, bi-phasic nanoglass with nominal stoichiometry Cu55Nb45. Three dimensional atom probe data suggest a nanoscale-phase-separated glassy structure having well defined Cu-rich and Nb-rich regions with a characteristic length scale of ≈3 nm. However, extended x-ray absorption fine structure analysis indicates subtle differences in the local environments of Cu and Nb. While the Cu atoms displayed a strong tendency to cluster and negligible structural order beyond the first coordination shell, the Nb atoms had a larger fraction of unlike neighbors (higher chemical order) and a distinctly better-ordered structural environment (higher topological order). This provides the first experimental indication that metallic glass formation may occur due to frustration arising from the competition between chemical ordering and clustering. These observations are complemented by classical as well as ab initio molecular dynamics simulations. Our study indicates that these nanoscale phase-separated glasses are quite distinct from the single phase nanoglasses (studied by Gleiter and others) in the following three respects: (i) they contain at least two structurally and compositionally distinct, nanodispersed, glassy phases, (ii) these phases are separated by comparatively sharp inter-phase boundaries, and (iii) thermally induced crystallization occurs via a complex, multi-step mechanism. Such materials, therefore, appear to constitute a new class of disordered systems that may be called a composite nanoglass.

  9. Local structure, composition, and crystallization mechanism of a model two-phase "composite nanoglass".

    PubMed

    Chattopadhyay, Soma; Kelly, S D; Shibata, Tomohiro; Balasubramanian, M; Srinivasan, S G; Du, Jincheng; Banerjee, Rajarshi; Ayyub, Pushan

    2016-02-14

    We report a detailed study of the local composition and structure of a model, bi-phasic nanoglass with nominal stoichiometry Cu55Nb45. Three dimensional atom probe data suggest a nanoscale-phase-separated glassy structure having well defined Cu-rich and Nb-rich regions with a characteristic length scale of ≈ 3 nm. However, extended x-ray absorption fine structure analysis indicates subtle differences in the local environments of Cu and Nb. While the Cu atoms displayed a strong tendency to cluster and negligible structural order beyond the first coordination shell, the Nb atoms had a larger fraction of unlike neighbors (higher chemical order) and a distinctly better-ordered structural environment (higher topological order). This provides the first experimental indication that metallic glass formation may occur due to frustration arising from the competition between chemical ordering and clustering. These observations are complemented by classical as well as ab initio molecular dynamics simulations. Our study indicates that these nanoscale phase-separated glasses are quite distinct from the single phase nanoglasses (studied by Gleiter and others) in the following three respects: (i) they contain at least two structurally and compositionally distinct, nanodispersed, glassy phases, (ii) these phases are separated by comparatively sharp inter-phase boundaries, and (iii) thermally induced crystallization occurs via a complex, multi-step mechanism. Such materials, therefore, appear to constitute a new class of disordered systems that may be called a composite nanoglass.

  10. Local structure in the disordered solid solution of cis- and trans-perinones.

    PubMed

    Teteruk, Jaroslav L; Glinnemann, Jürgen; Heyse, Winfried; Johansson, Kristoffer E; van de Streek, Jacco; Schmidt, Martin U

    2016-06-01

    The cis- and trans-isomers of the polycyclic aromatic compound perinone, C26H12N4O2, form a solid solution (Vat Red 14). This solid solution is isotypic to the crystal structures of cis-perinone (Pigment Red 194) and trans-perinone (Pigment Orange 34) and exhibits a combined positional and orientational disorder: In the crystal, each molecular position is occupied by either a cis- or trans-perinone molecule, both of which have two possible molecular orientations. The structure of cis-perinone exhibits a twofold orientational disorder, whereas the structure of trans-perinone is ordered. The crystal structure of the solid solution was determined by single-crystal X-ray analysis. Extensive lattice-energy minimizations with force-field and DFT-D methods were carried out on combinatorially complete sets of ordered models. For the disordered systems, local structures were calculated, including preferred local arrangements, ordering lengths, and probabilities for the arrangement of neighbouring molecules. The superposition of the atomic positions of all energetically favourable calculated models corresponds well with the experimentally determined crystal structures, explaining not only the atomic positions, but also the site occupancies and anisotropic displacement parameters. PMID:27240774

  11. SPOT4 Management Centre

    NASA Technical Reports Server (NTRS)

    Labrune, Yves; Labbe, X.; Roussel, A.; Vielcanet, P.

    1994-01-01

    In the context of the CNES SPOT4 program CISI is particularly responsible for the development of the SPOT4 Management Centre, part of the SPOT4 ground control system located at CNES Toulouse (France) designed to provide simultaneous control over two satellites. The main operational activities are timed to synchronize with satellite visibilities (ten usable passes per day). The automatic capability of this system is achieved through agenda services (sequence of operations as defined and planned by operator). Therefore, the SPOT4 Management Centre offers limited, efficient and secure human interventions for supervision and decision making. This paper emphasizes the main system characteristics as degree of automation, level of dependability and system parameterization.

  12. Elderly Care Centre

    NASA Astrophysics Data System (ADS)

    Wagiman, Aliani; Haja Bava Mohidin, Hazrina; Ismail, Alice Sabrina

    2016-02-01

    The demand for elderly centre has increased tremendously abreast with the world demographic change as the number of senior citizens rose in the 21st century. This has become one of the most crucial problems of today's era. As the world progress into modernity, more and more people are occupied with daily work causing the senior citizens to lose the care that they actually need. This paper seeks to elucidate the best possible design of an elderly care centre with new approach in order to provide the best service for them by analysing their needs and suitable activities that could elevate their quality of life. All these findings will then be incorporated into design solutions so as to enhance the living environment for the elderly especially in Malaysian context.

  13. Chromosomal localization and structure of the human type II IMP dehydrogenase gene

    SciTech Connect

    Glesne, D.; Huberman, E. |; Collart, F.; Varkony, T.; Drabkin, H.

    1994-05-01

    We determined the chromosomal localization and structure of the gene encoding human type II inosine 5{prime}-monophosphate dehydrogenase (IMPDH, EC 1.1.1.205), an enzyme associated with cellular proliferation, malignant transformation, and differentiation. Using polymerase chain reaction (PCR) primers specific for type II IMPDH, we screened a panel of human-Chinese hamster cell somatic hybrids and a separate deletion panel of chromosome 3 hybrids and localized the gene to 3p21.1{yields}p24.2. Two overlapping yeast artificial chromosome clones containing the full gene for type II IMPDH were isolated and a physical map of 117 kb of human genomic DNA in this region of chromosome 3 was constructed. The gene for type II IMPDH was localized and oriented on this map and found to span no more than 12.5 kb.

  14. International Seismological Centre

    USGS Publications Warehouse

    Spall, H.; Hughes, A.

    1979-01-01

    The International Seismological Centre had its origins when the British seismologist Professor John Milne returned to England from Japan in 1895 to retire at Shide on the Isle of Eight. In cooperation with the British Association for the Advancement of Science, Milne had set up a number of seismographic stations around the world and, while Tokyo, had published a Catalogue of 8,33 Earthquakes Recorded in Japan, 1885-1892. 

  15. Local mechanical properties of white matter structures in the human brain.

    PubMed

    Johnson, Curtis L; McGarry, Matthew D J; Gharibans, Armen A; Weaver, John B; Paulsen, Keith D; Wang, Huan; Olivero, William C; Sutton, Bradley P; Georgiadis, John G

    2013-10-01

    The noninvasive measurement of the mechanical properties of brain tissue using magnetic resonance elastography (MRE) has emerged as a promising method for investigating neurological disorders. To date, brain MRE investigations have been limited to reporting global mechanical properties, though quantification of the stiffness of specific structures in the white matter architecture may be valuable in assessing the localized effects of disease. This paper reports the mechanical properties of the corpus callosum and corona radiata measured in healthy volunteers using MRE and atlas-based segmentation. Both structures were found to be significantly stiffer than overall white matter, with the corpus callosum exhibiting greater stiffness and less viscous damping than the corona radiata. Reliability of both local and global measures was assessed through repeated experiments, and the coefficient of variation for each measure was less than 10%. Mechanical properties within the corpus callosum and corona radiata demonstrated correlations with measures from diffusion tensor imaging pertaining to axonal microstructure.

  16. Large local temperature gradient induced by surface plasmon heating of periodic metal structure

    NASA Astrophysics Data System (ADS)

    Shimada, Ryoko; Sakai, Hitomi

    Mixtures of several gas or solution having different concentration can be separated by the gradient of temperature. This is the so-called Soret effect. This phenomenon is quite important for chemical reaction and material condensation/separation. For activating large Soret effect, it would be useful to focus on the surface plasmon heating (SPH) of metal nanostructures that interact with light. In this work, a local temperate gradient was created with the aid of SPH achieved for periodic silver structures in a mesoscopic length scale fabricated by a nanosphere lithography method. Excitation of this periodic structure (by blue laser, for example) could create a localized periodic temperature gradient, as large as ~1,000 K/ μm, as suggested from preliminary heat-transfer calculation. Experimental and theoretical results will be presented on site

  17. Local structure in diatom biosilica probed by synchrotron x-ray diffraction

    NASA Astrophysics Data System (ADS)

    Dibiccari, Michael; Kwak, Seo-Young; Hind, Geoffrey; Dimasi, Elaine

    2006-03-01

    Diatoms are single-celled algae that form intricate outer shells, or frustrules, composed of biosilica. They have attracted attention in the context of nanotechnology, since the submicron architectures are genetically determined and thus potentially could be reproduced synthetically, by using organic additives that mimic the proteins responsible for controlling biological silicification. We have compared the local atomic structure of diatom biosilica to that of inorganic silica with synchrotron x-ray diffraction, analyzed as the Pair Distribution Function (PDF). Specimens of Thalassiosira weissflogii (Tw) were cleaned of organic matter using either hydrogen peroxide, commercial bleach, or sodium dodecyl sulfate treatments. Low resolution PDF measurements (qmax 13.6 å-1) were made of wet and dry Tw, pure silica microspheres, and diatomaceous earth containing 15% mineral impurities. All samples have similar PDFs, demonstrating that local structure in diatoms and synthetic silica are equivalent, and that the PDF method is insensitive to biological impurites.

  18. A Numerical Analysis on the Local Deformation of a Spacer Grid Structure for Nuclear Fuel Cells

    NASA Astrophysics Data System (ADS)

    Jang, Myung-Geun; Na, Geum Ju; Shin, Hyunho; Kim, Jong-Bong

    2016-08-01

    The result of a preliminary numerical investigation on local deformation characteristics of a multi-layered spacer-grid structure with five guide tubes is reported based on implicit finite element analysis. For the numerical analysis, displacements of top and bottom cross sections of each guide tube in a single-layer model were constrained while a lateral displacement was imposed on the single layer. Unlike the impact hammer test that is generally employed to characterize the deformation characteristics of the space-grid structure, the buckling phenomenon occurs locally in this study; it takes place at the inner grids around each tube and the degree of bucking is more apparent for tubes near the lateral surface where the lateral displacement was imposed.

  19. Bio-medical imaging: Localization of main structures in retinal fundus images

    NASA Astrophysics Data System (ADS)

    Basit, A.; Egerton, S. J.

    2013-12-01

    Retinal fundus images have three main structures, the optic disk, fovea and blood vessels. By examining fundus images, an ophthalmologist can diagnose various clinical disorders of the eye and the body, typically indicated by changes in the diameter, area, branching angles and tortuosity of the three ma in retinal structures. Knowledge of the optic disk position is an important diagnostic index fo r many diseases related to the retina. In this paper, localization of optic disc is discussed. Optic disk detection is based on morphological operationsand smoothing filters. Blood vessels are extracted using the green component of a colour retinal image with the help of a median filter. Maximum intensity values are validated with blood vessels to localize the optic disk location. The proposed method has shown significant improvements in results.

  20. R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

    PubMed Central

    Rahrig, Ryan R.; Leontis, Neocles B.; Zirbel, Craig L.

    2010-01-01

    Motivation: Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the ‘local alignment’ graph. Results: The algorithm is implemented in a program suite and web server called ‘R3D Align’. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments. Availability: R3D Align is freely available through a web server http://rna.bgsu.edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: r-rahrig@onu.edu PMID:20929913

  1. Scale-adaptive tensor algebra for local many-body methods of electronic structure theory

    SciTech Connect

    Liakh, Dmitry I

    2014-01-01

    While the formalism of multiresolution analysis (MRA), based on wavelets and adaptive integral representations of operators, is actively progressing in electronic structure theory (mostly on the independent-particle level and, recently, second-order perturbation theory), the concepts of multiresolution and adaptivity can also be utilized within the traditional formulation of correlated (many-particle) theory which is based on second quantization and the corresponding (generally nonorthogonal) tensor algebra. In this paper, we present a formalism called scale-adaptive tensor algebra (SATA) which exploits an adaptive representation of tensors of many-body operators via the local adjustment of the basis set quality. Given a series of locally supported fragment bases of a progressively lower quality, we formulate the explicit rules for tensor algebra operations dealing with adaptively resolved tensor operands. The formalism suggested is expected to enhance the applicability and reliability of local correlated many-body methods of electronic structure theory, especially those directly based on atomic orbitals (or any other localized basis functions).

  2. Study of localized structures of kinetic Alfvén wave and generation of turbulence

    SciTech Connect

    Kumari, Anju Sharma, R. P. Yadav, Nitin

    2015-06-15

    Localization of kinetic Alfvén waves (KAW) due to ponderomotive nonlinearity can be regarded as an important mechanism for heating the space plasmas. The present paper investigates the effect of background density fluctuations on the formation of large amplitude localized structures and turbulent spectrum of KAW applicable to magnetopause. The dynamical equations are derived, taking into account the ponderomotive nonlinearity of the KAW as well as the background fluctuations which are in the form of ion acoustic waves. The system is studied numerically as well as semi-analytically. The results reveal that the presence of density fluctuations affects the formation of localized structures. These fluctuations affecting the localization of KAW may also affect heating and acceleration of plasma. Respective turbulent scaling for the different amplitude of background fluctuations has also been studied. The relevance of the numerical results has been discussed with the THEMIS observations near the magnetopause [C. Chaston et al., Geophys. Res. Lett. 35, L17S08 (2008)].

  3. Crustal Structure Beneath Pleasant Valley, Nevada from Local and Regional Earthquake Travel Times

    NASA Astrophysics Data System (ADS)

    Kant, L. B.; Nabelek, J.; Braunmiller, J.

    2011-12-01

    In 1915 the Pleasant Valley fault in the Basin and Range Province of northern Nevada ruptured in a Mw~7 earthquake, one of the largest normal faulting earthquakes in U.S. history. We are currently operating a densely spaced linear array of broadband three-component seismometers across the Pleasant Valley fault to investigate the structure and the geometry of the fault zone. Here, we present a local crustal velocity model derived from P and S wave travel times of local and regional earthquakes recorded by the Pleasant Valley array. Regional events in northern California, eastern Nevada and Utah that occurred in line with the array are well recorded and provide constraints on upper mantle velocities. Many local seismic events were also observed. Only a few of these events were detected by the ANSS network, reflecting the limited detection capability in sparsely instrumented northern Nevada. The local event set includes earthquakes, mining blasts and sonic booms from nearby jet airplane flights. A subset of these events was located using Hypoinverse. Their travel time curves are used to estimate crustal structure and velocity in the Pleasant Valley region. This is an EarthScope FlexArray project.

  4. Nanoelectromechanics of Inorganic and Biological Systems: From Structural Imaging to Local Functionalities

    SciTech Connect

    Rodriguez, Brian; Kalinin, Sergei V; Jesse, Stephen; Thompson, G. L.; Vertegel, Alexey; Hohlbauch, Sophia; Proksch, Roger

    2008-01-01

    Coupling between electrical and mechanical phenomena is extremely common in inorganic materials, and nearly ubiquitous in biological systems, underpinning phenomena and devices ranging from SONAR to cardiac activity and hearing. This paper briefly summarizes the Scanning Probe Microscopy (SPM) approach, referred to as Piezoresponse Force Microscopy (PFM), for probing electromechanical coupling on the nanometer scales, and delineates some existing and emerging applications to probe local structure and functionality in inorganic ferroelectrics, calcified and connective tissues, and complex biosystems based on electromechanical detection.

  5. CONNECTING LOCAL STRUCTURE TO INTERFACE FORMATION: A Molecular Scale van der Waals Theory of Nonuniform Liquids

    NASA Astrophysics Data System (ADS)

    Weeks, John D.

    2002-10-01

    This article reviews a new and general theory of nonuniform fluids that naturally incorporates molecular scale information into the classical van der Waals theory of slowly varying interfaces. The method optimally combines two standard approximations, molecular (mean) field theory to describe interface formation and linear response (or Gaussian fluctuation) theory to describe local structure. Accurate results have been found in many different applications in nonuniform simple fluids and these ideas may have important implications for the theory of hydrophobic interactions in water.

  6. Experimental evidence of resonant tunneling via localized DQW states in an asymmetric triple barrier structure

    NASA Astrophysics Data System (ADS)

    Velásquez, Rober

    2003-04-01

    In this work we report on field-induced features appearing in the tunneling current traces of a biased asymmetric triple barrier resonant tunneling device in the presence of an in-plane magnetic field. A theoretical model that satisfactorily explains the origin of these features is discussed. The reported data evidences the localized nature of the quantum states in thin layer asymmetric double-quantum-well structures.

  7. Local concurrent error detection and correction in data structures using virtual backpointers

    NASA Technical Reports Server (NTRS)

    Li, C. C.; Chen, P. P.; Fuchs, W. K.

    1987-01-01

    A new technique, based on virtual backpointers, for local concurrent error detection and correction in linked data structures is presented. Two new data structures, the Virtual Double Linked List, and the B-tree with Virtual Backpointers, are described. For these structures, double errors can be detected in 0(1) time and errors detected during forward moves can be corrected in 0(1) time. The application of a concurrent auditor process to data structure error detection and correction is analyzed, and an implementation is described, to determine the effect on mean time to failure of a multi-user shared database system. The implementation utilizes a Sequent shared memory multiprocessor system operating on a shared databased of Virtual Double Linked Lists.

  8. Force and temperature characteristics of a fs-laser machined locally micro-structured FBG

    NASA Astrophysics Data System (ADS)

    Dutz, Franz J.; Marchi, Gabriele; Stephan, Valentin; Huber, Heinz P.; Roths, Johannes

    2016-05-01

    A locally micro-structured fiber Bragg grating (LMFBG) was manufactured by forming a circumferential groove in the middle of a type I fiber Bragg grating (FBG). The groove was directly ablated using a fs-laser and had a length of 86μm, a depth of 27μm and steep side walls. Due to the precisely machined geometry of the structure the reflection spectra can be accurately described with a fairly simple theoretical model. At several constant temperatures in the range from 5°C to 45°C this structure was exposed to various compressive loads in the range from 0N to -1.42N. Here the force and temperature sensitivity of the LMFBG are presented. This structure can be used for miniaturized compressive force sensing at variable temperatures, which is of particular interest for many bio-medical applications.

  9. Local structure of ZnO micro flowers and nanoparticles obtained by micro segmented flow synthesis

    SciTech Connect

    Li, Shuning; Roy, Amitava; Lichtenberg, Henning; Merchan, Gregory; Kumar, Challa S.S.R.; Köhler, J. Michael

    2012-03-07

    The micro-segmented flow technique was applied for continuous synthesis of ZnO micro- and nanoparticles with short residence times of 9.4 s and 21.4 s, respectively. The obtained particles were characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Small angle X-ray scattering (SAXS) and photoluminescence spectroscopy were used to determine the size and optical properties of ZnO nanoparticles. In addition, extended X-ray absorption fine structure (EXAFS) spectroscopy was employed to investigate local structural properties. The EXAFS measurements reveal a larger degree of structural disorder in the nanoparticles than the microparticles. These structural changes should be taken into consideration while evaluating the size-dependent visible emission of ZnO nanoparticles.

  10. Local atomic structure in equilibrium and supercooled liquid Zr(75.5)Pd(24.5).

    PubMed

    Mauro, N A; Fu, W; Bendert, J C; Cheng, Y Q; Ma, E; Kelton, K F

    2012-07-28

    Atomic structures were obtained in equilibrium and supercooled eutectic Zr(75.5)Pd(24.5) liquids by in situ high-energy synchrotron diffraction measurements using the beamline electrostatic levitation (BESL) technique, which provides a high-vacuum, containerless, environment. Reverse Monte Carlo fits to the x-ray static structure factors, constrained using partial pair correlation functions obtained from ab initio molecular dynamics simulations, indicate the presence of medium-range order (MRO) in the form of a strong tendency for Pd-Pd (solute-solute) avoidance. This order persists over the entire temperature range studied, from 170 °C above the equilibrium liquidus temperature to 263 °C below it. Further, a quantitative analysis of the atomic structures obtained indicates a modest degree of icosahedral-like local order around Pd atoms, with the clusters showing an increased tendency for face-sharing to form more extended structures with decreasing temperature. PMID:22852625

  11. AFM characterization of the shape of surface structures with localization factor.

    PubMed

    Bonyár, Attila

    2016-08-01

    Although with the use of scanning probe microscopy (SPM) methods the topographical imaging of surfaces is now widely available, the characterization of surface structures, especially their shape, and the processes which change these features is not trivial with the existing surface describing parameters. In this work the application of a parameter called localization factor is demonstrated for the quantitative characterization of surface structures and for processes which alter the shape of these structures. The theory and optimal operation range of this parameter are discussed with three application examples: microstructure characterization of gold thin films, characterization of the changes in the grain structure of these films during thermal annealing, and finally, characterization of the oxidation processes on a polished tin surface. PMID:27174696

  12. Three-dimensional local structure refinement using a full-potential XANES analysis

    SciTech Connect

    Smolentsev, G.; Soldatov, A. V.; Feiters, M. C.

    2007-04-01

    A technique of three-dimensional (3D) local structure refinement is proposed and demonstrated by applying it to the metal complex Ni(acacR){sub 2}. The method is based on the fitting of experimental x-ray absorption near-edge structure (XANES) using a multidimensional interpolation of spectra and full potential calculations of XANES. The low number of calculations required is the main advantage of the method, which allows a computationally time-expensive method using a non-muffin-tin potential to be applied. The possibility to determine bond angles in addition to bond lengths accessible to extended x-ray-absorption fine structure opens new perspectives of XANES as a 3D structure probe.

  13. Examination of the local structure in composite and lowdimensional semiconductor by X-ray Absorption Spectroscopy

    SciTech Connect

    Lawniczak-Jablonska, K.; Demchenko, I.N.; Piskorska, E.; Wolska,A.; Talik, E.; Zakharov, D.N.; Liliental-Weber, Z.

    2006-09-25

    X-ray absorption methods have been successfully used to obtain quantitative information about local atomic composition of two different materials. X-ray Absorption Near Edge Structure analysis and X-Ray Photoelectron Spectroscopy allowed us to determine seven chemical compounds and their concentrations in c-BN composite. Use of Extended X-ray Absorption Fine Structure in combination with Transmission Electron Microscopy enabled us to determine the composition and size of buried Ge quantum dots. It was found that the quantum dots consisted out of pure Ge core covered by 1-2 monolayers of a layer rich in Si.

  14. Local precision nets for monitoring movements of faults and large engineering structures

    NASA Technical Reports Server (NTRS)

    Henneberg, H. G.

    1978-01-01

    Along Bocono Fault were installed local high precision geodetic nets to observe the possible horizontal crustal deformations and movements. In the fault area there are few big structures which are also included in the mentioned investigation. In the near future, measurements shall be extended to other sites of Bocono Fault and also to the El Pilar Fault. In the same way and by similar methods high precision geodetic nets are applied in Venezuela to observe the behavior of big structures, as bridges and large dams and of earth surface deformations due to industrial activities.

  15. Local-global alignment for finding 3D similarities in protein structures

    DOEpatents

    Zemla, Adam T.

    2011-09-20

    A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

  16. A global/local analysis method for treating details in structural design

    NASA Technical Reports Server (NTRS)

    Aminpour, Mohammad A.; Mccleary, Susan L.; Ransom, Jonathan B.

    1993-01-01

    A method for analyzing global/local behavior of plate and shell structures is described. In this approach, a detailed finite element model of the local region is incorporated within a coarser global finite element model. The local model need not be nodally compatible (i.e., need not have a one-to-one nodal correspondence) with the global model at their common boundary; therefore, the two models may be constructed independently. The nodal incompatibility of the models is accounted for by introducing appropriate constraint conditions into the potential energy in a hybrid variational formulation. The primary advantage of this method is that the need for transition modeling between global and local models is eliminated. Eliminating transition modeling has two benefits. First, modeling efforts are reduced since tedious and complex transitioning need not be performed. Second, errors due to the mesh distortion, often unavoidable in mesh transitioning, are minimized by avoiding distorted elements beyond what is needed to represent the geometry of the component. The method is applied reduced to a plate loaded in tension and transverse bending. The plate has a central hole, and various hole sixes and shapes are studied. The method is also applied to a composite laminated fuselage panel with a crack emanating from a window in the panel. While this method is applied herein to global/local problems, it is also applicable to the coupled analysis of independently modeled components as well as adaptive refinement.

  17. The use of modal curvatures for damage localization in beam-type structures

    NASA Astrophysics Data System (ADS)

    Ciambella, J.; Vestroni, F.

    2015-03-01

    The localization of stiffness variation in damaged beams through modal curvatures, i.e., second derivative of mode shapes, is studied by exploiting a perturbative solution of the Euler-Bernoulli equation. It is shown that for low order modes the difference between undamaged and damaged modal curvatures has only one distinct peak if the damage is localized in a narrow region. This phenomenon is independent of the presence of experimental noise and of the technique used to reconstruct the curvature mode shapes from the displacement mode shapes. Broader damages cause the modal curvature difference to have several peaks outside the damage region that could result in a false damage localization. The same effect is present at higher modes for both narrow and broad damages. As a result, modal curvatures can be effectively used to localize structural damages only once they have been properly filtered. Here the perturbative solution is used to introduce an effective damage measure able to localize correctly narrow and broad damages and also single and multiple damages cases.

  18. Polychromatic X-ray Microdiffraction Characterization of Local Crystallographic Structure and Defect Distributions

    SciTech Connect

    Ice, G.E.; Barabash, R.I.; Pang, J.W. L.

    2007-12-19

    Three-dimensional (3D), nondestructive, spatially resolved characterization of local crystal structure is conveniently made with polychromatic x-ray microdiffraction. In general, polychromatic microdiffraction provides information about the local (subgrain) orientation, unpaired-dislocation density, and elastic strain. This information can be used for direct comparison to theoretical models. Practical microbeams use intense synchrotron x-ray sources and advanced x-ray focusing optics. By employing polychromatic x-ray beams and a virtual pinhole camera method, called differential aperture microscopy, 3D distributions of the local crystalline phase, orientation (texture), and elastic and plastic strain tensors can be measured with submicron 3D resolution. The local elastic strain tensor elements can typically be determined with uncertainties less than 100 ppm. Orientations can be quantified to {approx} 0.01{sup o} and the local unpaired dislocation-density tensor can be simultaneously characterized. The spatial resolution limit for hard x-ray polychromatic microdiffraction is < 40nm and existing instruments operate with {approx} 500 to 1000nm resolution. Because the 3D x-ray crystal microscope is a penetrating nondestructive tool, it is ideal for studies of mesoscale evolution in materials.

  19. Heterosynaptic structural plasticity on local dendritic segments of hippocampal CA1 neurons

    PubMed Central

    Oh, Won Chan; Parajuli, Laxmi Kumar; Zito, Karen

    2014-01-01

    SUMMARY Competition between synapses contributes to activity-dependent refinement of the nervous system during development. Does local competition between neighboring synapses drive circuit remodeling during experience-dependent plasticity in the cerebral cortex? Here, we examined the role of activity-mediated competitive interactions in regulating dendritic spine structure and function on hippocampal CA1 neurons. We found that high-frequency glutamatergic stimulation at individual spines, which leads to input-specific synaptic potentiation, induces shrinkage and weakening of nearby unstimulated synapses. This heterosynaptic plasticity requires potentiation of multiple neighboring spines, suggesting that a local threshold of neural activity exists beyond which inactive synapses are punished. Notably, inhibition of calcineurin, IP3Rs, or group I mGluRs blocked heterosynaptic shrinkage without blocking structural potentiation, and inhibition of CaMKII blocked structural potentiation without blocking heterosynaptic shrinkage. Our results support a model in which activity-induced shrinkage signal, and not competition for limited structural resources, drives heterosynaptic structural and functional depression during neural circuit refinement. PMID:25558061

  20. Environmental diel variation, parasite loads, and local population structuring of a mixed-mating mangrove fish.

    PubMed

    Ellison, Amy; Wright, Patricia; Taylor, D Scott; Cooper, Chris; Regan, Kelly; Currie, Suzie; Consuegra, Sofia

    2012-07-01

    Genetic variation within populations depends on population size, spatial structuring, and environmental variation, but is also influenced by mating system. Mangroves are some of the most productive and threatened ecosystems on earth and harbor a large proportion of species with mixed-mating (self-fertilization and outcrossing). Understanding population structuring in mixed-mating species is critical for conserving and managing these complex ecosystems. Kryptolebias marmoratus is a unique mixed-mating vertebrate inhabiting mangrove swamps under highly variable tidal regimes and environmental conditions. We hypothesized that geographical isolation and ecological pressures influence outcrossing rates and genetic diversity, and ultimately determine the local population structuring of K. marmoratus. By comparing genetic variation at 32 microsatellites, diel fluctuations of environmental parameters, and parasite loads among four locations with different degrees of isolation, we found significant differences in genetic diversity and genotypic composition but little evidence of isolation by distance. Locations also differed in environmental diel fluctuation and parasite composition. Our results suggest that mating system, influenced by environmental instability and parasites, underpins local population structuring of K. marmoratus. More generally, we discuss how the conservation of selfing species inhabiting mangroves and other biodiversity hotspots may benefit from knowledge of mating strategies and population structuring at small spatial scales. PMID:22957172

  1. STRUCTURE IN THE 3D GALAXY DISTRIBUTION. II. VOIDS AND WATERSHEDS OF LOCAL MAXIMA AND MINIMA

    SciTech Connect

    Way, M. J.; Gazis, P. R.; Scargle, Jeffrey D. E-mail: PGazis@sbcglobal.net

    2015-01-20

    The major uncertainties in studies of the multi-scale structure of the universe arise not from observational errors but from the variety of legitimate definitions and detection methods for individual structures. To facilitate the study of these methodological dependencies, we have carried out 12 different analyses defining structures in various ways. This has been done in a purely geometrical way by utilizing the HOP algorithm as a unique parameter-free method of assigning groups of galaxies to local density maxima or minima. From three density estimation techniques (smoothing kernels, Bayesian blocks, and self-organizing maps) applied to three data sets (the Sloan Digital Sky Survey Data Release 7, the Millennium simulation, and randomly distributed points) we tabulate information that can be used to construct catalogs of structures connected to local density maxima and minima. We also introduce a void finder that utilizes a method to assemble Delaunay tetrahedra into connected structures and characterizes regions empty of galaxies in the source catalog.

  2. Structure in the 3D Galaxy Distribution. II. Voids and Watersheds of Local Maxima and Minima

    NASA Astrophysics Data System (ADS)

    Way, M. J.; Gazis, P. R.; Scargle, Jeffrey D.

    2015-01-01

    The major uncertainties in studies of the multi-scale structure of the universe arise not from observational errors but from the variety of legitimate definitions and detection methods for individual structures. To facilitate the study of these methodological dependencies, we have carried out 12 different analyses defining structures in various ways. This has been done in a purely geometrical way by utilizing the HOP algorithm as a unique parameter-free method of assigning groups of galaxies to local density maxima or minima. From three density estimation techniques (smoothing kernels, Bayesian blocks, and self-organizing maps) applied to three data sets (the Sloan Digital Sky Survey Data Release 7, the Millennium simulation, and randomly distributed points) we tabulate information that can be used to construct catalogs of structures connected to local density maxima and minima. We also introduce a void finder that utilizes a method to assemble Delaunay tetrahedra into connected structures and characterizes regions empty of galaxies in the source catalog.

  3. Characterization of the Local Structure in Liquid Water by Various Order Parameters

    PubMed Central

    2015-01-01

    A wide range of geometric order parameters have been suggested to characterize the local structure of liquid water and its tetrahedral arrangement, but their respective merits have remained elusive. Here, we consider a series of popular order parameters and analyze molecular dynamics simulations of water, in the bulk and in the hydration shell of a hydrophobic solute, at 298 and 260 K. We show that these parameters are weakly correlated and probe different distortions, for example the angular versus radial disorders. We first combine these complementary descriptions to analyze the structural rearrangements leading to the density maximum in liquid water. Our results reveal no sign of a heterogeneous mixture and show that the density maximum arises from the depletion in interstitial water molecules upon cooling. In the hydration shell of the hydrophobic moiety of propanol, the order parameters suggest that the water local structure is similar to that in the bulk, with only a very weak depletion in ordered configurations, thus confirming the absence of any iceberg-type structure. Finally, we show that the main structural fluctuations that affect water reorientation dynamics in the bulk are angular distortions, which we explain by the jump hydrogen-bond exchange mechanism. PMID:26054933

  4. Near-Field Sound Localization Based on the Small Profile Monaural Structure

    PubMed Central

    Kim, Youngwoong; Kim, Keonwook

    2015-01-01

    The acoustic wave around a sound source in the near-field area presents unconventional properties in the temporal, spectral, and spatial domains due to the propagation mechanism. This paper investigates a near-field sound localizer in a small profile structure with a single microphone. The asymmetric structure around the microphone provides a distinctive spectral variation that can be recognized by the dedicated algorithm for directional localization. The physical structure consists of ten pipes of different lengths in a vertical fashion and rectangular wings positioned between the pipes in radial directions. The sound from an individual direction travels through the nearest open pipe, which generates the particular fundamental frequency according to the acoustic resonance. The Cepstral parameter is modified to evaluate the fundamental frequency. Once the system estimates the fundamental frequency of the received signal, the length of arrival and angle of arrival (AoA) are derived by the designed model. From an azimuthal distance of 3–15 cm from the outer body of the pipes, the extensive acoustic experiments with a 3D-printed structure show that the direct and side directions deliver average hit rates of 89% and 73%, respectively. The closer positions to the system demonstrate higher accuracy, and the overall hit rate performance is 78% up to 15 cm away from the structure body. PMID:26580618

  5. Environmental diel variation, parasite loads, and local population structuring of a mixed-mating mangrove fish

    PubMed Central

    Ellison, Amy; Wright, Patricia; Taylor, D Scott; Cooper, Chris; Regan, Kelly; Currie, Suzie; Consuegra, Sofia

    2012-01-01

    Genetic variation within populations depends on population size, spatial structuring, and environmental variation, but is also influenced by mating system. Mangroves are some of the most productive and threatened ecosystems on earth and harbor a large proportion of species with mixed-mating (self-fertilization and outcrossing). Understanding population structuring in mixed-mating species is critical for conserving and managing these complex ecosystems. Kryptolebias marmoratus is a unique mixed-mating vertebrate inhabiting mangrove swamps under highly variable tidal regimes and environmental conditions. We hypothesized that geographical isolation and ecological pressures influence outcrossing rates and genetic diversity, and ultimately determine the local population structuring of K. marmoratus. By comparing genetic variation at 32 microsatellites, diel fluctuations of environmental parameters, and parasite loads among four locations with different degrees of isolation, we found significant differences in genetic diversity and genotypic composition but little evidence of isolation by distance. Locations also differed in environmental diel fluctuation and parasite composition. Our results suggest that mating system, influenced by environmental instability and parasites, underpins local population structuring of K. marmoratus. More generally, we discuss how the conservation of selfing species inhabiting mangroves and other biodiversity hotspots may benefit from knowledge of mating strategies and population structuring at small spatial scales. PMID:22957172

  6. Near-Field Sound Localization Based on the Small Profile Monaural Structure.

    PubMed

    Kim, Youngwoong; Kim, Keonwook

    2015-01-01

    The acoustic wave around a sound source in the near-field area presents unconventional properties in the temporal, spectral, and spatial domains due to the propagation mechanism. This paper investigates a near-field sound localizer in a small profile structure with a single microphone. The asymmetric structure around the microphone provides a distinctive spectral variation that can be recognized by the dedicated algorithm for directional localization. The physical structure consists of ten pipes of different lengths in a vertical fashion and rectangular wings positioned between the pipes in radial directions. The sound from an individual direction travels through the nearest open pipe, which generates the particular fundamental frequency according to the acoustic resonance. The Cepstral parameter is modified to evaluate the fundamental frequency. Once the system estimates the fundamental frequency of the received signal, the length of arrival and angle of arrival (AoA) are derived by the designed model. From an azimuthal distance of 3-15 cm from the outer body of the pipes, the extensive acoustic experiments with a 3D-printed structure show that the direct and side directions deliver average hit rates of 89% and 73%, respectively. The closer positions to the system demonstrate higher accuracy, and the overall hit rate performance is 78% up to 15 cm away from the structure body. PMID:26580618

  7. Local chromatin structure of heterochromatin regulates repeated DNA stability, nucleolus structure, and genome integrity

    SciTech Connect

    Peng, Jamy C.

    2007-01-01

    Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in

  8. Local structure study of disordered crystalline materials with the atomic pair distribution function method

    NASA Astrophysics Data System (ADS)

    Qiu, Xiangyun

    The employed experimental method in this Ph.D. dissertation research is the atomic pair distribution function (PDF) technique specializing in high real space resolution local structure determination. The PDF is obtained via Fourier transform from powder total scattering data including the important local structural information in the diffuse scattering intensities underneath, and in-between, the Bragg peaks. Having long been used to study liquids and amorphous materials, the PDF technique has been recently successfully applied to highly crystalline materials owing to the advances in modern X-ray and neutron sources and computing power. An integral part of this thesis work has been to make the PDF technique accessible to a wider scientific community. We have recently developed the rapid acquisition PDF (RA-PDF) method featuring high energy X-rays coupled with an image plate area detector, allowing three to four orders of magnitude decrease of data collection time. Correspondingly in software development, I have written a complete X-ray data correction program PDFgetX2 (user friendly with GUI, 32,000+ lines). Those developments sweep away many barriers to the wide-spread application of the PDF technique in complex materials. The RA-PDF development also opens up new fields of research such as time-resolved studies, pump-probe measurements and so on, where the PDF analysis can provide unique insights. Two examples of the RA-PDF applications are described: the distorted T12 square nets in the new binary antimonide Ti2Sb and in-situ chemical reduction of CuO to Cu. The most intellectually enriching has been the local structure studies of the colossal magneto-resistive (CMR) manganites with intrinsic inhomogeneities. The strong coupling between electron, spin, orbital, and lattice degrees of freedom result in extremely rich and interesting phase diagrams. We have carried out careful PDF analysis of neutron powder diffraction data to study the local MnO6 octahedral

  9. Formation of localized structures in bistable systems through nonlocal spatial coupling. I. General framework.

    PubMed

    Colet, Pere; Matías, Manuel A; Gelens, Lendert; Gomila, Damià

    2014-01-01

    The present work studies the influence of nonlocal spatial coupling on the existence of localized structures in one-dimensional extended systems. We consider systems described by a real field with a nonlocal coupling that has a linear dependence on the field. Leveraging spatial dynamics we provide a general framework to understand the effect of the nonlocality on the shape of the fronts connecting two stable states. In particular we show that nonlocal terms can induce spatial oscillations in the front tails, allowing for the creation of localized structures, that emerge from pinning between two fronts. In parameter space the region where fronts are oscillatory is limited by three transitions: the modulational instability of the homogeneous state, the Belyakov-Devaney transition in which monotonic fronts acquire spatial oscillations with infinite wavelength, and a crossover in which monotonically decaying fronts develop spatial oscillations with a finite wavelength. We show how these transitions are organized by codimension 2 and 3 points and illustrate how by changing the parameters of the nonlocal coupling it is possible to bring the system into the region where localized structures can be formed.

  10. Exciton Localization in Extended π-Electron Systems: Comparison of Linear and Cyclic Structures.

    PubMed

    Thiessen, Alexander; Würsch, Dominik; Jester, Stefan-S; Aggarwal, A Vikas; Idelson, Alissa; Bange, Sebastian; Vogelsang, Jan; Höger, Sigurd; Lupton, John M

    2015-07-30

    We employ five π-conjugated model materials of different molecular shape-oligomers and cyclic structures-to investigate the extent of exciton self-trapping and torsional motion of the molecular framework following optical excitation. Our studies combine steady state and transient fluorescence spectroscopy in the ensemble with measurements of polarization anisotropy on single molecules, supported by Monte Carlo simulations. The dimer exhibits a significant spectral red shift within ∼100 ps after photoexcitation which is attributed to torsional relaxation. This relaxation mechanism is inhibited in the structurally rigid macrocyclic analogue. However, both systems show a high degree of exciton localization but with very different consequences: while, in the macrocycle, the exciton localizes randomly on different parts of the ring, scrambling polarization memory, in the dimer, localization leads to a deterministic exciton position with luminescence characteristics of a dipole. Monte Carlo simulations allow us to quantify the structural difference between the emitting and absorbing units of the π-conjugated system in terms of disorder parameters.

  11. Efficient determination of soft spots in amorphous solids using local structural information

    NASA Astrophysics Data System (ADS)

    Cubuk, Ekin; Schoenholz, Samuel; Malone, Brad; Liu, Andrea; Kaxiras, Efthimios

    2014-03-01

    Structural defects such as dislocations are also flow defects that control plastic flow in crystalline solids. In disordered solids, it is more challenging to identify such local regions that are susceptible to rearrangement. We propose an extremely fast method for identifying soft spots with high accuracy, which scales linearly with number of particles. We achieve this by training a supervised learning model with instances of local neighborhoods and their subsequent plastic flow behavior. By characterizing local neighborhoods with not just one structural quantity, such as bond orientational order, but a combination of multiple structural quantities, we are able to identify a population of regions that correlates just as strongly with rearrangements as do soft spots calculated from vibrational modes. This method does not require knowledge of the interparticle interactions and can readily be applied to experiments that measure the positions of constituent particles in a disordered packing. Furthermore, this also allows for the prediction of plastic behavior in systems like lithiated amorphous silicon, which is important for addressing the durability issues encountered in recent work on improving lithium-ion batteries.

  12. Disruption of Thermally-Stable Nanoscale Grain Structures by Strain Localization

    PubMed Central

    Khalajhedayati, Amirhossein; Rupert, Timothy J.

    2015-01-01

    Nanocrystalline metals with average grain sizes of only a few nanometers have recently been observed to fail through the formation of shear bands. Here, we investigate this phenomenon in nanocrystalline Ni which has had its grain structure stabilized by doping with W, with a specific focus on understanding how strain localization drives evolution of the nanoscale grain structure. Shear banding was initiated with both microcompression and nanoindentation experiments, followed by site-specific transmission electron microscopy to characterize the microstructure. Grain growth and texture formation were observed inside the shear bands, which had a wide variety of thicknesses. These evolved regions have well-defined edges, which rules out local temperature rise as a possible formation mechanism. No structural evolution was found in areas away from the shear bands, even in locations where significant plastic deformation had occurred, showing that plastic strain alone is not enough to cause evolution. Rather, intense strain localization is needed to induce mechanically-driven grain growth in a thermally-stable nanocrystalline alloy. PMID:26030826

  13. Rethinking the Changing Structures of Rural Local Government--State Power, Rural Politics and Local Political Strategies?

    ERIC Educational Resources Information Center

    Pemberton, Simon; Goodwin, Mark

    2010-01-01

    There is a notable absence in contemporary rural studies--of both a theoretical and empirical nature--concerning the changing nature of rural local government. Despite the scale and significance of successive rounds of local government reorganisation in the UK, very little has been written on this topic from a rural perspective. Instead research…

  14. Network community structure alterations in adult schizophrenia: identification and localization of alterations.

    PubMed

    Lerman-Sinkoff, Dov B; Barch, Deanna M

    2016-01-01

    A growing body of literature suggests functional connectivity alterations in schizophrenia. While findings have been mixed, evidence points towards a complex pattern of hyper-connectivity and hypo-connectivity. This altered connectivity can be represented and analyzed using the mathematical frameworks provided by graph and information theory to represent functional connectivity data as graphs comprised of nodes and edges linking the nodes. One analytic technique in this framework is the determination and analysis of network community structure, which is the grouping of nodes into linked communities or modules. This data-driven technique finds a best-fit structure such that nodes in a given community have greater connectivity with nodes in their community than with nodes in other communities. These community structure representations have been found to recapitulate known neural-systems in healthy individuals, have been used to identify novel functional systems, and have identified and localized community structure alterations in a childhood onset schizophrenia cohort. In the present study, we sought to determine whether community structure alterations were present in an adult onset schizophrenia cohort while stringently controlling for sources of imaging artifacts. Group level average graphs in healthy controls and individuals with schizophrenia exhibited visually similar network community structures and high amounts of normalized mutual information (NMI). However, testing of individual subject community structures identified small but significant alterations in community structure with alterations being driven by changes in node community membership in the somatosensory, auditory, default mode, salience, and subcortical networks. PMID:26793435

  15. Network community structure alterations in adult schizophrenia: identification and localization of alterations

    PubMed Central

    Lerman-Sinkoff, Dov B.; Barch, Deanna M.

    2015-01-01

    A growing body of literature suggests functional connectivity alterations in schizophrenia. While findings have been mixed, evidence points towards a complex pattern of hyper-connectivity and hypo-connectivity. This altered connectivity can be represented and analyzed using the mathematical frameworks provided by graph and information theory to represent functional connectivity data as graphs comprised of nodes and edges linking the nodes. One analytic technique in this framework is the determination and analysis of network community structure, which is the grouping of nodes into linked communities or modules. This data-driven technique finds a best-fit structure such that nodes in a given community have greater connectivity with nodes in their community than with nodes in other communities. These community structure representations have been found to recapitulate known neural-systems in healthy individuals, have been used to identify novel functional systems, and have identified and localized community structure alterations in a childhood onset schizophrenia cohort. In the present study, we sought to determine whether community structure alterations were present in an adult onset schizophrenia cohort while stringently controlling for sources of imaging artifacts. Group level average graphs in healthy controls and individuals with schizophrenia exhibited visually similar network community structures and high amounts of normalized mutual information (NMI). However, testing of individual subject community structures identified small but significant alterations in community structure with alterations being driven by changes in node community membership in the somatosensory, auditory, default mode, salience, and subcortical networks. PMID:26793435

  16. Network community structure alterations in adult schizophrenia: identification and localization of alterations.

    PubMed

    Lerman-Sinkoff, Dov B; Barch, Deanna M

    2016-01-01

    A growing body of literature suggests functional connectivity alterations in schizophrenia. While findings have been mixed, evidence points towards a complex pattern of hyper-connectivity and hypo-connectivity. This altered connectivity can be represented and analyzed using the mathematical frameworks provided by graph and information theory to represent functional connectivity data as graphs comprised of nodes and edges linking the nodes. One analytic technique in this framework is the determination and analysis of network community structure, which is the grouping of nodes into linked communities or modules. This data-driven technique finds a best-fit structure such that nodes in a given community have greater connectivity with nodes in their community than with nodes in other communities. These community structure representations have been found to recapitulate known neural-systems in healthy individuals, have been used to identify novel functional systems, and have identified and localized community structure alterations in a childhood onset schizophrenia cohort. In the present study, we sought to determine whether community structure alterations were present in an adult onset schizophrenia cohort while stringently controlling for sources of imaging artifacts. Group level average graphs in healthy controls and individuals with schizophrenia exhibited visually similar network community structures and high amounts of normalized mutual information (NMI). However, testing of individual subject community structures identified small but significant alterations in community structure with alterations being driven by changes in node community membership in the somatosensory, auditory, default mode, salience, and subcortical networks.

  17. Study of floristic diversity and the structural dynamics of some species providers of non woody forest products in the vegetable formations of the Centre East of Burkina Faso.

    PubMed

    Ky, J M K; Gnoula, C; Zerbo, P; Simpore, J; Nikiema, J B; Canini, A; Millogo-Rasolodimby, J

    2009-07-15

    The goal of this study is to contribute to a better knowledge of certain species providing Non Woody Forest Products (NWFP) in the Centre East of Burkina Faso. This study aims to determine the state of the resources in Vitellaria paradoxa, Balanites aegyptiaca, Tamarindus indica and Lannea microcarpa. For this purpose, an inventory of the vegetation was carried out in circular pieces of land of 1250 m2, as a sample of the zone of work, based on the chart of occupation of the grounds. We are identified 158 species comprising 90 genera and 47 families. Those species represent more than 90% of the trees from which various parts are used in food, traditional pharmacopeia and the craft industry. We also showed that because of the strong anthropisation of the zone, the bad pedoclimatic conditions and the permanent bush fires, the regeneration and growth of Vitellaria paradoxa, Balanites aegyptiaca, Tamarindus indica and Lannea microcarpa are disturbed.

  18. Photo-CIDNP 13C magic angle spinning NMR on bacterial reaction centres: exploring the electronic structure of the special pair and its surroundings.

    PubMed

    Matysik, J; Schulten, E; Alia; Gast, P; Raap, J; Lugtenburg, J; Hoff, A J; de Groot, H J

    2001-08-01

    Photochemically induced dynamic nuclear polarisation (photo-CIDNP) in intact bacterial reaction centres has been observed by 13C-solid state NMR under continuous illumination with white light. Strong intensity enhancement of 13C NMR signals of the aromatic rings allows probing the electronic ground state of the two BChl cofactors of the special pair at the molecular scale with atomic selectivity. Differences between the two BChl cofactors are discussed. Several aliphatic 13C atoms of cofactors, as well as 13C atoms of the imidazole ring of histidine residue(s), show nuclear-spin polarisation to the same extent as the aromatic nuclei of the cofactors. Mechanisms and applications of polarisation transfer are discussed. PMID:11592409

  19. Expression, purification, crystallization and preliminary X-ray structure analysis of wild-type and L(M196)H-mutant Rhodobacter sphaeroides reaction centres

    PubMed Central

    Gabdulkhakov, A. G.; Fufina, T. Y.; Vasilieva, L. G.; Mueller, U.; Shuvalov, V. A.

    2013-01-01

    The electron and proton transport mediated by protein-bound cofactors in photosynthesis have been investigated by various methods in order to determine the energetics, the dynamics and the pathway of this process. In purple bacteria, primary photosynthetic charge separation and the build-up of a proton gradient across the periplasmic membrane are catalyzed by the photosynthetic reaction centre (RC). Here, the purification, crystallization and preliminary X-ray analysis of wild-type and L(M196)H-mutant RCs of Rhodobacter sphaeroides are presented, enabling study of the influence of the protein environment of the primary electron donor on the spectral properties and photochemical activity of the RC. PMID:23695564

  20. Local Structure, Electronic Behavior, and Electrocatalytic Reactivity of CO-Reduced Platinum-Iron Oxide Nanoparticles

    SciTech Connect

    Duchesne, Paul N.; Chen, Guangxu; Zheng, Nanfeng; Zhang, Peng

    2014-02-18

    A series of platinum–iron oxide nanoparticles was synthesized using a “clean” CO-reduction method that employed different ratios of Pt-Fe precursor salts in oleylamine at elevated temperatures. High-resolution transmission electron microscopy (HRTEM) and energy-dispersive X-ray spectroscopy (EDS) studies revealed that nearly monodisperse (i.e., with relative standard deviations of less than 15%) nanoparticles with mean diameters of 3.5–4.4 nm and varied elemental compositions (Pt54Fe46 Pt70Fe30, and Pt87Fe13) were obtained. X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) measurements at the Pt L3- and Fe K-edges revealed that these nanoparticles all consisted of a Pt core with amorphous iron oxide on the surface. Furthermore, it was observed that the local structure (e.g., Pt–Pt bond distance and coordination number) and electronic behavior of the Pt–FeO nanoparticles (e.g., Pt d electron density and Fe valence state) are dependent on the Pt-Fe precursor ratios used in their synthesis. Quantum mechanical ab initio calculations were employed to interpret the results from X-ray spectroscopy and help elucidate the relationships between local structure and electronic properties in the nanoparticle samples. Finally, the surface reactivity of these nanoparticles in the oxygen reduction reaction (ORR) was explored, demonstrating higher electrocatalytic activity for all three platinum–iron oxide samples in comparison with a commercial Pt catalyst. The surface reactivity was also found to be sensitive to the Pt-Fe ratios of the nanoparticles and could be correlated with their local structure and electronic behavior.

  1. Global localization of 3D anatomical structures by pre-filtered Hough forests and discrete optimization.

    PubMed

    Donner, René; Menze, Bjoern H; Bischof, Horst; Langs, Georg

    2013-12-01

    The accurate localization of anatomical landmarks is a challenging task, often solved by domain specific approaches. We propose a method for the automatic localization of landmarks in complex, repetitive anatomical structures. The key idea is to combine three steps: (1) a classifier for pre-filtering anatomical landmark positions that (2) are refined through a Hough regression model, together with (3) a parts-based model of the global landmark topology to select the final landmark positions. During training landmarks are annotated in a set of example volumes. A classifier learns local landmark appearance, and Hough regressors are trained to aggregate neighborhood information to a precise landmark coordinate position. A non-parametric geometric model encodes the spatial relationships between the landmarks and derives a topology which connects mutually predictive landmarks. During the global search we classify all voxels in the query volume, and perform regression-based agglomeration of landmark probabilities to highly accurate and specific candidate points at potential landmark locations. We encode the candidates' weights together with the conformity of the connecting edges to the learnt geometric model in a Markov Random Field (MRF). By solving the corresponding discrete optimization problem, the most probable location for each model landmark is found in the query volume. We show that this approach is able to consistently localize the model landmarks despite the complex and repetitive character of the anatomical structures on three challenging data sets (hand radiographs, hand CTs, and whole body CTs), with a median localization error of 0.80 mm, 1.19 mm and 2.71 mm, respectively. PMID:23664450

  2. Global localization of 3D anatomical structures by pre-filtered Hough Forests and discrete optimization

    PubMed Central

    Donner, René; Menze, Bjoern H.; Bischof, Horst; Langs, Georg

    2013-01-01

    The accurate localization of anatomical landmarks is a challenging task, often solved by domain specific approaches. We propose a method for the automatic localization of landmarks in complex, repetitive anatomical structures. The key idea is to combine three steps: (1) a classifier for pre-filtering anatomical landmark positions that (2) are refined through a Hough regression model, together with (3) a parts-based model of the global landmark topology to select the final landmark positions. During training landmarks are annotated in a set of example volumes. A classifier learns local landmark appearance, and Hough regressors are trained to aggregate neighborhood information to a precise landmark coordinate position. A non-parametric geometric model encodes the spatial relationships between the landmarks and derives a topology which connects mutually predictive landmarks. During the global search we classify all voxels in the query volume, and perform regression-based agglomeration of landmark probabilities to highly accurate and specific candidate points at potential landmark locations. We encode the candidates’ weights together with the conformity of the connecting edges to the learnt geometric model in a Markov Random Field (MRF). By solving the corresponding discrete optimization problem, the most probable location for each model landmark is found in the query volume. We show that this approach is able to consistently localize the model landmarks despite the complex and repetitive character of the anatomical structures on three challenging data sets (hand radiographs, hand CTs, and whole body CTs), with a median localization error of 0.80 mm, 1.19 mm and 2.71 mm, respectively. PMID:23664450

  3. Modeling Structural and Mechanical Responses to Localized Erosional Processes on a Bivergent Orogenic Wedge

    NASA Astrophysics Data System (ADS)

    Marzen, R.; Morgan, J. K.

    2014-12-01

    Critical Coulomb wedge theory established that orogenic and accretionary wedges should develop self-similarly and maintain a critical taper that reflects the balance of strength of the wedge material and a basal décollement. However, a variety of geological processes can perturb that balance, forcing readjustment of the wedge. For example, glacial erosion and landsliding can concentrate erosion on a localized portion of the wedge slope, leaving that portion of the wedge with an out-of-equilibrium slope that would need to re-develop for the wedge to resume self-similar growth. We use the discrete element method to analyze how growing bivergent wedges with different cohesive strengths respond structurally and mechanically to erosional events localized along upper, middle, and lower segments of the pro-wedge. Mechanically, pro-wedge erosion results in a sudden decrease followed by a quick recovery of the mean stress and maximum shear stress throughout the pro-wedge. However, when erosion is localized in the mid- to lower portions of the pro-wedge, a zone of increased mean stress develops where the wedge is concentrating deformation to recover its taper. In contrast, when erosion is localized in the upper axial zone, there is almost no recovery of the wedge taper, reflecting the fact that the material at the top of the wedge is being carried passively in a transition zone between the pro-wedge and retro-wedge. Structurally, wedges composed of lower cohesion material recover their critical taper almost immediately through distributed deformation, while wedges of higher-cohesion material recover more slowly, and incompletely, by concentrating deformation along existing fault surfaces. As a result, localized erosional episodes can have a lasting effect on the wedge morphology when the wedge is composed of higher cohesion material.

  4. The effect of static and dynamic spatially structured disturbances on a locally dispersing population.

    PubMed

    Hiebeler, David E; Morin, Benjamin R

    2007-05-01

    Previous models of locally dispersing populations have shown that in the presence of spatially structured fixed habitat heterogeneity, increasing local spatial autocorrelation in habitat generally has a beneficial effect on such populations, increasing equilibrium population density. It has also been shown that with large-scale disturbance events which simultaneously affect contiguous blocks of sites, increasing spatial autocorrelation in the disturbances has a harmful effect, decreasing equilibrium population density. Here, spatial population models are developed which include both of these spatially structured exogenous influences, to determine how they interact with each other and with the endogenously generated spatial structure produced by the population dynamics. The models show that when habitat is fragmented and disturbance occurs at large spatial scales, the population cannot persist no matter how large its birth rate, an effect not seen in previous simpler models of this type. The behavior of the model is also explored when the local autocorrelation of habitat heterogeneity and disturbance events are equal, i.e. the two effects occur at the same spatial scale. When this scale parameter is very small, habitat fragmentation prevents the population from persisting because sites attempting to reproduce will drop most of their offspring on unsuitable sites; when the parameter is very large, large-scale disturbance events drive the population to extinction. Population levels reach their maximum at intermediate values of the scale parameter, and the critical values in the model show that the population will persist most easily at these intermediate scales of spatial influences. The models are investigated via spatially explicit stochastic simulations, traditional (infinite-dispersal) and improved (local-dispersal) mean-field approximations, and pair approximations.

  5. Demographic History, Population Structure, and Local Adaptation in Alpine Populations of Cardamine impatiens and Cardamine resedifolia

    PubMed Central

    Ometto, Lino; Li, Mingai; Bresadola, Luisa; Barbaro, Enrico; Neteler, Markus; Varotto, Claudio

    2015-01-01

    Species evolution depends on numerous and distinct forces, including demography and natural selection. For example, local adaptation and population structure affect the evolutionary history of species living along environmental clines. This is particularly relevant in plants, which are often characterized by limited dispersal ability and the need to respond to abiotic and biotic stress factors specific to the local environment. Here we study the demographic history and the possible existence of local adaptation in two related species of Brassicaceae, Cardamine impatiens and Cardamine resedifolia, which occupy separate habitats along the elevation gradient. Previous genome-wide analyses revealed the occurrence of distinct selective pressures in the two species, with genes involved in cold response evolving particularly fast in C. resedifolia. In this study we surveyed patterns of molecular evolution and genetic variability in a set of 19 genes, including neutral and candidate genes involved in cold response, across 10 populations each of C. resedifolia and C. impatiens from the Italian Alps (Trentino). We inferred the population structure and demographic history of the two species, and tested the occurrence of signatures of local adaptation in these genes. The results indicate that, despite a slightly higher population differentiation in C. resedifolia than in C. impatiens, both species are only weakly structured and that populations sampled at high altitude experience less gene flow than low-altitude ones. None of the genes showed signatures of positive selection, suggesting that they do not seem to play relevant roles in the current evolutionary processes of adaptation to alpine environments of these species. PMID:25933225

  6. Propagation of localized structures in relativistic magnetized electron-positron plasmas using particle-in-cell simulations

    SciTech Connect

    López, Rodrigo A.; Muñoz, Víctor; Viñas, Adolfo F.; Valdivia, Juan A.

    2015-09-15

    We use a particle-in-cell simulation to study the propagation of localized structures in a magnetized electron-positron plasma with relativistic finite temperature. We use as initial condition for the simulation an envelope soliton solution of the nonlinear Schrödinger equation, derived from the relativistic two fluid equations in the strongly magnetized limit. This envelope soliton turns out not to be a stable solution for the simulation and splits in two localized structures propagating in opposite directions. However, these two localized structures exhibit a soliton-like behavior, as they keep their profile after they collide with each other due to the periodic boundary conditions. We also observe the formation of localized structures in the evolution of a spatially uniform circularly polarized Alfvén wave. In both cases, the localized structures propagate with an amplitude independent velocity.

  7. Global-, local-, and intermediate-scale structures in prototype spiral galaxies

    NASA Technical Reports Server (NTRS)

    Roberts, William W., Jr.

    1993-01-01

    The relationship between galactic spiral structure and the matter in the underlying disk constitutes one of the central problems in galactic dynamics. In Bertin et al. (1989), disk matter characterized by a low-dispersive speed is shown to be capable of playing a key role in the generation of large-scale spiral structure. In Roberts et al. (1992), this self-gravitating, low-dispersion disk matter is shown to be capable of playing an essential role in the formation of structure on local and intermediate scales. Both in computed cases where large-scale spiral structure is present and in those where it is not, the same dominant physical processes and fundamental dynamical mechanisms are active on local scales. The new perception, in which large-scale and small-scale phenomena operate somewhat independently as evidenced in the computational studies, permits a range of flocculent, multiarmed, and grand design spiral types to be simulated. In particular, grand design galaxies with ragged appearances exhibiting spurs, arm branchings, and interarm bridges in addition to the major spiral arms, similar to those often observed, can be generated.

  8. Effects of Anions on Local Structure of Al and Si in Aluminosilicates.

    PubMed

    Miyazaki; Yokoyama

    1999-06-15

    Three kinds of amorphous aluminosilicates were synthesized by coprecipitation of silicic acid with aluminum hydroxide in the presence of different inorganic ions: sulfate, chloride, and nitrate. Although the bulk composition of the aluminosilicates obtained was not affected by anion species, their DTA spectra were significantly different, suggesting that their structures also differ. The local structure of Al and Si in the aluminosilicates was studied in detail by 27Al and 29Si MAS NMR. From the 27Al MAS NMR spectra and comparison between 29Si HD- and CP-MAS NMR spectra, it was concluded that the aluminosilicate obtained in the presence of sulfate ions has only a montmorillonite-like structure, whereas in the cases of chloride and nitrate, the solids are composed of three phases: aluminum hydroxide, silica, and the montmorillonite-like aluminosilicate. The difference in the local structure of Al and Si in the aluminosilicates was explained by the difference in interaction between the anions and aluminum ions. Copyright 1999 Academic Press.

  9. Effects of anions on local structure of Al and Si in aluminosilicates

    SciTech Connect

    Miyazaki, Akane; Yokoyama, Takushi

    1999-06-15

    Three kinds of amorphous aluminosilicates were synthesized by coprecipitation of silicic acid with aluminum hydroxide in the presence of different inorganic ions: sulfate, chloride, and nitrate. Although the bulk composition of the aluminosilicates obtained was not affected by anion species, their DTA spectra were significantly different, suggesting that their structures also differ. The local structure of Al and Si in the aluminosilicates was studied in detail by {sup 27}Al and {sup 29}Si MAS NMR. From the {sup 27}Al MAS NMR spectra and comparison between {sup 29}Si HD- and CP-MAS NMR spectra, it was concluded that the aluminosilicate obtained in the presence of sulfate ions has only a montmorillonite-like structure, whereas in the cases of chloride and nitrate, the solids are composed of three phases: aluminum hydroxide, silica, and the montmorillonite-like aluminosilicate. The difference in the local structure of Al and Si in the aluminosilicates was explained by the difference in interaction between the anions and aluminum ions.

  10. Factors influencing subcellular localization of the human papillomavirus L2 minor structural protein

    SciTech Connect

    Kieback, Elisa; Mueller, Martin . E-mail: Martin.Mueller@dkfz.de

    2006-02-05

    Two structural proteins form the capsids of papillomaviruses. The major structural protein L1 is the structural determinant of the capsids and is present in 360 copies arranged in 72 pentamers. The minor structural protein L2 is estimated to be present in twelve copies per capsid. Possible roles for L2 in interaction with cell surface receptors and in virion uptake have been suggested. As previously reported, L2 localizes in subnuclear domains identified as nuclear domain 10 (ND10). As it was demonstrated that L2 is able to recruit viral and cellular proteins to ND10, a possible role for L2 as a mediator in viral assembly has been proposed. In this study, we determined factors influencing the localization of L2 at ND10. Under conditions of moderate L2 expression level and in the absence of heterologous viral components, we observed that, in contrast to previous reports, L2 is mainly distributed homogeneously throughout the nucleus. L2, however, is recruited to ND10 at a higher expression level or in the presence of viral components derived from vaccinia virus or from Semliki Forest virus. We observed that translocation of L2 to ND10 is not a concentration-dependent accumulation but rather seems to be triggered by yet unidentified cellular factors. In contrast to HPV 11 and 16 L2, the HPV 18 L2 protein seems to require L1 for efficient nuclear accumulation.

  11. Local structure of Ge quantum dots determined by combined numerical analysis of EXAFS and XANES data.

    PubMed

    Zhang, Yuanpeng; Ersoy, Osman; Karatutlu, Ali; Little, William; Sapelkin, Andrei

    2016-01-01

    The sensitivity of X-ray absorption near-edge structure (XANES) to the local symmetry has been investigated in small (∼4 nm) matrix-free Ge quantum dots. The FDMNES package was used to calculate the theoretical XANES spectra that were compared with the experimental data of as-prepared and annealed nanoparticles. It was found that XANES data for an as-prepared sample can only be adequately described if the second coordination shell of the diamond-type structural model is included in the FDMNES calculations. This is in contrast to the extended X-ray absorption fine-structure data that show only the first-shell signal. These results suggest that, despite the high degree of disorder and a large surface-to-volume ratio, as-prepared small Ge quantum dots retain the diamond-type symmetry beyond the first shell. Furthermore, we utilized this sensitivity of XANES to the local symmetry to study annealed Ge quantum dots and found evidence for significant structural distortion which we attribute to the existence of surface disorder in the annealed oxygen-free Ge quantum dots. PMID:26698071

  12. Diversity, population structure, and evolution of local peach cultivars in China identified by simple sequence repeats.

    PubMed

    Shen, Z J; Ma, R J; Cai, Z X; Yu, M L; Zhang, Z

    2015-01-15

    The fruit peach originated in China and has a history of domestication of more than 4000 years. Numerous local cultivars were selected during the long course of cultivation, and a great morphological diversity exists. To study the diversity and genetic background of local peach cultivars in China, a set of 158 accessions from different ecological regions, together with 27 modern varieties and 10 wild accessions, were evaluated using 49 simple sequence repeats (SSRs) covering the peach genome. Broad diversity was also observed in local cultivars at the SSR level. A total of 648 alleles were amplified with an average of 13.22 observed alleles per locus. The number of genotypes detected ranged from 9 (UDP96015) to 58 (BPPCT008) with an average of 27.00 genotypes per marker. Eight subpopulations divided by STRUCTURE basically coincided with the dendrogram of genetic relationships and could be explained by the traditional groups. The 8 subpopulations were juicy honey peach, southwestern peach I, wild peach, Buddha peach + southwestern peach II, northern peach, southern crisp peach, ornamental peach, and Prunus davidiana + P. kansuensis. Most modern varieties carried the genetic backgrounds of juicy honey peach and southwestern peach I, while others carried diverse genetic backgrounds, indicating that local cultivars were partly used in modern breeding programs. Based on the traditional evolution pathway, a modified pathway for the development of local peach cultivars in China was proposed using the genetic background of subpopulations that were identified by SSRs. Current status and prospects of utilization of Chinese local peach cultivars were also discussed according to the SSR information.

  13. In situ localization of mRNAs coding for mouse testicular structural genes

    SciTech Connect

    Hecht, N.B. ); Penshow, J.D. )

    1987-11-01

    In situ hybridization histochemistry has been used to localize mRNA transcripts of five nuclear and cytoplasmic structural genes in the mouse testis. The mRNAs for three nuclear structural proteins involved in chromatin transformation during spermatogenesis (the two protamine variants of the mouse and one of the testis-specific proteins) are restricted solely to postmeiotic germ cells. In contrast, mRNAs for two other structural proteins, actin and {alpha} tubulin, are detected throughout spermatogenesis. Although present in premeiotic, meiotic, and postmeiotic cell types, the mRNA levels of actin and {alpha} tubulin differ considerably during spermiogenesis, the haploid phase of spermatogenesis. Actin mRNA levels decrease markedly as the male gamete differentiates during spermiogenesis whereas {alpha}-tubulin mRNAs are equally abundant in the haploid round and elongating spermatids.

  14. Spatially localized structure-function relations in the elastic properties of sheared articular cartilage

    NASA Astrophysics Data System (ADS)

    Silverberg, Jesse; Bonassar, Lawrence; Cohen, Itai

    2013-03-01

    Contemporary developments in therapeutic tissue engineering have been enabled by basic research efforts in the field of biomechanics. Further integration of technology in medicine requires a deeper understanding of the mechanical properties of soft biological materials and the structural origins of their response under extreme stresses and strains. Drawing on the science generated by the ``Extreme Mechanics'' community, we present experimental results on the mechanical properties of articular cartilage, a hierarchically structured soft biomaterial found in the joints of mammalian long bones. Measurements of the spatially localized structure and mechanical properties will be compared with theoretical descriptions based on networks of deformed rods, poro-visco-elasticity, and standard continuum models. Discrepancies between experiment and theory will be highlighted, and suggestions for how models can be improved will be given.

  15. Localization of surface modes along a periodic/quasiperiodic structure containing a left-handed material

    NASA Astrophysics Data System (ADS)

    Toledo-Solano, M.; Palomino-Ovando, M. A.; Lozada-Morales, R.

    2015-12-01

    We have investigated the optical properties of a one-dimensional (1-D) photonic periodic/quasiperiodic structure, designed as photonic crystal (PC)-Fibonacci (FN)-photonic crystal (PC) sections. The structure is composed of alternating layers of a right-handed material (RHM) and a left-handed material (LHM). The RHM dielectric function is frequency independent and the LHM (metamaterial) dielectric function and magnetic susceptibility are described according to the Drude model. Using attenuated total reflectivity geometry, we explore the coupling of light with the plasmons on the surface of the metamaterial layers of the hybrid structure. The excitation of surface modes in different frequency regions are investigated. We observed bands of surface modes with a significant selective spatial localization at which the intensity of the electric field is confined almost totally within one of the PC sections or within the FN one.

  16. G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design.

    PubMed

    Lee, Hui Sun; Im, Wonpil

    2016-04-01

    Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G-LoSA. G-LoSA aligns protein local structures in a sequence order independent way and provides a GA-score, a chemical feature-based and size-independent structure similarity score. Our benchmark validation shows the robust performance of G-LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure-centric comparative biology studies. In particular, G-LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G-LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer-aided drug design. We hope that G-LoSA can be a useful computational method for exploring interesting biological problems through large-scale comparison of protein local structures and facilitating drug discovery research and development. G-LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/. PMID:26813336

  17. Localized heuristic inverse quantitative structure activity relationship with bulk descriptors using numerical gradients.

    PubMed

    Stålring, Jonna; Almeida, Pedro R; Carlsson, Lars; Helgee Ahlberg, Ernst; Hasselgren, Catrin; Boyer, Scott

    2013-08-26

    State-of-the-art quantitative structure-activity relationship (QSAR) models are often based on nonlinear machine learning algorithms, which are difficult to interpret. From a pharmaceutical perspective, QSARs are used to enhance the chemical design process. Ultimately, they should not only provide a prediction but also contribute to a mechanistic understanding and guide modifications to the chemical structure, promoting compounds with desirable biological activity profiles. Global ranking of descriptor importance and inverse QSAR have been used for these purposes. This paper introduces localized heuristic inverse QSAR, which provides an assessment of the relative ability of the descriptors to influence the biological response in an area localized around the predicted compound. The method is based on numerical gradients with parameters optimized using data sets sampled from analytical functions. The heuristic character of the method reduces the computational requirements and makes it applicable not only to fragment based methods but also to QSARs based on bulk descriptors. The application of the method is illustrated on congeneric QSAR data sets, and it is shown that the predicted influential descriptors can be used to guide structural modifications that affect the biological response in the desired direction. The method is implemented into the AZOrange Open Source QSAR package. The current implementation of localized heuristic inverse QSAR is a step toward a generally applicable method for elucidating the structure activity relationship specifically for a congeneric region of chemical space when using QSARs based on bulk properties. Consequently, this method could contribute to accelerating the chemical design process in pharmaceutical projects, as well as provide information that could enhance the mechanistic understanding for individual scaffolds.

  18. Fusion of multichannel local and global structural cues for photo aesthetics evaluation.

    PubMed

    Luming Zhang; Yue Gao; Zimmermann, Roger; Qi Tian; Xuelong Li

    2014-03-01

    Photo aesthetic quality evaluation is a fundamental yet under addressed task in computer vision and image processing fields. Conventional approaches are frustrated by the following two drawbacks. First, both the local and global spatial arrangements of image regions play an important role in photo aesthetics. However, existing rules, e.g., visual balance, heuristically define which spatial distribution among the salient regions of a photo is aesthetically pleasing. Second, it is difficult to adjust visual cues from multiple channels automatically in photo aesthetics assessment. To solve these problems, we propose a new photo aesthetics evaluation framework, focusing on learning the image descriptors that characterize local and global structural aesthetics from multiple visual channels. In particular, to describe the spatial structure of the image local regions, we construct graphlets small-sized connected graphs by connecting spatially adjacent atomic regions. Since spatially adjacent graphlets distribute closely in their feature space, we project them onto a manifold and subsequently propose an embedding algorithm. The embedding algorithm encodes the photo global spatial layout into graphlets. Simultaneously, the importance of graphlets from multiple visual channels are dynamically adjusted. Finally, these post-embedding graphlets are integrated for photo aesthetics evaluation using a probabilistic model. Experimental results show that: 1) the visualized graphlets explicitly capture the aesthetically arranged atomic regions; 2) the proposed approach generalizes and improves four prominent aesthetic rules; and 3) our approach significantly outperforms state-of-the-art algorithms in photo aesthetics prediction.

  19. Structural and electronic properties of trans-polyacetylene under local strain

    NASA Astrophysics Data System (ADS)

    Ketabi, S. A.

    2016-06-01

    A theoretical study is presented to investigate the structural and electronic properties of trans-polyacetylene (trans-PA) molecule under local strain. The influence of a local bending or compression of the space between neighboring carbon atoms on the band gap of the molecule was studied. Making use of an effective difference equation based on tight-binding procedure the band structure of trans-PA has been calculated. Our results indicate that the energy gap of the strained molecule modified significantly which affects the electronic properties of the molecule. We found that the size of the molecular gap is proportional to the bending angle so that for the bending perpendicular to π-orbitals plane the band gap reduced drastically and for the parallel one the band gap gradually increased. Furthermore, the current-voltage characteristics of the strained trans-PA molecule are studied. We found that under the local strain the threshold voltage for the current flow through the bent molecule decreased (increased) depending on the bending is perpendicular (parallel) to the molecule plane.

  20. Structural damage localization by outlier analysis of signal-processed mode shapes - Analytical and experimental validation

    NASA Astrophysics Data System (ADS)

    Ulriksen, M. D.; Damkilde, L.

    2016-02-01

    Contrary to global modal parameters such as eigenfrequencies, mode shapes inherently provide structural information on a local level. Therefore, this particular modal parameter and its derivatives are utilized extensively for damage identification. Typically, more or less advanced mathematical methods are employed to identify damage-induced discontinuities in the spatial mode shape signals, hereby, potentially, facilitating damage detection and/or localization. However, by being based on distinguishing damage-induced discontinuities from other signal irregularities, an intrinsic deficiency in these methods is the high sensitivity towards measurement noise. In the present paper, a damage localization method which, compared to the conventional mode shape-based methods, has greatly enhanced robustness towards measurement noise is proposed. The method is based on signal processing of a spatial mode shape by means of continuous wavelet transformation (CWT) and subsequent application of a generalized discrete Teager-Kaiser energy operator (GDTKEO) to identify damage-induced mode shape discontinuities. In order to evaluate whether the identified discontinuities are in fact damage-induced, outlier analysis is conducted by applying the Mahalanobis metric to major principal scores of the sensor-located bands of the signal-processed mode shape. The method is tested analytically and benchmarked with other mode shape-based damage localization approaches on the basis of a free-vibrating beam and validated experimentally in the context of a residential-sized wind turbine blade subjected to an impulse load.

  1. Kinetic Model of Electric Potentials in Localized Collisionless Plasma Structures under Steady Quasi-gyrotropic Conditions

    NASA Technical Reports Server (NTRS)

    Schindler, K.; Birn, J.; Hesse, M.

    2012-01-01

    Localized plasma structures, such as thin current sheets, generally are associated with localized magnetic and electric fields. In space plasmas localized electric fields not only play an important role for particle dynamics and acceleration but may also have significant consequences on larger scales, e.g., through magnetic reconnection. Also, it has been suggested that localized electric fields generated in the magnetosphere are directly connected with quasi-steady auroral arcs. In this context, we present a two-dimensional model based on Vlasov theory that provides the electric potential for a large class of given magnetic field profiles. The model uses an expansion for small deviation from gyrotropy and besides quasineutrality it assumes that electrons and ions have the same number of particles with their generalized gyrocenter on any given magnetic field line. Specializing to one dimension, a detailed discussion concentrates on the electric potential shapes (such as "U" or "S" shapes) associated with magnetic dips, bumps, and steps. Then, it is investigated how the model responds to quasi-steady evolution of the plasma. Finally, the model proves useful in the interpretation of the electric potentials taken from two existing particle simulations.

  2. The impact of organisational culture on the delivery of person-centred care in services providing respite care and short breaks for people with dementia.

    PubMed

    Kirkley, Catherine; Bamford, Claire; Poole, Marie; Arksey, Hilary; Hughes, Julian; Bond, John

    2011-07-01

    Ensuring the development and delivery of person-centred care in services providing respite care and short breaks for people with dementia and their carers has a number of challenges for health and social service providers. This article explores the role of organisational culture in barriers and facilitators to person-centred dementia care. As part of a mixed-methods study of respite care and short breaks for people with dementia and their carers, 49 telephone semi-structured interviews, two focus groups (N= 16) and five face-to-face in-depth interviews involving front-line staff and operational and strategic managers were completed in 2006-2007. Qualitative thematic analysis of transcripts identified five themes on aspects of organisational culture that are perceived to influence person-centred care: understandings of person-centred care, attitudes to service development, service priorities, valuing staff and solution-focused approaches. Views of person-centred care expressed by participants, although generally positive, highlight a range of understandings about person-centred care. Some organisations describe their service as being person-centred without the necessary cultural shift to make this a reality. Participants highlighted resource constraints and the knowledge, attitudes and personal qualities of staff as a barrier to implementing person-centred care. Leadership style, the way that managers' support and value staff and the management of risk were considered important influences. Person-centred dementia care is strongly advocated by professional opinion leaders and is prescribed in policy documents. This analysis suggests that person-centred dementia care is not strongly embedded in the organisational cultures of all local providers of respite-care and short-break services. Provider organisations should be encouraged further to develop a shared culture at all levels of the organisation to ensure person-centred dementia care.

  3. Localized structures and front propagation in the Lengyel-Epstein model

    SciTech Connect

    Jensen, O.; Pannbacker, V.O.; Mosekilde, E.; Dewel, G.; Borckmans, P. Service de Chimie-Physique, Code Postal 231 Universite Libre de Bruxelles, 1050 Brussels )

    1994-08-01

    Pattern selection, localized structure formation, and front propagation are analyzed within the framework of a model for the chlorine dioxide--iodine--malonic acid reaction that represents a key to understanding recently obtained Turing structures. This model is distinguished from previously studied, simple reaction-diffusion models by producing a strongly subcritical transition to stripes. The wave number for the modes of maximum linear gain is calculated and compared with the dominant wave number for the finally selected, stationary structures grown from the homogeneous steady state or developed behind a traveling front. The speed of propagation for a front between the homogeneous steady state and a one-dimensional (1D) Turing structure is obtained. This velocity shows a characteristic change in behavior at the crossover between the subcritical and supercritical regimes for the Turing bifurcation. In the subcritical regime there is an interval where the front velocity vanishes as a result of a pinning of the front to the underlying structure. In 2D, two different nucleation mechanisms for hexagonal structures are illustrated on the Lengyel-Epstein and the Brusselator model. Finally, the observation of 1D and 2D spirals with Turing-induced cores is reported.

  4. Local weighting of nanometric track structure properties in macroscopic voxel geometries for particle beam treatment planning

    NASA Astrophysics Data System (ADS)

    Alexander, F.; Villagrasa, C.; Rabus, H.; Wilkens, J. J.

    2015-12-01

    The research project BioQuaRT within the European Metrology Research Programme aimed at correlating ion track structure characteristics with the biological effects of radiation and developed measurement and simulation techniques for determining ion track structure on different length scales from about 2 nm to about 10 μm. Within this framework, we investigated methods to translate track-structure quantities derived on a nanometre scale to macroscopic dimensions. Here we make use of parameterizations that link the energy of the projectile to the ionization pattern of the track using nanodosimetric ionization cluster size distributions. They were defined with data generated by simulations of ion tracks in liquid water using the Geant4 Monte Carlo toolkit with the Geant4-DNA processes. For the clinical situation with a mixed radiation field, where particles of various energies hit a cell from several directions, we have to find macroscopic relevant mean values. They can be determined by appropriate local weighting functions for the identified parameterization. We show that a stopping power weighted mean value of the mentioned track structure properties can describe the overall track structure in a cell exposed to a mixed radiation field. The parameterization, together with the presented stopping power weighting approach, show how nanometric track structure properties could be integrated into treatment planning systems without the need to perform time consuming simulations on the nanometer level for each individual patient.

  5. Centrosomes as signalling centres

    PubMed Central

    Arquint, Christian; Gabryjonczyk, Anna-Maria; Nigg, Erich A.

    2014-01-01

    Centrosomes—as well as the related spindle pole bodies (SPBs) of yeast—have been extensively studied from the perspective of their microtubule-organizing roles. Moreover, the biogenesis and duplication of these organelles have been the subject of much attention, and the importance of centrosomes and the centriole–ciliary apparatus for human disease is well recognized. Much less developed is our understanding of another facet of centrosomes and SPBs, namely their possible role as signalling centres. Yet, many signalling components, including kinases and phosphatases, have been associated with centrosomes and spindle poles, giving rise to the hypothesis that these organelles might serve as hubs for the integration and coordination of signalling pathways. In this review, we discuss a number of selected studies that bear on this notion. We cover different processes (cell cycle control, development, DNA damage response) and organisms (yeast, invertebrates and vertebrates), but have made no attempt to be comprehensive. This field is still young and although the concept of centrosomes and SPBs as signalling centres is attractive, it remains primarily a concept—in need of further scrutiny. We hope that this review will stimulate thought and experimentation. PMID:25047618

  6. Nuclear Science Centre, New Delhi

    SciTech Connect

    Mehta, G.; Potukuchi, P.; Roy, A.

    1995-08-01

    Argonne is collaborating with the Nuclear Science Centre (NSC), New Delhi, to develop a new type of superconducting accelerating structure for low-velocity heavy ions. A copper model has been evaluated and tests on the niobium prototype are currently in progress. Some technical details of this project are described in the Superconducting Linac Development section of this report. All funding for the prototype has come from the NSC, and they have also stationed two staff members at ATLAS for the past two years to gain experience and work on this project. Additional NSC personnel visited ATLAS for extended periods during 1994 for electronics and cryogenics experience and training. Two NSC staff members are scheduled to spend several months at ANL during 1995 to continue tests and developments of the prototype resonators and to initiate fabrication of the production models for their linac project.

  7. The local structure of SrLaGaO 4:Cr 3+ crystal

    NASA Astrophysics Data System (ADS)

    Zeng, Ti-Xian; Chen, Jia-Jun; Zhao, Bei-Jun; Zhu, Shi-Fu; Huang, Yi; Chen, Tai-Hong

    2008-07-01

    The local tetragonal distortion in the vicinity of substitutional Cr 3+ impurities in SrLaGaO 4 crystal was determined by fitting the calculated optical spectra and EPR parameter to the experimental values based on Zhao's semi-SCF d-orbit wave functions model of free Cr 3+ ions, the point-charge crystal field model and Macfarlane's perturbation loop method. This paper found that the local structures of SrLaGaO 4 were: R⊥‧=0.1907 nm and R∥‧=0.2237 nm (where R⊥‧ and R∥‧ denoted Cr 3+-O 2- distances perpendicular to and parallel with the C4 axis). The results agreed well with the experimental findings.

  8. Boundary-locality and perturbative structure of entanglement spectra in gapped systems.

    PubMed

    Alba, Vincenzo; Haque, Masudul; Läuchli, Andreas M

    2012-06-01

    The entanglement between two parts of a many-body system can be characterized in detail by the entanglement spectrum. Focusing on gapped phases of several one-dimensional systems, we show how this spectrum is dominated by contributions from the boundary between the parts. This contradicts the view of an "entanglement Hamiltonian" as a bulk entity. The boundary-local nature of the entanglement spectrum is clarified through its hierarchical level structure, through the combination of two single-boundary spectra to form a two-boundary spectrum, and finally through consideration of dominant eigenfunctions of the entanglement Hamiltonian. We show consequences of boundary-locality for perturbative calculations of the entanglement spectrum.

  9. The crystal structure of human adenylate kinase 6: An adenylate kinase localized to the cell nucleus.

    PubMed

    Ren, Hui; Wang, Liya; Bennett, Matthew; Liang, Yuhe; Zheng, Xiaofeng; Lu, Fei; Li, Lanfen; Nan, Jie; Luo, Ming; Eriksson, Staffan; Zhang, Chuanmao; Su, Xiao-Dong

    2005-01-11

    Adenylate kinases (AKs) play important roles in nucleotide metabolism in all organisms and in cellular energetics by means of phosphotransfer networks in eukaryotes. The crystal structure of a human AK named AK6 was determined by in-house sulfur single-wavelength anomalous dispersion phasing methods and refined to 2.0-A resolution with a free R factor of 21.8%. Sequence analyses revealed that human AK6 belongs to a distinct subfamily of AKs present in all eukaryotic organisms sequenced so far. Enzymatic assays show that human AK6 has properties similar with other AKs, particularly with AK5. Fluorescence microscopy showed that human AK6 is localized predominantly to the nucleus of HeLa cells. The identification of a nuclear-localized AK sheds light on nucleotide metabolism in the nucleus and the energetic communication between mitochondria and nucleus by means of phosphotransfer networks.

  10. Hierarchical mechanism of development of wealth and structure for a premodern local society

    NASA Astrophysics Data System (ADS)

    Matsuo, Miki Y.

    2011-06-01

    We propose a hierarchical model of social development composed of two associated hierarchies, each of which describes economic and noneconomic activities in society, respectively. The model is designed to explain the development of wealth distribution and social structure over 50 years in a premodern Japanese local society. Data analysis shows that the wealth distribution has a well-known universal power-law tail throughout the observed period, while the Pareto index gradually decreases with time. We further show that the noneconomic social properties, such as the household number, average family size, and number of collaterals in a household, of the local society, also have decreasing or increasing trends throughout the observed period. We show that the hierarchical model consistently demonstrates the correlations of these economic and noneconomic properties.

  11. Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

    PubMed Central

    Montano, Valeria; Didelot, Xavier; Foll, Matthieu; Linz, Bodo; Reinhardt, Richard; Suerbaum, Sebastian; Moodley, Yoshan; Jensen, Jeffrey D.

    2015-01-01

    Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g., transcription elongation factor NusA and tumor necrosis factor alpha-inducing protein Tipα) and hitherto unknown functional genes. PMID:25995212

  12. High-order spoof localized surface plasmons supported on a complementary metallic spiral structure

    PubMed Central

    Gao, Zhen; Gao, Fei; Zhang, Baile

    2016-01-01

    We experimentally demonstrate that multiple high-order spoof localized surface plasmons (spoof-LSPs) modes can be supported on a complementary metallic spiral structure, which were absent in the previously reported spoof-LSPs modes. Through exact numerical simulations and near-field imaging experiments, we directly observe these high-order spoof-LSPs modes at microwave frequencies. We also show that these higher-order spoof-LSPs modes exhibit larger frequency shifts caused by the local environmental refractive index change than the previously reported low-order spoof-LSPs modes. Hence the complementary MSS may find potential applications as plasmonic sensor in the microwave and terahertz frequencies. PMID:27079658

  13. Optimizing Data Centre Energy and Environmental Costs

    NASA Astrophysics Data System (ADS)

    Aikema, David Hendrik

    Data centres use an estimated 2% of US electrical power which accounts for much of their total cost of ownership. This consumption continues to grow, further straining power grids attempting to integrate more renewable energy. This dissertation focuses on assessing and reducing data centre environmental and financial costs. Emissions of projects undertaken to lower the data centre environmental footprints can be assessed and the emission reduction projects compared using an ISO-14064-2-compliant greenhouse gas reduction protocol outlined herein. I was closely involved with the development of the protocol. Full lifecycle analysis and verifying that projects exceed business-as-usual expectations are addressed, and a test project is described. Consuming power when it is low cost or when renewable energy is available can be used to reduce the financial and environmental costs of computing. Adaptation based on the power price showed 10--50% potential savings in typical cases, and local renewable energy use could be increased by 10--80%. Allowing a fraction of high-priority tasks to proceed unimpeded still allows significant savings. Power grid operators use mechanisms called ancillary services to address variation and system failures, paying organizations to alter power consumption on request. By bidding to offer these services, data centres may be able to lower their energy costs while reducing their environmental impact. If providing contingency reserves which require only infrequent action, savings of up to 12% were seen in simulations. Greater power cost savings are possible for those ceding more control to the power grid operator. Coordinating multiple data centres adds overhead, and altering at which data centre requests are processed based on changes in the financial or environmental costs of power is likely to increase this overhead. Tests of virtual machine migrations showed that in some cases there was no visible increase in power use while in others power use

  14. Gas phase structures and charge localization in small aluminum oxide anions: Infrared photodissociation spectroscopy and electronic structure calculations.

    PubMed

    Song, Xiaowei; Fagiani, Matias R; Gewinner, Sandy; Schöllkopf, Wieland; Asmis, Knut R; Bischoff, Florian A; Berger, Fabian; Sauer, Joachim

    2016-06-28

    We use cryogenic ion trap vibrational spectroscopy in combination with quantum chemical calculations to study the structure of mono- and dialuminum oxide anions. The infrared photodissociation spectra of D2-tagged AlO1-4 (-) and Al2O3-6 (-) are measured in the region from 400 to 1200 cm(-1). Structures are assigned based on a comparison to simulated harmonic and anharmonic IR spectra derived from electronic structure calculations. The monoaluminum anions contain an even number of electrons and exhibit an electronic closed-shell ground state. The Al2O3-6 (-) anions are oxygen-centered radicals. As a result of a delicate balance between localization and delocalization of the unpaired electron, only the BHLYP functional is able to qualitatively describe the observed IR spectra of all species with the exception of AlO3 (-). Terminal Al-O stretching modes are found between 1140 and 960 cm(-1). Superoxo and peroxo stretching modes are found at higher (1120-1010 cm(-1)) and lower energies (850-570 cm(-1)), respectively. Four modes in-between 910 and 530 cm(-1) represent the IR fingerprint of the common structural motif of dialuminum oxide anions, an asymmetric four-member Al-(O)2-Al ring. PMID:27369513

  15. Gas phase structures and charge localization in small aluminum oxide anions: Infrared photodissociation spectroscopy and electronic structure calculations

    NASA Astrophysics Data System (ADS)

    Song, Xiaowei; Fagiani, Matias R.; Gewinner, Sandy; Schöllkopf, Wieland; Asmis, Knut R.; Bischoff, Florian A.; Berger, Fabian; Sauer, Joachim

    2016-06-01

    We use cryogenic ion trap vibrational spectroscopy in combination with quantum chemical calculations to study the structure of mono- and dialuminum oxide anions. The infrared photodissociation spectra of D2-tagged AlO1-4- and Al2O3-6- are measured in the region from 400 to 1200 cm-1. Structures are assigned based on a comparison to simulated harmonic and anharmonic IR spectra derived from electronic structure calculations. The monoaluminum anions contain an even number of electrons and exhibit an electronic closed-shell ground state. The Al2O3-6- anions are oxygen-centered radicals. As a result of a delicate balance between localization and delocalization of the unpaired electron, only the BHLYP functional is able to qualitatively describe the observed IR spectra of all species with the exception of AlO3-. Terminal Al-O stretching modes are found between 1140 and 960 cm-1. Superoxo and peroxo stretching modes are found at higher (1120-1010 cm-1) and lower energies (850-570 cm-1), respectively. Four modes in-between 910 and 530 cm-1 represent the IR fingerprint of the common structural motif of dialuminum oxide anions, an asymmetric four-member Al-(O)2-Al ring.

  16. Hippocampal and amygdalar local structural differences in elderly patients with schizophrenia

    PubMed Central

    Prestia, Annapaola; Cavedo, Enrica; Boccardi, Marina; Muscio, Cristina; Adorni, Andrea; Geroldi, Cristina; Bonetti, Matteo; Thompson, Paul M.; Frisoni, Giovanni B.

    2015-01-01

    Objectives Morphological abnormalities have been reported for the hippocampi and amygdalae in young schizophrenia patients, but very little is known about the pattern of abnormalities in elderly schizophrenia patients. Here we investigated local structural differences in the hippocampi and amygdalae of elderly schizophrenia patients compared to healthy elderly subjects. We also related these differences to clinical symptom severity. Design 20 schizophrenia patients (mean age: 67.4±6.2 years, MMSE 22.8±4.4) and 20 healthy elderly subjects (70.3±7.5, 29.0±1.1) underwent high resolution magnetic resonance imaging of the brain. The Radial Atrophy Mapping technique was used to reconstruct the 3D shape of the amygdala and the hippocampus. Local differences in tissue reductions were computed between groups and permutation tests were run to correct for multiple comparisons, in statistical maps thresholded at p=0.05. Results Significant tissue reduction was observed bilaterally in the amygdala and hippocampus of schizophrenia patients. The basolateral-ventral-medial amygdalar nucleus showed the greatest involvement, with over 30% local tissue reduction. The centro-medial, cortical, and lateral nuclei were also atrophic in patients. The hippocampus showed significant tissue loss in the medio-caudal and antero-lateral aspects of CA1, and in medial section of its left head (pre- and para-subiculum;). In the left amygdala and hippocampus, local tissue volumes were significantly correlated with negative symptoms. Conclusions Tissue losses and altered morphology were found in elderly schizophrenia patients. Tissue loss mapped to amygdalo-hippocampal subregions known to have bidirectional and specific connections with frontal cortical and limbic structures and was related to clinical severity. PMID:24534522

  17. Protein Secondary Structure Prediction Using Local Adaptive Techniques in Training Neural Networks

    NASA Astrophysics Data System (ADS)

    Aik, Lim Eng; Zainuddin, Zarita; Joseph, Annie

    2008-01-01

    One of the most significant problems in computer molecular biology today is how to predict a protein's three-dimensional structure from its one-dimensional amino acid sequence or generally call the protein folding problem and difficult to determine the corresponding protein functions. Thus, this paper involves protein secondary structure prediction using neural network in order to solve the protein folding problem. The neural network used for protein secondary structure prediction is multilayer perceptron (MLP) of the feed-forward variety. The training set are taken from the protein data bank which are 120 proteins while 60 testing set is the proteins which were chosen randomly from the protein data bank. Multiple sequence alignment (MSA) is used to get the protein similar sequence and Position Specific Scoring matrix (PSSM) is used for network input. The training process of the neural network involves local adaptive techniques. Local adaptive techniques used in this paper comprises Learning rate by sign changes, SuperSAB, Quickprop and RPROP. From the simulation, the performance for learning rate by Rprop and Quickprop are superior to all other algorithms with respect to the convergence time. However, the best result was obtained using Rprop algorithm.

  18. Alkyl CH Stretch Vibrations as a Probe of Local Environment and Structure

    NASA Astrophysics Data System (ADS)

    Sibert, Edwin; Tabor, Daniel P.; Kidwell, Nathanael; Dean, Jacob C.; Zwier, Timothy S.

    2015-06-01

    The CH stretch region is a good candidate as a probe of structure and local environment. The functional groups are ubiquitous and their vibration spectra exhibit a surprising sensitivity to molecular structure. In this talk we briefly review our theoretical model Hamiltonian [J. Chem. Phys. 138 064308 (2013)] for describing vibrational spectra associated with the CH stretch of CH_2 groups and then describe an extension of it to molecules containing methyl and methoxy groups. Results are compared to the infrared spectroscopy of four molecules studied under supersonic expansion cooling in gas phase conditions. The molecules include 1,1-diphenylethane, 1,1-diphenylpropane, 2-methoxyphenol (guaiacol), and 1,3-dimethoxy-2-hydroxybenzene (syringol). The curvilinear local-mode Hamiltonian predicts most of the major spectral features considered in this study and provides insights into mode mixing. We conclude by returning to CH_2 groups and explain both why the CH stretch spectrum of cyclohexane is substantially modified when it forms a complex with an alkali metal and what these spectra tell us about the structure of the complex.

  19. A new EXAFS method for the local structure analysis of low-Z elements.

    PubMed

    Isomura, Noritake; Kamada, Masao; Nonaka, Takamasa; Nakamura, Eiken; Takano, Takumi; Sugiyama, Harue; Kimoto, Yasuji

    2016-01-01

    A unique analytical method is proposed for local structure analysis via extended X-ray absorption fine structure (EXAFS) spectroscopy. The measurement of electron energy distribution curves at various excitation photon energies using an electron energy analyzer is applied to determine a specific elemental Auger spectrum. To demonstrate the method, the N K-edge EXAFS spectra for a silicon nitride film were obtained via simultaneous measurement of the N KLL Auger and background spectra using dual-energy windows. The background spectrum was then used to remove the photoelectrons and secondary electron mixing in the energy distribution curves. The spectrum obtained following this subtraction procedure represents the `true' N K-edge EXAFS spectrum without the other absorptions that are observed in total electron yield N K-edge EXAFS spectra. The first nearest-neighbor distance (N-Si) derived from the extracted N K-edge EXAFS oscillation was in good agreement with the value derived from Si K-edge analysis. This result confirmed that the present method, referred to as differential electron yield (DEY)-EXAFS, is valid for deriving local surface structure information for low-Z elements. PMID:26698075

  20. Spatial localization of resistive drift wave structure in tokamak edge plasmas with an embedded magnetic island

    SciTech Connect

    Hu, Shilin; Qu, Hongpeng; Li, Jiquan; Kishimoto, Y.

    2014-10-15

    Resistive drift wave instability is investigated numerically in tokamak edge plasma confined by sheared slab magnetic field geometry with an embedded magnetic island. The focus is on the structural characteristics of eigenmode inside the island, where the density profile tends to be flattened. A transition of the dominant eigenmode occurs around a critical island width w{sub c}. For thin islands with a width below w{sub c}, two global long wavelength eigenmodes with approximately the same growth rate but different eigenfrequency are excited, which are stabilized by the magnetic island through two-dimensional mode coupling in both x and y (corresponding to radial and poloidal in tokamak) directions. On the other hand, a short wavelength eigenmode, which is destabilized by thick islands with a width above w{sub c}, dominates the edge fluctuation, showing a prominent structural localization in the region between the X-point and the O-point of the magnetic island. The main destabilization mechanism is identified as the mode coupling in the y direction, which is similar to the so-called toroidal coupling in tokamak plasmas. These three eigenmodes may coexist in the drift wave fluctuation for the island with a width around w{sub c}. It is demonstrated that the structural localization results mainly from the quasilinear flattening of density profile inside the magnetic island.

  1. The RNAsnp web server: predicting SNP effects on local RNA secondary structure.

    PubMed

    Sabarinathan, Radhakrishnan; Tafer, Hakim; Seemann, Stefan E; Hofacker, Ivo L; Stadler, Peter F; Gorodkin, Jan

    2013-07-01

    The function of many non-coding RNA genes and cis-regulatory elements of messenger RNA largely depends on the structure, which is in turn determined by their sequence. Single nucleotide polymorphisms (SNPs) and other mutations may disrupt the RNA structure, interfere with the molecular function and hence cause a phenotypic effect. RNAsnp is an efficient method to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package. The SNP effects are quantified in terms of empirical P-values, which, for computational efficiency, are derived from extensive pre-computed tables of distributions of substitution effects as a function of gene length and GC content. Here, we present a web service that not only provides an interface for RNAsnp but also features a graphical output representation. In addition, the web server is connected to a local mirror of the UCSC genome browser database that enables the users to select the genomic sequences for analysis and visualize the results directly in the UCSC genome browser. The RNAsnp web server is freely available at: http://rth.dk/resources/rnasnp/.

  2. The interplay of peptide sequence and local structure in TiO2 biomineralization.

    PubMed

    Choi, Noori; Tan, Lihan; Jang, Ji-ryang; Um, Yu Mi; Yoo, Pil J; Choe, Woo-Seok

    2012-10-01

    Using cyclic constrained TiO(2) binding peptides STB1 (CHKKPSKSC), RSTB1 (CHRRPSRSC) and linear peptide LSTB1 (AHKKPSKSA), it was shown that while affinity of the peptide to TiO(2) is essential to enable TiO(2) biomineralization, other factors such as biomineralization kinetics and peptide local structure need to be considered to predict biomineralization efficacy. Cyclic and linear TiO(2) binding peptides show significantly different biomineralization activities. Cyclic STB1 and RSTB1 could induce TiO(2) precipitation in the presence of titanium(IV)-bis-ammonium-lactato-dihydroxide (TiBALDH) precursor in water or tris buffer at pH 8. In contrast, linear LSTB1 was unable to mineralize TiO(2) under the same experimental conditions despite its high affinity to TiO(2) comparable with STB1 and/or RSTB1. LSTB1 being a flexible molecule could not render the stable condensation of TiBALDH precursor to form TiO(2) particles. However, in the presence of phosphate buffer ions, the structure of LSTB1 is stabilized, leading to efficient condensation of TiBALDH and TiO(2) particle formation. This study demonstrates that peptide-mediated TiO(2) mineralization is governed by a complicated interplay of peptide sequence, local structure, kinetics and the presence of mineralizing aider such as phosphate ions.

  3. Classification of trabeculae into three-dimensional rodlike and platelike structures via local inertial anisotropy.

    PubMed

    Vasilić, Branimir; Rajapakse, Chamith S; Wehrli, Felix W

    2009-07-01

    Trabecular bone microarchitecture is a significant determinant of the bone's mechanical properties and is thus of major clinical relevance in predicting fracture risk. The three-dimensional nature of trabecular bone is characterized by parameters describing scale, topology, and orientation of structural elements. However, none of the current methods calculates all three types of parameters simultaneously and in three dimensions. Here the authors present a method that produces a continuous classification of voxels as belonging to platelike or rodlike structures that determines their orientation and estimates their thickness. The method, dubbed local inertial anisotropy (LIA), treats the image as a distribution of mass density and the orientation of trabeculae is determined from a locally calculated tensor of inertia at each voxel. The orientation entropies of rods and plates are introduced, which can provide new information about microarchitecture not captured by existing parameters. The robustness of the method to noise corruption, resolution reduction, and image rotation is demonstrated. Further, the method is compared with established three-dimensional parameters including the structure-model index and topological surface-to-curve ratio. Finally, the method is applied to data acquired in a previous translational pilot study showing that the trabecular bone of untreated hypogonadal men is less platelike than that of their eugonadal peers.

  4. High-temperature phase transition and local structure of a hydrous anorthoclase

    NASA Astrophysics Data System (ADS)

    Yang, Y.; Wang, Z. P.; Tian, Z. Z.; Xia, Q. K.; Li, G. W.

    2016-02-01

    The in situ Raman spectra of a hydrous anorthoclase at temperatures of 20-800 °C have been measured using a LABRAM-HR spectrometer and Linkam TS 1500 heating stage. The frequencies of modes at 54, 99, 130 and 162 cm-1 related to M-O vibrations decrease sharply and then increase drastically or keep steady at temperatures above 200 °C. A knee point can be clearly seen at about 200 °C for those modes. The frequency of the mode at 282 cm-1 shows little temperature dependence. However, for the two strongest modes at 471 and 512 cm-1, the frequencies decrease linearly with increasing temperature. From evolution of the frequencies of modes at 54, 99, 130 and 162 cm-1 with temperature, the following conclusions can be drawn: (1) The distance of the local M-O bond shortens rather than lengthens at temperatures above 200 °C; (2) The abrupt changes of the local structure of M site induce a collapse of the framework structure and displacive phase transition at 200 °C; and (3) The H atoms incorporated in anorthoclase are located at the M site. These results are indicative for the structure and properties of anorthoclase at deep earth conditions.

  5. Local scale structures in Earth's thermospheric winds and their consequences for wind driven transport

    NASA Astrophysics Data System (ADS)

    Dhadly, Manbharat Singh

    In the traditional picture of Earth's upper thermosphere (~190--300 km), it is widely presumed that its convective stability and enormous kinematic viscosity attenuate wind gradients, and hence smooth out any structure present in the wind over scale size of several hundreds of kilometers. However, several independent experimental studies have shown that observed upper thermospheric wind fields at high latitudes contain stronger than expected local-scale spatial structures. The motivation of this dissertation is to investigate how the resulting local-scale gradients would distort neutral air masses and complicate thermospheric wind transport. To achieve this goal, we examined the behavior of a simple parameter that we refer to as the "distortion gradient". It incorporates all of the wind field's departures from uniformity, and is thus capable of representing all resulting contributions to the distortion or mixing of air masses. Climatological analysis of the distortion gradient using 2010, 2011, and 2012 wind data from the All-sky Scanning Doppler Imager (SDI) located at Poker Flat (65.12N, 147.47W) revealed the diurnal and seasonal trends in distortion of thermospheric masses. Distortion was observed to be dependent on geomagnetic activity and orientation of the interplanetary magnetic field. To understand the time-cumulative influence of these local-scale non-uniformities on thermospheric wind driven transport, time-resolved two-dimensional maps of the thermospheric vector wind fields were used to infer forward and backward air parcel trajectories. Tracing air parcel trajectories through a given geographic location indicates where they came from previously, and where they will go in the future. Results show that wind driven transport is very sensitive to small-scale details of the wind field. Any local-scale spatial wind gradients can significantly complicate air parcel trajectories. Transport of thermospheric neutral species in the presence of the local

  6. Electronic structure and local magnetism of 3d-5d impurity substituted CeFe2

    NASA Astrophysics Data System (ADS)

    Das, Rakesh; Das, G. P.; Srivastava, S. K.

    2016-04-01

    We present here a systematic first-principles study of electronic structure and local magnetic properties of Ce[Fe0.75M0.25]2 compounds, where M is a 3d, 4d or 5d transition or post-transition element, using the generalized gradient approximation of the density functional theory. The d-f band hybridizations existing in CeFe2 get modified by the impurity M in an orderly manner across a period for each impurity series: the hybridization is strongest for the Mn group impurity in the period and gets diminished on either side of it. The weakening of the d-f hybridization strength is also associated with a relative localization of the Ce 4f states with respect to the delocalized 4f states in CeFe2. The above effects are most prominent for 3d impurity series, while for 4d and 5d impurities, the hybridizations and relocalizations are relatively weak due primarily to the relatively extended nature of 4d and 5d wavefunctions. The Ce local moment is found to decrease from the CeFe2 value in proportion to the strength of relocalization, thus following almost the same orderly trend as obeyed by the d-f hybridization. Further, depending on the way the spin-up and spin-down densities of states of an impurity shift relative to the Fermi energy, the impurity local moments are highest for Mn or Fe group, reduce on either side, become zero for Ni to Ga, and are small but negative for V and Ti. The Ce hyperfine field is found to follow the M local moment in a linear fashion, and vice-versa.

  7. The Local Atomic Structure and Chemical Bonding in Sodium Tin Phases

    DOE PAGESBeta

    Baggetto, Loic; Bridges, Craig A.; Jumas, Dr. Jean-Claude; Mullins, David R.; Carroll, Kyler J.; Meisner, Roberta; Crumlin, Ethan; Liu, Xiason; Yang, Wanli; Veith, Gabriel M.

    2014-09-25

    To understand these electrochemically-derived materials we have reinvestigated the formation of Na-Sn alloys to identify all the phases which form when x ≥ 1 (NaxSn) and characterized the local bonding around the Sn atoms with X-ray diffraction, 119Sn M ssbauer spectroscopy, and X-ray absorption spectroscopies. The results from the well-defined crystallographic materials were compared to the spectroscopic measurements of the local Sn structures in the electrochemically prepared materials. The reinvestigation of the Na-Sn compounds yields a number of new results: (i) Na7Sn3 is a new thermodynamically-stable phase with a rhombohedral structure and R-3m space group; (ii) orthorhombic Na9Sn4 (Cmcm) hasmore » relatively slow formation kinetics suggesting why it does not form at room temperature during the electrochemical reaction; (iii) orthorhombic Na14.78Sn4 (Pnma), better described as Na16-xSn4, is Na-richer than cubic Na15Sn4 (I-43d). Characterization of electrochemically prepared Na-Sn alloys indicate that, at the exception of Na7Sn3 and Na15Sn4, different crystal structures than similar Na-Sn compositions prepared via classic solid state reactions are formed. These phases are composed of disordered structures characteristic of kinetic-driven solid-state amorphization reactions. In these structures, Sn coordinates in asymmetric environments, which differ significantly from the environments present in Na-Sn model compounds.« less

  8. The Local Atomic Structure and Chemical Bonding in Sodium Tin Phases

    SciTech Connect

    Baggetto, Loic; Bridges, Craig A.; Jumas, Dr. Jean-Claude; Mullins, David R.; Carroll, Kyler J.; Meisner, Roberta; Crumlin, Ethan; Liu, Xiason; Yang, Wanli; Veith, Gabriel M.

    2014-09-25

    To understand these electrochemically-derived materials we have reinvestigated the formation of Na-Sn alloys to identify all the phases which form when x ≥ 1 (NaxSn) and characterized the local bonding around the Sn atoms with X-ray diffraction, 119Sn M ssbauer spectroscopy, and X-ray absorption spectroscopies. The results from the well-defined crystallographic materials were compared to the spectroscopic measurements of the local Sn structures in the electrochemically prepared materials. The reinvestigation of the Na-Sn compounds yields a number of new results: (i) Na7Sn3 is a new thermodynamically-stable phase with a rhombohedral structure and R-3m space group; (ii) orthorhombic Na9Sn4 (Cmcm) has relatively slow formation kinetics suggesting why it does not form at room temperature during the electrochemical reaction; (iii) orthorhombic Na14.78Sn4 (Pnma), better described as Na16-xSn4, is Na-richer than cubic Na15Sn4 (I-43d). Characterization of electrochemically prepared Na-Sn alloys indicate that, at the exception of Na7Sn3 and Na15Sn4, different crystal structures than similar Na-Sn compositions prepared via classic solid state reactions are formed. These phases are composed of disordered structures characteristic of kinetic-driven solid-state amorphization reactions. In these structures, Sn coordinates in asymmetric environments, which differ significantly from the environments present in Na-Sn model compounds.

  9. Asymptotic near-nucleus structure of the electron-interaction potential in local effective potential theories

    SciTech Connect

    Qian, Zhixin; Sahni, Viraht

    2007-03-15

    In local effective potential theories of electronic structure, the electron correlations due to the Pauli exclusion principle, Coulomb repulsion, and correlation-kinetic effects, are all incorporated in the local electron-interaction potential v{sub ee}(r). In previous work, it has been shown that for spherically symmetric or sphericalized systems, the asymptotic near-nucleus expansion of this potential is v{sub ee}(r)=v{sub ee}(0)+{beta}r+O(r{sup 2}), with v{sub ee}(0) being finite. By assuming that the Schroedinger and local effective potential theory wave functions are analytic near the nucleus of atoms, we prove the following via quantal density functional theory (QDFT): (i) Correlations due to the Pauli principle and Coulomb correlations do not contribute to the linear structure; (ii) these Pauli and Coulomb correlations contribute quadratically; (iii) the linear structure is solely due to correlation-kinetic effects, the contributions of these effects being determined analytically. We also derive by application of adiabatic coupling constant perturbation theory via QDFT (iv) the asymptotic near-nucleus expansion of the Hohenberg-Kohn-Sham theory exchange v{sub x}(r) and correlation v{sub c}(r) potentials. These functions also approach the nucleus linearly with the linear term of v{sub x}(r) being solely due to the lowest-order correlation kinetic effects, and the linear term of v{sub c}(r) being due solely to the higher-order correlation kinetic contributions. The above conclusions are equally valid for systems of arbitrary symmetry, provided spherical averages of the properties are employed.

  10. Point process models for localization and interdependence of punctate cellular structures.

    PubMed

    Li, Ying; Majarian, Timothy D; Naik, Armaghan W; Johnson, Gregory R; Murphy, Robert F

    2016-07-01

    Accurate representations of cellular organization for multiple eukaryotic cell types are required for creating predictive models of dynamic cellular function. To this end, we have previously developed the CellOrganizer platform, an open source system for generative modeling of cellular components from microscopy images. CellOrganizer models capture the inherent heterogeneity in the spatial distribution, size, and quantity of different components among a cell population. Furthermore, CellOrganizer can generate quantitatively realistic synthetic images that reflect the underlying cell population. A current focus of the project is to model the complex, interdependent nature of organelle localization. We built upon previous work on developing multiple non-parametric models of organelles or structures that show punctate patterns. The previous models described the relationships between the subcellular localization of puncta and the positions of cell and nuclear membranes and microtubules. We extend these models to consider the relationship to the endoplasmic reticulum (ER), and to consider the relationship between the positions of different puncta of the same type. Our results do not suggest that the punctate patterns we examined are dependent on ER position or inter- and intra-class proximity. With these results, we built classifiers to update previous assignments of proteins to one of 11 patterns in three distinct cell lines. Our generative models demonstrate the ability to construct statistically accurate representations of puncta localization from simple cellular markers in distinct cell types, capturing the complex phenomena of cellular structure interaction with little human input. This protocol represents a novel approach to vesicular protein annotation, a field that is often neglected in high-throughput microscopy. These results suggest that spatial point process models provide useful insight with respect to the spatial dependence between cellular structures.

  11. Strain localization in ductile rocks: A comparison of natural and simulated pinch-and-swell structures

    NASA Astrophysics Data System (ADS)

    Peters, Max; Berger, Alfons; Herwegh, Marco; Regenauer-Lieb, Klaus

    2016-06-01

    We study pinch-and-swell structures in order to uncover the onset of strain localization and the change of deformation mechanisms in layered ductile rocks. To this end, boudinaged monomineralic veins embedded in an ultramylonitic matrix are analyzed quantitatively. The swells are built up by relatively undeformed original calcite grains, showing twinning and minor subgrain rotation recrystallization (SGR). Combined with progressive formation of high-angle misorientations between grains, indicative of SGR, severe grain size reduction defines the transition to the pinches. Accordingly, dynamically recrystallized grains have a strong crystallographic preferred orientation (CPO). Toward the necks, further grain size reduction, increasingly random misorientations, nucleation of new grains, and a loss of the CPO occur. We postulate that this microstructure marks the transition from dislocation to diffusion creep induced by strain localization. We confirm that the development of boudins is insensitive to original grain sizes and single-crystal orientations. In order to test these microstructural interpretations, a self-consistent numerical grain size evolution is implemented, based on thermo-mechanical principles, end-member flow laws and microphysical processes. Applying constant velocity and isothermal boundary conditions to a 3-layer finite element pure shear box, pinch-and-swell structures emerge out of the homogeneous layer through grain size softening at a critical state. Viscosity weakening due to elevated strain rates and dissipated heat from grain size reduction promotes strain rate weakening until a critical grain size is reached. At this point, a switch from dislocation to diffusion creep occurs. This state locks in at local steady states and is microstructurally expressed in pinches and swells, respectively. Thus, boudinage is identified as an energy attractor, identifying the high-energy steady state of an extending layered structure. We conclude from the

  12. TiO2 nanotube arrays for photocatalysis: Effects of crystallinity, local order, and electronic structure

    DOE PAGESBeta

    Liu, Jing; Hosseinpour, Pegah M.; Luo, Si; Heiman, Don; Menon, Latika; Arena, Dario A.; Lewis, Laura H.

    2014-11-19

    To furnish insight into correlations of electronic and local structure and photoactivity, arrays of short and long TiO₂ nanotubes were synthesized by electrochemical anodization of Ti foil, followed by thermal treatment in O₂ (oxidizing), Ar (inert), and H₂ (reducing) environments. The physical and electronic structures of these nanotubes were probed with x-ray diffraction, scanning electron microscopy, and synchrotron-based x-ray absorption spectroscopy, and correlated with their photocatalytic properties. The photocatalytic activity of the nanotubes was evaluated by monitoring the degradation of methyl orange under UV-VIS light irradiation. Results show that upon annealing at 350 °C all as-anodized amorphous TiO₂ nanotube samplesmore » partially transform to the anatase structure, with variations in the degree of crystallinity and in the concentration of local defects near the nanotubes' surface (~5 nm) depending on the annealing conditions. Degradation of methyl orange was not detectable for the as-anodized TiO₂ nanotubes regardless of their length. The annealed long nanotubes demonstrated detectable catalytic activity, which was more significant with the H₂-annealed nanotubes than with the Ar- and O₂-annealed nanotube samples. This enhanced photocatalytic response of the H₂-annealed long nanotubes relative to the other samples is positively correlated with the presence of a larger concentration of lattice defects (such as Ti3+ and anticipated oxygen vacancies) and a slightly lower degree of crystallinity near the nanotube surface. These physical and electronic structural attributes impact the efficacy of visible light absorption; moreover, the increased concentration of surface defects is postulated to promote the generation of hydroxyl radicals and thus accelerate the photodegradation of the methyl orange. The information obtained from this study provides unique insight into the role of the near-surface electronic and defect structure

  13. A new series of bis(ene-1,2-dithiolato)tungsten(IV), -(V), -(VI) complexes as reaction centre models of tungsten enzymes: preparation, crystal structures and spectroscopic properties.

    PubMed

    Sugimoto, Hideki; Hatakeda, Kohei; Toyota, Kazuo; Tatemoto, Susumu; Kubo, Minoru; Ogura, Takashi; Itoh, Shinobu

    2013-03-01

    The carbomethoxy substituted dithiolene ligand (L(COOMe)) enabled us to develop a series of new bis(ene-1,2-dithiolato)tungsten complexes including W(IV)O, W(IV)(OSiBuPh(2)), W(VI)O(2), W(VI)O(OSiBuPh(2)) and W(VI)O(S) core structures. By using these tungsten complexes, a systematic study of the terminal monodentate ligand effects has been performed on the structural, spectroscopic properties and reactivity. The structure and spectroscopic properties of the tungsten complexes have also been compared to those of the molybdenum complexes coordinated by the same ligand to investigate the effects of the metal ion (W vs. Mo). X-ray crystallographic analyses of the tungsten(IV) complexes have revealed that the tungsten centres adopt a distorted square pyramidal geometry with a dithiolene ligand having an ene-1,2-dithiolate form. On the other hand, the dioxotungsten(VI) complex exhibits an octahedral structure consisting of the bidentate L(COOMe) and two oxo groups, in which π-delocalization was observed between the W(VI)O(2) and ene-1,2-dithiolate units. The tungsten(IV) and dioxotungsten(VI) complexes are isostructural with the molybdenum counter parts. DFT calculation study of the W(VI)O(S) complex has indicated that the W=S bond of 2.2 Å is close to the bond length between the tungsten centre and ambiguously assigned terminal monodentate atom in aldehyde oxidoreductase of the tungsten enzyme. Resonance Raman (rR) spectrum of the W(VI)O(S) complex has shown the two inequivalent L(COOMe) ligands with respect to their bonding interactions with the tungsten centre, reproducing the appearance of two ν(C=C) stretches in the rR spectrum of aldehyde oxidoreductase. Sulfur atom transfer reaction from the W(VI)O(S) complex to triphenylphosphines has also been studied kinetically to demonstrate that the tungsten complex has a lower reactivity by about one-order of magnitude, when compared with its molybdenum counterpart.

  14. Local duality in spin structure functions g1(p) and g1(d)

    SciTech Connect

    Yelena Prok

    2006-02-01

    Inclusive double spin asymmetries obtained by scattering polarized electrons off polarized protons and deuterons have been analyzed to address the issue of quark hadron duality in the polarized spin structure functions gp 1 and gd 1. A polarized electron beam, solid polarized NH3 and ND3 targets and the CEBAF Large Acceptance Spectrometer (CLAS) in Hall B were used to collect the data. The resulting gp 1 and gd 1 were averaged over the nucleon resonance energy region (M local duality.

  15. Local Search Methods for Tree Chromosome Structure in a GA to Identify Functions

    NASA Astrophysics Data System (ADS)

    Matayoshi, Mitsukuni; Nakamura, Morikazu; Miyagi, Hayao

    In this paper, Local search methods for “Tree Chromosome Structure in a Genetic Algorithm to Identify Functions" which succeeds in function identifications are proposed. The proposed method aims at the identification success rate improvement and shortening identification time. The target functions of identification are composed of algebraic functions, primary transcendental functions, time series functions include a chaos function, and user-defined one-variable funcions. In testing, Kepler's the third law is added to Matayoshi's test functions(7)-(9). When some functions are identified, the improvement of identification rate and shortening time are indicated. However, we also report some ineffectual results, and give considerations.

  16. Soil resources and topography shape local tree community structure in tropical forests.

    PubMed

    Baldeck, Claire A; Harms, Kyle E; Yavitt, Joseph B; John, Robert; Turner, Benjamin L; Valencia, Renato; Navarrete, Hugo; Davies, Stuart J; Chuyong, George B; Kenfack, David; Thomas, Duncan W; Madawala, Sumedha; Gunatilleke, Nimal; Gunatilleke, Savitri; Bunyavejchewin, Sarayudh; Kiratiprayoon, Somboon; Yaacob, Adzmi; Supardi, Mohd N Nur; Dalling, James W

    2013-02-22

    Both habitat filtering and dispersal limitation influence the compositional structure of forest communities, but previous studies examining the relative contributions of these processes with variation partitioning have primarily used topography to represent the influence of the environment. Here, we bring together data on both topography and soil resource variation within eight large (24-50 ha) tropical forest plots, and use variation partitioning to decompose community compositional variation into fractions explained by spatial, soil resource and topographic variables. Both soil resources and topography account for significant and approximately equal variation in tree community composition (9-34% and 5-29%, respectively), and all environmental variables together explain 13-39% of compositional variation within a plot. A large fraction of variation (19-37%) was spatially structured, yet unexplained by the environment, suggesting an important role for dispersal processes and unmeasured environmental variables. For the majority of sites, adding soil resource variables to topography nearly doubled the inferred role of habitat filtering, accounting for variation in compositional structure that would previously have been attributable to dispersal. Our results, illustrated using a new graphical depiction of community structure within these plots, demonstrate the importance of small-scale environmental variation in shaping local community structure in diverse tropical forests around the globe.

  17. On-line structural damage localization and quantification using wireless sensors

    NASA Astrophysics Data System (ADS)

    Hsu, Ting-Yu; Huang, Shieh-Kung; Lu, Kung-Chung; Loh, Chin-Hsiung; Wang, Yang; Lynch, Jerome Peter

    2011-10-01

    In this paper, a wireless sensing system is designed to realize on-line damage localization and quantification of a structure using a frequency response function change method (FRFCM). Data interrogation algorithms are embedded in the computational core of the wireless sensing units to extract the necessary structural features, i.e. the frequency spectrum segments around eigenfrequencies, automatically from measured structural response for the FRFCM. Instead of the raw time history of the structural response, the extracted compact structural features are transmitted to the host computer. As a result, with less data transmitted from the wireless sensors, the energy consumed by the wireless transmission is reduced. To validate the performance of the proposed wireless sensing system, a six-story steel building with replaceable bracings in each story is instrumented with the wireless sensors for on-line damage detection during shaking table tests. The accuracy of the damage detection results using the wireless sensing system is verified through comparison with the results calculated from data recorded of a traditional wired monitoring system. The results demonstrate that, by taking advantage of collocated computing resources in wireless sensors, the proposed wireless sensing system can locate and quantify damage with acceptable accuracy and moderate energy efficiency.

  18. Social structure emerges via the interaction between local ecology and individual behaviour.

    PubMed

    Tanner, Colby J; Jackson, Andrew L

    2012-01-01

    1. The formation of groups is a fundamental aspect of social organization, but there are still many questions regarding how social structure emerges from individuals making non-random associations. 2. Although food distribution and individual phenotypic traits are known to separately influence social organization, this is the first study, to our knowledge, experimentally linking them to demonstrate the importance of their interaction in the emergence of social structure. 3. Using an experimental design in which food distribution was either clumped or dispersed, in combination with individuals that varied in exploratory behaviour, our results show that social structure can be induced in the otherwise non-social European shore crab (Carcinus maenas). 4. Regardless of food distribution, individuals with relatively high exploratory behaviour played an important role in connecting otherwise poorly connected individuals. In comparison, low exploratory individuals aggregated into cohesive, stable subgroups (moving together even when not foraging), but only in tanks where resources were clumped. No such non-foraging subgroups formed in environments where food was evenly dispersed. 5. Body size did not accurately explain an individual's role within the network for either type of food distribution. 6. Because of their synchronized movements and potential to gain social information, groups of low exploratory crabs were more effective than singletons at finding food. 7. Because social structure affects selection, and social structure is shown to be sensitive to the interaction between ecological and behavioural differences among individuals, local selective pressures are likely to reflect this interaction. PMID:21668891

  19. Three-dimensional velocity structure of the Galeras volcano (Colombia) from passive local earthquake tomography

    NASA Astrophysics Data System (ADS)

    Vargas, Carlos Alberto; Torres, Roberto

    2015-08-01

    A three-dimensional estimation of the Vp, Vs and Vp/Vs ratio structure at Galeras volcano was conducted by means of passive local earthquake tomography. 14,150 volcano-tectonic events recorded by 58 stations in the seismological network established for monitoring the volcanic activity by the Colombian Geological Survey - Pasto Volcano Observatory between the years 1989 and 2015, were inverted by using the LOTOS code. The seismic events are associated with shear-stress fractures in solid rock as a response to pressure induced by magma flow. Tomography resolution tests suggest a depth of imaging that yield 10 km from the summit of the main crater, illuminating a large portion of the volcanic structure and the interaction of tectonic features like the Buesaco and Silvia-Pijao faults. Full catalog tomographic inversion, that represents the stacked image of the volcanic structure or the most permanent features underneath the volcano, shows vertical structures aligned with seismicity beneath the main crater. We hypothesize that these structures correspond to a system of ducts or fractures through which magma and fluid phases flow up from deeper levels toward the top and related with the intersection of the surface traces of the Silvia-Pijao and Buesaco faults.

  20. HIERARCHICAL STELLAR STRUCTURES IN THE LOCAL GROUP DWARF GALAXY NGC 6822

    SciTech Connect

    Gouliermis, Dimitrios A.; Walter, Fabian; Schmeja, Stefan; Klessen, Ralf S.; De Blok, W. J. G. E-mail: walter@mpia-hd.mpg.d E-mail: rklessen@ita.uni-heidelberg.d

    2010-12-20

    We present a comprehensive study of the star cluster population and the hierarchical structure in the clustering of blue stars with ages {approx}<500 Myr in the Local Group dwarf irregular galaxy NGC 6822. Our observational material comprises the most complete optical stellar catalog of the galaxy from imaging with the Suprime-Cam at the 8.2 m Subaru Telescope. We identify 47 distinct star clusters with the application of the nearest-neighbor density method to this catalog for a detection threshold of 3{sigma} above the average stellar density. The size distribution of the detected clusters can be very well approximated by a Gaussian with a peak at {approx}68 pc. The total stellar masses of the clusters are estimated by extrapolating the cumulative observed stellar mass function of all clusters to be in the range 10{sup 3}-10{sup 4} M{sub sun}. Their number distribution is fitted very well by a power law with index {alpha} {approx} 1.5 {+-} 0.7, which is consistent with the cluster mass functions of other Local Group galaxies and the cluster initial mass function. In addition to the detected star clusters of the galaxy, the application of the nearest-neighbor density method for various density thresholds, other than 3{sigma}, enabled the identification of stellar concentrations in various lengthscales. The stellar density maps constructed with this technique provide a direct proof of hierarchically structured stellar concentrations in NGC 6822, in the sense that smaller dense stellar concentrations are located inside larger and looser ones. We illustrate this hierarchy by the so-called dendrogram, or structure tree of the detected stellar structures, which demonstrates that most of the detected structures split up into several substructures over at least three levels. We quantify the hierarchy of these structures with the use of the minimum spanning tree method. We find that structures detected at 1, 2, and 3{sigma} density thresholds are hierarchically constructed

  1. Implantable polymer/metal thin film structures for the localized treatment of cancer by Joule heating

    NASA Astrophysics Data System (ADS)

    Kan-Dapaah, Kwabena; Rahbar, Nima; Theriault, Christian; Soboyejo, Wole

    2015-04-01

    This paper presents an implantable polymer/metal alloy thin film structure for localized post-operative treatment of breast cancer. A combination of experiments and models is used to study the temperature changes due to Joule heating by patterned metallic thin films embedded in poly-dimethylsiloxane. The heat conduction within the device and the surrounding normal/cancerous breast tissue is modeled with three-dimensional finite element method (FEM). The FEM simulations are used to explore the potential effects of device geometry and Joule heating on the temperature distribution and lesion (thermal dose). The FEM model is validated using a gel model that mimics biological media. The predictions are also compared to prior results from in vitro studies and relevant in vivo studies in the literature. The implications of the results are discussed for the potential application of polymer/metal thin film structures in hyperthermic treatment of cancer.

  2. Fe local structure in Pt-free nitrogen-modified carbon based electrocatalysts: XAFS study

    NASA Astrophysics Data System (ADS)

    Witkowska, Agnieszka; Giuli, Gabriele; Renzi, Marco; Marzorati, Stefania; Yiming, Wubulikasimu; Nobili, Francesco; Longhi, Mariangela

    2016-05-01

    The paper presents a new results on the bonding environment (coordination number and geometry) and on oxidation states of Fe in nitrogen-modified Fe/C composites used as Pt-free catalysts for oxygen reduction in Direct Hydrogen Fuel Cells. Starting from glucose or fructose, two catalysts displaying different electrochemical performance were prepared and studied in the form of pristine powder and thin catalytic layer of electrode by Fe K-edge XAFS spectroscopy. The results show how the Fe local structure varies as a function of different synthesis conditions and how changes in the structural properties of the catalysts are related to fuel cell electrochemical performance increase during a cell activation period.

  3. Optimal sensor placement for maximum area coverage (MAC) for damage localization in composite structures

    NASA Astrophysics Data System (ADS)

    Thiene, M.; Sharif Khodaei, Z.; Aliabadi, M. H.

    2016-09-01

    In this paper an optimal sensor placement algorithm for attaining the maximum area coverage (MAC) within a sensor network is presented. The proposed novel approach takes into account physical properties of Lamb wave propagation (attenuation profile, direction dependant group velocity due to material anisotropy) and geometrical complexities (boundary reflections, presence of openings) of the structure. A feature of the proposed optimization approach lies in the fact that it is independent of characteristics of the damage detection algorithm (e.g. probability of detection) making it readily up-scalable to large complex composite structures such as aircraft stiffened composite panel. The proposed fitness function (MAC) is independent of damage parameters (type, severity, location). Statistical analysis carried out shows that the proposed optimum sensor network with MAC results in high probability of damage localization. Genetic algorithm is coupled with the fitness function to provide an efficient optimization strategy.

  4. Local structure study of Fe dopants in Ni-deficit Ni3Al alloys

    DOE PAGESBeta

    V. N. Ivanovski; Umicevic, A.; Belosevic-Cavor, J.; Lei, Hechang; Li, Lijun; Cekic, B.; Koteski, V.; Petrovic, C.

    2015-08-24

    We found that the local electronic and magnetic structure, hyperfine interactions, and phase composition of polycrystalline Ni–deficient Ni 3-x FexAl (x = 0.18 and 0.36) were investigated by means of 57 Fe Mössbauer spectroscopy. The samples were characterized by X–ray diffraction and magnetization measurements. The ab initio calculations performed with the projector augmented wave method and the calculations of the energies of iron point defects were done to elucidate the electronic structure and site preference of Fe doped Ni 3 Al. Moreover, the value of calculated electric field gradient tensor Vzz=1.6 1021Vm-2 matches well with the results of Mössbauer spectroscopymore » and indicates that the Fe atoms occupy Ni sites.« less

  5. Local structure of the halite-sylvine solid solution according to the computer simulation data

    SciTech Connect

    Urusov, V. S. Leonenko, E. V.

    2008-09-15

    The structural, elastic, and thermodynamic properties of halite NaCl and sylvine KCl and the miscibility properties of the NaCl-KCl solid solution found by computer simulation are in good agreement with the experimental data. Analysis of the relaxation of the solid solution structure suggests that both anion and cation sublattices are distorted; however, the anion sublattice is distorted much more strongly. Calculations of the local bond valence at all types of ions in the solid solution show opposite deviations from the balance at cations, whereas the general balance is retained. The values of the electrostatic potential in the ion positions reflect weakening of bonding in the solid solution with respect to its pure components. In addition, with an increase in the average interatomic distance in the first coordination sphere around cations, the modulus of the electrostatic potential at cations decreases.

  6. Oxygen Tuned Local Structure and Phase-Change Performance of Germanium Telluride.

    PubMed

    Zhou, Xilin; Du, Yonghua; Behera, Jitendra K; Wu, Liangcai; Song, Zhitang; Simpson, Robert E

    2016-08-10

    The effect of oxygen on the local structure of Ge atoms in GeTe-O materials has been investigated. Oxygen leads to a significant modification to the vibrational modes of Ge octahedra, which results from a decrease in its coordination. We find that a defective octahedral Ge network is the crucial fingerprint for rapid and reversible structural transitions in GeTe-based phase change materials. The appearance of oxide Raman modes confirms phase separation into GeO and TeO at high level O doping. Counterintuitively, despite the increase in crystallization temperature of oxygen doped GeTe-O phase change materials, when GeTe-O materials are used in electrical phase change memory cells, the electrical switching energy is lower than the pure GeTe material. This switching energy reduction is ascribed to the smaller change in volume, and therefore smaller enthalpy change, for the oxygen doped GeTe materials. PMID:27430363

  7. [Research of neuronal structures target localization based on Hilbert-Huang transform for neuronal discharges].

    PubMed

    Xue, Han; Qian, Zhiyu; Yang, Tianming

    2009-06-01

    Electrophysiological target localization is the key technology in microelectrode-guided stereotactic neurosurgery for Parkinson's disease (PD). A neuronal discharge signal analysis method based on Hilbert-Huang transform (HHT) was introduced. By decomposing the clinical microelectrode recording (MER) data of PD into intrinsic mode functions (IMFs), the marginal spectrums of IMFs were achieved, and the characteristic factor correlated with brain structure was explored, then the HHT characteristic factor curve of neuronal discharge signals of microelectrode piqure locus could be achieved. The structures of neuronal and boundaries can be distinguished by the characteristic factor curve, and then damage range and damage point can be identified. This method can assist clinicians in ascertaining operation target effectively and researching into the cases of PD.

  8. Structure and chromosomal localization of the human antidiuretic hormone receptor gene

    SciTech Connect

    Seibold, A.; Brabet, P.; Rosenthal, W.; Birnbaumer, M. )

    1992-11-01

    Applying a genomic DNA-expression approach, the authors cloned the gene and cDNA coding for the human antidiuretic hormone receptor, also called vasopressin V2 receptor' (V2R). The nucleotide sequence of both cloned DNAs provided the information to elucidate the structure of the isolated transcriptional unit. The structure of this gene is unusual in that it is the first G protein-coupled receptor gene that contains two very small intervening sequences, the second of which separates the region encoding the seventh transmembrane region from the rest of the open reading frame. The sequence information was used to synthesize appropriate oligonucleotides to be used as primers in the PCR. The V2R gene was localized by PCR using DNA from hybrid cells as template. The gene was found to reside in the q28-qter portion of the human X chromosome, a region identified as the locus for congential nephrogenic diabetes insipidus. 27 refs., 4 figs.

  9. Communication: Local structure-mobility relationships of confined fluids reverse upon supercooling.

    PubMed

    Bollinger, Jonathan A; Jain, Avni; Carmer, James; Truskett, Thomas M

    2015-04-28

    We examine the structural and dynamic properties of confined binary hard-sphere mixtures designed to mimic realizable colloidal thin films. Using computer simulations, governed by either Newtonian or overdamped Langevin dynamics, together with other techniques including a Fokker-Planck equation-based method, we measure the position-dependent and average diffusivities of particles along structurally isotropic and inhomogeneous dimensions of the fluids. At moderate packing fractions, local single-particle diffusivities normal to the direction of confinement are higher in regions of high total packing fraction; however, these trends are reversed as the film is supercooled at denser average packings. Auxiliary short-time measurements of particle displacements mirror data obtained for experimental supercooled colloidal systems. We find that average dynamics can be approximately predicted based on the distribution of available space for particle insertion across orders of magnitude in diffusivity regardless of the governing microscopic dynamics.

  10. Communication: Local structure-mobility relationships of confined fluids reverse upon supercooling

    NASA Astrophysics Data System (ADS)

    Bollinger, Jonathan A.; Jain, Avni; Carmer, James; Truskett, Thomas M.

    2015-04-01

    We examine the structural and dynamic properties of confined binary hard-sphere mixtures designed to mimic realizable colloidal thin films. Using computer simulations, governed by either Newtonian or overdamped Langevin dynamics, together with other techniques including a Fokker-Planck equation-based method, we measure the position-dependent and average diffusivities of particles along structurally isotropic and inhomogeneous dimensions of the fluids. At moderate packing fractions, local single-particle diffusivities normal to the direction of confinement are higher in regions of high total packing fraction; however, these trends are reversed as the film is supercooled at denser average packings. Auxiliary short-time measurements of particle displacements mirror data obtained for experimental supercooled colloidal systems. We find that average dynamics can be approximately predicted based on the distribution of available space for particle insertion across orders of magnitude in diffusivity regardless of the governing microscopic dynamics.

  11. Communication: Local structure-mobility relationships of confined fluids reverse upon supercooling.

    PubMed

    Bollinger, Jonathan A; Jain, Avni; Carmer, James; Truskett, Thomas M

    2015-04-28

    We examine the structural and dynamic properties of confined binary hard-sphere mixtures designed to mimic realizable colloidal thin films. Using computer simulations, governed by either Newtonian or overdamped Langevin dynamics, together with other techniques including a Fokker-Planck equation-based method, we measure the position-dependent and average diffusivities of particles along structurally isotropic and inhomogeneous dimensions of the fluids. At moderate packing fractions, local single-particle diffusivities normal to the direction of confinement are higher in regions of high total packing fraction; however, these trends are reversed as the film is supercooled at denser average packings. Auxiliary short-time measurements of particle displacements mirror data obtained for experimental supercooled colloidal systems. We find that average dynamics can be approximately predicted based on the distribution of available space for particle insertion across orders of magnitude in diffusivity regardless of the governing microscopic dynamics. PMID:25933745

  12. Local network structure of a-SiC:H and its correlation with dielectric function

    SciTech Connect

    Kageyama, Shota; Matsuki, Nobuyuki; Fujiwara, Hiroyuki

    2013-12-21

    The microscopic disordered structures of hydrogenated amorphous silicon carbide (a-Si{sub 1−x}C{sub x}:H) layers with different carbon contents have been determined based on the correlations between the dielectric function in the ultraviolet/visible region and the local bonding states studied by high-sensitivity infrared attenuated total reflection spectroscopy. We find that the microscopic structure of the a-Si{sub 1−x}C{sub x}:H layers fabricated by plasma-enhanced chemical vapor deposition shows a sharp structural transition at a boundary of x = 6.3 at. %. In the regime of x ≤ 6.3 at. %, (i) the amplitude of the a-SiC:H dielectric function reduces and (ii) the SiH{sub 2} content increases drastically with x, even though most of the C atoms are introduced into the tetrahedral sites without bonding with H. In the regime of x > 6.3 at. %, on the other hand, (i) the amplitude of the dielectric function reduces further and (ii) the concentration of the sp{sup 3} CH{sub n} (n = 2,3) groups increases. Moreover, we obtained the direct evidence that the sp{sup 2} C bonding state in the a-SiC matrix exists in the configuration of C = CH{sub 2} and the generation of the graphite-like C = CH{sub 2} unit suppresses the band gap widening significantly. At high C contents of x > 6.3 at. %, the a-SiC:H layers show quite porous structures due to the formation of microvoids terminated with the SiH{sub 2}/CH{sub n} groups. By taking the SiH{sub 2}/CH{sub n} microvoid generation in the network and the high-energy shift of the dielectric function by the local bonding states into account, the a-SiC:H dielectric function model has been established. From the analysis using this model, we have confirmed that the a-SiC:H optical properties in the ultraviolet/visible region are determined almost completely by the local network structures.

  13. Electronic transport in graphene structure: from weak to strong localization regimes

    NASA Astrophysics Data System (ADS)

    Lherbier, Aurelien

    2015-03-01

    Graphene, often named the wonder material for its many fascinating properties, has sparked out intense research activities over the last decade. Electronic transport in graphene became rapidly an important research field because of the early reported extremely high charge carrier mobility which triggered large expectations for nanoelectronic devices. Besides mobilities, graphene samples can exhibit particularly long electronic coherence lengths which allow for phase-related quantum transport phenomena such as the weak and strong localization transport regimes. This makes graphene a remarkable playground for fundamental studies of localization theory in low-dimensional systems. In this presentation, using tight-binding models enriched by first principle calculations, and a real-space Kubo-Greenwood method, multiscale simulations of the electronic transport in various graphene-based systems will be discussed. Such an approach allows for computing transport properties of systems containing millions of atoms reaching therefore the experimental sample size. In order to tailor graphene properties, chemical and/or structural modifications are widely used. However, such modifications act as scattering defects and usually deteriorate transport properties. Open a band gap while maintaining good mobility is a typical illustration of this dual problem. The influence of various chemical and structural defects will be analyzed. In particular, the consequences of unbalanced sublattice nitrogen doping in graphene and the case of highly defective graphene structures exhibiting strong Anderson insulator behaviors will be examined. Defects being even more detrimental for transport in 1D structures, a synthesis method that is free of defects is highly desirable. A solution is provided by a bottom-up chemistry approach where precursor monomers are self-assembled. The electronic transport and the potential for nanoelectronics of such defect-free carbon ribbons will also be discussed.

  14. Local and global semantic integration in an argument structure: ERP evidence from Korean.

    PubMed

    Nam, Yunju; Hong, Upyong

    2016-07-01

    The neural responses of Korean speakers were recorded while they read sentences that included local semantic mismatch between adjectives (A) and nouns (N) or/and global semantic mismatch between object nouns (N) and verbs (V), as well as the corresponding control sentences without any semantic anomalies. In Experiment 1 using verb-final declarative sentences (Nsubject [A-N]object V), the local A-N incongruence yielded an N400 effect at the object noun and a combination of N400 and a late negativity effect at the sentence final verb, whereas the global N-V incongruence yielded a biphasic N400 and P600 ERP pattern at the verb compared with the ERPs of same words in the control sentences respectively; in Experiment 2 using verb-initial object relative clause constructions ([Nsubject _V]rel [A-N]object …..) derived from the materials of Experiment 1, the effect of local incongruence changed notably such that not only an N400 but also an additional P600 effect was observed at the object noun, whereas the effect of the global incongruence remained largely the same (N400 and P600). Our theoretical interpretation of these results specifically focused on the reason for the P600 effects observed across different experiment conditions, which turned out to be attributable to (i) coordination of a semantic conflict, (ii) prediction disconfirmation, or (iii) argument structure processing breakdown.

  15. The effects of resource enrichment, dispersal, and predation on local and metacommunity structure.

    PubMed

    Cadotte, Marc W; Fortner, Allison M; Fukami, Tadashi

    2006-08-01

    Community structure is the observable outcome of numerous processes. We conducted a laboratory experiment using a microbial model system to disentangle effects of nutrient enrichment, dispersal, and predation on prey species richness and predator abundance at local and metacommunity scales. Prey species included: Chilomonas sp., Colpidium striatum, Colpoda cucullus, Paramecium tetraurelia, P. caudatum, Philodina sp., Spirostomum sp., Tetrahymena thermophila, and Uronema sp., and Stentor coeruleus was the predator used. We hypothesized that: (1) increased basal resources should maintain greater species richness and higher predator abundance; (2) dispersal should maintain greater species richness; and (3) predation should reduce species richness, especially in the high resource treatments relative to no-predator treatments. Our results support all three hypotheses. Further, we show that dispersal affects richness at the local community scale but not at the metacommunity scale. However, predation seems to have major effects at both the local and metacommunity scale. Overall, our results show that effects of resource enrichment, dispersal, and predation were mostly additive rather than interactive, indicating that it may be sometimes easier to understand their effects than generally thought due to complex interactive effects. PMID:16639564

  16. Structural health monitoring of localized internal corrosion in high temperature piping for oil industry

    NASA Astrophysics Data System (ADS)

    Eason, Thomas J.; Bond, Leonard J.; Lozev, Mark G.

    2015-03-01

    Crude oil is becoming more corrosive with higher sulfur concentration, chloride concentration, and acidity. The increasing presence of naphthenic acids in oils with various environmental conditions at temperatures between 150°C and 400°C can lead to different internal degradation morphologies in refineries that are uniform, non-uniform, or localized pitting. Improved corrosion measurement technology is needed to better quantify the integrity risk associated with refining crude oils of higher acid concentration. This paper first reports a consolidated review of corrosion inspection technology to establish the foundation for structural health monitoring of localized internal corrosion in high temperature piping. An approach under investigation is to employ flexible ultrasonic thin-film piezoelectric transducer arrays fabricated by the sol-gel manufacturing process for monitoring localized internal corrosion at temperatures up to 400°C. A statistical analysis of sol-gel transducer measurement accuracy using various time of flight thickness calculation algorithms on a flat calibration block is demonstrated.

  17. The effects of resource enrichment, dispersal, and predation on local and metacommunity structure.

    PubMed

    Cadotte, Marc W; Fortner, Allison M; Fukami, Tadashi

    2006-08-01

    Community structure is the observable outcome of numerous processes. We conducted a laboratory experiment using a microbial model system to disentangle effects of nutrient enrichment, dispersal, and predation on prey species richness and predator abundance at local and metacommunity scales. Prey species included: Chilomonas sp., Colpidium striatum, Colpoda cucullus, Paramecium tetraurelia, P. caudatum, Philodina sp., Spirostomum sp., Tetrahymena thermophila, and Uronema sp., and Stentor coeruleus was the predator used. We hypothesized that: (1) increased basal resources should maintain greater species richness and higher predator abundance; (2) dispersal should maintain greater species richness; and (3) predation should reduce species richness, especially in the high resource treatments relative to no-predator treatments. Our results support all three hypotheses. Further, we show that dispersal affects richness at the local community scale but not at the metacommunity scale. However, predation seems to have major effects at both the local and metacommunity scale. Overall, our results show that effects of resource enrichment, dispersal, and predation were mostly additive rather than interactive, indicating that it may be sometimes easier to understand their effects than generally thought due to complex interactive effects.

  18. Polarization dependent soft x-ray spectro-microscopy of local spin structures

    NASA Astrophysics Data System (ADS)

    Robertson, Maccallum; Agostino, Christopher; Im, Mi-Young; Montoya, Sergio; Fullerton, Eric; Fischer, Peter

    Quantitative information about element-specific contributions to local magnetic spin and orbital moments is readily available by XMCD spectroscopy and images of magnetic domain patterns with a few tens of nanometer spatial resolution. We show that the x-ray spectroscopic analysis of x-ray microscopy images provides quantitative information about local spin structures. We have investigated two prototypical multilayered PMA film systems prepared by sputtering, specifically (Co 0.3 nm/Pt 0.5 nm)x30 and (Fe 0.7nm/Gd 0.4nm)x100 systems. A spectroscopic sequence of full-field magnetic transmission soft x-ray microscopy (MTXM) images covering about 8mm field-of-views with a spatial resolution of about 20nm were recorded across the Co and Fe L edges, resp. To modulate the magnetic contrast, two sets of images were obtained with left and right circular polarization. Standard XMCD spectroscopy analysis procedures were applied to retrieve the local spectroscopic behavior. We observe a decrease of the L3/L2 ratio when approaching the domain walls, indicating a non-uniform spin configuration along the vertical profile of a domain, which we will discuss in view of both systems' magnetic anisotropies. U.S. DOE under Contract No. DE-AC02-05-CH11231.

  19. Waveform inversion for localized seismic structure and its application to D

    NASA Astrophysics Data System (ADS)

    Kawai, K.; Geller, R. J.; Fuji, N.; Konishi, K.

    2008-12-01

    In order to fully extract information on localized seismic structure from observed seismic data, we have developed a methodology for seismic waveform inversion. The calculation of synthetic seismograms and their partial derivatives are the key steps in such an inversion. We have developed accurate and efficient methods for calculating broadband synthetic seismograms for spherically symmetric transversely isotropic media for both shallow and deep events, which allows us to compute synthetics up to 2 Hz or higher frequencies (Kawai et al. 2006, GJI). Then, wWe formulate the inverse problem of waveform inversion for localized structure using the efficient algorithm of Geller and Hara (1993), computing partial derivatives for the 3-D anisotropic elastic parameters, including anelasticity, at particular points in space. Our method allows us to conduct both local and multi-scale global waveform inversion using pixel (or local shell) parameterization. We previouslyhave conducted waveform inversion for the vertical profile of the shear velocity in the lowermost mantle beneath Central America and the Arctic, beneath which the shear velocity is faster than the global average (Kawai et al., 2007ab, GRL). The obtained models suggest that the S-velocity increase in D'' may be localized in the zone from 100-200 km above the core-mantle boundary (CMB), while the S-velocity does not significantly deviate from PREM in the zone from 0-100 km above the CMB. In this studywork, we studied D'' beneath the Pacific, where the S-velocity is supposed thought to be slower than the global average on the basis of by many tomographic studies. models (e.g. Takeuchi 2007). We use the transverse component of broadband waveforms (for the period range, 8- 200 s). observed waveforms. We found 1-1.5% velocity decreases and increases in the zones from 400-500 km and from 300-400 km above the CMB, respectively. In addition, we found 0.5-1% velocity increases and decreases in the zones from 100-200 km

  20. Local structure based method for prediction of the biochemical function of proteins: Applications to glycoside hydrolases.

    PubMed

    Parasuram, Ramya; Mills, Caitlyn L; Wang, Zhouxi; Somasundaram, Saroja; Beuning, Penny J; Ondrechen, Mary Jo

    2016-01-15

    Thousands of protein structures of unknown or uncertain function have been reported as a result of high-throughput structure determination techniques developed by Structural Genomics (SG) projects. However, many of the putative functional assignments of these SG proteins in the Protein Data Bank (PDB) are incorrect. While high-throughput biochemical screening techniques have provided valuable functional information for limited sets of SG proteins, the biochemical functions for most SG proteins are still unknown or uncertain. Therefore, computational methods for the reliable prediction of protein function from structure can add tremendous value to the existing SG data. In this article, we show how computational methods may be used to predict the function of SG proteins, using examples from the six-hairpin glycosidase (6-HG) and the concanavalin A-like lectin/glucanase (CAL/G) superfamilies. Using a set of predicted functional residues, obtained from computed electrostatic and chemical properties for each protein structure, it is shown that these superfamilies may be sorted into functional families according to biochemical function. Within these superfamilies, a total of 18 SG proteins were analyzed according to their predicted, local functional sites: 13 from the 6-HG superfamily, five from the CAL/G superfamily. Within the 6-HG superfamily, an uncharacterized protein BACOVA_03626 from Bacteroides ovatus (PDB 3ON6) and a hypothetical protein BT3781 from Bacteroides thetaiotaomicron (PDB 2P0V) are shown to have very strong active site matches with exo-α-1,6-mannosidases, thus likely possessing this function. Also in this superfamily, it is shown that protein BH0842, a putative glycoside hydrolase from Bacillus halodurans (PDB 2RDY), has a predicted active site that matches well with a known α-L-galactosidase. In the CAL/G superfamily, an uncharacterized glycosyl hydrolase family 16 protein from Mycobacterium smegmatis (PDB 3RQ0) is shown to have local structural

  1. Capturing ultrafast photoinduced local structural distortions of BiFeO3

    PubMed Central

    Wen, Haidan; Sassi, Michel; Luo, Zhenlin; Adamo, Carolina; Schlom, Darrell G.; Rosso, Kevin M.; Zhang, Xiaoyi

    2015-01-01

    The interaction of light with materials is an intensively studied research forefront, in which the coupling of radiation energy to selective degrees of freedom offers contact-free tuning of functionalities on ultrafast time scales. Capturing the fundamental processes and understanding the mechanism of photoinduced structural rearrangement are essential to applications such as photo-active actuators and efficient photovoltaic devices. Using ultrafast x-ray absorption spectroscopy aided by density functional theory calculations, we reveal the local structural arrangement around the transition metal atom in a unit cell of the photoferroelectric archetype BiFeO3 film. The out-of-plane elongation of the unit cell is accompanied by the in-plane shrinkage with minimal change of interaxial lattice angles upon photoexcitation. This anisotropic elastic deformation of the unit cell is driven by localized electric field as a result of photoinduced charge separation, in contrast to a global lattice constant increase and lattice angle variations as a result of heating. The finding of a photoinduced elastic unit cell deformation elucidates a microscopic picture of photocarrier-mediated non-equilibrium processes in polar materials. PMID:26463128

  2. The local structure and ferromagnetism in Fe-implanted SrTiO₃ single crystals

    SciTech Connect

    Lobacheva, O. Chavarha, M.; Yiu, Y. M.; Sham, T. K.; Goncharova, L. V.

    2014-07-07

    We report a connection between the local structure of low-level Fe impurities and vacancies as the cause of ferromagnetic behavior observed in strontium titanate single crystals (STO), which were implanted with Fe and Si ions at different doses then annealed in oxygen. The effects of Fe doping and post-implantation annealing of STO were studied by X-ray Absorption Near Edge Structure (XANES) spectroscopy and Superconducting Quantum Interference Device magnetometry. XANES spectra for Fe and Ti K- and L-edge reveal the changes in the local environment of Fe and Ti following the implantation and annealing steps. The annealing in oxygen atmosphere partially healed implantation damages and changed the oxidation state of the implanted iron from metallic Fe⁰ to Fe²⁺/Fe³⁺ oxide. The STO single crystals were weak ferromagnets prior to implantation. The maximum saturation moment was obtained after our highest implantation dose of 2×10¹⁶ Fe atom/cm², which could be correlated with the metallic Fe⁰ phases in addition to the presence of O/Ti vacancies. After recrystallization annealing, the ferromagnetic response disappears. Iron oxide phases with Fe²⁺ and Fe³⁺ corresponding to this regime were identified and confirmed by calculations using Real Space Multiple Scattering program (FEFF9).

  3. Robust point matching for nonrigid shapes by preserving local neighborhood structures.

    PubMed

    Zheng, Yefeng; Doermann, David

    2006-04-01

    In previous work on point matching, a set of points is often treated as an instance of a joint distribution to exploit global relationships in the point set. For nonrigid shapes, however, the local relationship among neighboring points is stronger and more stable than the global one. In this paper, we introduce the lotion of a neighborhood structure for the general point matching problem. We formulate point matching as an optimization problem to preserve local neighborhood structures during matching. Our approach has a simple graph matching interpretation, where each point is a node in the graph, and two nodes are connected by an edge if they are neighbors. The optimal match between two graphs is the one that maximizes the number of matched edges. Existing techniques are leveraged to search for an optimal solution with the shape context distance used to initialize the graph matching, followed by relaxation labeling updates for refinement. Extensive experiments show the robustness of our approach under deformation, noise in point locations, outliers, occlusion, and rotation. It outperforms the shape context and TPS-RPM algorithms on most scenarios.

  4. Comparison of large-scale structures and velocities in the local universe

    NASA Technical Reports Server (NTRS)

    Yahil, Amos

    1994-01-01

    Comparison of the large-scale density and velocity fields in the local universe shows detailed agreement, strengthening the standard paradigm of the gravitational origin of these structures. Quantitative analysis can determine the cosmological density parameter, Omega, and biasing factor, b; there is virtually no sensitivity in any local analyses to the cosmologial constant, lambda. Comparison of the dipole anisotropy of the cosmic microwave background with the acceleration due to the Infrared Astronomy Satellite (IRAS) galaxies puts the linear growth factor in the range beta approximately equals Omega (exp 0.6)/b = 0.6(+0.7/-0.3) (95% confidence). A direct comparison of the density and velocity fields of nearby galaxies gives beta = 1.3 (+0.7/-0.6), and from nonlinear analysis the weaker limit (Omega greater than 0.45 for b greater than 0.5 (again 95% confidence). A tighter limit (Omega greater than 0.3 (4-6 sigma)), is obtained by a reconstruction of the probability distribution function of the initial fluctuations from which the structures observed today arose. The last two methods depend critically on the smooth velocity field determined from the observed velocities of nearby galaxies by the POTENT method. A new analysis of these velocities, with more than three times the data used to obtain the above quoted results, is now underway and promises to tighten the uncertainties considerably, as well as reduce systematic bias.

  5. Capturing ultrafast photoinduced local structural distortions of BiFeO3

    DOE PAGESBeta

    Wen, Haidan; Sassi, Michel JPC; Luo, Zhenlin; Adamo, Carolina; Schlom, Darrell; Rosso, Kevin M.; Zhang, Xiaoyi

    2015-10-14

    The interaction of light with materials is an intensively studied research forefront, in which the coupling of radiation energy to selective degrees of freedom offers contact-free tuning of functionalities on ultrafast time scales. Capturing the fundamental processes and understanding the mechanism of photoinduced structural rearrangement are essential to applications such as photo-active actuators and efficient photovoltaic devices. Using ultrafast x-ray absorption spectroscopy aided by density functional theory calculations, we reveal the local structural arrangement around the transition metal atom in a unit cell of the photoferroelectric archetype BiFeO3 film. The out-of-plane elongation of the unit cell is accompanied by themore » in-plane shrinkage with minimal change of interaxial lattice angles upon photoexcitation. This uniaxial elastic deformation of the unit cell is driven by localized electric field as a result of photoinduced charge separation, in contrast to a global lattice constant increase and lattice angle variations as a result of heating. The finding of a photoinduced elastic unit cell deformation elucidates a microscopic picture of photocarrier-mediated nonequilibrium processes in polar materials.« less

  6. Effects of the local resonance on the wave propagation in periodic frame structures: generalized Newtonian mechanics.

    PubMed

    Chesnais, Céline; Boutin, Claude; Hans, Stéphane

    2012-10-01

    This work is devoted to the study of the wave propagation in infinite two-dimensional structures made up of the periodic repetition of frames. Such materials are highly anisotropic and, because of lack of bracing, can present a large contrast between the shear and compression deformabilities. Moreover, when the thickness to length ratio of the frame elements is small, these elements can resonate in bending at low frequencies when compressional waves propagate in the structure. The frame size being small compared to the wavelength of the compressional waves, the homogenization method of periodic discrete media is extended to situations with local resonance, and it is applied to identify the macroscopic behavior at the leading order. In particular, the local resonance in bending leads to an effective mass different from the real mass and to the generalization of the Newtonian mechanics at the macroscopic scale. Consequently, compressional waves become dispersive and frequency bandgaps occur. The physical origin of these phenomena at the microscopic scale is also presented. Finally, a method is proposed for the design of such materials. PMID:23039554

  7. Capturing ultrafast photoinduced local structural distortions of BiFeO3

    NASA Astrophysics Data System (ADS)

    Wen, Haidan; Sassi, Michel; Luo, Zhenlin; Adamo, Carolina; Schlom, Darrell G.; Rosso, Kevin M.; Zhang, Xiaoyi

    2015-10-01

    The interaction of light with materials is an intensively studied research forefront, in which the coupling of radiation energy to selective degrees of freedom offers contact-free tuning of functionalities on ultrafast time scales. Capturing the fundamental processes and understanding the mechanism of photoinduced structural rearrangement are essential to applications such as photo-active actuators and efficient photovoltaic devices. Using ultrafast x-ray absorption spectroscopy aided by density functional theory calculations, we reveal the local structural arrangement around the transition metal atom in a unit cell of the photoferroelectric archetype BiFeO3 film. The out-of-plane elongation of the unit cell is accompanied by the in-plane shrinkage with minimal change of interaxial lattice angles upon photoexcitation. This anisotropic elastic deformation of the unit cell is driven by localized electric field as a result of photoinduced charge separation, in contrast to a global lattice constant increase and lattice angle variations as a result of heating. The finding of a photoinduced elastic unit cell deformation elucidates a microscopic picture of photocarrier-mediated non-equilibrium processes in polar materials.

  8. Capturing ultrafast photoinduced local structural distortions of BiFeO3

    SciTech Connect

    Wen, Haidan; Sassi, Michel JPC; Luo, Zhenlin; Adamo, Carolina; Schlom, Darrell; Rosso, Kevin M.; Zhang, Xiaoyi

    2015-10-14

    The interaction of light with materials is an intensively studied research forefront, in which the coupling of radiation energy to selective degrees of freedom offers contact-free tuning of functionalities on ultrafast time scales. Capturing the fundamental processes and understanding the mechanism of photoinduced structural rearrangement are essential to applications such as photo-active actuators and efficient photovoltaic devices. Using ultrafast x-ray absorption spectroscopy aided by density functional theory calculations, we reveal the local structural arrangement around the transition metal atom in a unit cell of the photoferroelectric archetype BiFeO3 film. The out-of-plane elongation of the unit cell is accompanied by the in-plane shrinkage with minimal change of interaxial lattice angles upon photoexcitation. This uniaxial elastic deformation of the unit cell is driven by localized electric field as a result of photoinduced charge separation, in contrast to a global lattice constant increase and lattice angle variations as a result of heating. The finding of a photoinduced elastic unit cell deformation elucidates a microscopic picture of photocarrier-mediated nonequilibrium processes in polar materials.

  9. The local structure and ferromagnetism in Fe-implanted SrTiO3 single crystals

    NASA Astrophysics Data System (ADS)

    Lobacheva, O.; Chavarha, M.; Yiu, Y. M.; Sham, T. K.; Goncharova, L. V.

    2014-07-01

    We report a connection between the local structure of low-level Fe impurities and vacancies as the cause of ferromagnetic behavior observed in strontium titanate single crystals (STO), which were implanted with Fe and Si ions at different doses then annealed in oxygen. The effects of Fe doping and post-implantation annealing of STO were studied by X-ray Absorption Near Edge Structure (XANES) spectroscopy and Superconducting Quantum Interference Device magnetometry. XANES spectra for Fe and Ti K- and L-edge reveal the changes in the local environment of Fe and Ti following the implantation and annealing steps. The annealing in oxygen atmosphere partially healed implantation damages and changed the oxidation state of the implanted iron from metallic Fe0 to Fe2+/Fe3+ oxide. The STO single crystals were weak ferromagnets prior to implantation. The maximum saturation moment was obtained after our highest implantation dose of 2 × 1016 Fe atom/cm2, which could be correlated with the metallic Fe0 phases in addition to the presence of O/Ti vacancies. After recrystallization annealing, the ferromagnetic response disappears. Iron oxide phases with Fe2+ and Fe3+ corresponding to this regime were identified and confirmed by calculations using Real Space Multiple Scattering program (FEFF9).

  10. Comparative study of local structure of two cyanobiphenyl liquid crystals by molecular dynamics method

    SciTech Connect

    Gerts, Egor D. Komolkin, Andrei V.; Burmistrov, Vladimir A.; Alexandriysky, Victor V.; Dvinskikh, Sergey V.

    2014-08-21

    Fully-atomistic molecular dynamics simulations were carried out on two similar cyanobiphenyl nematogens, HO-6OCB and 7OCB, in order to study effects of hydrogen bonds on local structure of liquid crystals. Comparable length of these two molecules provides more evident results on the effects of hydrogen bonding. The analysis of radial and cylindrical distribution functions clearly shows the differences in local structure of two mesogens. The simulations showed that anti-parallel alignment is preferable for the HO-6OCB. Hydrogen bonds between OH-groups are observed for 51% of HO-6OCB molecules, while hydrogen bonding between CN- and OH-groups occurs only for 16% of molecules. The lifetimes of H-bonds differ due to different mobility of molecular fragments (50 ps for N⋅⋅⋅H–O and 41 ps for O⋅⋅⋅H–O). Although the standard Optimized Potentials for Liquid Simulations - All-Atom force field cannot reproduce some experimental parameters quantitatively (order parameters are overestimated, diffusion coefficients are not reproduced well), the comparison of relative simulated results for the pair of mesogens is nevertheless consistent with the same relative experimental parameters. Thus, the comparative study of simulated and experimental results for the pair of similar liquid crystals still can be assumed plausible.

  11. Spatially localized structures and oscillons in atomic Bose-Einstein condensates confined in optical lattices

    NASA Astrophysics Data System (ADS)

    Charukhchyan, M. V.; Sedov, E. S.; Arakelian, S. M.; Alodjants, A. P.

    2014-06-01

    We consider the problem of formation of small-amplitude spatially localized oscillatory structures for atomic Bose-Einstein condensates confined in two- and three-dimensional optical lattices, respectively. Our approach is based on applying the regions with different signs of atomic effective masses where an atomic system exhibits effective hyperbolic dispersion within the first Brillouin zone. By using the kp method we have demonstrated mapping of the initial Gross-Pitaevskii equation on nonlinear Klein-Gordon and/or Ginzburg-Landau-Higgs equations, which is inherent in matter fields within ϕ4-field theories. Formation of breatherlike oscillating localized states—atomic oscillons—as well as kink-shaped states have been predicted in this case. Apart from classical field theories atomic field oscillons occurring in finite lattice structures possess a critical number of particles for their formation. The obtained results pave the way to simulating some analogues of fundamental cosmological processes occurring during our Universe's evolution and to modeling nonlinear hyperbolic metamaterials with condensed matter (atomic) systems.

  12. Effects of the local resonance on the wave propagation in periodic frame structures: generalized Newtonian mechanics.

    PubMed

    Chesnais, Céline; Boutin, Claude; Hans, Stéphane

    2012-10-01

    This work is devoted to the study of the wave propagation in infinite two-dimensional structures made up of the periodic repetition of frames. Such materials are highly anisotropic and, because of lack of bracing, can present a large contrast between the shear and compression deformabilities. Moreover, when the thickness to length ratio of the frame elements is small, these elements can resonate in bending at low frequencies when compressional waves propagate in the structure. The frame size being small compared to the wavelength of the compressional waves, the homogenization method of periodic discrete media is extended to situations with local resonance, and it is applied to identify the macroscopic behavior at the leading order. In particular, the local resonance in bending leads to an effective mass different from the real mass and to the generalization of the Newtonian mechanics at the macroscopic scale. Consequently, compressional waves become dispersive and frequency bandgaps occur. The physical origin of these phenomena at the microscopic scale is also presented. Finally, a method is proposed for the design of such materials.

  13. Structure of the pilus assembly protein TadZ from Eubacterium rectale: Implications for polar localization

    PubMed Central

    Xu, Qingping; Christen, Beat; Chiu, Hsiu-Ju; Jaroszewski, Lukasz; Klock, Heath E.; Knuth, Mark W.; Miller, Mitchell D.; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Figurski, David H.; Shapiro, Lucy; Wilson, Ian A.

    2011-01-01

    Summary The tad (tight adherence) locus encodes a protein translocation system that produces a novel variant of type IV pili. The pilus assembly protein TadZ (called CpaE in Caulobacter crescentus) is ubiquitous in tad loci, but is absent in other type IV pilus biogenesis systems. The crystal structure of TadZ from E. rectale (ErTadZ), in complex with ATP and Mg2+, was determined to 2.1 Å resolution. ErTadZ contains an atypical ATPase domain with a variant of a deviant Walker-A motif that retains ATP binding capacity while displaying only low intrinsic ATPase activity. The bound ATP plays an important role in dimerization of ErTadZ. The N-terminal atypical receiver domain resembles the canonical receiver domain of response regulators, but has a degenerate, stripped-down “active site”. Homology modeling of the N-terminal atypical receiver domain of CpaE indicates that it has a conserved protein-protein binding surface similar to that of the polar localization module of the social mobility protein FrzS, suggesting a similar function. Our structural results also suggest that TadZ localizes to the pole through the atypical receiver domain during early stage of pili biogenesis, and functions as a hub for recruiting other pili components, thus providing insights into the Tad pilus assembly process. PMID:22211578

  14. The role of impact structures in localizing explosive volcanism on a contracting planet: Mercury

    NASA Astrophysics Data System (ADS)

    Thomas, R. J.; Rothery, D. A.; Conway, S. J.; Anand, M.

    2015-10-01

    A long history of global contraction on Mercury is attested to by thousands of ridges and scarps, thought to be the surface expression of thrust faults[1]. The resulting compressive crustal stress presents an obstacle to surface volcanism on the planet, inhibiting magma ascent from depth. Nevertheless, volcanic vents and deposits indicate that explosive volcanism persisted on the planet until as recently as 1 Ga[2]. The common localization of this volcanism within impact craters and inwards of the rims of large impact basins [3]indicates that impact structures play a role in allowing volcanic eruption on this contracting body.By making a comparison with explosive volcanism within impact craters on the Moon, we investigate how ascending magma and impact structures interact on a local scale to facilitate such eruptions on Mercury. Additionally, in light of the surprisingly low number of large impact basins on Mercury[4], we investigate whether the detection of clusters of sites of explosive volcanism can provide evidence for the location of ancient impact basins that are no longer detectable morphologically.

  15. Structure of exhaust jets produced by magnetic reconnection localized in the out-of-plane direction

    NASA Astrophysics Data System (ADS)

    Pritchett, P. L.

    2015-01-01

    Three-dimensional electromagnetic particle-in-cell simulations are used to investigate the structure of exhaust jets produced by magnetic reconnection localized in the out-of-plane direction. The localized reconnection is produced by periodically blocking the cross-tail current density, a procedure that has effects analogous to those produced by the assumption of a region of anomalous resistivity in fluid treatments of reconnection. The width of the blocking region is varied between 4 and 24di, where di is the ion inertial length. After an initial displacement in the electron-drift direction, the jet front undergoes a marked expansion in the ion-drift direction, reaching a total cross-tail width of 15-20di regardless of the initial width. The jet front breaks up into small-scale finger structures of the order of 1-2di in width, which appears to be due to the action of the ballooning/interchange instability. Ahead of the front, the ion pressure Pixx is increased due to reflection of ions from the moving front and the penetration of high-speed ions in the jet through the front. The ion temperature Tixx exhibits a minimum within the front, while the electron temperature is enhanced in the front. The properties of the reconnection-generated fronts are compared and contrasted with those of interchange heads produced by a decreasing entropy profile.

  16. Capturing ultrafast photoinduced local structural distortion of BiFeO3

    SciTech Connect

    Wen, Haidan; Sassi, Michel; Luo, Zhenlin; Adamo, Carolina; Schlom, Darrell G.; Rosso, Kevin M.; Zhang, Xiaoyi

    2015-10-14

    The interaction of light with materials is an intensively studied research forefront, in which the coupling of radiation energy to selective degrees of freedom offers contact-free tuning of functionalities on ultrafast time scales. Capturing the fundamental processes and understanding the mechanism of photoinduced structural rearrangement are essential to applications such as photo-active actuators and efficient photovoltaic devices. Using ultrafast x-ray absorption spectroscopy aided by density functional theory calculations, we reveal the local structural arrangement around the transition metal atom in a unit cell of the photoferroelectric archetype BiFeO3 film. The out-of-plane elongation of the unit cell is accompanied by the in-plane shrinkage with minimal change of interaxial lattice angles upon photoexcitation. This anisotropic elastic deformation of the unit cell is driven by localized electric field as a result of photoinduced charge separation, in contrast to a global lattice constant increase and lattice angle variations as a result of heating. The finding of a photoinduced elastic unit cell deformation elucidates a microscopic picture of photocarrier-mediated non-equilibrium processes in polar materials.

  17. Widespread signatures of local mRNA folding structure selection in four Dengue virus serotypes

    PubMed Central

    2015-01-01

    Background It is known that mRNA folding can affect and regulate various gene expression steps both in living organisms and in viruses. Previous studies have recognized functional RNA structures in the genome of the Dengue virus. However, these studies usually focused either on the viral untranslated regions or on very specific and limited regions at the beginning of the coding sequences, in a limited number of strains, and without considering evolutionary selection. Results Here we performed the first large scale comprehensive genomics analysis of selection for local mRNA folding strength in the Dengue virus coding sequences, based on a total of 1,670 genomes and 4 serotypes. Our analysis identified clusters of positions along the coding regions that may undergo a conserved evolutionary selection for strong or weak local folding maintained across different viral variants. Specifically, 53-66 clusters for strong folding and 49-73 clusters for weak folding (depending on serotype) aggregated of positions with a significant conservation of folding energy signals (related to partially overlapping local genomic regions) were recognized. In addition, up to 7% of these positions were found to be conserved in more than 90% of the viral genomes. Although some of the identified positions undergo frequent synonymous / non-synonymous substitutions, the selection for folding strength therein is preserved, and thus cannot be trivially explained based on sequence conservation alone. Conclusions The fact that many of the positions with significant folding related signals are conserved among different Dengue variants suggests that a better understanding of the mRNA structures in the corresponding regions may promote the development of prospective anti- Dengue vaccination strategies. The comparative genomics approach described here can be employed in the future for detecting functional regions in other pathogens with very high mutations rates. PMID:26449467

  18. Gas-Expanded Liquids: Synergism of Experimental and Computational Determinations of Local Structure

    SciTech Connect

    Charles A. Eckert; Charles L. Liotta; Rigoberto Hernandez

    2007-06-26

    This project focuses on the characterization of a new class of solvent systems called gas-expanded liquids (GXLs), targeted for green-chemistry processing. The collaboration has adopted a synergistic approach combining elements of molecular dynamics (MD) simulation and spectroscopic experiments to explore the local solvent behavior that could not be studied by simulation or experiment alone. The major accomplishments from this project are: • Applied MD simulations to explore the non-uniform structure of CO2/methanol and CO2/acetone GXLs and studied their dynamic behavior with self-diffusion coefficients and correlation functions • Studied local solvent structure and solvation behavior with a combination of spectroscopy and MD simulations • Measured transport properties of heterocyclic solutes in GXLs through Taylor-Aris diffusion techniques and compared these findings to those of MD simulations • Probed local polarity and specific solute-solvent interactions with Diels-Alder and SN2 reaction studies The broader scientific impact resulting from the research activities of this contract have been recognized by two recent awards: the Presidential Green Chemistry Award (Eckert & Liotta) and a fellowship in the American Association for the Advancement of Science (Hernandez). In addition to the technical aspects of this contract, the investigators have been engaged in a number of programs extending the broader impacts of this project. The project has directly supported the development of two postdoctoral researcher, four graduate students, and five undergraduate students. Several of the undergraduate students were co-funded by a Georgia Tech program, the Presidential Undergraduate Research Award. The other student, an African-American female graduated from Georgia Tech in December 2005, and was co-funded through an NSF Research and Education for Undergraduates (REU) award.

  19. Combining global and local measures for structure-based druggability predictions.

    PubMed

    Volkamer, Andrea; Kuhn, Daniel; Grombacher, Thomas; Rippmann, Friedrich; Rarey, Matthias

    2012-02-27

    Predicting druggability and prioritizing certain disease modifying targets for the drug development process is of high practical relevance in pharmaceutical research. DoGSiteScorer is a fully automatic algorithm for pocket and druggability prediction. Besides consideration of global properties of the pocket, also local similarities shared between pockets are reflected. Druggability scores are predicted by means of a support vector machine (SVM), trained, and tested on the druggability data set (DD) and its nonredundant version (NRDD). The DD consists of 1069 targets with assigned druggable, difficult, and undruggable classes. In 90% of the NRDD, the SVM model based on global descriptors correctly classifies a target as either druggable or undruggable. Nevertheless, global properties suffer from binding site changes due to ligand binding and from the pocket boundary definition. Therefore, local pocket properties are additionally investigated in terms of a nearest neighbor search. Local similarities are described by distance dependent histograms between atom pairs. In 88% of the DD pocket set, the nearest neighbor and the structure itself conform with their druggability type. A discriminant feature between druggable and undruggable pockets is having less short-range hydrophilic-hydrophilic pairs and more short-range lipophilic-lipophilic pairs. Our findings for global pocket descriptors coincide with previously published methods affirming that size, shape, and hydrophobicity are important global pocket descriptors for automatic druggability prediction. Nevertheless, the variety of pocket shapes and their flexibility upon ligand binding limit the automatic projection of druggable features onto descriptors. Incorporating local pocket properties is another step toward a reliable descriptor-based druggability prediction. PMID:22148551

  20. Automated global structure extraction for effective local building block processing in XCS.

    PubMed

    Butz, Martin V; Pelikan, Martin; Llorà, Xavier; Goldberg, David E

    2006-01-01

    Learning Classifier Systems (LCSs), such as the accuracy-based XCS, evolve distributed problem solutions represented by a population of rules. During evolution, features are specialized, propagated, and recombined to provide increasingly accurate subsolutions. Recently, it was shown that, as in conventional genetic algorithms (GAs), some problems require efficient processing of subsets of features to find problem solutions efficiently. In such problems, standard variation operators of genetic and evolutionary algorithms used in LCSs suffer from potential disruption of groups of interacting features, resulting in poor performance. This paper introduces efficient crossover operators to XCS by incorporating techniques derived from competent GAs: the extended compact GA (ECGA) and the Bayesian optimization algorithm (BOA). Instead of simple crossover operators such as uniform crossover or one-point crossover, ECGA or BOA-derived mechanisms are used to build a probabilistic model of the global population and to generate offspring classifiers locally using the model. Several offspring generation variations are introduced and evaluated. The results show that it is possible to achieve performance similar to runs with an informed crossover operator that is specifically designed to yield ideal problem-dependent exploration, exploiting provided problem structure information. Thus, we create the first competent LCSs, XCS/ECGA and XCS/BOA, that detect dependency structures online and propagate corresponding lower-level dependency structures effectively without any information about these structures given in advance.

  1. Clinal resistance structure and pathogen local adaptation in a serpentine flax-flax rust interaction.

    PubMed

    Springer, Yuri P

    2007-08-01

    Because disease resistance is a hallmark signature of pathogen-mediated selection pressure on hosts, studies of resistance structure (the spatial distribution of disease resistance genes among conspecific host populations) can provide valuable insights into the influence of pathogens on host evolution and spatial variation in the magnitude of their effects. To date few studies of wild plant-pathogen interactions have characterized resistance structure by sampling across the host's biogeographic range, and only a handful have paired such investigations with studies of disease levels under natural conditions. I used a greenhouse cross-inoculation experiment to characterize genetic resistance of 16 populations of California dwarf flax (Hesperolinon californicum) to attack by multiple samples of the rust fungus Melampsora lini. I documented a latitudinal cline in resistance structure, manifest across the host's biogeographic range, which mirrored almost identically a cline in infection prevalence documented through field surveys of disease in study populations. These results provide empirical evidence for clinal patterns of antagonistic selection pressure, demonstrate that such patterns can be manifest across broad biogeographic scales, and suggest that rates of disease prevalence in wild plant populations may be tightly linked to the distribution of host resistance genes. Tests for local adaptation of the fungus revealed evidence of the phenomenon (significantly greater infection in sympatric plant-fungal pairings) as well as the potential for substantial bias to be introduced into statistical analyses by spatial patterns of host resistance structure.

  2. Examining the Local Structure of Titanium Carbide Derived Carbons: Experiment and Simulation

    NASA Astrophysics Data System (ADS)

    Llobet, Anna; Palmer, Jeremy; Yeon, Sun-Hwa; Fischer, John; Gogotsi, Yury; Gubbins, Keith

    2010-03-01

    Titanium Carbide derived carbons (Ti-CDCs) are amorphous nanoporous materials synthesized by high-temperature chlorination of crystalline TiC [1]. Judicious choice of the synthesis conditions allow for fine control over many of the structural features of Ti-CDCs, enabling them to be optimized for a wide variety of energy-related applications [2]. We have combined both experimental and computational methods to investigate the structural and functional properties of Ti-CDCs. Atomic pair distributions functions obtained from neutron diffraction experiments reveal that the synthesis temperature has a dramatic effect on the local structural ordering in these materials and consequently their functional properties. Atomistic models for Ti-CDCs have also been developed with the aid of molecular dynamics. These models reproduce the observed experimental trends and are used to gain new insight into the complex structure-function relationship. 1. Gogotsi, Y. 2006. Carbon nanomaterials. CRC Press, Boca Raton 2. Dash et al. 2006. Carbon 44:2489-2497

  3. Effect of turbulence characteristics on local flame structure of H2 air premixed flames

    NASA Astrophysics Data System (ADS)

    Nada, Y.; Tanahashi, M.; Miyauchi, T.

    2004-04-01

    Direct numerical simulations (DNS) of turbulent premixed flames are conducted to investigate effects of turbulence characteristics on the local flame structure. A detailed kinetic mechanism including 12 reactive species and 27 elementary reactions is used to represent the H2-air reaction in turbulence. Numerical conditions of DNS can be classified into a wrinkled-flamelets regime, a corrugated-flamelets regime and thin reaction zones near the boundary of Karlovitz number Ka=1.0 of the turbulent-combustion diagram. For all cases, the distribution of heat-release rate shows a three-dimensionally connected sheet-like feature, even though the heat-release rate highly fluctuates along the flamefront. The heat-release rate tends to increase at the flamefronts that are convex towards the burnt side. For the turbulent premixed flames in the corrugated-flamelets regime, the handgrip structure is produced by the intrusion of the coherent fine-scale eddy into the flame and the heat-release rate in this structure increases up to 1.2 times of that of a laminar flame. In the wrinkled-flamelets regime, the spire-like structure of the flamefront is created due to the coherent fine-scale eddies in turbulence. By identifying flame elements in turbulence, their statistical characteristics are also discussed. This article was chosen from Selected Proceedings of the Third International Symposium on Turbulence and Shear Flow Phenomena (Sendai, Japan, 24-27 June 2003) ed N Kasagi et al.

  4. Study of the Local Structure of II-Vi Ternary Alloys by Extended X-Ray Absorption Fine Structure

    NASA Astrophysics Data System (ADS)

    Pong, Way-Faung

    Bondlengths, Debye-Waller factors, and site occupancy in the diluted magnetic semiconductors Zn_ {rm 1 - x}Mn_{ rm x}Se and Hg_{ rm 1 - x}Mn_{rm x}Te, and the narrow-gap semiconductor Hg _{rm 1 - x}Cd _{rm x}Te have been measured using extended x-ray absorption fine structure (EXAFS). The nearest-neighbor bond lengths in all of these alloys are found to be constant as a function of alloy composition within the experimental uncertainty of 0.01A. Because the average cation-cation distance changes with Mn composition, these results necessarily imply distortion of the tetrahedral bond angles. In the case of Zn_{rm 1 - x}Mn_{rm x} Se, the anion sublattice is shown to suffer the largest distortion, but the cation sublattice also exhibits some relaxation. The repercussions of these results are discussed, in terms of the amount of cation and anion sublattice distortion at low temperature and its connection to the superexchange mechanism occurring between the Mn ^{+2} ions and mediated by the intervening anion in Zn_{rm 1 - x}Mn_{rm x} Se. From the NN bond length relaxation results shown in this study and those reported elsewhere for the III -V-based and II-VI-based ternary compounds and DMS alloys, it appears that substitution of Mn^{+2 } ions into II-VI-based compounds causes greater local distortion, in general, than otherwise observed when group II cations are substituted for one another. We believe that the tetrahedral bond weakening in DMS is due to MN 3d-orbital (t_2) and anion p-orbital hybridization in DMS, leaving fewer p-orbitals available for tetrahedral bonding. This leads to the weakening of the bond force constants alpha, beta, as well as the bond becoming more ionic as Mn^{+2} is substituted into the II-VI-based compounds. Finally, the experimentally extended electron energy loss fine structure (EXELFS) technique, with modulations in the differential inelastic electron scattering cross -section above an absorption core edge, has been used in recent years to

  5. Structural inheritance, segmentation, and rift localization in the Gulf of Aden oblique rift

    NASA Astrophysics Data System (ADS)

    Bellahsen, Nicolas; Leroy, Sylvie; Autin, Julia; d'Acremont, Elia; Razin, Philippe; Husson, Laurent; Pik, Raphael; Watremez, Louise; Baurion, Celine; Beslier, Marie-Odile; Khanbari, Khaled; Ahmed, Abdulhakim

    2013-04-01

    The structural evolution of the Gulf of Aden passive margins was controlled by its oblique divergence kinematics, inherited structures, and the Afar hot spot. The rifting between Arabia and Somalia started at 35 Ma just before the hot spot paroxysm (at 30Ma) and lasted until 18Ma, when oceanic spreading started. Fieldwork suggests that rift parallel normal faults initiated in the (future) distal margins, after a first stage of distributed rifting, and witness the rift localization, as confirmed by 4-layer analogue models. These faults arise either from crust or lithosphere scale buoyancy forces that are strongly controlled by the mantle temperature under the influence of the Afar hot spot. This implies a transition from a distributed mode to a localized one, sharper, both in space and time, in the West (close to the hot spot) than in the East (far away from the hot spot). In this framework, first order transform F.Z. are here (re-) defined by the fact that they deform continental crust. In the Gulf of Aden, as well as in other continental margins, it appears that these F.Z. are often, if not always, located at continental transfer or "transform" fault zones. Our detailed field-study of an offshore transfer fault zone in the southeastern Gulf of Aden (Socotra Island) shows that these structures are long-lived since early rifting until post rift times. During the early rifting, they are inherited structures reactivated as oblique normal faults before accommodating strike-slip motion. During the Ocean-Continent Transition (OCT) formation ("post syn-rift" times), a significant uplift occurred in the transfer fault zone footwall as shown by stratigraphic and LT thermochronology data. Second order transform F.Z. are defined as deforming only the OCT, thus initiated at the moment of its formation. In the western Gulf of Aden, the hot spot provoked a rift localization strongly oblique to the divergence and, as a consequence, several second order transform F.Z. formed (as

  6. Unraveling Local Dust Storm Structure on Mars: The Case of Northern Amazonis During Mars Year 24

    NASA Astrophysics Data System (ADS)

    Heavens, N. G.

    2015-12-01

    On an average Martian afternoon, two or three local dust storms are taking place somewhere on the planet. By definition, these storms range in area from a few square kilometers to hundreds of thousands, rarely surviving from sol to the next. After more than 40 years of observation, a great deal is known about where and when they occur, but very little is known about the structure and dynamics of individual storms. This contrast in our knowledge about local dust storms results from how they are observed. Daily global mapping of Mars in the visible has enabled an accurate census of storms as well as observation of their morphological diversity. However, even under ideal conditions, an individual storm is only observed by sounder-type instrumentation once or twice (if it is a large enough), providing an incomplete picture of structure of an individual storm. Early studies of cyclogenesis on Earth had a similar problem. Cyclones were many, but observations of individual cyclones, especially over the ocean, were sparse. The structure and dynamics of cyclones was unraveled by noting similarities in properties between certain classes of cyclones and using observational data to generate composite cyclones that could be analyzed and modeled. Variability within the composite also could be studied. Here I establish the existence of a well-defined class of Martian local dust storms defined by: (1) occurrence along the axis of the dark albedo feature in northern Amazonis Planitia (36 N, 155 W); (2) not being associated with lifting or cloudiness due to a baroclinic wave/frontal boundary at higher latitude; (3) being textured, that is, having dust clouds with sharp, well-defined features that are thought to indicate their clouds are supplied by the active lifting of dust; (4) having dust clouds organized in well-defined streets indicative of convective rolls. In Mars Year 24, such storms developed on thirteen occasions in northern fall and autumn. Using data from the Mars

  7. Shatter cones at the Keurusselkä impact structure and their relation to local jointing

    NASA Astrophysics Data System (ADS)

    Hasch, Maximilian; Reimold, Wolf Uwe; Raschke, Ulli; Zaag, Patrice Tristan

    2016-08-01

    Shatter cones are the only distinct meso- to macroscopic recognition criterion for impact structures, yet not all is known about their formation. The Keurusselkä impact structure, Finland, is interesting in that it presents a multitude of well-exposed shatter cones in medium- to coarse-grained granitoids. The allegedly 27 km wide Keurusselkä impact structure was formed about 1150 Ma ago in rocks of the Central Finland Granitoid Complex. Special attention was paid in this work to possible relationships between shatter cones and local, as well as regionally occurring, fracture or joint systems. A possible shatter cone find outside the previously suggested edge of the structure could mean that the Keurusselkä impact structure is larger than previously thought. The spacing between joints/fractures from regional joint systems was influenced by the impact, but impact-induced fractures strongly follow the regional joint orientation trends. There is a distinct relationship between shatter cones and joints: shatter cones occur on and against joint surfaces of varied orientations and belonging to the regional orientation trends. Planar fractures (PF) and planar deformation features (PDF) were found in three shatter cone samples from the central-most part of the impact structure, whereas other country rock samples from the same level of exposure but further from the assumed center lack shock deformation features. PDF occurrence is enhanced within 5 mm of shatter cone surfaces, which is interpreted to suggest that shock wave reverberation at preimpact joints could be responsible for this local enhancement of shock deformation. Some shatter cone surfaces are coated with a quasi-opaque material which is also found in conspicuous veinlets that branch off from shatter cone surfaces and resemble pseudotachylitic breccia veins. The vein-filling is composed of two mineral phases, one of which could be identified as a montmorillonitic phyllosilicate. The second phase could not be

  8. Should "Teacher Centred Teaching" Replace "Student Centred Learning"?

    ERIC Educational Resources Information Center

    Bailey, Patrick D.

    2008-01-01

    Mission statements of most HEIs across the UK support "student centred learning". In this paper, it is suggested that "teacher centred teaching" should also have a major role to play, improving the quality of the learning experience in higher education. Students are extremely diverse in their skills, weaknesses, and learning styles, but lecturers…

  9. Correction: Localized plasmon assisted structured illumination microscopy for wide-field high-speed dispersion-independent super resolution imaging.

    PubMed

    Ponsetto, Joseph Louis; Wei, Feifei; Liu, Zhaowei

    2016-02-14

    Correction for 'Localized plasmon assisted structured illumination microscopy for wide-field high-speed dispersion-independent super resolution imaging' by Joseph Louis Ponsetto et al., Nanoscale, 2014, 6, 5807-5812.

  10. Velocity structure around the Baikal rift zone from teleseismic and local earthquake traveltimes and geodynamic implications

    NASA Astrophysics Data System (ADS)

    Petit, Carole; Koulakov, Ivan; Deverchère, Jacques

    1998-10-01

    We present new results on the velocity structure of the Baikal rift zone, Asia, deduced from a comparative teleseismic and local tomography analysis. The aim of this paper is to better identify the role of deep mantle processes versus that of far-field tectonic effects on the occurrence of extensional tectonics within a continental plate. We use 36000 traveltimes of P-refracted waves from the ISC catalogues and Pg and Pn traveltimes of 578 earthquakes recorded by the Russian regional network to determine a velocity model by the use of local and teleseismic inversion procedures. The models show that some velocity patterns are continuous from the surface down to at least 400 km. Among them, a narrow negative anomaly goes through Mongolia and follows the southern and eastern margins of the Siberian craton: this structure is interpreted as a thin mantle plume rising beneath the rift axis. However, our results do not evidence any wide asthenospheric upwarp at this place. Other velocity anomalies observed near the surface are not deeply rooted. In particular, a negative anomaly is observed at shallow levels (48 km) beneath the northern third of Lake Baikal, which is disconnected from deeper structures. It may be explained by the existence of underplated magmatic material at the bottom of the crust. By comparing the geometry of deep-rooted anomalies to the present-day stress field patterns, we conclude that the sub-lithospheric mantle dynamics is not the main factor controlling extensional processes in the Baikal rift. However, it does contribute to a thermal weakening of the lithosphere along a mechanical discontinuity bounding the Siberian shield. We finally conclude that three favourable conditions are gathered in the Baikal area to generate extension: far-field extensional stress field, mechanical inherited lithospheric weakness and heat supply. Further studies should help to precise the genetic link between these three factors.

  11. Small but powerful: top predator local extinction affects ecosystem structure and function in an intermittent stream.

    PubMed

    Rodríguez-Lozano, Pablo; Verkaik, Iraima; Rieradevall, Maria; Prat, Narcís

    2015-01-01

    Top predator loss is a major global problem, with a current trend in biodiversity loss towards high trophic levels that modifies most ecosystems worldwide. Most research in this area is focused on large-bodied predators, despite the high extinction risk of small-bodied freshwater fish that often act as apex consumers. Consequently, it remains unknown if intermittent streams are affected by the consequences of top-predators' extirpations. The aim of our research was to determine how this global problem affects intermittent streams and, in particular, if the loss of a small-bodied top predator (1) leads to a 'mesopredator release', affects primary consumers and changes whole community structures, and (2) triggers a cascade effect modifying the ecosystem function. To address these questions, we studied the top-down effects of a small endangered fish species, Barbus meridionalis (the Mediterranean barbel), conducting an enclosure/exclosure mesocosm experiment in an intermittent stream where B. meridionalis became locally extinct following a wildfire. We found that top predator absence led to 'mesopredator release', and also to 'prey release' despite intraguild predation, which contrasts with traditional food web theory. In addition, B. meridionalis extirpation changed whole macroinvertebrate community composition and increased total macroinvertebrate density. Regarding ecosystem function, periphyton primary production decreased in apex consumer absence. In this study, the apex consumer was functionally irreplaceable; its local extinction led to the loss of an important functional role that resulted in major changes to the ecosystem's structure and function. This study evidences that intermittent streams can be affected by the consequences of apex consumers' extinctions, and that the loss of small-bodied top predators can lead to large ecosystem changes. We recommend the reintroduction of small-bodied apex consumers to systems where they have been extirpated, to restore

  12. Small but powerful: top predator local extinction affects ecosystem structure and function in an intermittent stream.

    PubMed

    Rodríguez-Lozano, Pablo; Verkaik, Iraima; Rieradevall, Maria; Prat, Narcís

    2015-01-01

    Top predator loss is a major global problem, with a current trend in biodiversity loss towards high trophic levels that modifies most ecosystems worldwide. Most research in this area is focused on large-bodied predators, despite the high extinction risk of small-bodied freshwater fish that often act as apex consumers. Consequently, it remains unknown if intermittent streams are affected by the consequences of top-predators' extirpations. The aim of our research was to determine how this global problem affects intermittent streams and, in particular, if the loss of a small-bodied top predator (1) leads to a 'mesopredator release', affects primary consumers and changes whole community structures, and (2) triggers a cascade effect modifying the ecosystem function. To address these questions, we studied the top-down effects of a small endangered fish species, Barbus meridionalis (the Mediterranean barbel), conducting an enclosure/exclosure mesocosm experiment in an intermittent stream where B. meridionalis became locally extinct following a wildfire. We found that top predator absence led to 'mesopredator release', and also to 'prey release' despite intraguild predation, which contrasts with traditional food web theory. In addition, B. meridionalis extirpation changed whole macroinvertebrate community composition and increased total macroinvertebrate density. Regarding ecosystem function, periphyton primary production decreased in apex consumer absence. In this study, the apex consumer was functionally irreplaceable; its local extinction led to the loss of an important functional role that resulted in major changes to the ecosystem's structure and function. This study evidences that intermittent streams can be affected by the consequences of apex consumers' extinctions, and that the loss of small-bodied top predators can lead to large ecosystem changes. We recommend the reintroduction of small-bodied apex consumers to systems where they have been extirpated, to restore

  13. Small but Powerful: Top Predator Local Extinction Affects Ecosystem Structure and Function in an Intermittent Stream

    PubMed Central

    Rodríguez-Lozano, Pablo; Verkaik, Iraima; Rieradevall, Maria; Prat, Narcís

    2015-01-01

    Top predator loss is a major global problem, with a current trend in biodiversity loss towards high trophic levels that modifies most ecosystems worldwide. Most research in this area is focused on large-bodied predators, despite the high extinction risk of small-bodied freshwater fish that often act as apex consumers. Consequently, it remains unknown if intermittent streams are affected by the consequences of top-predators’ extirpations. The aim of our research was to determine how this global problem affects intermittent streams and, in particular, if the loss of a small-bodied top predator (1) leads to a ‘mesopredator release’, affects primary consumers and changes whole community structures, and (2) triggers a cascade effect modifying the ecosystem function. To address these questions, we studied the top-down effects of a small endangered fish species, Barbus meridionalis (the Mediterranean barbel), conducting an enclosure/exclosure mesocosm experiment in an intermittent stream where B. meridionalis became locally extinct following a wildfire. We found that top predator absence led to ‘mesopredator release’, and also to ‘prey release’ despite intraguild predation, which contrasts with traditional food web theory. In addition, B. meridionalis extirpation changed whole macroinvertebrate community composition and increased total macroinvertebrate density. Regarding ecosystem function, periphyton primary production decreased in apex consumer absence. In this study, the apex consumer was functionally irreplaceable; its local extinction led to the loss of an important functional role that resulted in major changes to the ecosystem’s structure and function. This study evidences that intermittent streams can be affected by the consequences of apex consumers’ extinctions, and that the loss of small-bodied top predators can lead to large ecosystem changes. We recommend the reintroduction of small-bodied apex consumers to systems where they have been

  14. Investigation of Local Structures in Layered Niobates by Solid-state NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Liu, Ting

    Research on ion-exchangeable layered niobates has attracted great attention due to their unique structures and corresponding variations in properties and applications, such as ion conductors, solid acids, and water splitting catalysts. Families of layered niobates include double-layered or triple-layered Dion-Jacobson type perovskites (ALaNb2O7, A = Cs, Rb, K, H; AM2Nb3O10, A = Rb, K, H; M = Sr, Ca), layered niobates with both edge and corner sharing of NbO6 octahedra (KNb3O8, HNb3O6, Nb 6O17 and H4Nb6O17) and many others. Lately, more developments in the layered niobates through a variety of topochemical manipulations have been achieved. The topochemical reactions include ion exchange, exfoliation, substitution, and etc. As a result, many new materials have been successfully prepared, for example, solid solutions (ALa2NbTi2O10, ACaLaNb2TiO 10 and ACa2Nb3-xTaxO10, etc.), nanosheets (HNb3O8, H4Nb6O17, HLaNb2O7, HCa2Nb3O10, etc., to intercalate with organic molecules such as tetrabutylammonium hydroxide or n-butylamines), and nanoscrolls (from H2K2Nb 6O17). While these structural modifications often induce improvements in properties, the fundamental mechanisms of improvements in properties upon the modifications, especially local structural arrangements are poorly understood, which is often limited by structural characterizations. Particularly, the characterizations of the exfoliated nanosheets can be difficult by conventional X-ray diffraction (XRD) method due to disordered structures. Alternatively, solid-state nuclear magnetic resonance (NMR) spectroscopy is a useful tool to study local structures in solids. The structural information can be extracted by examining intrinsic interactions, such as quadrupolar, chemical shielding, and dipolar interactions, which are all associated with local environments surrounding a specific nucleus, 1H or 93Nb in layered niobates. The ultimate goal of this dissertation is to understand the relationships between local structures of

  15. Local probing of structure and property in dimensionally confined amorphous and crystalline structures by S/TEM

    NASA Astrophysics Data System (ADS)

    Yan, Aiming

    The characterization of materials' microstructure has been brought up to a new level since the invention and broad application of transmission electron microscope (TEM) thanks to the high-energy electron beam source which guarantees an unsurpassable spatial resolution and theoretical study of interaction between electron and matter. The advent of nano-world has imposed an urgent request to characterize nano-assemblies in nano- or even sub-nano-scale and scanning transmission electron microscopy (STEM) which typically utilizes an electron probe with a size of 1nm or even smaller has found its unique advantage to unravel the local structure, chemical and physical properties of these emerging nanostructures. Dimensionally constrained nanostructures such as thin films and nanopatterned systems have attracted people's attention for decades due to their novel chemical and physical properties and popularity in energy storage, biological integration and etc. This dissertation focuses on the unique characterization capability of S/TEM to study the local order in amorphous transparent conducting oxide thin films, disordering in 2-D layered materials, localized surface plasmons in nanoporous gold patterns on 2-D layered structures and crystallization process in dimensionally and spatially constrained oxide nanopatterns observed by in-situ TEM. Electron diffraction and x-ray diffraction are commonly used techniques to study the crystallinity in a certain material - crystalline or amorphous. In amorphous materials which lack long-range order, normal electron diffraction and x-ray diffraction techniques won't be able to extract any useful information regarding the ordering or disordering in the materials. We have developed a unique set of electron diffraction methods in both TEM and STEM, combined with density functional theory molecular dynamics of liquid quench to study the short-range (< 1 nm) and medium-range order (between 1 nm and 3 nm) in amorphous transparent oxide films

  16. Optical bullets in (2+1)D photonic structures and their interaction with localized defects

    NASA Astrophysics Data System (ADS)

    Dohnal, Tomas

    2005-11-01

    This dissertation studies light propagation in Kerr-nonlinear two dimensional waveguides with a Bragg resonant, periodic structure in the propagation direction. The model describing evolution of the electric field envelopes is the system of 2D Nonlinear Coupled Mode Equations (2D CME). The periodic structure induces a range of frequencies (frequency gap) in which linear waves do not propagate. It is shown that, similarly to the ID case of a fiber grating, the 2D nonlinear system supports localized solitary wave solutions, referred to as 2D gap solitons, which have frequencies inside the linear gap and can travel at, any speed smaller than or equal to the speed of light in the corresponding homogeneous medium. Such solutions are constructed numerically via Newton's iteration. Convergence is obtained only near the upper edge of the gap. Gap solitons with a nonzero velocity are constructed by numerically following a bifurcation curve parameterized by the velocity v. It is shown that gap solitons are saddle points of the corresponding Hamiltonian functional and that no (constrained) local minima of the Hamiltonian exist. The linear stability problem is formulated and reasons for the failure of the standard Hamiltonian PDE approach for determining linear stability are discussed. In the second part of the dissertation interaction of 2D gap solitons with localized defects is studied and trapping of slow enough 2D gap solitons is demonstrated. This study builds on [JOSA B 19, 1635 (2002)], where such trapping of 1D gap solitons is considered. Analogously to this 1D problem trapping in the 2D model is explained as a resonant energy transfer into one or more defect modes existent for the particular defect. For special localized defects exact linear modes are found explicitly via the separation of variables. Numerical computation of linear defect modes is used for more general defects. Corresponding nonlinear modes are then constructed via Newton's iteration by following a

  17. Analysis of local bond-orientational order for liquid gallium at ambient pressure: Two types of cluster structures.

    PubMed

    Chen, Lin-Yuan; Tang, Ping-Han; Wu, Ten-Ming

    2016-07-14

    In terms of the local bond-orientational order (LBOO) parameters, a cluster approach to analyze local structures of simple liquids was developed. In this approach, a cluster is defined as a combination of neighboring seeds having at least nb local-orientational bonds and their nearest neighbors, and a cluster ensemble is a collection of clusters with a specified nb and number of seeds ns. This cluster analysis was applied to investigate the microscopic structures of liquid Ga at ambient pressure (AP). The liquid structures studied were generated through ab initio molecular dynamics simulations. By scrutinizing the static structure factors (SSFs) of cluster ensembles with different combinations of nb and ns, we found that liquid Ga at AP contained two types of cluster structures, one characterized by sixfold orientational symmetry and the other showing fourfold orientational symmetry. The SSFs of cluster structures with sixfold orientational symmetry were akin to the SSF of a hard-sphere fluid. On the contrary, the SSFs of cluster structures showing fourfold orientational symmetry behaved similarly as the anomalous SSF of liquid Ga at AP, which is well known for exhibiting a high-q shoulder. The local structures of a highly LBOO cluster whose SSF displayed a high-q shoulder were found to be more similar to the structure of β-Ga than those of other solid phases of Ga. More generally, the cluster structures showing fourfold orientational symmetry have an inclination to resemble more to β-Ga.

  18. Analysis of local bond-orientational order for liquid gallium at ambient pressure: Two types of cluster structures.

    PubMed

    Chen, Lin-Yuan; Tang, Ping-Han; Wu, Ten-Ming

    2016-07-14

    In terms of the local bond-orientational order (LBOO) parameters, a cluster approach to analyze local structures of simple liquids was developed. In this approach, a cluster is defined as a combination of neighboring seeds having at least nb local-orientational bonds and their nearest neighbors, and a cluster ensemble is a collection of clusters with a specified nb and number of seeds ns. This cluster analysis was applied to investigate the microscopic structures of liquid Ga at ambient pressure (AP). The liquid structures studied were generated through ab initio molecular dynamics simulations. By scrutinizing the static structure factors (SSFs) of cluster ensembles with different combinations of nb and ns, we found that liquid Ga at AP contained two types of cluster structures, one characterized by sixfold orientational symmetry and the other showing fourfold orientational symmetry. The SSFs of cluster structures with sixfold orientational symmetry were akin to the SSF of a hard-sphere fluid. On the contrary, the SSFs of cluster structures showing fourfold orientational symmetry behaved similarly as the anomalous SSF of liquid Ga at AP, which is well known for exhibiting a high-q shoulder. The local structures of a highly LBOO cluster whose SSF displayed a high-q shoulder were found to be more similar to the structure of β-Ga than those of other solid phases of Ga. More generally, the cluster structures showing fourfold orientational symmetry have an inclination to resemble more to β-Ga. PMID:27421419

  19. Analysis of local bond-orientational order for liquid gallium at ambient pressure: Two types of cluster structures

    NASA Astrophysics Data System (ADS)

    Chen, Lin-Yuan; Tang, Ping-Han; Wu, Ten-Ming

    2016-07-01

    In terms of the local bond-orientational order (LBOO) parameters, a cluster approach to analyze local structures of simple liquids was developed. In this approach, a cluster is defined as a combination of neighboring seeds having at least nb local-orientational bonds and their nearest neighbors, and a cluster ensemble is a collection of clusters with a specified nb and number of seeds ns. This cluster analysis was applied to investigate the microscopic structures of liquid Ga at ambient pressure (AP). The liquid structures studied were generated through ab initio molecular dynamics simulations. By scrutinizing the static structure factors (SSFs) of cluster ensembles with different combinations of nb and ns, we found that liquid Ga at AP contained two types of cluster structures, one characterized by sixfold orientational symmetry and the other showing fourfold orientational symmetry. The SSFs of cluster structures with sixfold orientational symmetry were akin to the SSF of a hard-sphere fluid. On the contrary, the SSFs of cluster structures showing fourfold orientational symmetry behaved similarly as the anomalous SSF of liquid Ga at AP, which is well known for exhibiting a high-q shoulder. The local structures of a highly LBOO cluster whose SSF displayed a high-q shoulder were found to be more similar to the structure of β-Ga than those of other solid phases of Ga. More generally, the cluster structures showing fourfold orientational symmetry have an inclination to resemble more to β-Ga.

  20. Perturbation of chromatin structure globally affects localization and recruitment of splicing factors.

    PubMed

    Schor, Ignacio E; Llères, David; Risso, Guillermo J; Pawellek, Andrea; Ule, Jernej; Lamond, Angus I; Kornblihtt, Alberto R

    2012-01-01

    Chromatin structure is an important factor in the functional coupling between transcription and mRNA processing, not only by regulating alternative splicing events, but also by contributing to exon recognition during constitutive splicing. We observed that depolarization of neuroblastoma cell membrane potential, which triggers general histone acetylation and regulates alternative splicing, causes a concentration of SR proteins in nuclear speckles. This prompted us to analyze the effect of chromatin structure on splicing factor distribution and dynamics. Here, we show that induction of histone hyper-acetylation results in the accumulation in speckles of multiple splicing factors in different cell types. In addition, a similar effect is observed after depletion of the heterochromatic protein HP1α, associated with repressive chromatin. We used advanced imaging approaches to analyze in detail both the structural organization of the speckle compartment and nuclear distribution of splicing factors, as well as studying direct interactions between splicing factors and their association with chromatin in vivo. The results support a model where perturbation of normal chromatin structure decreases the recruitment efficiency of splicing factors to nascent RNAs, thus causing their accumulation in speckles, which buffer the amount of free molecules in the nucleoplasm. To test this, we analyzed the recruitment of the general splicing factor U2AF65 to nascent RNAs by iCLIP technique, as a way to monitor early spliceosome assembly. We demonstrate that indeed histone hyper-acetylation decreases recruitment of U2AF65 to bulk 3' splice sites, coincident with the change in its localization. In addition, prior to the maximum accumulation in speckles, ∼20% of genes already show a tendency to decreased binding, while U2AF65 seems to increase its binding to the speckle-located ncRNA MALAT1. All together, the combined imaging and biochemical approaches support a model where chromatin

  1. Local structural studies of oriented high-temperature superconducting cuprates by polarized XAFS spectroscopy

    NASA Astrophysics Data System (ADS)

    Haskel, Daniel

    1998-07-01

    Doping (Sr,Ba) in Lasb{2-x}(Sr,Ba)sb{x}CuOsb4 induces high Tsb{c} superconductivity in addition to profound changes in structural, magnetic and normal state electronic properties. The purpose of this thesis is to investigate the structural characteristics accompanying this doping by performing orientation dependent x-ray absorption fine structure (XAFS) measurements on magnetically aligned powders. This type of measurements allowed obtaining critical information at the La/(Sr,Ba) site previously unavailable, as detailed below. The measurements show that hole carriers introduced with Sr are polaronic in nature as evident from the two site configuration found for the O(2) apical neighboring Sr and the lack of temperature dependence in the O(2) distribution, which indicates that the hole states associated with each site are not discrete but rather broader than ksb{B}T up to T = 300K. There is a good theoretical argument suggesting each O(2) site is associated with holes being doped into O(1) 2psb{x,y}-Cu 3dsb{xsp2-ysp2} in-plane and O(2) 2psb{z}-Cu 3dsb{3zsp2-rsp2} out-of-plane electronic bands resulting in two different Jahn-Teller distortions of the CuOsb6 octahedra neighboring Sr, where the doped holes are peaked. Based on this argument, the predominance of out-of-plane character for the doped holes, as evidenced from the concentration dependence of the relative population of O(2) sites, would imply that theories of high Tsb{c} relying only on in-plane character of the doped holes are not complete in describing the properties of these cuprates. Our measurements showed that all structural phase transitions in Lasb{2-x}(Sr,Ba)sb{x}CuOsb4 have a significant order-disorder component, as opposed to the purely displacive models found in crystallographic studies. The CuOsb6 octahedra are locally tilted in the high-doping, high-temperature phases but fail to order over long range resulting in the average structures of the crystallographic studies. A critical parameter in

  2. Effect of Temperature on the Local Structure of Kaolinite Intercalated with Potassium Acetate

    SciTech Connect

    White, Claire E.; Provis, John L.; Gordon, Laura E.; Riley, Daniel P.; Proffen, Thomas; van Deventer, Jannie S.J.

    2011-09-06

    Kaolinite intercalated with potassium acetate is of great interest in the areas of environmental remediation and industrial application; however, its exact atomic structure and the changes which occur when heated have remained largely elusive. Here, neutron pair distribution function analysis is used to investigate the local structural characteristics of this complex material, revealing that hydrated potassium acetate exists as a single layer in the interlamellar spacing of kaolinite. Furthermore, the potassium ions within the intercalated complex are most likely associated with the resonance structure of the acetate molecules, and upon heating (and decomposition of the carbon containing molecules), these ions become strongly associated with the negative charge located on the oxygen atoms in the alumina layers of dehydroxylated kaolinite. Several possible orientations of hydrated potassium acetate within the interlamellar spacing of kaolinite have been proposed and investigated using density functional modeling, revealing the complex nature of this material. Nevertheless, this investigation has shown that the dehydroxylated form of the intercalated compound contains highly strained alumina and available alkali (potassium), making it a viable alternative to traditional aluminosilicates.

  3. Local structure of the metal-organic perovskite dimethylammonium manganese(ii) formate.

    PubMed

    Duncan, Helen D; Dove, Martin T; Keen, David A; Phillips, Anthony E

    2016-03-14

    We report total neutron scattering measurements on the metal-organic perovskite analogue dimethylammonium manganese(ii) formate, (CD3)2ND2[Mn(DCO2)3]. Reverse Monte Carlo modelling shows that, in both the disordered high-temperature and ordered low-temperature phases, the ammonium moiety forms substantially shorter hydrogen bonds (N...O = 2.4 Å and 2.6 Å) than are visible in the average crystal structures. These bonds result from a pincer-like motion of two adjacent formate ions about the dimethylammonium ion in such a way that the framework can adjust independently to the positions of nearest-neighbour dimethylammonium ions. At low temperatures the shortest hydrogen bond is less favourable, apparently because it involves a greater distortion of the framework. Furthermore, in the high-temperature phase, in addition to the three disordered nitrogen positions expected from the average crystal structure, there appear to be also smaller probability maxima between these positions, corresponding to orientations in which the dimethylammonium is hydrogen-bonded to the two oxygen atoms of a single formate ion. The spontaneous strain across the phase transition reveals a contraction of the framework about the dimethylammonium cation, continuing as the material is cooled below the transition temperature. These results provide direct evidence of the local atomic structure of the guest-framework hydrogen bonding, and in particular the distortions of the framework responsible for the phase transition in this system. PMID:26763144

  4. Bonding in elemental boron: a view from electronic structure calculations using maximally localized Wannier functions

    NASA Astrophysics Data System (ADS)

    Ogitsu, Tadashi; Gygi, Francois; Reed, John; Schwegler, Eric; Galli, Giulia

    2007-03-01

    Boron exhibits the most complex structure of all elemental solids, with more than 300 atoms per unit cell arranged in interconnecting icosahedra, and some crystallographic positions occupied with a probability of less than one. The precise determination of the ground state geometry of boron---the so-called β-boron structure--has been elusive and its electronic and bonding properties have been difficult to rationalize. Using lattice model Monte Carlo optimization techniques and ab-initio simulations, we have shown that a defective, quasi-ordered β solid is the most stable structure at zero as well as finite T. In the absence of partially occupied sites (POS), the perfect β-boron crystal is unstable; the presence of POS lower its internal energy below that of an ordered α-phase, not mere an entropic effect. We present a picture of the intricate and unique bonding in boron based on maximally localized Wannier (MLWF) functions, which indicates that the presence of POS provides a subtle, yet essential spatial balance between electron deficient and fully saturated bonds. This work was performed under the auspices of the U.S. Dept. of Energy at the University of California/ LLNL under contract no. W-7405-Eng-48.

  5. Condensation on superhydrophobic surfaces: the role of local energy barriers and structure length scale.

    PubMed

    Enright, Ryan; Miljkovic, Nenad; Al-Obeidi, Ahmed; Thompson, Carl V; Wang, Evelyn N

    2012-10-01

    Water condensation on surfaces is a ubiquitous phase-change process that plays a crucial role in nature and across a range of industrial applications, including energy production, desalination, and environmental control. Nanotechnology has created opportunities to manipulate this process through the precise control of surface structure and chemistry, thus enabling the biomimicry of natural surfaces, such as the leaves of certain plant species, to realize superhydrophobic condensation. However, this "bottom-up" wetting process is inadequately described using typical global thermodynamic analyses and remains poorly understood. In this work, we elucidate, through imaging experiments on surfaces with structure length scales ranging from 100 nm to 10 μm and wetting physics, how local energy barriers are essential to understand non-equilibrium condensed droplet morphologies and demonstrate that overcoming these barriers via nucleation-mediated droplet-droplet interactions leads to the emergence of wetting states not predicted by scale-invariant global thermodynamic analysis. This mechanistic understanding offers insight into the role of surface-structure length scale, provides a quantitative basis for designing surfaces optimized for condensation in engineered systems, and promises insight into ice formation on surfaces that initiates with the condensation of subcooled water.

  6. Magnetoelastic evidence for a local structural transformation in Co-rich glasses

    NASA Astrophysics Data System (ADS)

    O'Handley, R. C.; Grant, N. J.

    1983-04-01

    The magnetostriction of Fe-rich glasses is large and positive ( λ = +32×10 -6) whereas that of polycrystalline α-Fe is small and negative ( λ = -7×10 -6). This is understood to be a consequence of the sharp difference in local atomic order between these two materials: a 12-fold coordinated short-range order dominated by trigonal prismatic arrangements of Fe about B atoms in the glass, versus an eight-fold coordinated bcc structure in the crystal. Co-rich glases on the other hand show temperature and compositional dependences which closely parallel those of polycrystalline hcp (ɛ) cobalt and Co-Fe alloys. Specifically: (1) the addition of iron to ɛ-Co (polycrystalline λ = -16×10 -6) drives a martensitic transformation to the γ (fcc) phase in Co 1- xFe x at approximately x = 0.07. Near this composition λ = 0 and for x 62 0.09, λ is positive. Similar behavior is observed with the addition of iron to amorphous Co 80B 20 ( λ = -4×10 -6) in the series (Co 1- xFe x) 80B 20 where λ passes through zero at x = 0.06. (2) The martensitic transformation from the hcp to the fcc phase can also be thermally driven and is observed in Co at 420°C, near which temperature λ again changes sign and is positive in the high-temperature phase. Similarly, amorphous Co 80B 20 shows by extrapolation to above crystallization [1] (and Co 78Fe 2B 20, Co 72Mn 8B 20 and Co 70Cr 10B 20 show explicitly [2]) a thermally induced transition to a positive magnetostriction phase at 400°C. To the extent that the magnetostriction of polycrystalline cobalt signals the occurrence of the long-range ε-γ transformation, the magnetostriction of amorphous cobalt-rich alloys can be taken to indicate a similar, but local, transformation in the glasses. These transformations are reversible in both the crystals and glasses. In the amorphous materials most other macroscopic manifestations of the cooperative, local atomic rearrangements involved in the transformation are masked by the random

  7. Sure Start Children's Centres: time to make them better known.

    PubMed

    Thompson, Christine

    2010-01-01

    Health services have traditionally been available to local communities through general practices, health visitors and midwives. Since the introduction of the Sure Start Local programme in 1997 and Sure Start Children's Centres in 2004, an increasing number of children's centres are working with their local NHS to provide health services for the under fives, and improve the accessibility of these services to local families. Sure Start Children's Centres were set up in England as part of the Department for Children, Schools and Families' Children's Plan to improve outcomes for children and their families and contribute to the strategic objectives of Every Child Matters. Children's centres offer a range of integrated services from child health and maternity services to parenting and childcare provisions. They also deliver key health promotion activities and programmes that contribute to the public health priorities of Primary Care Trusts, e.g. breast-feeding, smoking in pregnancy, physical activity and healthy eating. There are now 3,500 children's centres offering easily accessible services to more than 2.4 million children and families across England. Health professionals are asked work proactively together to raise awareness of these among local communities so that more families can benefit from the services they offer. PMID:20518370

  8. Bone tissue incorporates in vitro gallium with a local structure similar to gallium-doped brushite.

    PubMed

    Korbas, M; Rokita, E; Meyer-Klaucke, W; Ryczek, J

    2004-01-01

    During mineral growth in rat bone-marrow stromal cell cultures, gallium follows calcium pathways. The dominant phase of the cell culture mineral constitutes the poorly crystalline hydroxyapatite (HAP). This model system mimics bone mineralization in vivo. The structural characterization of the Ga environment was performed by X-ray absorption spectroscopy at the Ga K-edge. These data were compared with Ga-doped synthetic compounds (poorly crystalline hydroxyapatite, amorphous calcium phosphate and brushite) and with strontium-treated bone tissue, obtained from the same culture model. It was found that Sr(2+) substitutes for Ca(2+) in the HAP crystal lattice. In contrast, the replacement by Ga(3+) yielded a much more disordered local environment of the probe atom in all investigated cell culture samples. The coordination of Ga ions in the cell culture minerals was similar to that of Ga(3+), substituted for Ca(2+), in the Ga-doped synthetic brushite (Ga-DCPD). The Ga atoms in the Ga-DCPD were coordinated by four oxygen atoms (1.90 A) of the four phosphate groups and two oxygen atoms at 2.02 A. Interestingly, the local environment of Ga in the cell culture minerals was not dependent on the onset of Ga treatment, the Ga concentration in the medium or the age of the mineral. Thus, it was concluded that Ga ions were incorporated into the precursor phase to the HAP mineral. Substitution for Ca(2+ )with Ga(3+) distorted locally this brushite-like environment, which prevented the transformation of the initially deposited phase into the poorly crystalline HAP. PMID:14648284

  9. A single frequency component-based re-estimated MUSIC algorithm for impact localization on complex composite structures

    NASA Astrophysics Data System (ADS)

    Yuan, Shenfang; Bao, Qiao; Qiu, Lei; Zhong, Yongteng

    2015-10-01

    The growing use of composite materials on aircraft structures has attracted much attention for impact monitoring as a kind of structural health monitoring (SHM) method. Multiple signal classification (MUSIC)-based monitoring technology is a promising method because of its directional scanning ability and easy arrangement of the sensor array. However, for applications on real complex structures, some challenges still exist. The impact-induced elastic waves usually exhibit a wide-band performance, giving rise to the difficulty in obtaining the phase velocity directly. In addition, composite structures usually have obvious anisotropy, and the complex structural style of real aircrafts further enhances this performance, which greatly reduces the localization precision of the MUSIC-based method. To improve the MUSIC-based impact monitoring method, this paper first analyzes and demonstrates the influence of measurement precision of the phase velocity on the localization results of the MUSIC impact localization method. In order to improve the accuracy of the phase velocity measurement, a single frequency component extraction method is presented. Additionally, a single frequency component-based re-estimated MUSIC (SFCBR-MUSIC) algorithm is proposed to reduce the localization error caused by the anisotropy of the complex composite structure. The proposed method is verified on a real composite aircraft wing box, which has T-stiffeners and screw holes. Three typical categories of 41 impacts are monitored. Experimental results show that the SFCBR-MUSIC algorithm can localize impact on complex composite structures with an obviously improved accuracy.

  10. Photographic observation of magnetic domain structure with three-dimensional local magnetization direction

    NASA Astrophysics Data System (ADS)

    Meguro, Sakae; Akahane, Koichi; Saito, Shin

    2016-07-01

    The direction of magnetization of a magnetic material is possibly oriented three-dimensionally because of the presence of magnetic anisotropy field, self-demagnetizing field, and stray field. Therefore, the three-dimensional detection of the direction of magnetization is required. The method of magnetic domain observation by photographic imaging utilizing the Kerr effect is widely used. If the perpendicular magnetization components exist, there is a problem that obliquely incident light has superimposed longitudinal Kerr and polar Kerr effects. To perform the three-dimensional detection of magnetization direction, it is necessary to eliminate the influence of the polar Kerr effect from the Kerr effect of obliquely incident light. We report the photographic observation of the magnetic domain structure and the detection of the three-dimensional local magnetization direction using the Kerr effect, applying only an in-plane saturation magnetic field.

  11. Local structure of disordered Au-Cu and Au-Ag alloys

    NASA Astrophysics Data System (ADS)

    Frenkel, A. I.; Machavariani, V. Sh.; Rubshtein, A.; Rosenberg, Yu.; Voronel, A.; Stern, E. A.

    2000-10-01

    X-ray-absorption fine structure (XAFS) and x-ray-diffraction (XRD) measurements of disordered alloys AuxCu1-x and Au0.5Ag0.5 prepared by melt spinning were performed. In the Au0.5Ag0.5 alloy, no significant local deviations of the atoms from the average fcc lattice were detected while in AuxCu1-x alloys, significant deviations of atoms from the average fcc lattice were found. Mean-square vibrations of the Cu-Cu distances revealed by the XAFS in AuxCu1-x alloys indicate the weakening of contact between Cu atoms in the dilute limit. Our computer simulation for AuxCu1-x clusters of 105 atoms reproduces the main features of both the XAFS and XRD data.

  12. Structure and chromosomal localization of a human water channel (AQP3) gene

    SciTech Connect

    Ishibashi, Kenichi; Sasaki, Sei; Saito, Fumiko

    1995-05-20

    A cDNA encoding rat AQP3, a water channel and a member of the MIP family, that is expressed predominantly in kidney medulla and colon was cloned recently. To determine the structure, tissue distribution, and chromosomal localization of the human AQP3 gene, the authors screened a human kidney cDNA library with rat AQP3 probe and isolated a cDNA coding for human AQP3 protein. The deduced amino acid sequence of human AQP3 was 91% identical to rat AQP3. Human AQP3 mRNA was expressed in colon, kidney, liver, pancreas, lung, peripheral leukocytes, spleen, and prostate. The human AQP3 gene was mapped to 7q36.2-q36.3 by chromosome fluorescence in situ hybridization. 10 refs., 3 figs.

  13. Effects of local structural transformation of lipid-like compounds on delivery of messenger RNA

    PubMed Central

    Li, Bin; Luo, Xiao; Deng, Binbin; Giancola, JoLynn B.; McComb, David W.; Schmittgen, Thomas D.; Dong, Yizhou

    2016-01-01

    Lipid-like nanoparticles (LLNs) have shown great potential for RNA delivery. Lipid-like compounds are key components in LLNs. In this study, we investigated the effects of local structural transformation of lipid-like compounds on delivery of messenger RNA. Our results showed that position change of functional groups on lipid-like compounds can dramatically improve delivery efficiency. We then optimized formulation ratios of TNT-b10 LLNs, a lead material, increasing delivery efficiency over 2-fold. More importantly, pegylated TNT-b10 LLNs is stable for over four weeks and is over 10-fold more efficient than that of its counterpart TNT-a10 LLNs. Additionally, the optimal formulation O-TNT-b10 LLNs is capable of delivering mRNA encoding luciferase in vivo. These results provide useful insights into the design of next generation LLNs for mRNA delivery. PMID:26916931

  14. Structure, Function, and Localization of Gβ5–RGS Complexes

    PubMed Central

    Slepak, Vladlen Z.

    2012-01-01

    Members of the R7 subfamily of regulator of G protein signaling (RGS) proteins (RGS6, 7, 9, and 11) exist as heterodimers with the G protein beta subunit Gβ5. These protein complexes are only found in neurons and are defined by the presence of three domains: DEP/DHEX, Gβ5/GGL, and RGS. This article summarizes published work in the following areas: (1) the functional significance of structural organization of Gβ5–R7 complexes, (2) regional distribution of Gβ5–R7 in the nervous system and regulation of R7 family expression, (3) subcellular localization of Gβ5–R7 complexes, and (4) novel binding partners of Gβ5–R7 proteins. The review points out some contradictions between observations made by different research groups and highlights the importance of using alternative experimental approaches to obtain conclusive information about Gβ5–R7 function in vivo. PMID:20374716

  15. Local electronic structure and magnetic properties of 3d transition metal doped GaAs

    NASA Astrophysics Data System (ADS)

    Lin, He; Duan, Haiming

    2008-05-01

    The local electronic structure and magnetic properties of GaAs doped with 3d transition metal (Sc, Ti, V, Cr, Mn, Fe, Co, Ni) were studied by using discrete variational method (DVM) based on density functional theory. The calculated result indicated that the magnetic moment of transition metal increases first and then decreases, and reaches the maximum value when Mn is doped into GaAs. In the case of Mn concentration of 1.4%, the magnetic moment of Mn is in good agreement with the experimental result. The coupling between impure atoms in the system with two impure atoms was found to have obvious variation. For different transition metal, the coupling between the impure atom and the nearest neighbor As also has different variation.

  16. Surface structure and hole localization in bismuth vanadate: A first principles study

    SciTech Connect

    Kweon, Kyoung E.; Hwang, Gyeong S.

    2013-09-23

    The monoclinic and tetragonal phases of bismuth vanadate (BiVO{sub 4}) have been found to exhibit significantly different photocatalytic activities for water splitting. To assess a possible surface effect on the phase-dependent behavior, we calculate and compare the geometries and electronic structures of the monoclinic and tetragonal BiVO{sub 4} (001) surfaces using hybrid density functional theory. The relaxed atomic configurations of these two surfaces are found to be nearly identical, while an excess hole shows a relatively stronger tendency to localize at the surface than the bulk in both phases. Possible factors for the phase-dependent photocatalytic activity of BiVO{sub 4} are discussed.

  17. Stochasticity, periodicity and localized light structures in partially mode-locked fibre lasers

    PubMed Central

    Churkin, D. V.; Sugavanam, S.; Tarasov, N.; Khorev, S.; Smirnov, S. V.; Kobtsev, S. M.; Turitsyn, S. K.

    2015-01-01

    Physical systems with co-existence and interplay of processes featuring distinct spatio-temporal scales are found in various research areas ranging from studies of brain activity to astrophysics. The complexity of such systems makes their theoretical and experimental analysis technically and conceptually challenging. Here, we discovered that while radiation of partially mode-locked fibre lasers is stochastic and intermittent on a short time scale, it exhibits non-trivial periodicity and long-scale correlations over slow evolution from one round-trip to another. A new technique for evolution mapping of intensity autocorrelation function has enabled us to reveal a variety of localized spatio-temporal structures and to experimentally study their symbiotic co-existence with stochastic radiation. Real-time characterization of dynamical spatio-temporal regimes of laser operation is set to bring new insights into rich underlying nonlinear physics of practical active- and passive-cavity photonic systems. PMID:25947951

  18. Bridging the pressure gap: Can we get local quantitative structural information at 'near-ambient' pressures?

    NASA Astrophysics Data System (ADS)

    Woodruff, D. P.

    2016-10-01

    In recent years there have been an increasing number of investigations aimed at 'bridging the pressure gap' between UHV surface science experiments on well-characterised single crystal surfaces and the much higher (ambient and above) pressures relevant to practical catalyst applications. By applying existing photon-in/photon-out methods and developing instrumentation to allow photoelectron emission to be measured in higher-pressure sample environments, it has proved possible to obtain surface compositions and spectroscopic fingerprinting of chemical and molecular states of adsorbed species at pressures up to a few millibars. None of these methods, however, provide quantitative structural information on the local adsorption sites of isolated atomic and molecular adsorbate species under these higher-pressure reaction conditions. Methods for gaining this information are reviewed and evaluated.

  19. Gap eigenmode of radially localized helicon waves in a periodic structure

    NASA Astrophysics Data System (ADS)

    Chang, L.; Breizman, B. N.; Hole, M. J.

    2013-02-01

    An ElectroMagnetic Solver (Chen et al 2006 Phys. Plasmas 13 123507) is employed to model a spectral gap and a gap eigenmode in a periodic structure in the whistler frequency range. A radially localized helicon mode (Breizman and Arefiev 2000 Phys. Rev. Lett. 84 3863) is considered. We demonstrate that the computed gap frequency and gap width agree well with a theoretical analysis, and find a discrete eigenmode inside the gap by introducing a defect to the system's periodicity. The axial wavelength of the gap eigenmode is close to twice the system's periodicity, which is consistent with Bragg's law. Such an eigenmode could be excited by energetic electrons, similar to the excitation of toroidal Alfvén eigenmodes by energetic ions in tokamaks. Experimental identification of this mode is conceivable on the large plasma device (Gekelman et al 1991 Rev. Sci. Instrum. 62 2875).

  20. Arbitrary Lagrangian-Eulerian Method with Local Structured Adaptive Mesh Refinement for Modeling Shock Hydrodynamics

    SciTech Connect

    Anderson, R W; Pember, R B; Elliott, N S

    2001-10-22

    A new method that combines staggered grid Arbitrary Lagrangian-Eulerian (ALE) techniques with structured local adaptive mesh refinement (AMR) has been developed for solution of the Euler equations. This method facilitates the solution of problems currently at and beyond the boundary of soluble problems by traditional ALE methods by focusing computational resources where they are required through dynamic adaption. Many of the core issues involved in the development of the combined ALEAMR method hinge upon the integration of AMR with a staggered grid Lagrangian integration method. The novel components of the method are mainly driven by the need to reconcile traditional AMR techniques, which are typically employed on stationary meshes with cell-centered quantities, with the staggered grids and grid motion employed by Lagrangian methods. Numerical examples are presented which demonstrate the accuracy and efficiency of the method.

  1. Primary structure and cellular localization of callinectin, an antimicrobial peptide from the blue crab.

    PubMed

    Noga, Edward J; Stone, Kathryn L; Wood, Abbey; Gordon, William L; Robinette, David

    2011-04-01

    We report the complete amino acid sequence of callinectin, a 32 amino acid, proline-, arginine-rich antimicrobial peptide (AMP) with four cysteines and having the sequence WNSNRRFRVGRPPVVGRPGCVCFRAPCPCSNY-amide. The primary structure of callinectin is highly similar to arasins, AMPs recently identified in the small spider crab (Hyas araneus). Callinectin exists in three isomers that vary in the functional group on the tryptophan (W) residue. The most prevalent isomer had a hydroxy-N-formylkynurenine group, while the other two isomers had either N-formylkynurenine or hydroxy-tryptophan. Using a sequence highly similar to native callinectin, we chemically synthesized a peptide which we called callinectin-like peptide (CLP). Via immuno-electron microscopy, affinity-purified rabbit antibodies raised to CLP successfully localized the site of callinectin in blue crab hemocytes to the large electron-dense granules that are found primarily in large granule hemocytes.

  2. Fluvial processes and local lithology controlling abundance, structure, and composition of mussel beds

    PubMed Central

    Vannote, Robin L.; Minshall, G. Wayne

    1982-01-01

    In the Salmon River Canyon, Idaho, the fresh-water pearl mussel, Margaritifera falcata, attains maximum density and age in river reaches where large block-boulders structurally stabilize cobbles and interstitial gravels. We hypothesize that block-boulders prevent significant bed scour during major floods, and these boulder-sheltered mussel beds, although rare, may be critical for population recruitment elsewhere within the river, especially after periodic flood scour of less protected mussel habitat. Mussel shells in Indian middens adjacent to these boulder-stabilized areas suggest that prehistoric tribes selectively exploited the high-density old-aged mussel beds. Locally, canyon reaches are aggrading with sand and gravel, and M. falcata is being replaced by Gonidea angulata. PMID:16593208

  3. Primary structure and cellular localization of callinectin, an antimicrobial peptide from the blue crab

    PubMed Central

    Noga, Edward J.; Stone, Kathryn L.; Wood, Abbey; Gordon, William L.; Robinette, David

    2011-01-01

    We report the complete amino acid sequence of callinectin, a 32 amino acid, proline-, arginine-rich AMP with four cysteines and having the sequence WNSNRRFRVGRPPVVGRPGCVCFRAPCPCSNY-amide. The primary structure of callinectin is highly similar to arasins, AMPs recently identified in the small spider crab (Hyas araneus). Callinectin exists in three isomers that vary in the functional group on the tryptophan (W) residue. The most prevalent isomer had a hydroxy-N-formylkynurenine group, while the other two isomers had either N-formylkynurenine or hydroxy-tryptophan. Using a sequence highly similar to native callinectin, we chemically synthesized a peptide which we called callinectin-like peptide (CLP). Via immunoelectron microscopy, affinity-purified rabbit antibodies raised to CLP successfully localized the site of callinectin in blue crab hemocytes to the large electron-dense granules that are found primarily in large granule hemocytes. PMID:21115038

  4. Effects of local structural transformation of lipid-like compounds on delivery of messenger RNA

    NASA Astrophysics Data System (ADS)

    Li, Bin; Luo, Xiao; Deng, Binbin; Giancola, Jolynn B.; McComb, David W.; Schmittgen, Thomas D.; Dong, Yizhou

    2016-02-01

    Lipid-like nanoparticles (LLNs) have shown great potential for RNA delivery. Lipid-like compounds are key components in LLNs. In this study, we investigated the effects of local structural transformation of lipid-like compounds on delivery of messenger RNA. Our results showed that position change of functional groups on lipid-like compounds can dramatically improve delivery efficiency. We then optimized formulation ratios of TNT-b10 LLNs, a lead material, increasing delivery efficiency over 2-fold. More importantly, pegylated TNT-b10 LLNs is stable for over four weeks and is over 10-fold more efficient than that of its counterpart TNT-a10 LLNs. Additionally, the optimal formulation O-TNT-b10 LLNs is capable of delivering mRNA encoding luciferase in vivo. These results provide useful insights into the design of next generation LLNs for mRNA delivery.

  5. Bonding nature of local structural motifs in amorphous GeTe.

    PubMed

    Deringer, Volker L; Zhang, Wei; Lumeij, Marck; Maintz, Stefan; Wuttig, Matthias; Mazzarello, Riccardo; Dronskowski, Richard

    2014-09-26

    Despite its simple chemical constitution and unparalleled technological importance, the phase-change material germanium telluride (GeTe) still poses fundamental questions. In particular, the bonding mechanisms in amorphous GeTe have remained elusive to date, owing to the lack of suitable bond-analysis tools. Herein, we introduce a bonding indicator for amorphous structures, dubbed "bond-weighted distribution function" (BWDF), and we apply this method to amorphous GeTe. The results underline a peculiar role of homopolar Ge-Ge bonds, which locally stabilize tetrahedral fragments but not the global network. This atom-resolved (i.e., chemical) perspective has implications for the stability of amorphous "zero bits" and thus for the technologically relevant resistance-drift phenomenon.

  6. Structure and chromosomal localization of the gene encoding the human myelin protein zero (MPZ)

    SciTech Connect

    Hayasaka, Kiyoshi; Himoro, Masato; Takada, Goro ); Wang, Yimin; Takata, Mizuho; Minoshima, Shinsei; Shimizu, Nobuyoshi; Miura, Masayuki; Uyemura, Keiichi )

    1993-09-01

    The authors describe the cloning, characterization, and chromosomal mapping of the human myelin protein zero (MPZ) gene (a structural protein of myelin and an adhesive glycoprotein of the immunoglobulin superfamily). The gene is about 7 kb long and consists of six exons corresponding of the functional domains. All exon-intron junction sequences conform to the GT/AG rule. The 5[prime]-flanking region of the gene has a TA-rich element (TATA-like box), two CAAT boxes, and a single defined transcription initiation site detected by the primer extension method. The gene for human MPZ was assigned to chromosome 1q22-q23 by spot blot hybridization of flow-sorted human chromosomes and fluorescence in situ hybridization. The localization of the MPZ gene coincides with the locus for Charcot-Marie-Tooth disease type 1B, determined by linkage analysis. 20 refs., 3 figs., 1 tab.

  7. Maskless direct micro-structuring of PDMS by femtosecond laser localized rapid curing

    NASA Astrophysics Data System (ADS)

    Selvaraj, Hamsapriya; Tan, Bo; Venkatakrishnan, K.

    2011-07-01

    Polydimethylsiloxane (PDMS) is widely used to build biomedical microdevices because of its excellent properties. Prototyping 2D and 3D PDMS microdevices normally requires a long curing time and must go through multiple steps. In this paper, we propose femtosecond laser stereolithography for the rapid prototyping of PDMS 2D and 3D microstructures. This work presents a new way of rapid curing of PDMS resin on a microsecond timescale using femtosecond laser pulses of megahertz pulse frequency. The proposed technique permits single-step curing and is capable of fabricating 2D and 3D structures in micro-scale. The rapid localized curing can be explained by the volume-constrained quick temperature rise due to the accumulated heating at repetitive irradiation. The rapid cooling following the curing limits the decomposition and, therefore, the PDMS retains its mechanical strength.

  8. Local structure controls the nonaffine shear and bulk moduli of disordered solids.

    PubMed

    Schlegel, M; Brujic, J; Terentjev, E M; Zaccone, A

    2016-01-01

    Paradigmatic model systems, which are used to study the mechanical response of matter, are random networks of point-atoms, random sphere packings, or simple crystal lattices; all of these models assume central-force interactions between particles/atoms. Each of these models differs in the spatial arrangement and the correlations among particles. In turn, this is reflected in the widely different behaviours of the shear (G) and compression (K) elastic moduli. The relation between the macroscopic elasticity as encoded in G, K and their ratio, and the microscopic lattice structure/order, is not understood. We provide a quantitative analytical connection between the local orientational order and the elasticity in model amorphous solids with different internal microstructure, focusing on the two opposite limits of packings (strong excluded-volume) and networks (no excluded-volume). The theory predicts that, in packings, the local orientational order due to excluded-volume causes less nonaffinity (less softness or larger stiffness) under compression than under shear. This leads to lower values of G/K, a well-documented phenomenon which was lacking a microscopic explanation. The theory also provides an excellent one-parameter description of the elasticity of compressed emulsions in comparison with experimental data over a broad range of packing fractions.

  9. Structural effects of the local anesthetic bupivacaine hydrochloride on the human erythrocyte membrane and molecular models.

    PubMed

    Suwalsky, Mario; Schneider, Carlos; Villena, Fernando; Norris, Beryl; Cárdenas, Hernán; Cuevas, Francisco; Sotomayor, Carlos P

    2002-01-01

    The interaction of the local anesthetic bupivacaine with the human erythrocyte membrane and molecular models is described. The latter consisted of isolated unsealed human erythrocyte membranes (IUM), large unilamellar vesicles (LUV) of dimyristoylphosphatidylcholine (DMPC), and phospholipid multilayers built-up of DMPC and dimyristoylphosphatidylethanolamine (DMPE), representatives of phospholipid classes located in the outer and inner monolayers of the human erythrocyte membrane, respectively. Optical and scanning electron microscopy revealed that bupivacaine induced erythrocyte spheroechinocytosis. According to the bilayer couple hypothesis, this result implied that bupivacaine inserted in the outer monolayer of the erythrocyte membrane. Experiments performed on IUM and DMPC LUV by fluorescence spectroscopy and X-ray diffraction on DMPC and DMPE multilayers confirmed this result. Changes in the molecular organization of membranes alter lipid-protein interactions and induce functional perturbation of membrane proteins such as Na(+) channels. Since local anesthetics may control the influx of Na(+) into the human erythrocyte, in order to relate the structural perturbations induced by bupivacaine in these systems to Na(+) transport, the interaction of this anesthetic with isolated toad skin was also studied. Electrophysiological measurements indicated a significant decrease in the potential difference and in the short-circuit current of the skin after the application of the anesthetic, reflecting inhibition of the active transport of ions. These results suggest that bupivacaine-induced conformational changes of the lipid molecules alter the lipid-protein boundaries of the outer moiety of the erythrocyte membrane, thus interfering with the function of neighboring sodium channels. PMID:12482399

  10. Inverse solution technique of steady-state responses for local nonlinear structures

    NASA Astrophysics Data System (ADS)

    Wang, Xing; Guan, Xin; Zheng, Gangtie

    2016-03-01

    An inverse solution technique with the ability of obtaining complete steady-state primary harmonic responses of local nonlinear structures in the frequency domain is proposed in the present paper. In this method, the nonlinear dynamic equations of motion is first condensed from many to only one algebraic amplitude-frequency equation of relative motion. Then this equation is transformed into a polynomial form, and with its frequency as the unknown variable, the polynomial equation is solved by tracing all the solutions of frequency with the increase of amplitude. With this solution technique, some complicated dynamic behaviors such as sharp tuning, anomalous jumps, breaks in responses and detached resonance curves could be obtained. The proposed method is demonstrated and validated through a finite element beam under force excitations and a lumped parameter model with a local nonlinear element under base excitations. The phenomenon of detached resonance curves in the frequency response and its coupling effects with multiple linear modes in the latter example are observed.

  11. Locally-tailored structure of an elastomeric substrate for stretchable circuits

    NASA Astrophysics Data System (ADS)

    Park, Chan Woo; Jung, Soon Won; Na, Bock Soon; Oh, Ji-Young; Park, Nae-Man; Lee, Sang Seok; Bon Koo, Jae

    2016-02-01

    We demonstrate a new process for fabricating a hybrid elastomeric polydimethylsiloxane (PDMS) substrate, which can provide a high ratio (as large as ∼50) of the elastic modulus between the active device region and the interconnect area, as well as a locally tailored surface profile for each region. For this process, a Si master mold with a dual surface profile is prepared, where locally flat regions are distributed within a wavy-surfaced area. The stiffer elastomeric islands for active devices are formed on the flat regions by photolithography of a photo-patternable and hard PDMS layer (E ∼ 160 MPa), over which a soft PDMS layer (E ∼ 2 to 3 MPa) is casted. By releasing the whole PDMS layer from the mold, a hybrid silicone substrate with stiff and flat islands embedded within a soft and wavy matrix is obtained. In this hybrid structure, active devices located on the stiff regions can provide high reliability under stretched conditions, while most strain is accommodated by wavy interconnects within the soft area. Such beneficial effects are demonstrated by organic thin film transistors produced on the hybrid substrate.

  12. Localization of fluorescently labeled structures in frozen-hydrated samples using integrated light electron microscopy.

    PubMed

    Faas, F G A; Bárcena, M; Agronskaia, A V; Gerritsen, H C; Moscicka, K B; Diebolder, C A; van Driel, L F; Limpens, R W A L; Bos, E; Ravelli, R B G; Koning, R I; Koster, A J

    2013-03-01

    Correlative light and electron microscopy is an increasingly popular technique to study complex biological systems at various levels of resolution. Fluorescence microscopy can be employed to scan large areas to localize regions of interest which are then analyzed by electron microscopy to obtain morphological and structural information from a selected field of view at nm-scale resolution. Previously, an integrated approach to room temperature correlative microscopy was described. Combined use of light and electron microscopy within one instrument greatly simplifies sample handling, avoids cumbersome experimental overheads, simplifies navigation between the two modalities, and improves the success rate of image correlation. Here, an integrated approach for correlative microscopy under cryogenic conditions is presented. Its advantages over the room temperature approach include safeguarding the native hydrated state of the biological specimen, preservation of the fluorescence signal without risk of quenching due to heavy atom stains, and reduced photo bleaching. The potential of cryo integrated light and electron microscopy is demonstrated for the detection of viable bacteria, the study of in vitro polymerized microtubules, the localization of mitochondria in mouse embryonic fibroblasts, and for a search into virus-induced intracellular membrane modifications within mammalian cells. PMID:23261400

  13. Local structure controls the nonaffine shear and bulk moduli of disordered solids

    NASA Astrophysics Data System (ADS)

    Schlegel, M.; Brujic, J.; Terentjev, E. M.; Zaccone, A.

    2016-01-01

    Paradigmatic model systems, which are used to study the mechanical response of matter, are random networks of point-atoms, random sphere packings, or simple crystal lattices; all of these models assume central-force interactions between particles/atoms. Each of these models differs in the spatial arrangement and the correlations among particles. In turn, this is reflected in the widely different behaviours of the shear (G) and compression (K) elastic moduli. The relation between the macroscopic elasticity as encoded in G, K and their ratio, and the microscopic lattice structure/order, is not understood. We provide a quantitative analytical connection between the local orientational order and the elasticity in model amorphous solids with different internal microstructure, focusing on the two opposite limits of packings (strong excluded-volume) and networks (no excluded-volume). The theory predicts that, in packings, the local orientational order due to excluded-volume causes less nonaffinity (less softness or larger stiffness) under compression than under shear. This leads to lower values of G/K, a well-documented phenomenon which was lacking a microscopic explanation. The theory also provides an excellent one-parameter description of the elasticity of compressed emulsions in comparison with experimental data over a broad range of packing fractions.

  14. Evaluating mental workload of two-dimensional and three-dimensional visualization for anatomical structure localization.

    PubMed

    Foo, Jung-Leng; Martinez-Escobar, Marisol; Juhnke, Bethany; Cassidy, Keely; Hisley, Kenneth; Lobe, Thom; Winer, Eliot

    2013-01-01

    Visualization of medical data in three-dimensional (3D) or two-dimensional (2D) views is a complex area of research. In many fields 3D views are used to understand the shape of an object, and 2D views are used to understand spatial relationships. It is unclear how 2D/3D views play a role in the medical field. Using 3D views can potentially decrease the learning curve experienced with traditional 2D views by providing a whole representation of the patient's anatomy. However, there are challenges with 3D views compared with 2D. This current study expands on a previous study to evaluate the mental workload associated with both 2D and 3D views. Twenty-five first-year medical students were asked to localize three anatomical structures--gallbladder, celiac trunk, and superior mesenteric artery--in either 2D or 3D environments. Accuracy and time were taken as the objective measures for mental workload. The NASA Task Load Index (NASA-TLX) was used as a subjective measure for mental workload. Results showed that participants viewing in 3D had higher localization accuracy and a lower subjective measure of mental workload, specifically, the mental demand component of the NASA-TLX. Results from this study may prove useful for designing curricula in anatomy education and improving training procedures for surgeons.

  15. Local conditions for the Pauli potential in order to yield self-consistent electron densities exhibiting proper atomic shell structure

    NASA Astrophysics Data System (ADS)

    Finzel, Kati

    2016-01-01

    The local conditions for the Pauli potential that are necessary in order to yield self-consistent electron densities from orbital-free calculations are investigated for approximations that are expressed with the help of a local position variable. It is shown that those local conditions also apply when the Pauli potential is given in terms of the electron density. An explicit formula for the Ne atom is given, preserving the local conditions during the iterative procedure. The resulting orbital-free electron density exhibits proper shell structure behavior and is in close agreement with the Kohn-Sham electron density. This study demonstrates that it is possible to obtain self-consistent orbital-free electron densities with proper atomic shell structure from simple one-point approximations for the Pauli potential at local density level.

  16. Local conditions for the Pauli potential in order to yield self-consistent electron densities exhibiting proper atomic shell structure.

    PubMed

    Finzel, Kati

    2016-01-21

    The local conditions for the Pauli potential that are necessary in order to yield self-consistent electron densities from orbital-free calculations are investigated for approximations that are expressed with the help of a local position variable. It is shown that those local conditions also apply when the Pauli potential is given in terms of the electron density. An explicit formula for the Ne atom is given, preserving the local conditions during the iterative procedure. The resulting orbital-free electron density exhibits proper shell structure behavior and is in close agreement with the Kohn-Sham electron density. This study demonstrates that it is possible to obtain self-consistent orbital-free electron densities with proper atomic shell structure from simple one-point approximations for the Pauli potential at local density level.

  17. Local Arsenic Structure in Shallow Implants in Si following SPER: an EXAFS and MEIS study

    SciTech Connect

    Pepponi, G.; Giubertoni, D.; Gennaro, S.; Bersani, M.; Anderle, M.; Grisenti, R.; Werner, M.; Berg, J. A. van den

    2006-11-13

    Solid phase epitaxial regrowth (SPER) has been investigated in the last few years as a possible method to form ultra shallow dopant distributions in silicon with a high level of electrical. Despite the interest for this process, few investigations were related to arsenic. Apart from the fact that it is easier to form shallow distribution with arsenic than with boron, it is also well known that at the moderate temperatures implied by SPER (500-700 deg. C) arsenic easily deactivates, probably by forming inactive clusters around point defects in silicon. In order to have a better understanding of the SPER process for arsenic implanted silicon in shallow regime, an EXAFS (extended x-ray absorption fine structure) and MEIS (medium energy ion scattering) study is reported in this paper. Silicon samples were implanted at 3 keV with arsenic ions (dose was 2E15 at/cm2 producing a 11 nm amorphous layer) and then annealed in nitrogen at temperatures ranging from 500 to 700 deg. C to have different levels of recrystallisation. From the comparison of the recrystallised fraction as measured by MEIS with the electrical activation measured by Hall effect it results evident that a full regrowth of the lattice is not reflected by a high electrical activation. The activated arsenic corresponds to less than one third of the apparently substitutional dopant for all the samples analyzed. This lack of activation was further investigated by EXAFS: the samples that according to MEIS are fully recrystallised do not reveal a clear local order around As atoms suggesting that either the As atoms are not yet completely relocated within the lattice sites or a deactivation occurred resulting in a more disordered local structure.

  18. Local and regional effects on community structure of dung beetles in a mainland-island scenario.

    PubMed

    da Silva, Pedro Giovâni; Hernández, Malva Isabel Medina

    2014-01-01

    Understanding the ecological mechanisms driving beta diversity is a major goal of community ecology. Metacommunity theory brings new ways of thinking about the structure of local communities, including processes occurring at different spatial scales. In addition to new theories, new methods have been developed which allow the partitioning of individual and shared contributions of environmental and spatial effects, as well as identification of species and sites that have importance in the generation of beta diversity along ecological gradients. We analyzed the spatial distribution of dung beetle communities in areas of Atlantic Forest in a mainland-island scenario in southern Brazil, with the objective of identifying the mechanisms driving composition, abundance and biomass at three spatial scales (mainland-island, areas and sites). We sampled 20 sites across four large areas, two on the mainland and two on the island. The distribution of our sampling sites was hierarchical and areas are isolated. We used standardized protocols to assess environmental heterogeneity and sample dung beetles. We used spatial eigenfunctions analysis to generate the spatial patterns of sampling points. Environmental heterogeneity showed strong variation among sites and a mild increase with increasing spatial scale. The analysis of diversity partitioning showed an increase in beta diversity with increasing spatial scale. Variation partitioning based on environmental and spatial variables suggests that environmental heterogeneity is the most important driver of beta diversity at the local scale. The spatial effects were significant only at larger spatial scales. Our study presents a case where environmental heterogeneity seems to be the main factor structuring communities at smaller scales, while spatial effects are more important at larger scales. The increase in beta diversity that occurs at larger scales seems to be the result of limitation in species dispersal ability due to habitat

  19. Human phenol sulfotransferase STP2 gene: Molecular cloning, structural characterization, and chromosomal localization

    SciTech Connect

    Her, C.; Raftogianis, R.; Weinshilboum, R.M.

    1996-05-01

    Sulfonation is an important pathway in the biotransformation of many drugs, xenobiotics, neurotransmitters, and steroid hormones. The thermostable (TS) form of phenol sulfotransferase (PST) preferentially catalyzes the sulfonation of {open_quotes}simple{close_quotes} planar phenols, and levels of activity of TS PST in human tissues are controlled by inheritance. Two different human liver TS PST cDNAs have been cloned that encode proteins with amino acid sequences that are 96% identical. We have determined the structure and chromosomal localization of the gene for one of these two cDNAs, STP2, as a step toward understanding molecular genetic mechanisms involved in the regulation of this enzyme activity in humans. STP2 spans approximately 5.1 kb and contains nine exons that range in length from 74 to 347 bp. The locations of most STP2 exon-intron splice junctions are identical to those of a gene for the thermolabile form of PST in humans, STM; a rat PST gene; a human estrogen ST (EST) gene, STE; and a guinea pig EST gene. The two initial STP2 exons, IA and IB, were identified by performing 5{prime}-rapid amplification of cDNA ends with human liver cDNA as template. Exons IA and IB are noncoding and represent two different human liver TS PST cDNA 5{prime}untranslated region sequences. The two apparent 5{prime}-ons IA and IB, contain no canonical TATA boxes, but do contain CCAAT elements. STP2 was localized to human chromosome 16 by performing the PCR with DNA from NIGMS human/rodent somatic cell hybrids as template. Structural characterization of STP2 will make it possible to begin to study molecular genetic mechanisms involved in the regulation of TS PST activity in human tissues. 63 refs., 7 figs., 1 tab.

  20. Local and Regional Effects on Community Structure of Dung Beetles in a Mainland-Island Scenario

    PubMed Central

    da Silva, Pedro Giovâni; Hernández, Malva Isabel Medina

    2014-01-01

    Understanding the ecological mechanisms driving beta diversity is a major goal of community ecology. Metacommunity theory brings new ways of thinking about the structure of local communities, including processes occurring at different spatial scales. In addition to new theories, new methods have been developed which allow the partitioning of individual and shared contributions of environmental and spatial effects, as well as identification of species and sites that have importance in the generation of beta diversity along ecological gradients. We analyzed the spatial distribution of dung beetle communities in areas of Atlantic Forest in a mainland-island scenario in southern Brazil, with the objective of identifying the mechanisms driving composition, abundance and biomass at three spatial scales (mainland-island, areas and sites). We sampled 20 sites across four large areas, two on the mainland and two on the island. The distribution of our sampling sites was hierarchical and areas are isolated. We used standardized protocols to assess environmental heterogeneity and sample dung beetles. We used spatial eigenfunctions analysis to generate the spatial patterns of sampling points. Environmental heterogeneity showed strong variation among sites and a mild increase with increasing spatial scale. The analysis of diversity partitioning showed an increase in beta diversity with increasing spatial scale. Variation partitioning based on environmental and spatial variables suggests that environmental heterogeneity is the most important driver of beta diversity at the local scale. The spatial effects were significant only at larger spatial scales. Our study presents a case where environmental heterogeneity seems to be the main factor structuring communities at smaller scales, while spatial effects are more important at larger scales. The increase in beta diversity that occurs at larger scales seems to be the result of limitation in species dispersal ability due to habitat