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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. Local light-induced spin manipulation in two magnetic centre metallic chains

    NASA Astrophysics Data System (ADS)

    Hartenstein, T.; Li, C.; Lefkidis, G.; Hübner, W.

    2008-08-01

    In this paper localized optically induced spin dynamics is presented, based on highly correlational ab initio calculations. Two-magnetic-centre metallic chains are chosen as a material on which the total spin is always found to lie on one of the magnetic centres only. Switching is achieved through a Λ-process driven by a laser pulse whose parameters are optimized with a genetic algorithm. Locally switching the spin on the iron side of a Co-Na-Fe cluster is given as an example of local spin manipulation.

  4. Theoretical studies of the dependence of EPR g-factors on local structure for the trigonal Er3+-VK centres in KMgF3 and KZnF3

    NASA Astrophysics Data System (ADS)

    Chai, Rui-Peng; Kuang, Xiao-Yu; Liang, Liang; Yu, Geng-Hua

    2015-05-01

    The dependence of the EPR g-factors on the local structural parameter for a 4f11 configuration ion Er3+ in a trigonal crystal-field has been studied by diagonalizing the 364×364 complete energy matrices. Our studies indicate that the EPR spectra of the trigonal Er3+-VK centers in KMgF3 and KZnF3 may be attributed to the translation of the cubic Kramers doublet Γ7. Furthermore, the EPR g-factors of the trigonal Er3+-VK centers may be interpreted reasonably by the shifts ΔZ≈0.340 Å and ΔZ≈0.303 Å of the Er3+ ions toward the charge compensator VK along the C3 axis for the KMgF3:Er3+ and the KZnF3:Er3+ systems respectively.

  5. 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.

  6. 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

  7. 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

  8. 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

  9. 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…

  10. 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.

  11. Localized structure of Euglena bioconvection

    NASA Astrophysics Data System (ADS)

    Iima, Makoto; Shoji, Erika; Awazu, Akinori; Nishimori, Hiraku; Izumi, Shunsuke; Hiroshima University Collaboration

    2013-11-01

    Bioconvection of a suspension of Euglena gracilis, a photosensitive flagellate whose body length is approximately 50 micrometers, was experimentally studied. Under strong light intensity, Euglena has a negative phototaxis; they tend to go away from the light source. When the bright illumination is given from the bottom, a large scale spatio-temporal pattern is generated as a result of interaction between Euglena and surrounding flow. Recently, localized convection pattern had been reported, however, the generation process and interaction of the localized convection cells has not been analyzed. We performed experimental study to understand the localization mechanism, in particular, the onset of bioconvection and lateral localization behavior due to phototaxis. Experiments started from different initial condition suggests a bistability near the onset of the convection as binary fluid convection that also shows localized convection cells. Dynamics of localized convections cells, which is similar to the binary fluid convection case although the basic equations are not the same, is also reported.

  12. 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…

  13. 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…

  14. 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

  15. 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.

  16. 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

  17. Introduction: Dissipative localized structures in extended systems

    NASA Astrophysics Data System (ADS)

    Tlidi, Mustapha; Taki, Majid; Kolokolnikov, Theodore

    2007-09-01

    Localized structures belong to the class of dissipative structures found far from equilibrium. Contributions from the most representative groups working on a various fields of natural science such as biology, chemistry, plant ecology, mathematics, optics, and laser physics are presented. The aim of this issue is to gather specialists from these fields towards a cross-fertilization among these active areas of research and thereby to present an overview of the state of art in the formation and the characterization of dissipative localized structures. Nonlinear optics and laser physics have an important part in this issue because of potential applications in information technology. In particular, localized structures could be used as "bits" for parallel information storage and processing.

  18. 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.

  19. Patterns and localized structures in population dynamics

    NASA Astrophysics Data System (ADS)

    Clerc, M. G.; Escaff, D.; Kenkre, V. M.

    2005-11-01

    Patterns, fronts, and localized structures of a prototypical model for population dynamics interaction are studied. The physical content of the model is the coexistence of a simple random walk for the motion of the individuals with a nonlinearity in the competitive struggle for resources which simultaneously stresses the Allee effect and interaction at a distance. Mathematically, the model is variational and exhibits coexistence between different stable extended states. Solutions are obtained, the phase diagram is constructed, and the emergence of localized structures is investigated.

  20. Local backbone structure prediction of proteins.

    PubMed

    de Brevern, Alexandre G; Benros, Cristina; Gautier, Romain; Valadié, Héléne; Hazout, Serge; Etchebest, Catherine

    2004-01-01

    A statistical analysis of the PDB structures has led us to define a new set of small 3D structural prototypes called Protein Blocks (PBs). This structural alphabet includes 16 PBs, each one is defined by the (phi, psi) dihedral angles of 5 consecutive residues. The amino acid distributions observed in sequence windows encompassing these PBs are used to predict by a Bayesian approach the local 3D structure of proteins from the sole knowledge of their sequences. LocPred is a software which allows the users to submit a protein sequence and performs a prediction in terms of PBs. The prediction results are given both textually and graphically. PMID:15724288

  1. How Good Is Our School? The Child at the Centre: The Health Promoting School--The Role of Local Authorities and Their Partners. Self-Evaluation Series

    ERIC Educational Resources Information Center

    Her Majesty's Inspectorate of Education, 2004

    2004-01-01

    To become effective health promoting establishments which achieve the maximum impact on children, young people and families and on the local community, schools and pre-school centres need to operate within a strategic framework developed at the highest levels within their local council and community area. Effective councils are committed to…

  2. Quantum structure based infrared detector research and development within Acreo’s centre of excellence IMAGIC

    NASA Astrophysics Data System (ADS)

    Andersson, J. Y.; Höglund, L.; Noharet, B.; Wang, Q.; Ericsson, P.; Wissmar, S.; Asplund, C.; Malm, H.; Martijn, H.; Hammar, M.; Gustafsson, O.; Hellström, S.; Radamson, H.; Holtz, P. O.

    2010-07-01

    Acreo has a long tradition of working with quantum structure based infrared (IR) detectors and arrays. This includes QWIP (quantum well infrared photodetector), QDIP (quantum dot infrared photodetector), and InAs/GaInSb based photon detectors of different structure and composition. It also covers R&D on uncooled microbolometers. The integrated thermistor material of such detectors is advantageously based on quantum structures that are optimised for high temperature coefficient and low noise. Especially the SiGe material system is preferred due to the compatibility with silicon technology. The R&D work on IR detectors is a prominent part of Acreo's centre of excellence "IMAGIC" on imaging detectors and systems for non-visible wavelengths. IMAGIC is a collaboration between Acreo, several industry partners and universities like the Royal Institute of Technology (KTH) and Linköping University.

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

    PubMed Central

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

    2005-01-01

    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. PMID:16511113

  4. Structure Process, Weak Values and Local Momentum

    NASA Astrophysics Data System (ADS)

    Hiley, B. J.

    2016-03-01

    We explain how weak values and the local momentum can be better understood in terms of Bohm's notion of structure process. The basic ideas of this approach can be expressed in a fully algebraic way, generalising Heisenberg's original matrix mechanics. This approach leads to questions that are now being experimentally investigated by our group at University College London.

  5. 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...

  6. Local structures of homogeneous Hall MHD turbulence

    NASA Astrophysics Data System (ADS)

    Miura, H.; Araki, K.

    2011-12-01

    Local structures of decaying homogeneous and isotropic Hall MHD turbulence are studied by means of direct numerical simulations. Regions of strong vorticity and strong current density in Hall MHD turbulence are compared to those of single-fluid MHD turbulence. An analysis by the use of a low-pass filter reveals that the introduction of the Hall term can modify not only small-scale structures of the current density but also structures of the vorticity field, especially at the scales smaller than the ion skin depth.

  7. 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

  8. A structural alphabet for local protein structures: improved prediction methods.

    PubMed

    Etchebest, Catherine; Benros, Cristina; Hazout, Serge; de Brevern, Alexandre G

    2005-06-01

    Three-dimensional protein structures can be described with a library of 3D fragments that define a structural alphabet. We have previously proposed such an alphabet, composed of 16 patterns of five consecutive amino acids, called Protein Blocks (PBs). These PBs have been used to describe protein backbones and to predict local structures from protein sequences. The Q16 prediction rate reaches 40.7% with an optimization procedure. This article examines two aspects of PBs. First, we determine the effect of the enlargement of databanks on their definition. The results show that the geometrical features of the different PBs are preserved (local RMSD value equal to 0.41 A on average) and sequence-structure specificities reinforced when databanks are enlarged. Second, we improve the methods for optimizing PB predictions from sequences, revisiting the optimization procedure and exploring different local prediction strategies. Use of a statistical optimization procedure for the sequence-local structure relation improves prediction accuracy by 8% (Q16 = 48.7%). Better recognition of repetitive structures occurs without losing the prediction efficiency of the other local folds. Adding secondary structure prediction improved the accuracy of Q16 by only 1%. An entropy index (Neq), strongly related to the RMSD value of the difference between predicted PBs and true local structures, is proposed to estimate prediction quality. The Neq is linearly correlated with the Q16 prediction rate distributions, computed for a large set of proteins. An "expected" prediction rate QE16 is deduced with a mean error of 5%. PMID:15822101

  9. 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…

  10. A structured methodology to calculate traffic emissions inventories for city centres.

    PubMed

    Ariztegui, Javier; Casanova, Jesus; Valdes, Manuel

    2004-12-01

    This study presents a methodology to estimate traffic emissions inventories for the case of city centres. It deals with the problem in a structured manner, identifying the sources and the formats of the input data as well as labelling the steps needed to perform the calculation. It describes a method to calculate the total mileage driven around the city using the concept of mileage per zone. Although the methodology employs a classical approach through the use of emission factors developed for mean speeds, it also discusses the possibility of applying these factors to instantaneous speeds. Finally, the study focuses on the influence of two critical factors: time resolution and the estimate of the total mileage. In both cases, the results indicate that the assumptions made are adequate and yield accurate results. The methodology has been applied to the city of Madrid as an example. PMID:15504496

  11. Single centre outcomes from definitive chemo-radiotherapy and single modality radiotherapy for locally advanced oesophageal cancer

    PubMed Central

    Gray, Joanna; McDonald, Alexander; McIntosh, David; MacLaren, Vivienne; Hennessy, Aisling; Grose, Derek

    2016-01-01

    Background Definitive chemo-radiotherapy (dCRT) has been advocated as an alternative to surgical resection for the treatment of locally advanced oesophageal cancer (OC). We have retrospectively reviewed 4 years’ experience of patients (pts) who underwent contemporary staging and were treated with concurrent chemo-radiotherapy (dCRT) or single modality radical radiotherapy (RT) with curative intent. Methods Retrospective analysis permitted identification of consecutive patients who underwent contemporary staging prior to non-surgical treatment for locally advanced oesophageal carcinoma. The primary outcomes were overall survival (OS) and disease-free survival (DFS), adjusted for baseline differences in age, tumour staging and histological cell type. All patients were treated with either dCRT or single modality RT within a single centre between 2009 and 2012. Results We identified 235 patients in total [median age 69.8 years, male =130 pts, female =105 pts, adenocarcinoma (ACA) =85 pts, squamous =150 pts]. A total of 190 pts received dCRT and 45 patients were treated with RT. All patients were staged with CT of chest, abdomen and pelvis, 226 patients underwent endoscopic ultrasound (EUS), and 183 patients had PET-CT. Patients treated with dCRT demonstrated longer OS (27 vs. 25 months respectively, P=0.02) and DFS (31 vs. 16 months respectively, P=0.01) compared to those treated with RT. More advanced tumour stage (stage 3 vs. stage 1/2) at presentation conferred poorer OS (32 vs. 38.2 months, P=0.02) and DFS (11 vs. 28 months, P=0.013). We demonstrated an acceptable toxicity profile with only 77 patients (32.8%) suffering grade 3 toxicity and 9 patients (4.2%) experiencing grade 4 toxicity by CTC criteria. The NG/PEG feeding rates were 4% across all treated patients. Conclusions This retrospective analysis is in keeping with current treatment paradigms emphasising the importance and safety of concurrent CRT in maximising curative potential for patients undergoing

  12. 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

  13. Guanine quadruplex structures localize to heterochromatin.

    PubMed

    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

  14. 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.

  15. 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

  16. 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

  17. Towards structural controllability of local-world networks

    NASA Astrophysics Data System (ADS)

    Sun, Shiwen; Ma, Yilin; Wu, Yafang; Wang, Li; Xia, Chengyi

    2016-05-01

    Controlling complex networks is of vital importance in science and engineering. Meanwhile, local-world effect is an important ingredient which should be taken into consideration in the complete description of real-world complex systems. In this letter, structural controllability of a class of local-world networks is investigated. Through extensive numerical simulations, firstly, effects of local world size M and network size N on structural controllability are examined. For local-world networks with sparse topological configuration, compared to network size, local-world size can induce stronger influence on controllability, however, for dense networks, controllability is greatly affected by network size and local-world effect can be neglected. Secondly, relationships between controllability and topological properties are analyzed. Lastly, the robustness of local-world networks under targeted attacks regarding structural controllability is discussed. These results can help to deepen the understanding of structural complexity and connectivity patterns of complex systems.

  18. 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.

  19. Structures of Local Rearrangements in Soft Colloidal Glasses

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

    We image local structural rearrangements in soft colloidal glasses under small periodic perturbations induced by thermal cycling. Local structural entropy S2 positively correlates with observed rearrangements in colloidal glasses. The high S2 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 S2 spots are capable of predicting local rearrangements long before the relaxations occur, while fluctuation-created high S2 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 S2. 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.

  20. 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

  1. 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

  2. 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

  3. Studies on crystal structures, active-centre geometry and depurinating mechanism of two ribosome-inactivating proteins.

    PubMed Central

    Huang, Q; Liu, S; Tang, Y; Jin, S; Wang, Y

    1995-01-01

    Two ribosome-inactivating proteins, trichosanthin and alpha-momorcharin, have been studied in the forms of complexes with ATP or formycin, by an X-ray-crystallographic method at 1.6-2.0 A (0.16-0.20 nm) resolution. The native alpha-momorcharin had been studied at 2.2 A resolution. Structures of trichosanthin were determined by a multiple isomorphous replacement method. Structures of alpha-momorcharin were determined by a molecular replacement method using refined trichosanthin as the searching model. Small ligands in all these complexes have been recognized and built on the difference in electron density. All these structures have been refined to achieve good results, both in terms of crystallography and of ideal geometry. These two proteins show considerable similarity in their three-dimensional folding and to that of related proteins. On the basis of these structures, detailed geometries of the active centres of these two proteins are described and are compared with those of related proteins. In all complexes the interactions between ligand atoms and protein atoms, including hydrophobic forces, aromatic stacking interactions and hydrogen bonds, are found to be specific towards the adenine base. The relationship between the sequence conservation of ribosome-inactivating proteins and their active-centre geometry was analysed. A depurinating mechanism of ribosome-inactivating proteins is proposed on the basis of these results. The N-7 atom of the substrate base group is proposed to be protonated by an acidic residue in the active centre. Images Figure 1 PMID:7619070

  4. Rodlike localized structure in isotropic pattern-forming systems

    NASA Astrophysics Data System (ADS)

    Bordeu, Ignacio; Clerc, Marcel G.

    2015-10-01

    Stationary two-dimensional localized structures have been observed in a wide variety of dissipative systems. The existence, stability properties, dynamical evolution, and bifurcation diagram of an azimuthal symmetry breaking, rodlike localized structure in the isotropic prototype model of pattern formation, the Swift-Hohenberg model, is studied. These rodlike structures persist under the presence of nongradient perturbations. Interaction properties of the rodlike structures are studied. This allows us to envisage the possibility of different crystal-like configurations.

  5. Finding Common Ground: Creating Local Governance Structures.

    ERIC Educational Resources Information Center

    Mutchler, Sue E.; And Others

    As federal, state, and local policy makers attend to the economic, educational, social, and health-related needs of children, they are beginning to share a vision of a "seamless web" of high-quality, comprehensive, continuous services for children and their families. It remains a challenging goal because of the complexity of children's needs and…

  6. XAFS study on the impact of local structure on electrochemical performance for Co3O4 nanowire arrays

    NASA Astrophysics Data System (ADS)

    Jiang, Shan; Cheng, Weiren; He, Jingfu; Huang, Junheng; Liu, Qinghua; Jiang, Yong; Wei, Shiqiang

    2016-05-01

    Determining the local structure of catalyst materials is critical for understanding the mechanism of enhanced electrochemical activity in semiconductor electrode. Here, using X-ray absorption fine structure (XAFS) spectra, we reveal that the local disorder structure is formed for the mixed-phase Co3O4 nanowire arrays due to the interaction between the phases of Co3O4 and Co2(OH)2CO3. Comparing to pure Co3O4 nanowire arrays, the mixed phase sample is richer in Co2+ and the electronic structure is changed by the local structure, which are demonstrated by the X-ray absorption near-edge structure (XANES) spectra. It is deduced that the mixed-phase Co3O4 nanowire arrays with abundant Co2+ sites provide more redox centres in electrochemical reaction than the pure Co3O4 nanowire arrays.

  7. 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.

  8. 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.

  9. 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.

  10. Structure and redox properties of the haem centre in the C357M mutant of cytochrome P450cam.

    PubMed

    Murugan, Rajamanickam; Mazumdar, Shyamalava

    2005-07-01

    The effects of site-specific mutation of the axial cysteine (C357M) to a methionine residue in cytochrome P450cam on the enzyme's coordination geometry and redox potential have been investigated. The absorption spectra of the haem centre in the C357M mutant of the enzyme showed close similarity to those of cytochrome c both in the oxidised and reduced forms. A well-defined absorption peak at 695 nm, similar to that seen in the case of cytochrome c and characteristic of methionine ligation to the ferric haem, was observed. The results indicated that the haem of C357M cytochrome P450cam is possibly axially coordinated to a methionine and a histidine, analogously to cytochrome c. The circular dichroism spectra in the visible and the far-UV regions suggested that the tertiary structure of the haem cavity in the C357M mutant cytochrome P450cam was distinctly different from that in the wild-type enzyme or in cytochrome c, although the secondary structure of the mutant remained identical to that of the wild-type cytochrome P450cam. Comparison of the natures of the CD spectra in the 400 nm and 695 nm regions of the C357M mutant of cytochrome P450cam with those of horse cytochrome c suggested (R) chirality at the sulfur atom of the iron-bound methionine residue in the mutant. The redox potential of the haem centre, estimated by redox titration of the C357M mutant, was found to be +260 mV, which is much higher than that in the wild-type enzyme and similar to the redox potential of cytochrome c. This supported the concept that axial ligation of the haem plays the major role in tuning the redox potential of the haem centre in haem proteins. PMID:15912551

  11. 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.

  12. Global-local finite element analysis of composite structures

    SciTech Connect

    Deibler, J.E.

    1992-06-01

    The development of layered finite elements has facilitated analysis of laminated composite structures. However, the analysis of a structure containing both isotropic and composite materials remains a difficult problem. A methodology has been developed to conduct a ``global-local`` finite element analysis. A ``global`` analysis of the entire structure is conducted at the appropriate loads with the composite portions replaced with an orthotropic material of equivalent materials properties. A ``local`` layered composite analysis is then conducted on the region of interest. The displacement results from the ``global`` analysis are used as loads to the ``local`` analysis. the laminate stresses and strains can then be examined and failure criteria evaluated.

  13. Global-local finite element analysis of composite structures

    SciTech Connect

    Deibler, J.E.

    1992-06-01

    The development of layered finite elements has facilitated analysis of laminated composite structures. However, the analysis of a structure containing both isotropic and composite materials remains a difficult problem. A methodology has been developed to conduct a global-local'' finite element analysis. A global'' analysis of the entire structure is conducted at the appropriate loads with the composite portions replaced with an orthotropic material of equivalent materials properties. A local'' layered composite analysis is then conducted on the region of interest. The displacement results from the global'' analysis are used as loads to the local'' analysis. the laminate stresses and strains can then be examined and failure criteria evaluated.

  14. 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.

  15. Locally refined block-centred finite-difference groundwater models: Evaluation of parameter sensitivity and the consequences for inverse modelling

    USGS Publications Warehouse

    Mehl, S.; Hill, M.C.

    2002-01-01

    Models with local grid refinement, as often required in groundwater models, pose special problems for model calibration. This work investigates the calculation of sensitivities and the performance of regression methods using two existing and one new method of grid refinement. The existing local grid refinement methods considered are: (a) a variably spaced grid in which the grid spacing becomes smaller near the area of interest and larger where such detail is not needed, and (b) telescopic mesh refinement (TMR), which uses the hydraulic heads or fluxes of a regional model to provide the boundary conditions for a locally refined model. The new method has a feedback between the regional and local grids using shared nodes, and thereby, unlike the TMR methods, balances heads and fluxes at the interfacing boundary. Results for sensitivities are compared for the three methods and the effect of the accuracy of sensitivity calculations are evaluated by comparing inverse modelling results. For the cases tested, results indicate that the inaccuracies of the sensitivities calculated using the TMR approach can cause the inverse model to converge to an incorrect solution.

  16. Local structure analyzers as determinants of preattentive pattern discrimination.

    PubMed

    Kröse, B J

    1987-01-01

    Contemporary literature suggests that preattentive texture or pattern discrimination is induced by differences between local structure features or "textons." This paper presents a model for the description of such local structure features based on the computation of local autocorrelations within the image. By means of this structure model a measure of structure dissimilarity is introduced. Experiments have been carried out to test a hypothesized relation between the detectability of a target pattern in a field of background patterns and the value of the structure dissimilarity measure. The experimental results show that it seems justified to relate, in a quantitative way, the detectability of the target pattern to the value of the structure dissimilarity measure. PMID:3828403

  17. Glass formation and local topological instability of atomic structure

    SciTech Connect

    Egami, T.

    1997-12-31

    A direct connection between the local topology of the atomic structure of liquids and glasses and thermodynamic quantities through the atomic level stresses is suggested for metallic alloys. In particular the role of local topological instability in the phase transformation involving liquid and glass will be discussed. It is pointed out that a single local geometrical criterion can explain various phase transformations, such as melting, glass transition, and glass formation by solid state reaction and liquid quenching.

  18. 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…

  19. Localized vibrations: moles in structure-land

    NASA Astrophysics Data System (ADS)

    van der Maas, John H.

    1992-03-01

    Functional groups reveal specific information about their direct surroundings; in fact, they form the moles, the undercover agents, in molecules. However, as with agents, the information is produced in coded form (spectral data) so one has to know the code in detail before the message is completely understood. The substantially improved accuracy (wavenumber, intensity) and sensitivity brought about by FT-instruments, in combination with computer software, offer extended spectral information. Functional groups can now be examined in great detail. Obviously the amount of deducible structural items is group dependent, implying that one has to pursue the probing qualities of a functionality prior to use. The OH-group, and more in particular the OH-stretching vibration, proves to be an extremely good mole. Its potentials are demonstrated on conformational studies of various saturated alcohols, the presence of OH(DOT)(DOT)(DOT)(pi) bridges, the strength and type of OH(DOT)(DOT)(DOT)O bridges, all in an apolar solvent, and on the disclosure of different hydrogen bonds in some solid samples.

  20. Proteins comparison through probabilistic optimal structure local alignment

    PubMed Central

    Micale, Giovanni; Pulvirenti, Alfredo; Giugno, Rosalba; Ferro, Alfredo

    2014-01-01

    Multiple local structure comparison helps to identify common structural motifs or conserved binding sites in 3D structures in distantly related proteins. Since there is no best way to compare structures and evaluate the alignment, a wide variety of techniques and different similarity scoring schemes have been proposed. Existing algorithms usually compute the best superposition of two structures or attempt to solve it as an optimization problem in a simpler setting (e.g., considering contact maps or distance matrices). Here, we present PROPOSAL (PROteins comparison through Probabilistic Optimal Structure local ALignment), a stochastic algorithm based on iterative sampling for multiple local alignment of protein structures. Our method can efficiently find conserved motifs across a set of protein structures. Only the distances between all pairs of residues in the structures are computed. To show the accuracy and the effectiveness of PROPOSAL we tested it on a few families of protein structures. We also compared PROPOSAL with two state-of-the-art tools for pairwise local alignment on a dataset of manually annotated motifs. PROPOSAL is available as a Java 2D standalone application or a command line program at http://ferrolab.dmi.unict.it/proposal/proposal.html. PMID:25228906

  1. Protein tertiary structure recognition using optimized Hamiltonians with local interactions.

    PubMed Central

    Goldstein, R A; Luthey-Schulten, Z A; Wolynes, P G

    1992-01-01

    Protein folding codes embodying local interactions including surface and secondary structure propensities and residue-residue contacts are optimized for a set of training proteins by using spin-glass theory. A screening method based on these codes correctly matches the structure of a set of test proteins with proteins of similar topology with 100% accuracy, even with limited sequence similarity between the test proteins and the structural homologs and the absence of any structurally similar proteins in the training set. PMID:1409599

  2. 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

  3. Structure of local interactions in complex financial dynamics

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    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.

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

    PubMed

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

    2014-10-01

    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. PMID:25377487

  5. 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.

  6. Global/local methods for probabilistic structural analysis

    NASA Technical Reports Server (NTRS)

    Millwater, H. R.; Wu, Y.-T.

    1993-01-01

    A probabilistic global/local method is proposed to reduce the computational requirements of probabilistic structural analysis. A coarser global model is used for most of the computations with a local more refined model used only at key probabilistic conditions. The global model is used to establish the cumulative distribution function (cdf) and the Most Probable Point (MPP). The local model then uses the predicted MPP to adjust the cdf value. The global/local method is used within the advanced mean value probabilistic algorithm. The local model can be more refined with respect to the g1obal model in terms of finer mesh, smaller time step, tighter tolerances, etc. and can be used with linear or nonlinear models. The basis for this approach is described in terms of the correlation between the global and local models which can be estimated from the global and local MPPs. A numerical example is presented using the NESSUS probabilistic structural analysis program with the finite element method used for the structural modeling. The results clearly indicate a significant computer savings with minimal loss in accuracy.

  7. Structure and local structure of perovskite based materials

    NASA Astrophysics Data System (ADS)

    Rossell Abrodos, Marta Dacil

    Perovskites, with general formula ABX3, where A and B are cations and X is an anion, form a very important class of inorganic crystals whose physical properties are extensively used in many technological applications. The basic, so-called aristotype structure, consists of an infinite array of corner-linked anion octahedra, with the A cations in the spaces between the octahedra and a B cation at the center of each octahedron. Interesting physical properties are often related to the flexibility of the perovskite structure to deform or to form non-stoichiometric compositions. In this thesis, four perovskite-related systems are studied. Transmission electron microscopy (TEM) is of prime interest to analyze the influence of the structure and microstructure on the physical properties of these systems. (1) The anion-deficient Sr4Fe6O12+delta (delta < 1) derivatives. These materials are mixed conducting oxides with high oxygen and electronic conductivity. A complete characterization of the structure of these anion-deficient compounds is deduced from electron diffraction and high-resolution TEM. The presence of anion vacancies in the Sr4Fe6O12+delta (delta < 1) structure is suggested to have an influence on the transport properties. (2) The CaRMnSnO6 (R = La, Pr, Nd, Sm-Dy) double perovskites. A random distribution of the Ca and R cations over the A positions and Mn and Sn cations over the B positions is found. Due to a random distribution of the Mn 3+ and Sn4+ cations, a spin glass behavior was found for CaLaMnSnO6. (3) The K3AlF6 elpasolite-type (or ordered double perovskite) structure. This compound is of high technological importance since it is a basic component of the melts for low temperature electrolysis in aluminum smelting. A sequence of phase transitions at different temperatures in K3AlF6 along with the data on unit cell dimensions and space symmetry of three major polymorphs is reported. (4) Ca 2Fe2O5 brownmillerite-type thin films deposited on three different

  8. 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.

  9. The Local Physical Structure of Amorphous Boron Carbide Thin Films

    NASA Astrophysics Data System (ADS)

    Paquette, M. M.; Li, Wenjing; Driver, M. S.; Oyler, N. A.; Caruso, A. N.

    2011-03-01

    Thin-film amorphous hydrogenated boron carbide (a-B5 C:Hx) and technical boron carbide (B4 C:Cy) are important materials in next-generation solid-state neutron detectors and refractory electronics. Optimizing the electrical carrier transport and electronic structure of these films for the stated applications has been severely hindered by: (1) their lack of long-range periodicity; (2) the ability of boron-rich solids to form complex polyhedra; and, (3) the possibility that carbon atoms incorporate into the polyhedral structures in an intraicosahedral fashion or that they bridge polyhedral structures in an intericosahedral fashion. The use of traditional spectroscopies that are sensitive to local coordination environment have been inadequate in the determination of the local physical structure because of either poor resolution or very low interaction cross sections. However, magic spinning angle (MAS) solid-state nuclear magnetic resonance (SSNMR), does have the signal-to-noise and rigor to extract the local physical coordination structure of these materials, despite the challenges associated with deltahedra-based structures. This poster will describe the progress and challenges in structure determination through a comparison of unknown samples to known calibration standards using MAS techniques, in the context of furthering the general understanding of the electronic structure of a-B5 C:Hx and B4 C:Cy thin films.

  10. 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.

  11. Confidence-Guided Local Structure Prediction with HHfrag

    PubMed Central

    Kalev, Ivan; Habeck, Michael

    2013-01-01

    We present a method to assess the reliability of local structure prediction from sequence. We introduce a greedy algorithm for filtering and enrichment of dynamic fragment libraries, compiled with remote-homology detection methods such as HHfrag. After filtering false hits at each target position, we reduce the fragment library to a minimal set of representative fragments, which are guaranteed to have correct local structure in regions of detectable conservation. We demonstrate that the location of conserved motifs in a protein sequence can be predicted by examining the recurrence and structural homogeneity of detected fragments. The resulting confidence score correlates with the local RMSD of the representative fragments and allows us to predict torsion angles from sequence with better accuracy compared to existing machine learning methods. PMID:24146881

  12. Correlation of Local Structure and Electronic Properties of Glass Materials

    NASA Astrophysics Data System (ADS)

    Lordi, Vincenzo; Adelstein, Nicole

    2015-03-01

    Wide band gap glasses such as silica and its derivatives are typically considered insulators. However, electronic transport in glasses can be important for certain applications, such as when used as the host material for a scintillator radiation detector. Here we explore the relationship between local structure in glass materials and the corresponding electronic properties of carrier transport and charge trapping. We present a novel analysis that decomposes the distribution of localized band tail states in terms of specific local structural features in the glass. Comparison of the structure-related transport properties of different glass compositions is given, using silica and sodium silicate as prototypes. Prepared by LLNL under Contract DE-AC52-07NA27344.

  13. Influences of consolidation processes on local paper structure

    NASA Astrophysics Data System (ADS)

    Sung, Yongjoo

    The accurate measurement of the structural parameters such as thickness, grammage, apparent density and surface topography, and the proper evaluation of the variation of each parameter, are very important not only for predicting the end use properties of the paper, but also for diagnosing the pa permaking processes. The difficulty of the measurement of thickness at fine scale ˜1 mm has been an impediment to the understanding of local paper structure. To address this problem, a twin laser profilometer instrument (TLP) for non-contacting measurement of local thickness and surface topography was developed, characterized and calibrated in this work. The fundamental relationships between structural parameters were reexamined with various handsheet samples. The effects of wet pressing on the local paper structure were evaluated using laboratory static press and commercial press felts. The different press pressure had no significant influence on the local density variation of the handsheet samples. The influences of felts on the surface topography were also successfully observed. The different densification effects of soft nip and hard nip calendering processes were evaluated by direct comparison of structural parameters before and after processing. The much higher selective reduction in local thickness (larger reduction for the thicker area) by the hard nip calendering process resulted in different relationships between structural parameters. The various periodic variations in the paper structure were also detected, analyzed and identified. The effects of different forming elements such as the conventional foil system and the velocity induced drainage (VID) system on the paper structure and end use properties were evaluated with pilot machine trials and commercial product produced using different forming elements. Generally, the VID samples showed better formation, less two sidedness in the fine distribution through thickness direction, and less densification during

  14. 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.

  15. Exploiting orientation-selective DEER: determining molecular structure in systems containing Cu(ii) centres.

    PubMed

    Bowen, Alice M; Jones, Michael W; Lovett, Janet E; Gaule, Thembanikosi G; McPherson, Michael J; Dilworth, Jonathan R; Timmel, Christiane R; Harmer, Jeffrey R

    2016-02-17

    Orientation-selective DEER (Double Electron-Electron Resonance) measurements were conducted on a series of rigid and flexible molecules containing Cu(ii) ions. A system with two rigidly held Cu(ii) ions was afforded by the protein homo-dimer of copper amine oxidase from Arthrobacter globiformis. This system provided experimental DEER data between two Cu(ii) ions with a well-defined distance and relative orientation to assess the accuracy of the methodology. Evaluation of orientation-selective DEER (os DEER) on systems with limited flexibility was probed using a series of porphyrin-based Cu(ii)-nitroxide and Cu(ii)-Cu(ii) model systems of well-defined lengths synthesized for this project. Density functional theory was employed to generate molecular models of the conformers for each porphyrin-based Cu(ii) dimer studied. Excellent agreement was found between DEER traces simulated using these computed conformers and the experimental data. The performance of different parameterised structural models in simulating the experimental DEER data was also investigated. The results of this analysis demonstrate the degree to which the DEER data define the relative orientation of the two Cu(ii) ions and highlight the need to choose a parameterised model that captures the essential features of the flexibility (rotational freedom) of the system being studied. PMID:26837391

  16. Bacterial pathogen gene regulation: a DNA-structure-centred view of a protein-dominated domain.

    PubMed

    Dorman, Charles J; Colgan, Aoife; Dorman, Matthew J

    2016-07-01

    The mechanisms used by bacterial pathogens to regulate the expression of their genes, especially their virulence genes, have been the subject of intense investigation for several decades. Whole genome sequencing projects, together with more targeted studies, have identified hundreds of DNA-binding proteins that contribute to the patterns of gene expression observed during infection as well as providing important insights into the nature of the gene products whose expression is being controlled by these proteins. Themes that have emerged include the importance of horizontal gene transfer to the evolution of pathogens, the need to impose regulatory discipline upon these imported genes and the important roles played by factors normally associated with the organization of genome architecture as regulatory principles in the control of virulence gene expression. Among these architectural elements is the structure of DNA itself, its variable nature at a topological rather than just at a base-sequence level and its ability to play an active (as well as a passive) part in the gene regulation process. PMID:27252403

  17. 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…

  18. Local Function Conservation in Sequence and Structure Space

    PubMed Central

    Weinhold, Nils; Sander, Oliver; Domingues, Francisco S.; Lengauer, Thomas; Sommer, Ingolf

    2008-01-01

    We assess the variability of protein function in protein sequence and structure space. Various regions in this space exhibit considerable difference in the local conservation of molecular function. We analyze and capture local function conservation by means of logistic curves. Based on this analysis, we propose a method for predicting molecular function of a query protein with known structure but unknown function. The prediction method is rigorously assessed and compared with a previously published function predictor. Furthermore, we apply the method to 500 functionally unannotated PDB structures and discuss selected examples. The proposed approach provides a simple yet consistent statistical model for the complex relations between protein sequence, structure, and function. The GOdot method is available online (http://godot.bioinf.mpi-inf.mpg.de). PMID:18604264

  19. 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

  20. Local Structure of Implicated Pd in Si Using PAC

    NASA Astrophysics Data System (ADS)

    Brett, D. A.; Dogra, R.; Byrne, A. P.; Ridgway, M. C.; Bartels, J.; Vianden, R.

    2004-11-01

    TDPAC has been employed to study the local structure of implanted palladium in silicon utilizing 87 75 keV γ γ cascade of probe nucleus 100Pd. The observed hyperfine parameters revealed the presence of Pd V defect pair only in highly doped n-type silicon. A dumbbell structure with substitutional palladium and silicon vacancy as nearest neigbor is suggested for this defect.

  1. 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.

  2. 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.

  3. 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

  4. 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…

  5. 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…

  6. 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.

  7. Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes.

    PubMed

    Martin, Juliette; Regad, Leslie; Etchebest, Catherine; Camproux, Anne-Claude

    2008-11-15

    Interresidue protein contacts in proteins structures and at protein-protein interface are classically described by the amino acid types of interacting residues and the local structural context of the contact, if any, is described using secondary structures. In this study, we present an alternate analysis of interresidue contact using local structures defined by the structural alphabet introduced by Camproux et al. This structural alphabet allows to describe a 3D structure as a sequence of prototype fragments called structural letters, of 27 different types. Each residue can then be assigned to a particular local structure, even in loop regions. The analysis of interresidue contacts within protein structures defined using Voronoï tessellations reveals that pairwise contact specificity is greater in terms of structural letters than amino acids. Using a simple heuristic based on specificity score comparison, we find that 74% of the long-range contacts within protein structures are better described using structural letters than amino acid types. The investigation is extended to a set of protein-protein complexes, showing that the similar global rules apply as for intraprotein contacts, with 64% of the interprotein contacts best described by local structures. We then present an evaluation of pairing functions integrating structural letters to decoy scoring and show that some complexes could benefit from the use of structural letter-based pairing functions. PMID:18491388

  8. PredyFlexy: flexibility and local structure prediction from sequence

    PubMed Central

    de Brevern, Alexandre G.; Bornot, Aurélie; Craveur, Pierrick; Etchebest, Catherine; Gelly, Jean-Christophe

    2012-01-01

    Protein structures are necessary for understanding protein function at a molecular level. Dynamics and flexibility of protein structures are also key elements of protein function. So, we have proposed to look at protein flexibility using novel methods: (i) using a structural alphabet and (ii) combining classical X-ray B-factor data and molecular dynamics simulations. First, we established a library composed of structural prototypes (LSPs) to describe protein structure by a limited set of recurring local structures. We developed a prediction method that proposes structural candidates in terms of LSPs and predict protein flexibility along a given sequence. Second, we examine flexibility according to two different descriptors: X-ray B-factors considered as good indicators of flexibility and the root mean square fluctuations, based on molecular dynamics simulations. We then define three flexibility classes and propose a method based on the LSP prediction method for predicting flexibility along the sequence. This method does not resort to sophisticate learning of flexibility but predicts flexibility from average flexibility of predicted local structures. The method is implemented in PredyFlexy web server. Results are similar to those obtained with the most recent, cutting-edge methods based on direct learning of flexibility data conducted with sophisticated algorithms. PredyFlexy can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/predyflexy/. PMID:22689641

  9. 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

  10. 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.

  11. Comments on valence-bond structures and charge-shift + recoupled-pair bonding for symmetrical 4-electron 3-centre bonding units

    NASA Astrophysics Data System (ADS)

    Harcourt, Richard D.

    2016-07-01

    Consideration is given to two charge-shift bonding schemes for a symmetrical 4-electron 3-centre hyperbonding unit with three overlapping atomic orbitals. One of these schemes includes the other scheme and the Hach-Rundle-Pimentel 3-centre molecular orbital model as special cases. SF4 and [Cu(H2O)6]2+ are used to illustrate aspects of charge-shift bonding and recoupled-pair bonding theory by generating the increased-valence structures that are associated with the preferred scheme.

  12. Early detection of local buckling in structural members

    NASA Astrophysics Data System (ADS)

    Ali, Bashir; Sundaresan, Mannur J.; Schulz, Mark J.; Hughes, Derke

    2005-05-01

    Most structural health monitoring analyses to date have focused on the determination of damage in the form of crack growth in metallic materials or delamination or other types of damage growth in composite materials. However, in many applications, local instability in the form of buckling can be the precursor to more extensive damage and unstable failure of the structure. If buckling could be detected in the very early stages, there is a possibility of taking preventive measures to stabilize and save the structure. Relatively few investigations have addressed this type of damage initiation in structures. Recently, during the structural health monitoring of a wind turbine blade, local buckling was identified as the cause of premature failure. A stress wave propagation technique was used in this test to detect the precursor to the buckling failure in the form of early changes in the local curvature of the blade. These conditions have also been replicated in the laboratory and results are reported in this paper. A composite column was subjected to axial compression to induce various levels of buckling deformation. Two different techniques were used to detect the precursors to buckling in this column. The first identifier is the change in the vibration shapes and natural frequencies of the column. The second is the change in the characteristics of diagnostic Lamb waves during the buckling deformation. Experiments indicate that very small changes in curvature during the initial stages of buckling are detectable using the structural health monitoring techniques. The experimental vibration characteristics of the column with slight initial curvatures compared qualitatively with finite element results. The finite element analysis is used to identify the frequencies that are most sensitive to buckling deformation, and to select suitable locations for the placement of sensors that can detect even small changes in the local curvature.

  13. 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

  14. Topological framework for local structure analysis in condensed matter.

    PubMed

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

    2015-10-27

    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

  15. 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.

  16. Binding-activated localization microscopy of DNA structures.

    PubMed

    Schoen, Ingmar; Ries, Jonas; Klotzsch, Enrico; Ewers, Helge; Vogel, Viola

    2011-09-14

    Many nucleic acid stains show a strong fluorescence enhancement upon binding to double-stranded DNA. Here we exploit this property to perform superresolution microscopy based on the localization of individual binding events. The dynamic labeling scheme and the optimization of fluorophore brightness yielded a resolution of ∼14 nm (fwhm) and a spatial sampling of 1/nm. We illustrate our approach with two different DNA-binding dyes and apply it to visualize the organization of the bacterial chromosome in fixed Escherichia coli cells. In general, the principle of binding-activated localization microscopy (BALM) can be extended to other dyes and targets such as protein structures. PMID:21838238

  17. Fluctuations and local ice structure in model supercooled water

    NASA Astrophysics Data System (ADS)

    Overduin, S. D.; Patey, G. N.

    2015-09-01

    Large-scale simulations (up to 32 000 molecules) are used to analyze local structures and fluctuations for the TIP4P/2005 and TIP5P water models, under deeply supercooled conditions, near previously proposed liquid-liquid critical points. Bulk freezing does not occur in our simulations, but correlations between molecules with local ice-like structure (ice-like molecules) are strong and long ranged (˜4 nm), exceeding the shortest dimension of smaller simulation cells at the lowest temperatures considered. Correlations between ice-like molecules decay slowly at low temperature, on the order of a hundred nanoseconds. Local ice-like structure is strongly correlated with highly tetrahedral liquid structure at all times, both structures contribute to density fluctuations, and to the associated anomalous scattering. For the TIP4P/2005 and TIP5P models, we show that the apparent spontaneous liquid-liquid phase separations, recently reported [T. Yagasaki, M. Matsumoto, and H. Tanaka, Phys. Rev. E 89, 020301 (2014)] for small rectangular simulation cells below the proposed critical points, exhibit strong system size dependence and do not occur at all in the largest systems we consider. Furthermore, in the smaller rectangular systems where layers of different densities do occur, we find that the appearance of a region of low density is always accompanied simultaneously by an excess of local ice density, with no separation in time. Our results suggest that the density differences observed in direct simulations for the two models considered here are likely due to long-range correlations between ice-like molecules and do not provide strong evidence of liquid-liquid phase separation.

  18. Monaural sound localization based on structure-induced acoustic resonance.

    PubMed

    Kim, Keonwook; Kim, Youngwoong

    2015-01-01

    A physical structure such as a cylindrical pipe controls the propagated sound spectrum in a predictable way that can be used to localize the sound source. This paper designs a monaural sound localization system based on multiple pyramidal horns around a single microphone. The acoustic resonance within the horn provides a periodicity in the spectral domain known as the fundamental frequency which is inversely proportional to the radial horn length. Once the system accurately estimates the fundamental frequency, the horn length and corresponding angle can be derived by the relationship. The modified Cepstrum algorithm is employed to evaluate the fundamental frequency. In an anechoic chamber, localization experiments over azimuthal configuration show that up to 61% of the proper signal is recognized correctly with 30% misfire. With a speculated detection threshold, the system estimates direction 52% in positive-to-positive and 34% in negative-to-positive decision rate, on average. PMID:25668214

  19. Monaural Sound Localization Based on Structure-Induced Acoustic Resonance

    PubMed Central

    Kim, Keonwook; Kim, Youngwoong

    2015-01-01

    A physical structure such as a cylindrical pipe controls the propagated sound spectrum in a predictable way that can be used to localize the sound source. This paper designs a monaural sound localization system based on multiple pyramidal horns around a single microphone. The acoustic resonance within the horn provides a periodicity in the spectral domain known as the fundamental frequency which is inversely proportional to the radial horn length. Once the system accurately estimates the fundamental frequency, the horn length and corresponding angle can be derived by the relationship. The modified Cepstrum algorithm is employed to evaluate the fundamental frequency. In an anechoic chamber, localization experiments over azimuthal configuration show that up to 61% of the proper signal is recognized correctly with 30% misfire. With a speculated detection threshold, the system estimates direction 52% in positive-to-positive and 34% in negative-to-positive decision rate, on average. PMID:25668214

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. Local and near surface structure from diffraction (Preface)

    SciTech Connect

    Barabash, Rozaliya; Ice, Gene E

    2010-01-01

    This special topic of Materials Science and Engineering A highlights novel applications of X-ray and neutron diffraction for the analysis of a range of materials, including conventional and nanostructured materials, thin films, bio-inspired materials, and superalloys. The development of ultra-brilliant synchrotron X-ray sources and recent advances in neutron diffraction provide important new opportunities for the analysis of local and near surface material structures at multiple length scales.

  5. 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…

  6. 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.

  7. Analyzing the sequence-structure relationship of a library of local structural prototypes.

    PubMed

    Benros, Cristina; de Brevern, Alexandre G; Hazout, Serge

    2009-01-21

    We present a thorough analysis of the relation between amino acid sequence and local three-dimensional structure in proteins. A library of overlapping local structural prototypes was built using an unsupervised clustering approach called "hybrid protein model" (HPM). The HPM carries out a multiple structural alignment of local folds from a non-redundant protein structure databank encoded into a structural alphabet composed of 16 protein blocks (PBs). Following previous research focusing on the HPM protocol, we have considered gaps in the local structure prototype. This methodology allows to have variable length fragments. Hence, 120 local structure prototypes were obtained. Twenty-five percent of the protein fragments learnt by HPM had gaps. An investigation of tight turns suggested that they are mainly derived from three PB series with precise locations in the HPM. The amino acid information content of the whole conformational classes was tackled by multivariate methods, e.g., canonical correlation analysis. It points out the presence of seven amino acid equivalence classes showing high propensities for preferential local structures. In the same way, definition of "contrast factors" based on sequence-structure properties underline the specificity of certain structural prototypes, e.g., the dependence of Gly or Asn-rich turns to a limited number of PBs, or, the opposition between Pro-rich coils to those enriched in Ser, Thr, Asn and Glu. These results are so useful to analyze the sequence-structure relationships, but could also be used to improve fragment-based method for protein structure prediction from sequence. PMID:18977232

  8. Local Structure of Cerium in Aluminophosphate and Silicophosphate Glasses

    SciTech Connect

    J Rygel; Y Chen; C Pantano; T Shibata; J Du; L Kokou; R Woodman; J Belcher

    2011-12-31

    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.

  9. 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.

  10. 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

  11. 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

  12. Local structural excitations in model glass systems under applied load

    NASA Astrophysics Data System (ADS)

    Swayamjyoti, S.; Löffler, J. F.; Derlet, P. M.

    2016-04-01

    The potential-energy landscape of a model binary Lennard-Jones structural glass is investigated as a function of applied external strain, in terms of how local structural excitations (LSEs) respond to the load. Using the activation relaxation technique and nudged elastic band methods, the evolving structure and barrier energy of such LSEs are studied in detail. For the case of a tensile/compressive strain, the LSE barrier energies generally decrease/increase, whereas under pure shear, it may either increase or decrease resulting in a broadening of the barrier energy distribution. It is found that how a particular LSE responds to an applied strain is strongly controlled by the LSE's far-field internal stress signature prior to loading.

  13. Electronic-structure calculation for metals by local optimization

    SciTech Connect

    Woodward, C.; Min, B.I.; Benedek, R.; Garner, J.

    1989-03-15

    Recent work by Car and Parrinello has generated considerable interest in the calculation of electronic structure by nonlinear optimization. The technique introduced by these authors, dynamical simulated annealing, is designed for problems that involve energy barriers. When local optimization suffices to determine the energy minimum, more direct methods are available. In this paper we apply the algorithm suggested by Williams and Soler to calculate the electronic structure of metals, using a plane-wave expansion for the electronic orbitals and an electron-ion pseudopotential of the Kleinman-Bylander form. Radial pseudopotentials were taken from the compilation of Bachelet, Hamann, and Schlueter. Calculations are performed to optimize the electronic structure (i) with fixed atomic configuration, or (ii) with the atomic volume being optimized simultaneously. It is found that the dual optimization (ii) converges in essentially the same number of steps as the static lattice optimization (i). Numerical results are presented for Li, K, Al, and simple-cubic P.

  14. Phase behavior and local structure of liquid crystalline polymers

    NASA Astrophysics Data System (ADS)

    Fynewever, Herb

    In this work we use a combination of theory and computer simulation to study the phase behavior of liquid crystalline polymers and the local structure of polymer melts. We review experimental and simulation evidence which shows that long and stiff molecules form orientationally ordered phases at packing fractions intermediate between the liquid and the solid. With the aid of a two-molecule simulation, we are able to apply Onsager's theory [Ann. N. Y. Acad. Sci. 51, 627 (1949)] for liquid crystal formation to flexible molecules without any additional approximations. Our results have a quantitative advantage over other theories in comparison with computer simulation data such as for the liquid-liquid crystal phase diagram. We also study the local structure of polymer melts using a two-molecule simulation to apply the density functional theories of Donley, Curro, and McCoy [J. Chem. Phys. 101 , 3205 (1994)1; and Yethiraj and Woodward [J. Chem. Phys 102 , 5499 (1995)]. The accuracy of these methods rivals that of integral equation theories in their predictions of local order. Further, the two-molecule simulation facilitates a more direct calculation of the equation of state via the monitoring of orientational correlations.

  15. 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.

  16. High Resolution Local Structure-Constrained Image Upsampling.

    PubMed

    Zhao, Yang; Wang, Ronggang; Wang, Wenmin; Gao, Wen

    2015-11-01

    With the development of ultra-high-resolution display devices, the visual perception of fine texture details is becoming more and more important. A method of high-quality image upsampling with a low cost is greatly needed. In this paper, we propose a fast and efficient image upsampling method that makes use of high-resolution local structure constraints. The average local difference is used to divide a bicubic-interpolated image into a sharp edge area and a texture area, and these two areas are reconstructed separately with specific constraints. For reconstruction of the sharp edge area, a high-resolution gradient map is estimated as an extra constraint for the recovery of sharp and natural edges; for the reconstruction of the texture area, a high-resolution local texture structure map is estimated as an extra constraint to recover fine texture details. These two reconstructed areas are then combined to obtain the final high-resolution image. The experimental results demonstrated that the proposed method recovered finer pixel-level texture details and obtained top-level objective performance with a low time cost compared with state-of-the-art methods. PMID:26186777

  17. 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

  18. Local measurement of optically induced photocurrent in semiconductor structures

    NASA Astrophysics Data System (ADS)

    Benesova, Marketa; Dobis, Pavel; Tomanek, Pavel; Uhdeova, Nadezda

    2003-07-01

    Photocurrent (PC) spectroscopic techniques have demonstrated to be helpful experimental method to investigate the local properties of bulk semiconductors, microstructures, surfaces and interfaces. We have measured locally induced PC of semiconductor quantum structures using a technique of reflection Scanning Near-field Optical Microscope (r-SNOM) in combination with Ti:Sapphire laser and tuning dye laser and with He-Ne laser. The r-SNOM employs an uncoated and/or Au-metalized single-mode fiber tip both in illumination and collection mode. Taking opportunity of the high lateral resolution of the microscope and combining it with fast micro-PL, it is possible to locate e.g. defects in a multiple quantum well grown by molecular beam epitaxy. Near-field characteristics of measured quantities are also discussed.

  19. 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.

  20. Unimodal biometric system based on local topology structure preserving projections

    NASA Astrophysics Data System (ADS)

    Liu, Huanxi; Lv, Xiaowei; Li, Xiong; Liu, Yuncai

    2009-11-01

    We propose a unified unimodal biometric system that is suitable for most individual modalities, e.g., face and gait. The proposed system consists of three steps: (1) preprocessing raw biometric data, (2) determining the intrinsic low-dimensional subspace of preprocessed data by local topology structure preserving projections (LTSPP), and (3) performing the classification in the determined subspace using the intraclass distance sum. In the proposed system, LTSPP is a novel subspace algorithm that focuses not only on the class information but also on the local topology structure. In terms of representing the separability of different classes, LTSPP projects the interclass margin data far apart. Meanwhile, LTSPP preserves the intraclass topology structures by using linear reconstruction coefficients. Compared with other subspace methods, LTSPP possesses more discriminant abilities and is more suitable for biometric recognition. In addition, both preprocessing each raw datum into unit and performing the classification using the intraclass distance sum are helpful to improve the recognition rates. We carry out various recognition experiments using the Yale and HumanID gait databases. The encouraging experimental results demonstrate the effectiveness of our unified unimodal biometric system, and the proposed LTSPP algorithm for this system can yield the best recognition rates compared to the other algorithms.

  1. 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

  2. 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

  3. Local structure studies of materials using pair distribution function analysis

    NASA Astrophysics Data System (ADS)

    Peterson, Joseph W.

    A collection of pair distribution function studies on various materials is presented in this dissertation. In each case, local structure information of interest pushes the current limits of what these studies can accomplish. The goal is to provide insight into the individual material behaviors as well as to investigate ways to expand the current limits of PDF analysis. Where possible, I provide a framework for how PDF analysis might be applied to a wider set of material phenomena. Throughout the dissertation, I discuss 0 the capabilities of the PDF method to provide information pertaining to a material's structure and properties, ii) current limitations in the conventional approach to PDF analysis, iii) possible solutions to overcome certain limitations in PDF analysis, and iv) suggestions for future work to expand and improve the capabilities PDF analysis.

  4. Local Strain Evaluation of Strained-SOI Structures

    NASA Astrophysics Data System (ADS)

    Usuda, Koji; Mizuno, Tomohisa; Numata, Toshinori; Tezuka, Tsutomu; Sugiyama, Naoharu; Moriyama, Yoshihiko; Nakaharai, Shu; Takagi, Shin-Ichi

    The strain relaxation within a strained-Si on SiGe on insulator (SGOI) structure might be one of the key issues in development of strained-Si MOSFET devices for high-performance ULSIs. In order to investigate the strain relaxation within the thin strained-Si layers, a new characterization technique to directly evaluate a local strain variation in the layers is required. Hence, we have developed the nano-beam electron diffraction (NBD) method which has a lateral resolution of 10 nm and a strain resolution of 0.1%. In this paper, we discuss a detailed investigation of whether the NBD method could be utilized to clarify a strain in a strained-Si layer on the SGOI structures.

  5. Local structures of copper-doped ZnO films

    NASA Astrophysics Data System (ADS)

    Ma, Qing; Buchholz, D. Bruce; Chang, Robert P. H.

    2008-12-01

    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 Cu2+ state, which provides the necessary unpaired spins for ferromagnetism. Therefore, Cu2+/Zn2+ 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 CuZn-O bond found in these films is a prerequisite for the spin alignments in a substitutionally copper-doped zinc oxide film.

  6. 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.

  7. Local structures surrounding Zr in nanostructurally stabilized cubic zirconia: Structural origin of phase stability

    SciTech Connect

    Soo, Y. L.; Chen, P. J.; Huang, S. H.; Shiu, T. J.; Tsai, T. Y.; Chow, Y. H.; Lin, Y. C.; Weng, S. C.; Chang, S. L.; Wang, G.; Cheung, C. L.; Sabirianov, R. F.; Mei, W. N.; Namavar, F.; Haider, H.; Garvin, K. L.; Lee, J. F.; Lee, H. Y.; Chu, P. P.

    2008-12-01

    Local environment surrounding Zr atoms in the thin films of nanocrystalline zirconia (ZrO{sub 2}) has been investigated by using the extended x-ray absorption fine structure (EXAFS) technique. These films prepared by the ion beam assisted deposition exhibit long-range structural order of cubic phase and high hardness at room temperature without chemical stabilizers. The local structure around Zr probed by EXAFS indicates a cubic Zr sublattice with O atoms located on the nearest tetragonal sites with respect to the Zr central atoms, as well as highly disordered locations. Similar Zr local structure was also found in a ZrO{sub 2} nanocrystal sample prepared by a sol-gel method. Variations in local structures due to thermal annealing were observed and analyzed. Most importantly, our x-ray results provide direct experimental evidence for the existence of oxygen vacancies arising from local disorder and distortion of the oxygen sublattice in nanocrystalline ZrO{sub 2}. These oxygen vacancies are regarded as the essential stabilizing factor for the nanostructurally stabilized cubic zirconia.

  8. 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

  9. 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.

  10. A variable-radius measure of local hospital market structure.

    PubMed Central

    Phibbs, C S; Robinson, J C

    1993-01-01

    OBJECTIVE. To provide a radius measure of the structure of local hospital markets that varies with hospital characteristics and is available for all hospitals in the United States. DATA SOURCES. 1982 American Hospital Association (AHA) Survey of Hospitals, 1982 Area Resource File (ARF), and 1983 California Office of Statewide Health Planning and Development (OSHPD) discharge abstracts. STUDY DESIGN. The OSHPD data were used to measure the radii necessary to capture 75 percent and 90 percent of each hospital's admissions. These radii were used as the dependent variables in regression models in which the independent variables were from the AHA and ARF. To estimate predicted market radii, the estimated parameters from the California models were applied to all nonfederal, short-term, general hospitals in the continental United States. These radii were used to define each hospital's service area, and all other hospitals within the calculated radii were considered potential competitors. Using this definition, we calculated two measures of local market structure: the number of other hospitals within the radius and a Herfindahl-Hirschman Index based on the distribution of hospital bed shares in the market. DATA EXTRACTION METHODS. These measures were calculated for all nonfederal, short-term, acute care hospitals in the continental United States for whom complete data were available (N = 4,884). CONCLUSIONS. These measures are available from the authors on computer-readable diskette, matched to hospital identifiers. PMID:8344822

  11. Fine structure of the electron paramagnetic resonance spectrum of Fe3+ centres in LiTaO3

    NASA Astrophysics Data System (ADS)

    Vazhenin, V. A.; Guseva, V. B.; Artyomov, M. Yu; Route, R. K.; Fejer, M. M.; Byer, R. L.

    2003-01-01

    The electron paramagnetic resonance spectrum of trigonal Fe3+ centres has been investigated and parameters of the spin Hamiltonian obtained for nominally pure congruent LiTaO3 crystals annealed at ~1500 K under Li2O vapour pressure corresponding to the pressure over the stoichiometric lithium tantalate. The possibility of calculating the zero-field splitting of the ground state of the impurity ion on the basis of the superposition model is discussed.

  12. Matt: local flexibility aids protein multiple structure alignment.

    PubMed

    Menke, Matthew; Berger, Bonnie; Cowen, Lenore

    2008-01-01

    Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins are aligned against each other optimally, and the final alignment chains these together in geometrically consistent ways. Ye and Godzik have recently suggested that adding geometric flexibility may help better model protein structures in a variety of contexts. We introduce the program Matt (Multiple Alignment with Translations and Twists), an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations. After a dynamic programming assembly guided by these "bent" alignments, geometric consistency is restored in the final step before the alignment is output. Matt is tested against other recent multiple protein structure alignment programs on the popular Homstrad and SABmark benchmark datasets. Matt's global performance is competitive with the other programs on Homstrad, but outperforms the other programs on SABmark, a benchmark of multiple structure alignments of proteins with more distant homology. On both datasets, Matt demonstrates an ability to better align the ends of alpha-helices and beta-strands, an important characteristic of any structure alignment program intended to help construct a structural template library for threading approaches to the inverse protein-folding problem. The related question of whether Matt alignments can be used to distinguish distantly homologous structure pairs from pairs of proteins that are not homologous is also considered. For this purpose, a p-value score based on the length of the common core and average root

  13. Structural heterogeneity regarding local Shwartzman activity of lipid A.

    PubMed

    Mashimo, J; Tanaka, C; Arata, S; Akiyama, Y; Hata, S; Hirayama, T; Egawa, K; Kasai, N

    1988-01-01

    The relation of chemical structure to local Shwartzman activity of lipid A preparations purified by thin-layer chromatography from five bacterial strains was examined. Two lipid A fractions from E. coli F515--Ec-A2 and Ec-A3--exhibited strong activity, similar to that of previous synthetic E. coli-type lipid A (compound 506 or LA-15-PP). The Ec-A3 fraction contained a component that appeared to be structurally identical to compound 506, and the main component of Ec-A2 fraction was structurally similar to compound 506 except that it carried a 3-hydroxytetradecanoyl group at the C-3' position of the backbone in place of a 3-tetradecanoyloxytetradecanoyl group. Free lipid A (12 C) and purified lipid A fractions, Ec-A2 (12 C) and Ec-A3 (12 C), respectively, obtained from bacteria grown at 12 C, exhibited activity comparable to Ec-A2 or Ec-A3. In these preparations, a large part of the 3-dodecanoyloxytetradecanoyl group might be replaced by 3-hexadecenoyloxytetradecanoyl group. Salmonella minnesota R595 free lipid A also contained at least two active lipid A components as seen in E. coli lipid A, but the third component corresponding to the synthetic Salmonella-type lipid A (compound 516 or LA-16-PP) exhibited low activity. A lipid A fraction, Cv-A4 from Chromobacterium violaceum IFO 12614, which was proposed to have two acyloxyacyl groups at the C-2 and C-2' positions with other acyl groups, exhibited weaker activity than the free lipid A or LPS. The purified lipid A fractions from Pseudomonas diminuta JCM 2788 and Pseudomonas vesicularis JCM 1477 contained an unusual backbone with 2,3-diamino-2,3-dideoxy-D-glucose disaccharide phosphomonoester, and these lipid A (Pd-A3 and Pv-A3) exhibited strong activity comparable to the E. coli lipid A. Thus, the present results show that the local Shwartzman reaction can be expressed by partly different lipid A structures in both hydrophilic backbone and fatty acyl residues; when they have the same backbone the potency varies

  14. Superoxide reductase from Giardia intestinalis: structural characterization of the first SOR from a eukaryotic organism shows an iron centre that is highly sensitive to photoreduction.

    PubMed

    Sousa, Cristiana M; Carpentier, Philippe; Matias, Pedro M; Testa, Fabrizio; Pinho, Filipa; Sarti, Paolo; Giuffrè, Alessandro; Bandeiras, Tiago M; Romão, Célia V

    2015-11-01

    Superoxide reductase (SOR), which is commonly found in prokaryotic organisms, affords protection from oxidative stress by reducing the superoxide anion to hydrogen peroxide. The reaction is catalyzed at the iron centre, which is highly conserved among the prokaryotic SORs structurally characterized to date. Reported here is the first structure of an SOR from a eukaryotic organism, the protozoan parasite Giardia intestinalis (GiSOR), which was solved at 2.0 Å resolution. By collecting several diffraction data sets at 100 K from the same flash-cooled protein crystal using synchrotron X-ray radiation, photoreduction of the iron centre was observed. Reduction was monitored using an online UV-visible microspectrophotometer, following the decay of the 647 nm absorption band characteristic of the iron site in the glutamate-bound, oxidized state. Similarly to other 1Fe-SORs structurally characterized to date, the enzyme displays a tetrameric quaternary-structure arrangement. As a distinctive feature, the N-terminal loop of the protein, containing the characteristic EKHxP motif, revealed an unusually high flexibility regardless of the iron redox state. At variance with previous evidence collected by X-ray crystallography and Fourier transform infrared spectroscopy of prokaryotic SORs, iron reduction did not lead to dissociation of glutamate from the catalytic metal or other structural changes; however, the glutamate ligand underwent X-ray-induced chemical changes, revealing high sensitivity of the GiSOR active site to X-ray radiation damage. PMID:26527141

  15. Local structure of solid Rb at megabar pressures

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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 μm2, 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.

  16. Local structure of solid Rb at megabar pressures.

    PubMed

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

    2015-06-01

    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(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. PMID:26049504

  17. Structuring Lecture Videos by Automatic Projection Screen Localization and Analysis.

    PubMed

    Li, Kai; Wang, Jue; Wang, Haoqian; Dai, Qionghai

    2015-06-01

    We present a fully automatic system for extracting the semantic structure of a typical academic presentation video, which captures the whole presentation stage with abundant camera motions such as panning, tilting, and zooming. Our system automatically detects and tracks both the projection screen and the presenter whenever they are visible in the video. By analyzing the image content of the tracked screen region, our system is able to detect slide progressions and extract a high-quality, non-occluded, geometrically-compensated image for each slide, resulting in a list of representative images that reconstruct the main presentation structure. Afterwards, our system recognizes text content and extracts keywords from the slides, which can be used for keyword-based video retrieval and browsing. Experimental results show that our system is able to generate more stable and accurate screen localization results than commonly-used object tracking methods. Our system also extracts more accurate presentation structures than general video summarization methods, for this specific type of video. PMID:26357345

  18. 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.

  19. 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. PMID:23103433

  20. Efficient reanalysis of structures by a direct modification method. [local stiffness modifications of large structures

    NASA Technical Reports Server (NTRS)

    Raibstein, A. I.; Kalev, I.; Pipano, A.

    1976-01-01

    A procedure for the local stiffness modifications of large structures is described. It enables structural modifications without an a priori definition of the changes in the original structure and without loss of efficiency due to multiple loading conditions. The solution procedure, implemented in NASTRAN, involved the decomposed stiffness matrix and the displacement vectors of the original structure. It solves the modified structure exactly, irrespective of the magnitude of the stiffness changes. In order to investigate the efficiency of the present procedure and to test its applicability within a design environment, several real and large structures were solved. The results of the efficiency studies indicate that the break-even point of the procedure varies between 8% and 60% stiffness modifications, depending upon the structure's characteristics and the options employed.

  1. Using Local Born and Local Rytov Fourier Modeling and Migration Methods for Investigation of Heterogeneous Structures

    SciTech Connect

    Fehler, M.C.; Huang, L.-J.

    1998-12-10

    During the past few years, there has been interest in developing migration and forward modeling approaches that are both fast and reliable particularly in regions that have rapid spatial variations in structure. The authors have been investigating a suite of modeling and migration methods that are implemented in the wavenumber-space domains and operate on data in the frequency domain. The best known example of these methods is the split-step Fourier method (SSF). Two of the methods that the authors have developed are the extended local Born Fourier (ELBF) approach and the extended local Rytov Fourier (ELRF) approach. Both methods are based on solutions of the scalar (constant density) wave equation, are computationally fast and can reliably model effects of both deterministic and random structures. The authors have investigated their reliability for migrating both 2D synthetic data and real 2D field data. The authors have found that the methods give images that are better than those that can be obtained using other methods like the SSF and Kirchhoff migration approaches. More recently, the authors have developed an approach for solving the acoustic (variable density) wave equation and have begun to investigate its applicability for modeling one-way wave propagation. The methods will be introduced and their ability to model seismic wave propagation and migrate seismic data will be investigated. The authors will also investigate their capability to model forward wave propagation through random media and to image zones of small scale heterogeneity such as those associated with zones of high permeability.

  2. 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.

  3. Local Structure Fixation in the Composite Manufacturing Chain

    NASA Astrophysics Data System (ADS)

    Girdauskaite, Lina; Krzywinski, Sybille; Rödel, Hartmut; Wildasin-Werner, Andrea; Böhme, Ralf; Jansen, Irene

    2010-12-01

    Compared to metal materials, textile reinforced composites show interesting features, but also higher production costs because of low automation rate in the manufacturing chain at this time. Their applicability is also limited due to quality problems, which restrict the production of complex shaped dry textile preforms. New technologies, design concepts, and cost-effective manufacturing methods are needed in order to establish further fields of application. This paper deals with possible ways to improve the textile deformation process by locally applying a fixative to the structure parallel to the cut. This hinders unwanted deformation in the textile stock during the subsequent stacking and formation steps. It is found that suitable thermoplastic binders, applied in the appropriate manner do not restrict formation of the textile and have no negative influence on the mechanical properties of the composite.

  4. Local atomic structure in disordered and nanocrystalline catalytic materials.

    SciTech Connect

    Dmowski, W.; Egami, T.; Swider-Lyons, K.; Dai, Sheng; Overbury, Steven {Steve} H

    2007-01-01

    The power of the atomic pair density function method to study the local atomic structure of dispersed materials is discussed for three examples (I) supercapacitor hydrous ruthenia, (II) electroctalyst platinum-iron phosphate and (III) nanoparticle gold catalyst. Hydrous ruthenia appears to be amorphous, but was found to be nanocomposite with RuO{sub 2} nanocrystals supporting electronic and hydrous boundaries protonic conductivity. A platinum-iron phosphate electrocatalyst, that exhibits activity for the oxygen reduction reaction has platinum in a non-metallic state. In catalysts comprised of gold nanoparticles supported on TiO{sub 2}, atomic correlations in the second atomic shell were observed suggesting interaction with the support that could modify gold chemical activity.

  5. 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.

  6. Polariton Local States in Periodic Bragg Multiple Quantum Well Structures

    NASA Astrophysics Data System (ADS)

    Deych, Lev; Yamilov, Alexey; Lisyansky, Alexander

    2000-11-01

    We analytically study defect polariton states in Bragg MQW structures, and defect induced changes in transmission and reflection spectra. Defect layers can differ from the host layers in three different ways: in the exciton-light coupling strength, in the exciton resonance frequency, and in interwell spacing. We show that a single defect leads to two local polariton modes in the photonic band gap. These modes lead to peculiarities in reflection and transmission spectra. Each type of defect can be reproduced experimentally, and we show that each of them play distinctly different roles in the optical properties of the system. We obtain closed analytical expressions for respective local frequencies, as well as for reflection and transmission coefficients. On the basis of the results obtained, we give practical recommendation for experimental observation of the studied effects in samples used in Refs. [1,2]. [1] M.Hübner, J. Kuhl, T. Stroucken, A. Knorr, S.W. Koch, R. Hey, K. Ploog, Phys. Rev. Lett. 76, 4199 (1996). [2] M.Hübner, J.P. Prineas, C. Ell, P. Brick, E.S. Lee, G. Khitrova, H.M. Gibbs, S.W. Koch, Phys. Rev. Lett. 83, 2841 (1999).

  7. Structural evidence for Scc4-dependent localization of cohesin loading

    PubMed Central

    Hinshaw, Stephen M; Makrantoni, Vasso; Kerr, Alastair; Marston, Adèle L; Harrison, Stephen C

    2015-01-01

    The cohesin ring holds newly replicated sister chromatids together until their separation at anaphase. Initiation of sister chromatid cohesion depends on a separate complex, Scc2NIPBL/Scc4Mau2 (Scc2/4), which loads cohesin onto DNA and determines its localization across the genome. Proper cohesin loading is essential for cell division, and partial defects cause chromosome missegregation and aberrant transcriptional regulation, leading to severe developmental defects in multicellular organisms. We present here a crystal structure showing the interaction between Scc2 and Scc4. Scc4 is a TPR array that envelops an extended Scc2 peptide. Using budding yeast, we demonstrate that a conserved patch on the surface of Scc4 is required to recruit Scc2/4 to centromeres and to build pericentromeric cohesion. These findings reveal the role of Scc4 in determining the localization of cohesin loading and establish a molecular basis for Scc2/4 recruitment to centromeres. DOI: http://dx.doi.org/10.7554/eLife.06057.001 PMID:26038942

  8. 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.

  9. Pressure dependence of the local structure of iridium ditelluride across the structural phase transition

    NASA Astrophysics Data System (ADS)

    Paris, E.; Joseph, B.; Iadecola, A.; Marini, C.; Ishii, H.; Kudo, K.; Pascarelli, S.; Nohara, M.; Mizokawa, T.; Saini, N. L.

    2016-04-01

    The local structure of IrTe2 has been studied by iridium L3-edge x-ray absorption spectroscopy (XAS) measurements as a function of pressure, performed at two temperatures (100 and 295 K) across the structural phase transition at ˜270 K. Extended x-ray absorption fine structure (EXAFS) and x-ray absorption near-edge structure (XANES) spectra show pressure-dependent anomalies, suggesting phase transitions that are characterized by different local atomic displacements. The high-temperature phase of IrTe2 (trigonal at 295 K) reveals a clear anomaly in the Ir-Te correlations at ˜4 GPa, while the low-temperature phase (at 100 K) shows a smaller change at ˜6 GPa, likely to be associated with transitions in lower-symmetry phases. XANES spectra, measuring higher-order atomic correlations, also show nonlinear pressure dependence in the local geometry at the anomalous pressures. These nonlinear changes suggest that IrTe2 goes through lower local symmetry phases with increasing pressure.

  10. Predicting the bifurcation structure of localized snaking patterns

    NASA Astrophysics Data System (ADS)

    Makrides, Elizabeth; Sandstede, Björn

    2014-02-01

    We expand upon a general framework for studying the bifurcation diagrams of localized spatially oscillatory structures. Building on work by Beck et al., the present work provides rigorous analytical results on the effects of perturbations to systems exhibiting snaking behavior. Starting with a reversible variational system possessing an additional Z2 symmetry, we elucidate the distinct effects of breaking symmetry and breaking variational structure, and characterize the resulting changes in both the bifurcation diagram and the solutions themselves. We show how to predict the branch reorganization and drift speeds induced by any particular given perturbative term, and illustrate our results via numerical continuation. We further demonstrate the utility of our methods in understanding the effects of particular perturbations breaking reversibility. Our approach yields an analytical explanation for previous numerical results on the effects of perturbations in the one-dimensional cubic-quintic Swift-Hohenberg model and allows us to make predictions on the effects of perturbations in more general settings, including planar systems. While our numerical results involve the Swift-Hohenberg model system, we emphasize the general applicability of the analytical results.

  11. Local geometry and elasticity in compact chromatin structure.

    PubMed

    Koslover, Elena F; Fuller, Colin J; Straight, Aaron F; Spakowitz, Andrew J

    2010-12-15

    The hierarchical packaging of DNA into chromatin within a eukaryotic nucleus plays a pivotal role in both the accessibility of genomic information and the dynamics of replication. Our work addresses the role of nanoscale physical and geometric properties in determining the structure of chromatin at the mesoscale level. We study the packaging of DNA in chromatin fibers by optimization of regular helical morphologies, considering the elasticity of the linker DNA as well as steric packing of the nucleosomes and linkers. Our model predicts a broad range of preferred helix structures for a fixed linker length of DNA; changing the linker length alters the predicted ensemble. Specifically, we find that the twist registry of the nucleosomes, as set by the internucleosome repeat length, determines the preferred angle between the nucleosomes and the fiber axis. For moderate to long linker lengths, we find a number of energetically comparable configurations with different nucleosome-nucleosome interaction patterns, indicating a potential role for kinetic trapping in chromatin fiber formation. Our results highlight the key role played by DNA elasticity and local geometry in regulating the hierarchical packaging of the genome. PMID:21156136

  12. Local Geometry and Elasticity in Compact Chromatin Structure

    PubMed Central

    Koslover, Elena F.; Fuller, Colin J.; Straight, Aaron F.; Spakowitz, Andrew J.

    2010-01-01

    The hierarchical packaging of DNA into chromatin within a eukaryotic nucleus plays a pivotal role in both the accessibility of genomic information and the dynamics of replication. Our work addresses the role of nanoscale physical and geometric properties in determining the structure of chromatin at the mesoscale level. We study the packaging of DNA in chromatin fibers by optimization of regular helical morphologies, considering the elasticity of the linker DNA as well as steric packing of the nucleosomes and linkers. Our model predicts a broad range of preferred helix structures for a fixed linker length of DNA; changing the linker length alters the predicted ensemble. Specifically, we find that the twist registry of the nucleosomes, as set by the internucleosome repeat length, determines the preferred angle between the nucleosomes and the fiber axis. For moderate to long linker lengths, we find a number of energetically comparable configurations with different nucleosome-nucleosome interaction patterns, indicating a potential role for kinetic trapping in chromatin fiber formation. Our results highlight the key role played by DNA elasticity and local geometry in regulating the hierarchical packaging of the genome. PMID:21156136

  13. Photonic crystal structures for efficent localization or extraction of light

    NASA Astrophysics Data System (ADS)

    Vuckovic, Jelena

    Three-dimensional (3D) photonic crystals offer the opportunity of light manipulation in all directions in space, but they are very difficult to fabricate. On the other hand, planar photonic crystals are much simpler to make, but they exhibit only a "quasi-3D" confinement, resulting from the combined action of 2D photonic crystal and internal reflection. The imperfect confinement in the third dimension produces some unwanted out-of-plane loss, which is usually a limiting factor in performance of these structures. This thesis proposes how to fully take advantage of the relatively simple fabrication of planar photonic crystals, by addressing a problem of loss-reduction. One of the greatest challenges in photonics is a construction of optical microcavities with small mode volumes and large quality factors, for efficient localization of light. Beside standard applications of these structures (such as lasers or filters), they can potentially be used for cavity QED experiments, or as building blocks for quantum networks. This work also presents the design and fabrication of optical microcavities based on planar photonic crystals, with mode volumes of the order of one half of cubic wavelength of light (measured in material) and with Q factors predicted to be even larger than 10 4. In addition to photonic crystals fabricated in semiconductors, we also address interesting properties of metallic photonic crystals and present our theoretical and experimental work on using them to improve the output of light emissive devices. Feature sizes of structures presented here are below those achievable by photolithography. Therefore, a high resolution lithography is necessary for their fabrication. The presently used e-beam writing techniques suffer from limitations in speed and wafer throughput, and they represent a huge obstacle to commercialization of photonic crystals. Our preliminary work on electron beam projection lithography, the technique that could provide us with the speed

  14. 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

  15. 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.

  16. Localized structural fluctuations promote amyloidogenic conformations in transthyretin

    PubMed Central

    Lim, Kwang Hun; Dyson, H. Jane; Kelly, Jeffery W.; Wright, Peter E.

    2013-01-01

    The process of transthyretin (TTR) misfolding and aggregation, including amyloid formation, appears to cause a number of degenerative diseases. During amyloid formation, the native protein undergoes a tetramer-to-folded monomer transition, followed by local unfolding of the monomer to an assembly-competent amyloidogenic intermediate. Here we use NMR relaxation dispersion to probe conformational exchange at physiological pH between native monomeric transthyretin (the F87M/L110M variant) and a small population of a transiently formed amyloidogenic intermediate. The dispersion experiments show that a majority of the residues in the β-sheet containing β-strands D, A, G and H undergo conformational fluctuations on μs-ms time scales. Exchange broadening is greatest for residues in the outer β-strand H, which hydrogen bonds to β-strand H’ of a neighboring subunit in the tetramer, but the associated structural fluctuations propagate across the entire β-sheet. Fluctuations in the other β-sheet are limited to the outer β-strand F, which packs against strand F’ in the tetramer, while the B, C, and E β-strands of this sheet remain stable. The structural changes were also investigated under more forcing amyloidogenic conditions (pH 6.4–3.7), where β-strand D and regions of the D-E and E-F loops were additionally destabilized, increasing the population of the amyloidogenic intermediate and accelerating amyloid formation. Strands B, C, and E appear to maintain native-like conformations in the partially unfolded, amyloidogenic state of wild type TTR. In the case of the protective mutant T119M, the conformational fluctuations are suppressed under both physiological and mildly acidic conditions, indicating that the dynamic properties of TTR correlate well with its aggregation propensity. PMID:23318953

  17. 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

  18. The Local Universe of Disk Galaxies: Energy, Mass, and Structure

    NASA Astrophysics Data System (ADS)

    Driver, Simon P.

    2015-08-01

    This talk will explore three themes: (1) Our understanding of the space density of disk systems in the nearby (z<0.1) Universe, their global properties including their panchromatic (FUV-far-IR) information (energy outputs), their dust properties (masses and temperatures), their (specific) star-formation rates, and ultimately the amount of stellar mass locked up in disc components. (2) The completeness of our local surveys, with a particular focus on the severe impact of low surface brightness selection bias, and how these can be overcome using the upcoming deep imaging studies. (3) The complexity of automated structural decomposition and experiences and results from profiling 8000 galaxies at z<0.06 allowing us to derive key relations such as the mass-size relation of disc systems. The data shown is drawn from the Galaxy And Mass Assembly survey. The GAMA survey builds upon the SDSS legacy by extending 2mags deeper spectroscopically (r<19.8mag) and also including panchromatic data from GALEX, VST, VISTA, WISE and Herschel-Atlas and shortly ASKAP for 300,000 galaxies over 250sq deg of sky. This talk will be aligned with the GAMA Panchromatic Data Release where all imaging data products will be publicly released.

  19. Beamlet Imaging and Local Inversion for Complex Structures

    NASA Astrophysics Data System (ADS)

    Wu, R.; Luo, M.; Chen, L.

    2003-12-01

    Beamlet decomposition of wavefields is defined as wavelet transform applied to wavefield along spatial axes. Beamlets has both spatial and directional localization satisfying the Heisenberg uncertainty principle. We have used both Gabor-Daubechies frame and local-cosine basis for the decomposition. The theory of local perturbations and wave propagators in beamlet domain has been developed. In this presentation we will summarize the theory and method of beamlet propagation and imaging, and show the 2D and 3D imaging (prestack depth migration) results for SEG/EAGE salt models. The high-resolution and high quality images demonstrate the excellent performance and wide-angle capacity of beamlet imaging. Based on beamlet imaging in angle-domain, a method of local AVA (amplitude versus angle) and local inversion is proposed to estimate the medium parameters near a local discontinuity (reflector). The local image matrices derived during the amplitude-preserving imaging process can be reduced to common refection-angle image (CRAI) gathers and common dip-angle image (CDAI) gathers. CDAI gathers can be used to determine the dip-angle of the reflector and CRAI gathers are then used for local AVA analysis. In the target area, local inversion can be conducted based on local AVA and velocity analyses. Preliminary numerical tests of local AVA analysis will be shown to demonstrate the feasibility of the approach.

  20. Strength through structure: visualization and local assessment of the trabecular bone structure

    NASA Astrophysics Data System (ADS)

    Räth, C.; Monetti, R.; Bauer, J.; Sidorenko, I.; Müller, D.; Matsuura, M.; Lochmüller, E.-M.; Zysset, P.; Eckstein, F.

    2008-12-01

    The visualization and subsequent assessment of the inner human bone structures play an important role for better understanding the disease- or drug-induced changes of bone in the context of osteoporosis giving prospect for better predictions of bone strength and thus of the fracture risk of osteoporotic patients. In this work, we show how the complex trabecular bone structure can be visualized using μCT imaging techniques at an isotropic resolution of 26 μm. We quantify these structures by calculating global and local topological and morphological measures, namely Minkowski functionals (MFs) and utilizing the (an-)isotropic scaling index method (SIM) and by deriving suitable texture measures based on MF and SIM. Using a sample of 151 specimens taken from human vertebrae in vitro, we correlate the texture measures with the mechanically measured maximum compressive strength (MCS), which quantifies the strength of the bone probe, by using Pearson's correlation coefficient. The structure parameters derived from the local measures yield good correlations with the bone strength as measured in mechanical tests. We investigate whether the performance of the texture measures depends on the MCS value by selecting different subsamples according to MCS. Considering the whole sample the results for the newly defined parameters are better than those obtained for the standard global histomorphometric parameters except for bone volume/total volume (BV/TV). If a subsample consisting only of weak bones is analysed, the local structural analysis leads to similar and even better correlations with MCS as compared to BV/TV. Thus, the MF and SIM yield additional information about the stability of the bone especially in the case of weak bones, which corroborates the hypothesis that the bone structure (and not only its mineral mass) constitutes an important component of bone stability.

  1. 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.

  2. 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

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

    PubMed

    Nwaka, Solomon; Ochem, Alexander; Besson, Dominique; Ramirez, Bernadette; Fakorede, Foluke; Botros, Sanaa; Inyang, Uford; Mgone, Charles; Adae-Mensah, Ivan; Konde, Victor; Nyasse, Barthelemy; Okole, Blessed; Guantai, Anastasia; Loots, Glaudina; Atadja, Peter; Ndumbe, Peter; Sanou, Issa; Olesen, Ole; Ridley, Robert; Ilunga, Tshinko

    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. 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

  5. Tidal effects on the spatial structure of the Local Group

    NASA Astrophysics Data System (ADS)

    Pasetto, S.; Chiosi, C.

    2009-05-01

    Aims: The spatial distribution of galaxies in the Local Group (LG) is the footprint of its formation mechanism and the gravitational interactions among its members and the external massive galaxies or galaxy groups. Using a 3D-geometrical description of the spatial distribution of all the members of the LG (not only the satellites of the MW and M 31) based on present-day data of positions and distances, we found in our previous study that all galaxies (MW, M 31, their satellites, and even the most distant objects) are confined within a slab of about 200 kpc thickness. Examining how external galaxies or groups would gravitationally affect (and eventually alter) the planar structure (and its temporal evolution) of the LG, they found that the external force field acts parallel to the plane determined by geometry and studied this with the Least Action Principle. Methods: In this paper, we thoroughly investigated the role played by the tidal forces exerted by external galaxies or galaxy groups on the LG galaxies (the most distant dwarfs in particular) in shaping their large-scale distribution. We studied in particular an idea based on the well-known effect of tidal interactions, according to which a system of mass-points can undergo not only tidal stripping but also tidal compression and thus become flatter. Results: Excluding the dwarf galaxies tightly bound to the MW and M 31, the same tidal forces can account for the planar distribution of the remaining dwarf galaxies. We analytically recover our previous results and prove that a planar distribution of the LG dwarf galaxies is compatible with the external force field. We also highlight the physical cause of this result.

  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. Expectation and Locality Effects in German Verb-final Structures

    PubMed Central

    Levy, Roger P.; Keller, Frank

    2013-01-01

    Probabilistic expectations and memory limitations are central factors governing the real-time comprehension of natural language, but how the two factors interact remains poorly understood. One respect in which the two factors have come into theoretical conflict is the documentation of both locality effects, in which more dependents preceding a governing verb increase processing difficulty at the verb, and anti-locality effects, in which more preceding dependents facilitate processing at the verb. However, no controlled study has previously demonstrated both locality and anti-locality effects in the same type of dependency relation within the same language. Additionally, many previous demonstrations of anti-locality effects have been potentially confounded with lexical identity, plausibility, and sentence position. Here, we provide new evidence of both locality and anti-locality effects in the same type of dependency relation in a single language—verb-final constructions in German—while controlling for lexical identity, plausibility, and sentence position. In main clauses, we find clear anti-locality effects, with the presence of a preceding dative argument facilitating processing at the final verb; in subject-extracted relative clauses with identical linear ordering of verbal dependents, we find both anti-locality and locality effects, with processing facilitated when the verb is preceded by a dative argument alone, but hindered when the verb is preceded by both the dative argument and an adjunct. These results indicate that both expectations and memory limitations need to be accounted for in any complete theory of online syntactic comprehension. PMID:24558294

  9. 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

  10. 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

  11. Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure.

    PubMed

    Mahajan, Swapnil; de Brevern, Alexandre G; Offmann, Bernard; Srinivasan, Narayanaswamy

    2014-01-01

    Conformational changes in proteins are extremely important for their biochemical functions. Correlation between inherent conformational variations in a protein and conformational differences in its homologues of known structure is still unclear. In this study, we have used a structural alphabet called Protein Blocks (PBs). PBs are used to perform abstraction of protein 3-D structures into a 1-D strings of 16 alphabets (a-p) based on dihedral angles of overlapping pentapeptides. We have analyzed the variations in local conformations in terms of PBs represented in the ensembles of 801 protein structures determined using NMR spectroscopy. In the analysis of concatenated data over all the residues in all the NMR ensembles, we observe that the overall nature of inherent local structural variations in NMR ensembles is similar to the nature of local structural differences in homologous proteins with a high correlation coefficient of .94. High correlation at the alignment positions corresponding to helical and β-sheet regions is only expected. However, the correlation coefficient by considering only the loop regions is also quite high (.91). Surprisingly, segregated position-wise analysis shows that this high correlation does not hold true to loop regions at the structurally equivalent positions in NMR ensembles and their homologues of known structure. This suggests that the general nature of local structural changes is unique; however most of the local structural variations in loop regions of NMR ensembles do not correlate to their local structural differences at structurally equivalent positions in homologues. PMID:23730714

  12. 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

  13. 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.

  14. The DESY Grid Centre

    NASA Astrophysics Data System (ADS)

    Haupt, A.; Gellrich, A.; Kemp, Y.; Leffhalm, K.; Ozerov, D.; Wegner, P.

    2012-12-01

    DESY is one of the world-wide leading centers for research with particle accelerators, synchrotron light and astroparticles. DESY participates in LHC as a Tier-2 center, supports on-going analyzes of HERA data, is a leading partner for ILC, and runs the National Analysis Facility (NAF) for LHC and ILC in the framework of the Helmholtz Alliance, Physics at the Terascale. For the research with synchrotron light major new facilities are operated and built (FLASH, PETRA-III, and XFEL). DESY furthermore acts as Data-Tier1 centre for the Neutrino detector IceCube. Established within the EGI-project DESY operates a grid infrastructure which supports a number of virtual Organizations (VO), incl. ATLAS, CMS, and LHCb. Furthermore, DESY hosts some of HEP and non-HEP VOs, such as the HERA experiments and ILC as well as photon science communities. The support of the new astroparticle physics VOs IceCube and CTA is currently set up. As the global structure of the grid offers huge resources which are perfect for batch-like computing, DESY has set up the National Analysis Facility (NAF) which complements the grid to allow German HEP users for efficient data analysis. The grid infrastructure and the NAF use the same physics data which is distributed via the grid. We call the conjunction of grid and NAF the DESY Grid Centre. In the contribution to CHEP2012 we will in depth discuss the conceptional and operational aspects of our multi-VO and multi-community Grid Centre and present the system setup. We will in particular focus on the interplay of Grid and NAF and present experiences of the operations.

  15. 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

  16. 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'…

  17. 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.

  18. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.

    PubMed

    Sarver, Michael; Zirbel, Craig L; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B

    2008-01-01

    New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, "Find RNA 3D" (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs whose

  19. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

    PubMed Central

    Sarver, Michael; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B.

    2010-01-01

    New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, “Find RNA 3D” (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs

  20. 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.

  1. 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.

  2. Local structure determination in strained-layer semiconductors

    NASA Astrophysics Data System (ADS)

    Woicik, Joseph C.

    The theory of elasticity accurately describes the deformations of macroscopic bodies under the action of applied stress [1]. In this review, we examine the internal mechanisms of elasticity for strained-layer semiconductor heterostructures. In particular, we present extended x-ray-absorption fine structure (EXAFS) and x-ray diffraction (XRD) measurements to show how the bond lengths and bond angles in semiconductor thin-alloy films change with strain when they are grown coherently on substrates with different lattice constants. The structural distortions measured by experiment are compared to valence-force field (VFF) calculations and other theoretical models. Atomic switching and interfacial strain at buried interfaces are also discussed.

  3. Locally resonant periodic structures with low-frequency band gaps

    NASA Astrophysics Data System (ADS)

    Cheng, Zhibao; Shi, Zhifei; Mo, Y. L.; Xiang, Hongjun

    2013-07-01

    Presented in this paper are study results of dispersion relationships of periodic structures composited of concrete and rubber, from which the frequency band gap can be found. Two models with fixed or free boundary conditions are proposed to approximate the bound frequencies of the first band gap. Studies are conducted to investigate the low-frequency and directional frequency band gaps for their application to engineering. The study finds that civil engineering structures can be designed to block harmful waves, such as earthquake disturbance.

  4. 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

  5. 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…

  6. 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…

  7. Structure and chromosomal localization of the human renal kallikrein gene

    SciTech Connect

    Evans, B.A.; Yun, Z.X.; Close, J.A.; Tregear, G.W.; Kitamura, N.; Nakanish, S.; Callen, D.F.; Baker, E.; Hyland, V.J.; Sutherland, G.R.; Richards, R.I.

    1988-05-03

    Glandular kallikreins are a family of proteases encoded by a variable number of genes in different mammalian species. In all species examined, however, one particular kallikrein is functionally conserved in its capacity to release the vasoactive peptide, Lys-bradykinin, from low molecular weight kininogen. This kallikrein is found in the kidney, pancreas, and salivary gland, showing a unique pattern of tissue-specific expression relative to other members of the family. The authors have isolated a genomic clone carrying the human renal kallikrein gene and compared the nucleotide sequence of its promoter region with those of the mouse renal kallikrein gene and another mouse kallikrein gene expressed in a distinct cell type. They find four sequence elements conserved between renal kallikrein genes from the two species. They have also shown that the human gene is localized to 19q13, a position analogous to that of the kallikrein gene family on mouse chromosome 7.

  8. Evaluation of local structure alphabets based on residue burial.

    PubMed

    Karchin, Rachel; Cline, Melissa; Karplus, Kevin

    2004-05-15

    Residue burial, which describes a protein residue's exposure to solvent and neighboring atoms, is key to protein structure prediction, modeling, and analysis. We assessed 21 alphabets representing residue burial, according to their predictability from amino acid sequence, conservation in structural alignments, and utility in one fold-recognition scenario. This follows upon our previous work in assessing nine representations of backbone geometry.1 The alphabet found to be most effective overall has seven states and is based on a count of C(beta) atoms within a 14 A-radius sphere centered at the C(beta) of a residue of interest. When incorporated into a hidden Markov model (HMM), this alphabet gave us a 38% performance boost in fold recognition and 23% in alignment quality. PMID:15103615

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks.

    PubMed

    Agarwal, Garima; Mahajan, Swapnil; Srinivasan, Narayanaswamy; de Brevern, Alexandre G

    2011-01-01

    Structure comparison tools can be used to align related protein structures to identify structurally conserved and variable regions and to infer functional and evolutionary relationships. While the conserved regions often superimpose well, the variable regions appear non superimposable. Differences in homologous protein structures are thought to be due to evolutionary plasticity to accommodate diverged sequences during evolution. One of the kinds of differences between 3-D structures of homologous proteins is rigid body displacement. A glaring example is not well superimposed equivalent regions of homologous proteins corresponding to α-helical conformation with different spatial orientations. In a rigid body superimposition, these regions would appear variable although they may contain local similarity. Also, due to high spatial deviation in the variable region, one-to-one correspondence at the residue level cannot be determined accurately. Another kind of difference is conformational variability and the most common example is topologically equivalent loops of two homologues but with different conformations. In the current study, we present a refined view of the "structurally variable" regions which may contain local similarity obscured in global alignment of homologous protein structures. As structural alphabet is able to describe local structures of proteins precisely through Protein Blocks approach, conformational similarity has been identified in a substantial number of 'variable' regions in a large data set of protein structural alignments; optimal residue-residue equivalences could be achieved on the basis of Protein Blocks which led to improved local alignments. Also, through an example, we have demonstrated how the additional information on local backbone structures through protein blocks can aid in comparative modeling of a loop region. In addition, understanding on sequence-structure relationships can be enhanced through our approach. This has been

  14. 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

  15. 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.

  16. 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

  17. HYPLOSP: a knowledge-based approach to protein local structure prediction.

    PubMed

    Chen, Ching-Tai; Lin, Hsin-Nan; Sung, Ting-Yi; Hsu, Wen-Lian

    2006-12-01

    Local structure prediction can facilitate ab initio structure prediction, protein threading, and remote homology detection. However, the accuracy of existing methods is limited. In this paper, we propose a knowledge-based prediction method that assigns a measure called the local match rate to each position of an amino acid sequence to estimate the confidence of our method. Empirically, the accuracy of the method correlates positively with the local match rate; therefore, we employ it to predict the local structures of positions with a high local match rate. For positions with a low local match rate, we propose a neural network prediction method. To better utilize the knowledge-based and neural network methods, we design a hybrid prediction method, HYPLOSP (HYbrid method to Protein LOcal Structure Prediction) that combines both methods. To evaluate the performance of the proposed methods, we first perform cross-validation experiments by applying our knowledge-based method, a neural network method, and HYPLOSP to a large dataset of 3,925 protein chains. We test our methods extensively on three different structural alphabets and evaluate their performance by two widely used criteria, Maximum Deviation of backbone torsion Angle (MDA) and Q(N), which is similar to Q(3) in secondary structure prediction. We then compare HYPLOSP with three previous studies using a dataset of 56 new protein chains. HYPLOSP shows promising results in terms of MDA and Q(N) accuracy and demonstrates its alphabet-independent capability. PMID:17245815

  18. 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

  19. 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.

  20. Free amino and imino-bridged centres attached to organic chains bonded to structurally ordered silica for dye removal from aqueous solution.

    PubMed

    Rehman, Fozia; Volpe, Pedro L O; Airoldi, Claudio

    2014-01-15

    Ordered mesoporous SBA-15 type silica was synthesized by sol gel polymerization and reacted with 3-aminopropyltriethoxysilane (AP) or triethylenetetramine (TE), to attach pendant chains or bridging molecules, with basic centres. The materials were characterized by elemental analysis, infrared spectroscopy, and nuclear magnetic resonance in the solid state, X-ray diffractometry, scanning and transmission electron microscopy. The nitrogen sorption/desorption data for SBA-15 and the organofunctionalized SBA-15AP and SBA-15TE silicas resulted in IV type isotherms with hysteresis loops of the H1 type, surface areas of 800; 213 and 457 m(2) g(-1) and average pore diameters of 8.0; 3.2 and 6.8 nm, respectively. The ordered structural features of the mesoporous silica remained preserved after post-functionalization with pendant and bridged organic chains. Sorption data for organofunctionalized silicas gave highly selective sorption capacities for anionic water soluble Reactive Blue dye, with 0.064 and 0.072 mmol g(-1). Negligible sorption was observed with the unmodified mesoporous silica. The results suggest that organofunctionalized silica can be a simple, efficient, inexpensive and suitable method for the effective and selective removal of anionic organic dye pollutants from aqueous solutions. PMID:24374243

  1. 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.

  2. Interplay between Microscopic Diffusion and Local Structure of Liquid Water

    SciTech Connect

    Cunsolo, A.; Orecchini, A; Petrillo, C.; Sacchetti, F.

    2010-11-29

    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.

  3. 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.

  4. 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

  5. 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

    2015-01-01

    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

  6. 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

  7. 33 CFR 208.10 - Local flood protection works; maintenance and operation of structures and facilities.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Local flood protection works; maintenance and operation of structures and facilities. 208.10 Section 208.10 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE FLOOD CONTROL REGULATIONS § 208.10 Local flood protection works;...

  8. 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…

  9. 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,…

  10. 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

  11. 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.

  12. Localized surface plasmon microscopy of submicron domain structures of mixed lipid bilayers

    PubMed Central

    Watanabe, Koyo; Miyazaki, Ryosuke; Terakado, Goro; Okazaki, Takashi; Morigaki, Kenichi; Kano, Hiroshi

    2012-01-01

    We propose scanning localized surface plasmon microscopy of mixed lipid bilayers with submicron domain structures. Our observation technique, which employs localized surface plasmons excited on a flat metal surface as a sensing probe, provides non-label and non-contact imaging with the spatial resolution of ∼ 170 nm. We experimentally show that submicron domain structures of mixed lipid bilayers can be observed. A detailed analysis finds that the domains are classified into two groups. PMID:23024897

  13. 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.

  14. The European standards of Haemophilia Centres

    PubMed Central

    Giangrande, Paul; Calizzani, Gabriele; Menichini, Ivana; Candura, Fabio; Mannucci, Pier Mannuccio; Makris, Michael

    2014-01-01

    Introduction The European haemophilia community of professionals and patients has agreed on the principles of haemophilia care to address comprehensive optimal delivery of care which is nowadays scattered throughout Europe. Many of the health facilities call themselves Haemophilia Centres despite their variation in size, expertise and services provided. Only a small number of countries have Haemophilia Centre accreditation systems in place. Methods In the framework of the European Haemophilia Network project, following an inclusive process of stakeholder involvement, the European Guidelines for the certification of haemophilia centres have been developed in order to set quality standards for European Haemophilia Centres and criteria for their certification. Results The Guidelines define the standards and criteria for the designation of two levels of care delivery: European Haemophilia Treatment Centres, providing local routine care, and European Haemophilia Comprehensive Care Centres, providing specialised and multi-disciplinary care and functioning as tertiary referral centres. Additionally, they define standards about general requirements, patient care, provision of an advisory service and establishment of network of clinical and specialised services. Conclusions The implementation of the European Guidelines for the certification of Haemophilia Centres will contribute to the reduction of health inequalities through the standardisation of quality of care in European Union Member States and could represent a model to be taken into consideration for other rare disease groups. PMID:24922293

  15. Centres of excellence.

    PubMed

    Watson, J M

    1980-05-16

    The present Government may not be enthusiastic about health centres. But Dr Joyce M. Watson, of Glasgow University Department of General Practice and based at Woodside Health Centre in Glasgow, writes with enthusiasm of their advantages for the practice of medicine and the care of patients. PMID:10247174

  16. Local structural differences in homologous proteins: specificities in different SCOP classes.

    PubMed

    Joseph, Agnel Praveen; Valadié, Hélène; Srinivasan, Narayanaswamy; de Brevern, Alexandre G

    2012-01-01

    The constant increase in the number of solved protein structures is of great help in understanding the basic principles behind protein folding and evolution. 3-D structural knowledge is valuable in designing and developing methods for comparison, modelling and prediction of protein structures. These approaches for structure analysis can be directly implicated in studying protein function and for drug design. The backbone of a protein structure favours certain local conformations which include α-helices, β-strands and turns. Libraries of limited number of local conformations (Structural Alphabets) were developed in the past to obtain a useful categorization of backbone conformation. Protein Block (PB) is one such Structural Alphabet that gave a reasonable structure approximation of 0.42 Å. In this study, we use PB description of local structures to analyse conformations that are preferred sites for structural variations and insertions, among group of related folds. This knowledge can be utilized in improving tools for structure comparison that work by analysing local structure similarities. Conformational differences between homologous proteins are known to occur often in the regions comprising turns and loops. Interestingly, these differences are found to have specific preferences depending upon the structural classes of proteins. Such class-specific preferences are mainly seen in the all-β class with changes involving short helical conformations and hairpin turns. A test carried out on a benchmark dataset also indicates that the use of knowledge on the class specific variations can improve the performance of a PB based structure comparison approach. The preference for the indel sites also seem to be confined to a few backbone conformations involving β-turns and helix C-caps. These are mainly associated with short loops joining the regular secondary structures that mediate a reversal in the chain direction. Rare β-turns of type I' and II' are also identified

  17. Local Structural Differences in Homologous Proteins: Specificities in Different SCOP Classes

    PubMed Central

    Joseph, Agnel Praveen; Valadié, Hélène; Srinivasan, Narayanaswamy; de Brevern, Alexandre G.

    2012-01-01

    The constant increase in the number of solved protein structures is of great help in understanding the basic principles behind protein folding and evolution. 3-D structural knowledge is valuable in designing and developing methods for comparison, modelling and prediction of protein structures. These approaches for structure analysis can be directly implicated in studying protein function and for drug design. The backbone of a protein structure favours certain local conformations which include α-helices, β-strands and turns. Libraries of limited number of local conformations (Structural Alphabets) were developed in the past to obtain a useful categorization of backbone conformation. Protein Block (PB) is one such Structural Alphabet that gave a reasonable structure approximation of 0.42 Å. In this study, we use PB description of local structures to analyse conformations that are preferred sites for structural variations and insertions, among group of related folds. This knowledge can be utilized in improving tools for structure comparison that work by analysing local structure similarities. Conformational differences between homologous proteins are known to occur often in the regions comprising turns and loops. Interestingly, these differences are found to have specific preferences depending upon the structural classes of proteins. Such class-specific preferences are mainly seen in the all-β class with changes involving short helical conformations and hairpin turns. A test carried out on a benchmark dataset also indicates that the use of knowledge on the class specific variations can improve the performance of a PB based structure comparison approach. The preference for the indel sites also seem to be confined to a few backbone conformations involving β-turns and helix C-caps. These are mainly associated with short loops joining the regular secondary structures that mediate a reversal in the chain direction. Rare β-turns of type I’ and II’ are also

  18. Control of local structures and photophysical properties of zinc porphyrin-based supramolecular assemblies structurally organized by regioselective ligand coordination.

    PubMed

    Sakuma, Takao; Sakai, Hayato; Araki, Yasuyuki; Wada, Takehiko; Hasobe, Taku

    2016-02-10

    Nano- and micro-sized molecular assemblies of zinc porphyrins [5,10,15,20-tetrakis(4-carboxyphenyl)porphyrinato-zinc(ii) (ZnTCPP)] utilizing bridging nitrogen ligands such as diazabicycro[2.2.2]octane (DABCO) were prepared to demonstrate the regioselective coordination by two different synthetic strategies such as (i) the solvothermal method and (ii) the colloidal metal organic framework (MOF) method. The initial organization process is a planar checkerboard patterned formation (2D platform) of zinc porphyrins organized by paddlewheel secondary building units (PSBUs) between carboxylate and zinc ions. Then, DABCO moieties are decorated on zinc atoms in the metal centres of the porphyrin rings (m-cPDC) in the solvothermal method, whereas the metal centres in the porphyrin rings (n-uPDC) remain uncoordinated in the colloidal MOF method. These internal structural changes between m-cPDC and n-uPDC are in sharp contrast with the corresponding reference systems using ZnTCPP and a 4,4'-bipyridine (BPY) ligand (i.e., m-cPBC and n-cPBC). Concretely, the metal centres of zinc porphyrins in n-uPDC were unsaturated and uncoordinated with the DABCO ligands, which was confirmed by XRD and steady-state spectroscopic measurements. These different coordination features have great effect on the spectroscopic and photophysical properties. For example, the average fluorescence lifetime of m-cPDC is much smaller than that of n-uPDC because of the acceleration of nonradiative processes, which are highly related with the coordination of DABCO to the Zn(ii) centre of the ZnTCPP unit. Finally, fluorescence quenching experiments via photoinduced electron transfer (PET) utilizing an electron acceptor: benzoquinone (BQ) were performed. The apparent association constant (Kapp) of n-uPDC is larger than that of m-cPDC. This suggested that the unsaturated ZnTCPP units embedded in n-uPDC easily accommodate guest molecules as compared to the other systems. PMID:26821786

  19. Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins

    PubMed Central

    Whitten, Steven T.; García-Moreno E., Bertrand; Hilser, Vincent J.

    2005-01-01

    Local conformational fluctuations in proteins can affect the coupling between ligand binding and global structural transitions. This finding was established by monitoring quantitatively how the population distribution in the ensemble of microstates of staphylococcal nuclease was affected by proton binding. Analysis of acid unfolding and proton-binding data with an ensemble-based model suggests that local fluctuations: (i) can be effective modulators of ligand-binding affinities, (ii) are important determinants of the cooperativity of ligand-driven global structural transitions, and (iii) are well represented thermodynamically as local unfolding processes. These studies illustrate how an ensemble-based description of proteins can be used to describe quantitatively the interdependence of local conformational fluctuations, ligand-binding processes, and global structural transitions. This level of understanding of the relationship between conformation, energy, and dynamics is required for a detailed mechanistic understanding of allostery, cooperativity, and other complex functional and regulatory properties of macromolecules. PMID:15767576

  20. 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

  1. Anti-pruritic Effect of Sertaconazole 2% Cream in Atopic Dermatitis Subjects: A Prospective, Randomized, Double-blind, Vehicle-controlled, Multi-centre Clinical Trial of Efficacy, Safety and Local Tolerability.

    PubMed

    Ständer, Sonja; Metz, Martin; Ramos F, Mac H; Maurer, Marcus; Schoepke, Nicole; Tsianakas, Athanasios; Zeidler, Claudia; Luger, Thomas A

    2016-08-23

    This study was a prospective, parallel-group, randomized, double-blind, vehicle-controlled, multi-centre clinical trial to compare the efficacy of topical sertaconazole 2% cream with vehicle in reducing chronic pruritus in subjects with atopic dermatitis, and to assess its safety and local tolerability. A total of 70 subjects applied either of the 2 treatments twice daily for a period of 4 weeks on affected, itchy skin areas. Treatment efficacy was evaluated primarily considering the item itch intensity on a 5-point verbal rating scale. Insomnia, state of atopic dermatitis (Scoring Atopic Dermatitis; SCORAD), quality of life and therapy benefit were also assessed. No significant difference between active treatment and vehicle was found at any of the time-points for any of the investigated parameters. Under the experimental conditions of the study, sertaconazole 2% cream did not exert anti-pruritic effects that were better than vehicle in subjects with atopic dermatitis who had chronic pruritus. Trial registration ClinicalTrials.gov #NCT01792713. PMID:26527564

  2. Local field enhancement on metallic periodic surface structures produced by femtosecond laser pulses

    SciTech Connect

    Ionin, Andrei A; Kudryashov, Sergei I; Ligachev, A E; Makarov, Sergei V; Mel'nik, N N; Rudenko, A A; Seleznev, L V; Sinitsyn, D V; Khmelnitskii, R A

    2013-04-30

    Periodic surface structures on aluminium are produced by femtosecond laser pulses for efficient excitation of surface electromagnetic waves using a strong objective (NA = 0.5). The local electromagnetic field enhancement on the structures is measured using the technique of surface-enhanced Raman scattering from pyridine molecules. (extreme light fields and their applications)

  3. 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

  4. Local structure and superconductivity of the Ce1-xLaxRu2 Laves phase system

    NASA Astrophysics Data System (ADS)

    Saini, N. L.; Agrestini, S.; Amato, E.; Filippi, M.; di Castro, D.; Bianconi, A.; Manfrinetti, P.; Palenzona, A.; Marcelli, A.

    2004-09-01

    We have studied local structure of the Laves phase Ce1-xLaxRu2 superconductor by Ru K-edge extended x-ray absorption fine-structure measurements focusing on the small La concentration regime where the transition temperature Tc passes through a local maximum. We find that correlated Debye-Waller factor of the Ru-Ru bonds follows Tc with the varying La concentration in the system. Although, this remarkable Tc correlation on the local atomic structure suggests important role of the electron-lattice interactions, the band-structure effects seem more likely the reason to drive the anomalous superconducting behavior and the Tc maximum in this 4f system.

  5. 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.

  6. 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.

  7. 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.

  8. Local structure of NiAl compounds investigated by extended X-ray absorption fine-structure spectroscopy.

    PubMed

    Tian, J S; Han, G M; Wei, H; Jin, T; Dargusch, M S

    2012-07-01

    The local structures of pure NiAl and Ti-, Co-doped NiAl compounds have been obtained utilizing extended X-ray absorption fine-structure (EXAFS) spectroscopy. The results provide experimental evidence that Ni antisite defects exist in the Ni-rich NiAl compounds. The site preference of Ti and Co has been confirmed. Ti occupies the Al sublattice, while Co occupies the Ni sublattice. The structure parameters obtained by EXAFS were consistent with the X-ray diffraction results. Owing to the precipitation of α-Cr, the local structure of NiAl-Cr has not been obtained, making the site preference of Cr unclear. PMID:22713881

  9. 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.

  10. 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

  11. In silico local structure approach: a case study on outer membrane proteins.

    PubMed

    Martin, Juliette; de Brevern, Alexandre G; Camproux, Anne-Claude

    2008-04-01

    The detection of Outer Membrane Proteins (OMP) in whole genomes is an actual question, their sequence characteristics have thus been intensively studied. This class of protein displays a common beta-barrel architecture, formed by adjacent antiparallel strands. However, due to the lack of available structures, few structural studies have been made on this class of proteins. Here we propose a novel OMP local structure investigation, based on a structural alphabet approach, i.e., the decomposition of 3D structures using a library of four-residue protein fragments. The optimal decomposition of structures using hidden Markov model results in a specific structural alphabet of 20 fragments, six of them dedicated to the decomposition of beta-strands. This optimal alphabet, called SA20-OMP, is analyzed in details, in terms of local structures and transitions between fragments. It highlights a particular and strong organization of beta-strands as series of regular canonical structural fragments. The comparison with alphabets learned on globular structures indicates that the internal organization of OMP structures is more constrained than in globular structures. The analysis of OMP structures using SA20-OMP reveals some recurrent structural patterns. The preferred location of fragments in the distinct regions of the membrane is investigated. The study of pairwise specificity of fragments reveals that some contacts between structural fragments in beta-sheets are clearly favored whereas others are avoided. This contact specificity is stronger in OMP than in globular structures. Moreover, SA20-OMP also captured sequential information. This can be integrated in a scoring function for structural model ranking with very promising results. PMID:17932925

  12. Control of Grain Structure in Pure Copper by a Local Heating

    NASA Astrophysics Data System (ADS)

    Shibayanagi, Toshiya; Tsukamoto, Masahiro; Abe, Nobuyuki

    The present work deals with a preferential grain growth process in a localized region utilizing local heating method in order to fabricate some unique microstructures different from those fabricated in the homogeneous way of microstructure evolution. A Monte Carlo simulation of grain growth under a heterogeneous temperature gradient, i.e. spot heating, was performed. Steep temperature gradient brought about a preferential grain growth in the higher temperature region, showing that the local heating was effective for the control of grain structure of polycrystalline materials. Such type of preferential grain growth became less significant under the mild temperature gradient. Local heating of pure copper foil with 0.2mm in thickness utilizing laser beam was performed by changing the irradiation conditions. In the case of 200W for laser power and 18mm/s for sweep velocity, some grains were observed to have larger grain sizes than their surrounding grains, suggesting a possibility of preferential grain growth in the localized region.

  13. Local structure of NaNbO3: A neutron scattering study

    NASA Astrophysics Data System (ADS)

    Jiang, Lu; Mitchell, D. C.; Dmowski, W.; Egami, T.

    2013-07-01

    We report the results of a neutron diffraction study of structural evolution in sodium niobate, NaNbO3, which is the parent compound for lead-free ferroelectric materials, as a function of temperature from 15 to 930 K over six phases. The Rietveld analysis of the high-resolution powder neutron diffraction data shows the variation in the structure from cubic to rhombohedral ferroelectric structures. However, the refinements on local structure by the pair distribution function (PDF) method indicates that there are only three basic patterns of the local structure, and the ground states of NaNbO3 in the low-temperature antiferroelectric and ferroelectric phases have the R3c symmetry, even though in the long range the system shows the Pbcm symmetry or the coexistence of two phases. The origin of the complex phase behavior and its implications on the performance as lead-free ferroelectrics are discussed.

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

    NASA Astrophysics Data System (ADS)

    Yang, Yue

    2016-02-01

    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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. Prediction of compounds in different local structure-activity relationship environments using emerging chemical patterns.

    PubMed

    Namasivayam, Vigneshwaran; Gupta-Ostermann, Disha; Balfer, Jenny; Heikamp, Kathrin; Bajorath, Jürgen

    2014-05-27

    Active compounds can participate in different local structure-activity relationship (SAR) environments and introduce different degrees of local SAR discontinuity, depending on their structural and potency relationships in data sets. Such SAR features have thus far mostly been analyzed using descriptive approaches, in particular, on the basis of activity landscape modeling. However, compounds in different local SAR environments have not yet been predicted. Herein, we adapt the emerging chemical patterns (ECP) method, a machine learning approach for compound classification, to systematically predict compounds with different local SAR characteristics. ECP analysis is shown to accurately assign many compounds to different local SAR environments across a variety of activity classes covering the entire range of observed local SARs. Control calculations using random forests and multiclass support vector machines were carried out and a variety of statistical performance measures were applied. In all instances, ECP calculations yielded comparable or better performance than controls. The approach presented herein can be applied to predict compounds that complement local SARs or prioritize compounds with different SAR characteristics. PMID:24803014

  20. 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 .

  1. 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.

  2. Linking Slow Dynamics and Local Structure in Simple Models of Glass-Forming Liquids

    NASA Astrophysics Data System (ADS)

    Coslovich, D.; Pastore, G.

    2008-07-01

    Establishing a relation between the dynamical features of supercooled liquids, their structural properties and the nature of intermolecular interactions is a key issue in the description of the glass transition. To investigate this point we perform molecular dynamics simulations for three model glass-forming liquids with different types of local order. Our results show that the roughness of the energy landscape, estimated from the amplitude of average energy barriers, and the localization of unstable modes provide useful means to rationalize the link between structure and dynamics in glass-forming liquids.

  3. Global and local structural similarity in protein–protein complexes: Implications for template-based docking

    PubMed Central

    Kundrotas, Petras J.; Vakser, Ilya A.

    2016-01-01

    The increasing amount of structural information on protein–protein interactions makes it possible to predict the structure of protein–protein complexes by comparison/alignment of the interacting proteins to the ones in cocrystallized complexes. In the predictions based on structure similarity, the template search is performed by structural alignment of the target interactors with the entire structures or with the interface only of the subunits in cocrystallized complexes. This study investigates the scope of the structural similarity that facilitates the detection of a broad range of templates significantly divergent from the targets. The analysis of the target-template similarity is based on models of protein–protein complexes in a large representative set of heterodimers. The similarity of the biological and crystal packing interfaces, dissimilar interface structural motifs in overall similar structures, interface similarity to the full structure, and local similarity away from the interface were analyzed. The structural similarity at the protein–protein interfaces only was observed in ~25% of target-template pairs with sequence identity <20% and primarily homodimeric templates. For ~50% of the target-template pairs, the similarity at the interface was accompanied by the similarity of the whole structure. However, the structural similarity at the interfaces was still stronger than that of the noninterface parts. The study provides insights into structural and functional diversity of protein–protein complexes, and relative performance of the interface and full structure alignment in docking. PMID:23946125

  4. 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.

  5. Multi-spacecraft analysis of local structure of Heliospheric Current Sheet

    NASA Astrophysics Data System (ADS)

    Arrazola, D.; Blanco, Juan Jose; Rodriguez-Pacheco, Javier; Hidalgo, Miguel Angel; Medina, Jose

    Local variability of the Heliospheric Current Sheet (HCS) has been studied. Its local magnetic structure is observed as a boundary through which the magnetic field inverts its direction toward or away from Sun. In this work, we have used data from ACE, WIND, STEREO A and B spacecrafts. Solar wind features and magnetic field variations obtained from each spacecraft and for each event analyzed have been used to estimate temporal and spatial dependences in the local HCS structure. Their connection with the neutral line at the corona has been also determined. We have grouped the selected events according to their magnetic connection, with the aim of analyzing possible variations on the local orientation. Events studied cover from the ascending phase of solar cycle 23 to the next minimum around 2007. It has been observed that when spacecrafts are close to each other and/or magnetically well connected, clear variations on the local orientation are not observed. In these cases, the elapsed time was less than 2 hours. This fact could be interpreted as if there were not temporal variations on the local structure of the HCS in the range of 2 hours. On the other hand, the analysis shows that angular variation has a growing trend with elapsed time between different spacecraft. This can be related to the fact that spacecrafts are magnetically bad connected. In these cases, variations in local HCS orientation are observed. To evaluate changes of the HCS local orientations it has been used MVA, CVA and HYTARO methods. Results and future goals are summarized in this work.

  6. 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.

  7. 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.

  8. 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.

  9. Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry.

    PubMed

    Karchin, Rachel; Cline, Melissa; Mandel-Gutfreund, Yael; Karplus, Kevin

    2003-06-01

    An important problem in computational biology is predicting the structure of the large number of putative proteins discovered by genome sequencing projects. Fold-recognition methods attempt to solve the problem by relating the target proteins to known structures, searching for template proteins homologous to the target. Remote homologs that may have significant structural similarity are often not detectable by sequence similarities alone. To address this, we incorporated predicted local structure, a generalization of secondary structure, into two-track profile hidden Markov models (HMMs). We did not rely on a simple helix-strand-coil definition of secondary structure, but experimented with a variety of local structure descriptions, following a principled protocol to establish which descriptions are most useful for improving fold recognition and alignment quality. On a test set of 1298 nonhomologous proteins, HMMs incorporating a 3-letter STRIDE alphabet improved fold recognition accuracy by 15% over amino-acid-only HMMs and 23% over PSI-BLAST, measured by ROC-65 numbers. We compared two-track HMMs to amino-acid-only HMMs on a difficult alignment test set of 200 protein pairs (structurally similar with 3-24% sequence identity). HMMs with a 6-letter STRIDE secondary track improved alignment quality by 62%, relative to DALI structural alignments, while HMMs with an STR track (an expanded DSSP alphabet that subdivides strands into six states) improved by 40% relative to CE. PMID:12784210

  10. Control of localized surface plasmon resonance energy in monolayer structures of gold and silver nanoparticles.

    PubMed

    Yokota, Hiroki; Taniguchi, Taichi; Watanabe, Taichi; Kim, DaeGwi

    2015-10-28

    Monolayer structures of Au and Ag nanoparticles (NPs) were fabricated by a dipping method to realize the control of localized surface plasmon resonance (LSPR) energy. The mean inter-particle distance in the monolayer was controlled by changing the concentration of NPs in the colloidal solution used for the monolayer assembly. The extinction-peak energy of the monolayer structure was red-shifted with decreasing inter-particle distance, reflecting plasmon coupling between NPs. PMID:26411840

  11. Assessing a novel approach for predicting local 3D protein structures from sequence.

    PubMed

    Benros, Cristina; de Brevern, Alexandre G; Etchebest, Catherine; Hazout, Serge

    2006-03-01

    We developed a novel approach for predicting local protein structure from sequence. It relies on the Hybrid Protein Model (HPM), an unsupervised clustering method we previously developed. This model learns three-dimensional protein fragments encoded into a structural alphabet of 16 protein blocks (PBs). Here, we focused on 11-residue fragments encoded as a series of seven PBs and used HPM to cluster them according to their local similarities. We thus built a library of 120 overlapping prototypes (mean fragments from each cluster), with good three-dimensional local approximation, i.e., a mean accuracy of 1.61 A Calpha root-mean-square distance. Our prediction method is intended to optimize the exploitation of the sequence-structure relations deduced from this library of long protein fragments. This was achieved by setting up a system of 120 experts, each defined by logistic regression to optimize the discrimination from sequence of a given prototype relative to the others. For a target sequence window, the experts computed probabilities of sequence-structure compatibility for the prototypes and ranked them, proposing the top scorers as structural candidates. Predictions were defined as successful when a prototype <2.5 A from the true local structure was found among those proposed. Our strategy yielded a prediction rate of 51.2% for an average of 4.2 candidates per sequence window. We also proposed a confidence index to estimate prediction quality. Our approach predicts from sequence alone and will thus provide valuable information for proteins without structural homologs. Candidates will also contribute to global structure prediction by fragment assembly. PMID:16385557

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. Pressure Induced Local Structure Distortions in Cu(pyz)F2(H2O)2

    SciTech Connect

    Musfeldt, J.L.; Carr, G.; Liu, Z.; Li, S.; Kang, C.L., Jena, P.; Manson, J.L.; Schlueter, J.A. Whangbo, M.H.

    2011-06-06

    We employed infrared spectroscopy along with complementary lattice dynamics and spin density calculations to investigate pressure-driven local structure distortions in the copper coordination polymer Cu(pyz)F{sub 2}(H{sub 2}O){sub 2}. Here, pyz is pyrazine. Our study reveals rich and fully reversible local lattice distortions that buckle the pyrazine ring, disrupt the bc-plane O-H {hor_ellipsis} F hydrogen-bonding network, and reinforce magnetic property switching. The resiliency of the soft organic ring is a major factor in the stability of this material. Interestingly, the collective character of the lattice vibrations masks direct information on the Cu-N and Cu-O linkages through the series of pressure-induced Jahn-Teller axis switching transitions, although Cu-F bond softening is clearly identified above 3 GPa. These findings illustrate the importance of combined bulk and local probe techniques for microscopic structure determination in complex materials.

  17. Pressure-Induced Local Structure Distortions in Cu(pyz)F(2)(H(2)O)(2)

    SciTech Connect

    J Musfeldt; Z Liu; S Li; J Kang; C Lee; P Jena; J Manson; J Schlueter; G Carr; M Whangbo

    2011-12-31

    We employed infrared spectroscopy along with complementary lattice dynamics and spin density calculations to investigate pressure-driven local structure distortions in the copper coordination polymer Cu(pyz)F{sub 2}(H{sub 2}O){sub 2}. Here, pyz is pyrazine. Our study reveals rich and fully reversible local lattice distortions that buckle the pyrazine ring, disrupt the bc-plane O-H {hor_ellipsis} F hydrogen-bonding network, and reinforce magnetic property switching. The resiliency of the soft organic ring is a major factor in the stability of this material. Interestingly, the collective character of the lattice vibrations masks direct information on the Cu-N and Cu-O linkages through the series of pressure-induced Jahn-Teller axis switching transitions, although Cu-F bond softening is clearly identified above 3 GPa. These findings illustrate the importance of combined bulk and local probe techniques for microscopic structure determination in complex materials.

  18. 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.

  19. 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.

  20. Role of zinc finger structure in nuclear localization of transcription factor Sp1

    SciTech Connect

    Ito, Tatsuo; Azumano, Makiko; Uwatoko, Chisana; Itoh, Kohji Kuwahara, Jun

    2009-02-27

    Transcription factor Sp1 is localized in the nucleus and regulates gene expression. Our previous study demonstrated that the carboxyl terminal region of Sp1 containing 3-zinc finger region as DNA binding domain can also serve as nuclear localization signal (NLS). However, the nuclear transport mechanism of Sp1 has not been well understood. In this study, we performed a gene expression study on mutant Sp1 genes causing a set of amino acid substitutions in zinc finger domains to elucidate nuclear import activity. Nuclear localization of the GFP-fused mutant Sp1 proteins bearing concomitant substitutions in the first and third zinc fingers was highly inhibited. These mutant Sp1 proteins had also lost the binding ability as to the GC box sequence. The results suggest that the overall tertiary structure formed by the three zinc fingers is essential for nuclear localization of Sp1 as well as dispersed basic amino acids within the zinc fingers region.

  1. Multistage structural evolution in simple monatomic supercritical fluids: superstable tetrahedral local order.

    PubMed

    Ryltsev, R E; Chtchelkatchev, N M

    2013-11-01

    The local order units of dense simple liquid are typically three-dimensional (close packed) clusters: hcp, fcc, and icosahedrons. We show that the fluid demonstrates the superstable tetrahedral local order up to temperatures several orders of magnitude higher than the melting temperature and down to critical density. While the solid-like local order (hcp, fcc) disappears in the fluid at much lower temperatures and far above critical density. We conclude that the supercritical fluid shows the temperature (density)-driven two-stage "melting" of the three-dimensional local order. We also find that the structure relaxation times in the supercritical fluid are much larger than ones estimated for weakly interactive gas even far above the melting line. PMID:24329208

  2. 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

  3. 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…

  4. 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…

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

    PubMed

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

    2016-01-01

    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

  6. 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.

  7. Observation of electro-activated localized structures in broad area VCSELs.

    PubMed

    Parravicini, J; Brambilla, M; Columbo, L; Prati, F; Rizza, C; Tissoni, G; Agranat, A J; DelRe, E

    2014-12-01

    We demonstrate experimentally the electro-activation of a localized optical structure in a coherently driven broad-area vertical-cavity surface-emitting laser (VCSEL) operated below threshold. Control is achieved by electro-optically steering a writing beam through a pre-programmable switch based on a photorefractive funnel waveguide. PMID:25606953

  8. 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.

  9. 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.

  10. 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…

  11. 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.

  12. 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.

  13. Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet.

    PubMed

    de Brevern, Alexandre G; Joseph, Agnel Praveen

    2011-05-01

    Protein structure analysis and prediction methods are based on non-redundant data extracted from the available protein structures, regardless of the species from which the protein originates. Hence, these datasets represent the global knowledge on protein folds, which constitutes a generic distribution of amino acid sequence-protein structure (AAS-PS) relationships. In this study, we try to elucidate whether the AAS-PS relationship could possess specificities depending on the specie. For this purpose, we have chosen three different species: Saccharomyces cerevisiae, Plasmodium falciparum and Arabidopsis thaliana. We analyzed the AAS-PS behaviors of the proteins from these three species and compared it to the "expected" distribution of a classical non-redundant databank. With the classical secondary structure description, only slight differences in amino acid preferences could be observed. With a more precise description of local protein structures (Protein Blocks), significant changes could be highlighted. S. cerevisiae's AAS-PS relationship is close to the general distribution, while striking differences are observed in the case of A. thaliana. P. falciparum is the most distant one. This study presents some interesting view-points on AAS-PS relationship. Certain species exhibit unique preferences for amino acids to be associated with protein local structural elements. Thus, AAS-PS relationships are species dependent. These results can give useful insights for improving prediction methodologies which take the species specific information into account. PMID:21333657

  14. 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.

  15. Theoretical studies of the structures and local aromaticity of conjugated polycyclic hydrocarbons using three aromatic indices

    NASA Astrophysics Data System (ADS)

    Sakai, Shogo; Kita, Yuki

    2013-07-01

    The structures and local aromaticity of some conjugated polycyclic hydrocarbons (from the butadienoid, acene, and phenylene series) are studied using ab initio MO and density functional methods. The aromaticities of the molecules are estimated using three indices: the nucleus-independent chemical shift (NICS), the harmonic oscillator model of aromaticity (HOMA), and the index of deviation from aromaticity (IDA). Assessment of the relationships between the structures and the aromatic indices shows that the IDA values correspond best to the characteristics of the conjugated polycyclic hydrocarbon structures.

  16. 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.

  17. 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.

  18. Local, global and electronic structure of supported gold nanoclusters determined by EXAFS, XRD and XPS methods

    NASA Astrophysics Data System (ADS)

    Aldea, Nicolae; Rednic, Vasile; Pintea, Stelian; Marginean, Petru; Barz, Bogdan; Gluhoi, Andreea; Nieuwenhuys, Bernard E.; Neumann, Manfred; Yaning, Xie; Matei, Florica

    2009-07-01

    We analyze gold nanoclusters as supported catalysts by extended X-ray absorption fine structure, X-ray diffraction and X-ray photoelectron spectroscopy in order to determine their local, global and electronic structure. The present study points out a strong deformation of the local structure of the metal due to its interaction with oxide supports. We determine the particle size distribution and microstrain functions of the Au nanoclusters by X-ray diffraction method. Based on X-ray absorption fine structure spectroscopy analysis we show that the entire local structure of the investigated systems is strongly distorted regarding the average Au-Au coordination number. The distances between atoms are practically the same as standard Au foil. The strong metal-support interaction is confirmed by the change in shape of the electron transition probability densities that appear in the Au L III-edge. From XPS investigations we find electronic states corresponding to gold as well as to the oxide supports.

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

    PubMed Central

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

    2009-01-01

    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 4–5.5 month old infants are sensitive to the global structure of Glass patterns by measuring Visual Evoked Potentials (VEPs). 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. PMID:19642888

  20. 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

  1. 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

  2. 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…

  3. Crust structure of northern Morocco and southern Iberian Peninsula from local earthquake tomography

    NASA Astrophysics Data System (ADS)

    El moudnib, L.; Villasenor, A.; Harnafi, M.; Himmi, M.; Gallart, J.

    2012-12-01

    We have estimated the P-wave velocity structure under northern Morocco and Alboran Sea and Southern Spain using an iterative simultaneous inversion method of local earthquake arrival-time data for velocity and hypocentral parameters. For this investigation we applied this tomographic method to 40714 P-wave arrival times from 2429 local events recorded by 124 both temporary and permanent seismic stations of local and regional networks from January 2000 to June 2009. The P wave arrival times used are calculated by the finite difference technique which allows a flexible parameterization of the velocity model. Twenty layers with a thickness of 4km for each one were postulated to obtain the three-dimensional P-wave structure along the complex Ibero-Maghribean boundary region. The hypocenter location of the global earthquake dataset has been remarkably improved by the obtained three-dimensional velocity model (RMS reduced to 27.3%). At the uppermost level of the crust the results suggest that the most prominent feature is the very low velocity zone associated with flysch units north of the Strait of Gibraltar, and in northern Morocco extending from Al-Hoceima region to the Alboran ridge. Conversely, a high velocity anomaly is observed in the area of the Ronda Peridotites, but a similar structure is not observed in the Beni-Boussera region in Morocco. The inverted velocity model is generally consistent with geology structure of the entire area and yields more details at depth of the geology structures and tectonic units. Moreover, it shows an accurate identification at depth of the shape and the geometry of the geology structures in the area. The tomographic cross section profiles reveal a vertical downgoing highly velocity materials in the whole area and show a thick crust in either the western part of the Alboran sea or northern Morocco region compared with the eastern one. keywords: local earthquake, P arrival-time, simultaneous inversion, hypocenter relocation

  4. LOCUSTRA: accurate prediction of local protein structure using a two-layer support vector machine approach.

    PubMed

    Zimmermann, Olav; Hansmann, Ulrich H E

    2008-09-01

    Constraint generation for 3d structure prediction and structure-based database searches benefit from fine-grained prediction of local structure. In this work, we present LOCUSTRA, a novel scheme for the multiclass prediction of local structure that uses two layers of support vector machines (SVM). Using a 16-letter structural alphabet from de Brevern et al. (Proteins: Struct., Funct., Bioinf. 2000, 41, 271-287), we assess its prediction ability for an independent test set of 222 proteins and compare our method to three-class secondary structure prediction and direct prediction of dihedral angles. The prediction accuracy is Q16=61.0% for the 16 classes of the structural alphabet and Q3=79.2% for a simple mapping to the three secondary classes helix, sheet, and coil. We achieve a mean phi(psi) error of 24.74 degrees (38.35 degrees) and a median RMSDA (root-mean-square deviation of the (dihedral) angles) per protein chain of 52.1 degrees. These results compare favorably with related approaches. The LOCUSTRA web server is freely available to researchers at http://www.fz-juelich.de/nic/cbb/service/service.php. PMID:18763837

  5. 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

  6. 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

  7. 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…

  8. Winnipeg Centre Project.

    ERIC Educational Resources Information Center

    Manitoba Dept. of Education, Winnipeg.

    The Winnipeg Centre Project is a field-based, work-study program that attempts to create more appropriate education for the inner-city child. Sponsored by the Planning and Research Branch of the Department of Colleges and Universities Affairs and administered by Brandon University in consultation with the Winnipeg School Division, the project is…

  9. 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.

  10. 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

  11. 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.

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

    PubMed Central

    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

  13. Connections between structural jamming, local metabasin features, and relaxation dynamics in a supercooled glassy liquid

    NASA Astrophysics Data System (ADS)

    Frechero, M. A.; Alarcón, L. M.; Schulz, E. P.; Appignanesi, G. A.

    2007-01-01

    Dynamics in glass-forming liquids in the supercooled regime vary considerably from one point of the sample to another suggesting the existence of regions with different degrees of jamming. In fact, the existence of relatively compact regions with particles with an enhanced propensity for motion has been detected in model glassy systems. In turn, the structural relaxation has been shown to be accomplished by means of a series of fast transitions between metabasins in the potential energy landscape involving the collective motion of a substantial number of particles arranged in relatively compact clusters (democratic clusters or d clusters). In this work we shall complete this picture by identifying the connections between local structural jamming, metabasin confining strength, and d clusters. Thus we shall demonstrate that the degree of jamming of the local structure dictates the confining strength of the local metabasin and that the local high propensity regions and the d clusters are not only similar in nature but that they share a significant amount of particles.

  14. The Kohn-Sham kinetic energy density as indicator of the electron localization: atomic shell structure.

    PubMed

    Navarrete-López, Alejandra M; Garza, Jorge; Vargas, Rubicelia

    2008-03-14

    In this report, it is shown that the Kohn-Sham (KS) kinetic energy density (KED) contains the average local electrostatic potential (ALEP) and the average local ionization energy (ALIE); the shell structure in atomic systems is presented as one application of the KS-KED. By writing the KS-KED from the KS equations, this quantity was divided in three contributions: orbital, Coulomb, and exchange correlation. By studying several closed and open shell atoms, the shell structure was established by the maxima presented by the Coulomb contribution and the minima in the orbital contribution of the KS-KED. The exchange-correlation contribution to the KS-KED does not show maxima or minima, but this quantity shows bumps where the division between shells is expected. The results obtained in this work were compared with other shell structure indicators such as the electron localization function, the ALEP, the ALIE, and the radial distribution function. The most important result in this work is related to the fact that even when the ALEP and the ALIE functions were built with different arguments to each other, they are contained in the KS-KED. In this way, the KS-KED shows its importance to reveal the electron localization in atomic systems. PMID:18345880

  15. 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.

  16. 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

  17. The temperature and structure of the local hot bubble from DXL mission

    NASA Astrophysics Data System (ADS)

    Liu, Wenhao

    2016-04-01

    DXL (Diffuse X-rays from the Local Galaxy) is a sounding rocket mission designed to quantify and characterize the contribution of Solar Wind Charge eXchange (SWCX) to the diffuse X-ray background. Based on the results from the DXL mission, we estimated the SWCX contribution to the soft X-ray background from the Rosat All Sky Survey (RASS). After removing the SWCX contamination, we were able to measure the temperature and emission measure of the “cleaned” local hot bubble, and to build its 3-Dimensional structure.Submitted for the DXL Collaboration

  18. High-order spoof localized surface plasmons supported on a complementary metallic spiral structure

    NASA Astrophysics Data System (ADS)

    Gao, Zhen; Gao, Fei; Zhang, Baile

    2016-04-01

    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.

  19. Visualizing cell structure and function with point-localization superresolution imaging

    PubMed Central

    Sengupta, Prabuddha; Van Engelenburg, Schuyler; Lippincott-Schwartz, Jennifer

    2012-01-01

    Fundamental to the success of cell and developmental biology is the ability to tease apart molecular organization in cells and tissues by localizing specific proteins with respect to one another in a native cellular context. However, many key cellular structures (from mitochondrial cristae to nuclear pores) lie below the diffraction limit of visible light, precluding analysis of their organization by conventional approaches. Point-localization superresolution microscopy techniques, such as PALM and STORM, are poised to resolve, with unprecedented clarity, the organizational principles of macromolecular complexes within cells, thus leading to deeper insights into cellular function in both health and disease. PMID:23237943

  20. Localization and the invariant probability measure for a structural dynamic system

    NASA Astrophysics Data System (ADS)

    Kissel, Glen J.

    2009-03-01

    In the one-dimensional classical analogs to Anderson localization, whether optical, acoustical or structural dynamic, the periodic system has its periodicity disrupted by having one or more of its parameters randomly disordered. Such randomized systems can be modeled via an infinite product of random transfer matrices. In the case where the transfer matrices are 2x2, the upper (and positive) Lyapunov exponent of the random matrix product is identified as the localization factor (inverse localization length) for the disordered one-dimensional model. It is this localization factor which governs the confinement of energy transmission along the disordered system, and for which the localization phenomenon has been of interest. The theorem of Furstenberg for infinite products of random matrices allows us to calculate this upper Lyapunov exponent. In Furstenberg's master formula we integrate with respect to the probability measure of the random matrices, but also with respect to the invariant probability measure of the direction of the vector propagated by the long chain of random matrices. This invariant measure is difficult to find analytically, and, as a result, either an approximating assumption is frequently made, or, less frequently, the invariant measure is determined numerically. Here we calculate the invariant measure numerically using a Monte Carlo bin counting technique and then numerically integrate Furstenberg's formula to arrive at the localization factor for both continuous and discrete disorder of the mass. This result is cross checked with the (modified) Wolf algorithm.

  1. 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.

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

    PubMed

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

    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. PMID:26395735

  3. FBG and FOPS for local and global structural health monitoring on a single fiber

    NASA Astrophysics Data System (ADS)

    Maheshwari, Muneesh; Tjin, Swee Chuan; Ching, Wei Wen; Asundi, A.

    2015-04-01

    Fiber Bragg grating (FBG) sensors and fiber optic polarimetric sensors (FOPS) have been widely researched and implemented for structural health monitoring (SHM). FBG essentially provides localized strain information, while FOPS gives a global indication of the structural health of materials. An FBG written on the polarization maintaining (PM) fiber can thus be used for both global structural monitoring and local strain sensing. However each sensor has to be used with its own hardware and processing. For gratings written on PM fibers two Bragg reflections, corresponding to two modes of polarization, are observed. While both Bragg wavelengths shift under longitudinal strain in unison, their relative peak amplitude does not change. In this paper, a novel concept is proposed which makes the peak amplitudes responsive to the longitudinal strain. This relative amplitude of both the peaks is used for the first time to determine the state of polarization (SOP) with no additional optical systems. With this additional information on SOP, PM-FBGs can be used for both, local and global SHM simultaneously. Further, a new design has been proposed which gives improved information on the damaged location in beam structures. This can be further extended to other complex geometries.

  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 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.

  6. Identification of spatially-localized flow structures via sparse proper orthogonal decomposition

    NASA Astrophysics Data System (ADS)

    Dhingra, Neil; Jovanovic, Mihailo; Schmid, Peter

    2013-11-01

    Proper Orthogonal Decomposition (POD) has become a standard tool for identification of the most energetic flow structures in fluid flows. It relies on the maximization of a quadratic form subject to a quadratic equality constraint, which can be readily accomplished via a singular value decomposition. For spatially homogeneous (or nearly homogeneous) flows, the resulting flow structures are global (or have large support) in the spatial domain of interest. By augmenting the optimization problem with an additional penalty term that promotes sparsity in the physical space, we are able to obtain energetic flow structures that become increasingly localized as our emphasis on sparsity increases. The resulting optimization problem, formulated in terms of an augmented Lagrangian functional, is solved using the Alternating Direction Method of Multipliers followed by a postprocessing step. The sparse POD algorithm is applied to the linearized Navier-Stokes equations for a plane channel flow, and the emergence of spatially localized structures is observed for increasing penalty terms. This test case and the underlying optimization techniques build the foundation for further studies into the relevance and role of localized perturbations on the overall behavior of general shear flows.

  7. 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.

  8. 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

  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. PMID:26874493

  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. 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

  12. Average and local structure, debye temperature, and structural rigidity in some oxide compounds related to phosphor hosts.

    PubMed

    Denault, Kristin A; Brgoch, Jakoah; Kloss, Simon D; Gaultois, Michael W; Siewenie, Joan; Page, Katharine; Seshadri, Ram

    2015-04-01

    The average and local structure of the oxides Ba2SiO4, BaAl2O4, SrAl2O4, and Y2SiO5 are examined to evaluate crystal rigidity in light of recent studies suggesting that highly connected and rigid structures yield the best phosphor hosts. Simultaneous momentum-space refinements of synchrotron X-ray and neutron scattering yield accurate average crystal structures, with reliable atomic displacement parameters. The Debye temperature ΘD, which has proven to be a useful proxy for structural rigidity, is extracted from the experimental atomic displacement parameters and compared with predictions from density functional theory calculations and experimental low-temperature heat capacity measurements. The role of static disorder on the measured displacement parameters, and the resulting Debye temperatures, are also analyzed using pair distribution function of total neutron scattering, as refined over varying distance ranges of the pair distribution function. The interplay between optimal bonding in the structure, structural rigidity, and correlated motion in these structures is examined, and the different contributions are delineated. PMID:25815799

  13. Local Adaptation and Vector-Mediated Population Structure in Plasmodium vivax Malaria

    PubMed Central

    Gonzalez-Ceron, Lilia; Carlton, Jane M.; Gueye, Amy; Fay, Michael; McCutchan, Thomas F.; Su, Xin-zhuan

    2008-01-01

    Plasmodium vivax in southern Mexico exhibits different infectivities to 2 local mosquito vectors, Anopheles pseudopunctipennis and Anopheles albimanus. Previous work has tied these differences in mosquito infectivity to variation in the central repeat motif of the malaria parasite's circumsporozoite (csp) gene, but subsequent studies have questioned this view. Here we present evidence that P. vivax in southern Mexico comprised 3 genetic populations whose distributions largely mirror those of the 2 mosquito vectors. Additionally, laboratory colony feeding experiments indicate that parasite populations are most compatible with sympatric mosquito species. Our results suggest that reciprocal selection between malaria parasites and mosquito vectors has led to local adaptation of the parasite. Adaptation to local vectors may play an important role in generating population structure in Plasmodium. A better understanding of coevolutionary dynamics between sympatric mosquitoes and parasites will facilitate the identification of molecular mechanisms relevant to disease transmission in nature and provide crucial information for malaria control. PMID:18385220

  14. 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.

  15. 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.

  16. 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.

  17. Local structure of germanium-sulfur, germanium-selenium, and germanium-tellurium vitreous alloys

    SciTech Connect

    Bordovsky, G. A.; Terukov, E. I.; Anisimova, N. I.; Marchenko, A. V.; Seregin, P. P.

    2009-09-15

    {sup 119}Sn and {sup 129}Te ({sup 129}I) Moessbauer spectroscopy showed that chalcogen-enriched Ge{sub 100-y}X{sub y} (X = S, Se, Te) glasses are constructed of structural units including two-coordinated chalcogen atoms in chains such as Ge-X-Ge- and Ge-X-X-Ge-. Germanium in these glasses is only tetravalent and four-coordinated, and only chalcogen atoms are in the local environment of germanium atoms. Chalcogen-depleted glasses are constructed of structural units including two-coordinated (in Ge-X-Ge- chains) and three-coordinated chalcogen atoms (in -Ge-X-Ge- chains). Germanium in these glasses stabilizes in both the tetravalent four-coordinated and divalent three-coordinated states, and only chalcogen atoms are in the local environment of germanium atoms.

  18. GSATools: analysis of allosteric communication and functional local motions using a structural alphabet

    PubMed Central

    Pandini, Alessandro; Fornili, Arianna; Fraternali, Franca; Kleinjung, Jens

    2013-01-01

    Motivation: GSATools is a free software package to analyze conformational ensembles and to detect functional motions in proteins by means of a structural alphabet. The software integrates with the widely used GROMACS simulation package and can generate a range of graphical outputs. Three applications can be supported: (i) investigation of the conformational variability of local structures; (ii) detection of allosteric communication; and (iii) identification of local regions that are critical for global functional motions. These analyses provide insights into the dynamics of proteins and allow for targeted design of functional mutants in theoretical and experimental studies. Availability: The C source code of the GSATools, along with a set of pre-compiled binaries, is freely available under GNU General Public License from http://mathbio.nimr.mrc.ac.uk/wiki/GSATools. Contact: alessandro.pandini@kcl.ac.uk or jkleinj@nimr.mrc.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23740748

  19. 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)].

  20. 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.

  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. 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

  3. 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.

  4. 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.

  5. SPOT4 Management Centre

    NASA Astrophysics Data System (ADS)

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

    1994-11-01

    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.

  6. Local atomic order, electronic structure and electron transport properties of Cu-Zr metallic glasses

    SciTech Connect

    Antonowicz, J. Pietnoczka, A.; Pękała, K.; Latuch, J.; Evangelakis, G. A.

    2014-05-28

    We studied atomic and electronic structures of binary Cu-Zr metallic glasses (MGs) using combined experimental and computational methods including X-ray absorption fine structure spectroscopy, electrical resistivity, thermoelectric power (TEP) measurements, molecular dynamics (MD) simulations, and ab-initio calculations. The results of MD simulations and extended X-ray absorption fine structure analysis indicate that atomic order of Cu-Zr MGs and can be described in terms of interpenetrating icosahedral-like clusters involving five-fold symmetry. MD configurations were used as an input for calculations of theoretical electronic density of states (DOS) functions which exhibits good agreement with the experimental X-ray absorption near-edge spectra. We found no indication of minimum of DOS at Fermi energy predicted by Mott's nearly free electron (NFE) model for glass-forming alloys. The theoretical DOS was subsequently used to test Mott's model describing the temperature variation of electrical resistivity and thermoelectric power of transition metal-based MGs. We demonstrate that the measured temperature variations of electrical resistivity and TEP remain in a contradiction with this model. On the other hand, the experimental temperature dependence of electrical resistivity can be explained by incipient localization of conduction electrons. It is shown that weak localization model works up to relatively high temperatures when localization is destroyed by phonons. Our results indicate that electron transport properties of Cu-Zr MGs are dominated by localization effects rather than by electronic structure. We suggest that NFE model fails to explain a relatively high glass-forming ability of binary Cu-Zr alloys.

  7. 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.

  8. Local atomic order, electronic structure and electron transport properties of Cu-Zr metallic glasses

    NASA Astrophysics Data System (ADS)

    Antonowicz, J.; Pietnoczka, A.; Pekała, K.; Latuch, J.; Evangelakis, G. A.

    2014-05-01

    We studied atomic and electronic structures of binary Cu-Zr metallic glasses (MGs) using combined experimental and computational methods including X-ray absorption fine structure spectroscopy, electrical resistivity, thermoelectric power (TEP) measurements, molecular dynamics (MD) simulations, and ab-initio calculations. The results of MD simulations and extended X-ray absorption fine structure analysis indicate that atomic order of Cu-Zr MGs and can be described in terms of interpenetrating icosahedral-like clusters involving five-fold symmetry. MD configurations were used as an input for calculations of theoretical electronic density of states (DOS) functions which exhibits good agreement with the experimental X-ray absorption near-edge spectra. We found no indication of minimum of DOS at Fermi energy predicted by Mott's nearly free electron (NFE) model for glass-forming alloys. The theoretical DOS was subsequently used to test Mott's model describing the temperature variation of electrical resistivity and thermoelectric power of transition metal-based MGs. We demonstrate that the measured temperature variations of electrical resistivity and TEP remain in a contradiction with this model. On the other hand, the experimental temperature dependence of electrical resistivity can be explained by incipient localization of conduction electrons. It is shown that weak localization model works up to relatively high temperatures when localization is destroyed by phonons. Our results indicate that electron transport properties of Cu-Zr MGs are dominated by localization effects rather than by electronic structure. We suggest that NFE model fails to explain a relatively high glass-forming ability of binary Cu-Zr alloys.

  9. 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.

  10. Global and local health monitoring of civil structures using smart ferroelectric sensors and electronically steerable antennas

    NASA Astrophysics Data System (ADS)

    Varadan, Vijay K.; Varadan, Vasundara V.

    1994-09-01

    In this paper, the global and local health monitoring of civil structures using RF antennas and ferroelectric sensors is presented. The sensors are fabricated with interdigital transducers printed on a piezoelectric polymer or ceramic type film. They in turn are mounted onto an ultra thin Penn State's novel RF antenna. The wave form measurements may be monitored at a remote location via the antennas in the sensors and an outside antenna.

  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. 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.

  13. 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.

  14. 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.

  15. 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.

  16. The effects of localized damping on structural response. [of the large space telescope

    NASA Technical Reports Server (NTRS)

    Merchant, D. H.; Gates, R. M.; Ice, M. W.; Vanderlinden, J. W.

    1975-01-01

    The effect of localized structural damping on the excitability of higher order normal modes of the large space telescope was investigated. A preprocessor computer program was developed to incorporate Voigt structural joint damping models in a NASTRAN finite-element dynamic model. A postprocessor computer program was developed to select critical modes for low-frequency attitude control problems and for higher frequency fine-stabilization problems. The mode selection is accomplished by ranking the flexible modes based on coefficients for rate gyro, position gyro, and optical sensors, and on image-plane motions due to sinusoidal or random power spectral density force and torque inputs.

  17. 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.

  18. Probing the local structure of high-{Tc} superconductors using XAFS spectroscopy

    SciTech Connect

    Bridges, F.; Booth, C.H.; Li, G.G.; Bauer, E.D.; Boyce, J.; Claeson, T.

    1996-12-31

    X-ray Absorption Fine-Structure (XAFS) is a local structural probe that is complementary to diffraction techniques. The authors discuss the types of information that can be obtained using this probe and then consider several examples, including the distortion about Co in YBa{sub 2}Cu{sub 3}O{sub 7} (YBCO), an unusual negative correlation of atom pair displacements in HgBa{sub 2}CuO{sub 4+{delta}}, and the distortions about the O(4) atom in thin films and single crystals of YBCO.

  19. 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.

  20. Local spin flip in two- and three-magnetic-center structures: A first-principles approach

    NASA Astrophysics Data System (ADS)

    Lefkidis, G.; Li, C.; Hartenstein, T.; Hübner, W.

    2010-01-01

    We present a fully ab initio theory of ultrafast spin switching in nanostructures using optical control theory and including spin-orbit coupling thus realizing Λ processes. These processes are investigated using high-level quantum chemistry in structures with one, two, and three magnetic centers, where the spin localization and transferability are discussed with respect to their geometry. In particular we study metallic chains with two and three magnetic centers interconnected with Na atoms. We discuss the prerequisites for such scenarios for all structures.

  1. Local structure investigation of Co doped ZnO thin films prepared by RF sputtering technique

    NASA Astrophysics Data System (ADS)

    Yadav, A. K.; Haque, S. Maidul; Shukla, D.; Phase, D. M.; Jha, S. N.; Bhattacharyya, D.

    2016-05-01

    Co doped ZnO thin films have been prepared using rf magnetron sputtering technique with varying Co doping concentration. GIXRD has been used to probe long range order and Zn, Co and Oxygen K-edge XAFS measurements have been used for investigating local structure around Zn and Co atoms. GIXRD results show wurzite structure of the samples while XANES and EXAFS results at Zn and Co K edge show that Co is going at Zn site in ZnO matrix and no other phase is present. These results are further confirmed by O K edge and Co L2,3 edge XANES measurements.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  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. PMID:24580304

  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. PMID:26035080

  11. 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

  12. Multi-damage localization in plate structure using frequency response function-based indices

    NASA Astrophysics Data System (ADS)

    Gao, Hai-yang; Guo, Xing-lin; Ouyang, Huajiang; Yang, Xiu-ming

    2015-07-01

    Vibration signal and its derivative have shown some promise in structural damage detection in previous research. However, the theoretical and practical difficulties of multi-damage detection in plate structures based on dynamic responses remain. In this paper, an efficient damage localization index based on frequency response function (FRF) is presented. The imaginary part of FRF (IFRF) is extracted to derive the new localization index due to its relation to modal flexibility. For avoiding the finite element model error, two-dimensional gapped smoothing method (GSM) is employed without the need for baseline data from a presumably undamaged structure. Experimental studies on a steel plate with two localized defects in different boundary conditions are performed. The results are compared with some typical damage indices in the literature, such as mode shapes, uniform load surface and IFRF. In order to mitigate the inherent disadvantages of GSM in anti-noise ability, a simple statistical treatment based on Thompson outlier analysis is finally used for noise suppression. The effect of damage level and boundary condition on the detection results is also investigated.

  13. Average structure and local configuration of excess oxygen in UO2+x

    PubMed Central

    Wang, Jianwei; Ewing, Rodney C.; Becker, Udo

    2014-01-01

    Determination of the local configuration of interacting defects in a crystalline, periodic solid is problematic because defects typically do not have a long-range periodicity. Uranium dioxide, the primary fuel for fission reactors, exists in hyperstoichiometric form, UO2+x. Those excess oxygen atoms occur as interstitial defects, and these defects are not random but rather partially ordered. The widely-accepted model to date, the Willis cluster based on neutron diffraction, cannot be reconciled with the first-principles molecular dynamics simulations present here. We demonstrate that the Willis cluster is a fair representation of the numerical ratio of different interstitial O atoms; however, the model does not represent the actual local configuration. The simulations show that the average structure of UO2+x involves a combination of defect structures including split di-interstitial, di-interstitial, mono-interstitial, and the Willis cluster, and the latter is a transition state that provides for the fast diffusion of the defect cluster. The results provide new insights in differentiating the average structure from the local configuration of defects in a solid and the transport properties of UO2+x. PMID:24642875

  14. 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

  15. 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

  16. Local chromatin structure of heterochromatin regulates repeatedDNA stability, nucleolus structure, and genome integrity

    SciTech Connect

    Peng, Jamy C.

    2007-05-05

    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

  17. 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…

  18. Can Chemistry Teachers' Centres Survive?

    ERIC Educational Resources Information Center

    Garforth, F. M.

    1972-01-01

    The difficulties faced by the Hull Chemistry Teachers' Centre in England are discussed. The lack of finances and time, as well as organizational difficulties in relationship with Science Centres and universities are among the problems. (TS)

  19. ARX model-based damage sensitive features for structural damage localization using output-only measurements

    NASA Astrophysics Data System (ADS)

    Roy, Koushik; Bhattacharya, Bishakh; Ray-Chaudhuri, Samit

    2015-08-01

    The study proposes a set of four ARX model (autoregressive model with exogenous input) based damage sensitive features (DSFs) for structural damage detection and localization using the dynamic responses of structures, where the information regarding the input excitation may not be available. In the proposed framework, one of the output responses of a multi-degree-of-freedom system is assumed as the input and the rest are considered as the output. The features are based on ARX model coefficients, Kolmogorov-Smirnov (KS) test statistical distance, and the model residual error. At first, a mathematical formulation is provided to establish the relation between the change in ARX model coefficients and the normalized stiffness of a structure. KS test parameters are then described to show the sensitivity of statistical distance of ARX model residual error with the damage location. The efficiency of the proposed set of DSFs is evaluated by conducting numerical studies involving a shear building and a steel moment-resisting frame. To simulate the damage scenarios in these structures, stiffness degradation of different elements is considered. It is observed from this study that the proposed set of DSFs is good indicator for damage location even in the presence of damping, multiple damages, noise, and parametric uncertainties. The performance of these DSFs is compared with mode shape curvature-based approach for damage localization. An experimental study has also been conducted on a three-dimensional six-storey steel moment frame to understand the performance of these DSFs under real measurement conditions. It has been observed that the proposed set of DSFs can satisfactorily localize damage in the structure.

  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. 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.

  3. Modeling the local structure and energetics of protozeolitic nanoclusters in hydrothermally stable aluminosilicate mesostructures.

    PubMed

    Li, Hong; Mahanti, S D; Pinnavaia, Thomas J

    2005-02-24

    The density functional theory (DFT) method is used to investigate the structure and bonding of silica and aluminosilicate nanoclusters containing five- and six-membered oxygen rings. The clusters, which are derived from the BEA zeolite structure, are considered as models of the protozeolitic clusters that are incorporated into the pore walls of steam stable aluminosilicate mesostructures assembled from zeolite seeds. Two locally different Brønsted acid sites in the aluminosilicate structure are identified for the adsorption of a water molecule. The sterically more open acid site is favored for water binding. The stability of the aluminosilicate structure in the presence of H2O molecule is studied by breaking an Al-O bond and inserting a water molecule into the five-membered ring structure. We find that an excitation energy at least 18 times larger than the room-temperature thermal energy is needed to break the stable five-membered ring structure, implying a high hydrothermal stability and acidity for this aluminosilicate structure. PMID:16851274

  4. Localization of binding sites in protein structures by optimization of a composite scoring function.

    PubMed

    Rossi, Andrea; Marti-Renom, Marc A; Sali, Andrej

    2006-10-01

    The rise in the number of functionally uncharacterized protein structures is increasing the demand for structure-based methods for functional annotation. Here, we describe a method for predicting the location of a binding site of a given type on a target protein structure. The method begins by constructing a scoring function, followed by a Monte Carlo optimization, to find a good scoring patch on the protein surface. The scoring function is a weighted linear combination of the z-scores of various properties of protein structure and sequence, including amino acid residue conservation, compactness, protrusion, convexity, rigidity, hydrophobicity, and charge density; the weights are calculated from a set of previously identified instances of the binding-site type on known protein structures. The scoring function can easily incorporate different types of information useful in localization, thus increasing the applicability and accuracy of the approach. To test the method, 1008 known protein structures were split into 20 different groups according to the type of the bound ligand. For nonsugar ligands, such as various nucleotides, binding sites were correctly identified in 55%-73% of the cases. The method is completely automated (http://salilab.org/patcher) and can be applied on a large scale in a structural genomics setting. PMID:16963645

  5. Localization of binding sites in protein structures by optimization of a composite scoring function

    PubMed Central

    Rossi, Andrea; Marti-Renom, Marc A.; Sali, Andrej

    2006-01-01

    The rise in the number of functionally uncharacterized protein structures is increasing the demand for structure-based methods for functional annotation. Here, we describe a method for predicting the location of a binding site of a given type on a target protein structure. The method begins by constructing a scoring function, followed by a Monte Carlo optimization, to find a good scoring patch on the protein surface. The scoring function is a weighted linear combination of the z-scores of various properties of protein structure and sequence, including amino acid residue conservation, compactness, protrusion, convexity, rigidity, hydrophobicity, and charge density; the weights are calculated from a set of previously identified instances of the binding-site type on known protein structures. The scoring function can easily incorporate different types of information useful in localization, thus increasing the applicability and accuracy of the approach. To test the method, 1008 known protein structures were split into 20 different groups according to the type of the bound ligand. For nonsugar ligands, such as various nucleotides, binding sites were correctly identified in 55%–73% of the cases. The method is completely automated (http://salilab.org/patcher) and can be applied on a large scale in a structural genomics setting. PMID:16963645

  6. Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.

    PubMed Central

    Young, M A; Ravishanker, G; Beveridge, D L; Berman, H M

    1995-01-01

    Sequence-dependent bending of the helical axes in 112 oligonucleotide duplex crystal structures resident in the Nucleic Acid Database have been analyzed and compared with the use of bending dials, a computer graphics tool. Our analysis includes structures of both A and B forms of DNA and considers both uncomplexed forms of the double helix as well as those bound to drugs and proteins. The patterns in bending preferences in the crystal structures are analyzed by base pair steps, and emerging trends are noted. Analysis of the 66 B-form structures in the Nucleic Acid Database indicates that uniform trends within all pyrimidine-purine and purine-pyrimidine steps are not necessarily observed but are found particularly at CG and GC steps of dodecamers. The results support the idea that AA steps are relatively straight and that larger roll bends occur at or near the junctions of these A-tracts with their flanking sequences. The data on 16 available crystal structures of protein-DNA complexes indicate that the majority of the DNA bends induced via protein binding are sharp localized kinks. The analysis of the 30 available A-form DNA structures indicates that these structures are also bent and show a definitive preference for bending into the deep major groove over the shallow minor groove. PMID:7647248

  7. 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

  8. Metal-dielectric composite optical structures with novel dynamic tunable localized surface-plasmonic effects

    NASA Astrophysics Data System (ADS)

    Feng, Yuyang; Willatzen, Morten; Andersen, Niels L.

    2007-05-01

    A tunable MEMS sub-wavelength surface plasmonic apparatus is proposed based on localized surface-plasmon resonance effects. Optical tunneling is obtained through Surface Plasmon Polaritons (SPP) and Localized Surface Plasmon (LSP) by using a periodic sub-wavelength narrow-grooved metal-dielectric-metal (MDM) composite structure. Only p-polarized light can excite the SPP and LSP resonantly. The excited LSP mode with a strong field enhancement at the incident side grooves, resonantly excites the LSP mode on the other side of the thin structure. Then, with matched radiative modes, photons are radiated and tunneled. Nano/micro electromechanical actuation of small elastic deformations makes it possible to dynamically tune the localized surface plasmons via shape changes. Numerical simulations based on the Finite-Difference Time-Domain (FDTD) method are carried out on sub-wavelength structures and the results discussed. The MDM concept provides a new method to achieve real-time, dynamic tunable control and manipulation of light transmission and reflection via LSP which is different from novel tunable SPP apparatus where refractive index modulation is obtained using a voltage-controlled liquid crystal or tunable spaced air-gapped micro-prisms based on a convential SPP arrangement. This is important for the manipulation of LSP and plasmonic device design applications. Furthermore, a proposed Localized Surface Plasmon Resonance (LSPR) sensor mechanism with MDM-LSPR are demonstrated with numerical results. We believe that the MDM-LSPR is a novel principle for LSPR sensors in dielectric sensing for chemical or biologic applications which compares to current LSPR sensors with nano-particle LSPR and nanosphere lithography (NSL).

  9. 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

  10. 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

  11. Expression, purification, crystallization and preliminary X-ray structure analysis of wild-type and L(M196)H-mutant Rhodobacter sphaeroides reaction centres.

    PubMed

    Gabdulkhakov, A G; Fufina, T Y; Vasilieva, L G; Mueller, U; Shuvalov, V A

    2013-05-01

    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

  12. 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. PMID:19947178

  13. 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.

  14. In situ KPFM imaging of local photovoltaic characteristics of structured organic photovoltaic devices.

    PubMed

    Watanabe, Satoshi; Fukuchi, Yasumasa; Fukasawa, Masako; Sassa, Takafumi; Kimoto, Atsushi; Tajima, Yusuke; Uchiyama, Masanobu; Yamashita, Takashi; Matsumoto, Mutsuyoshi; Aoyama, Tetsuya

    2014-02-12

    Here, we discuss the local photovoltaic characteristics of a structured bulk heterojunction, organic photovoltaic devices fabricated with a liquid carbazole, and a fullerene derivative based on analysis by scanning kelvin probe force microscopy (KPFM). Periodic photopolymerization induced by an interference pattern from two laser beams formed surface relief gratings (SRG) in the structured films. The surface potential distribution in the SRGs indicates the formation of donor and acceptor spatial distribution. Under illumination, the surface potential reversibly changed because of the generation of fullerene anions and hole transport from the films to substrates, which indicates that we successfully imaged the local photovoltaic characteristics of the structured photovoltaic devices. Using atomic force microscopy, we confirmed the formation of the SRG because of the material migration to the photopolymerized region of the films, which was induced by light exposure through photomasks. The structuring technique allows for the direct fabrication and the control of donor and acceptor spatial distribution in organic photonic and electronic devices with minimized material consumption. This in situ KPFM technique is indispensable to the fabrication of nanoscale electron donor and electron acceptor spatial distribution in the devices. PMID:24450927

  15. Local structure reconstruction in hydrogenated amorphous silicon from angular correlation and synchrotron diffraction studies

    NASA Astrophysics Data System (ADS)

    Britton, D. T.; Minani, E.; Knoesen, D.; Schut, H.; Eijt, S. W. H.; Furlan, F.; Giles, C.; Härting, M.

    2006-02-01

    Hydrogenated amorphous silicon (a-Si:H) is a widely used thin film semiconductor material which is still incompletely understood. It is generally assumed to form a continuous random network, with a high concentration of coordination defects (dangling bonds), which are hydrogen terminated. Neither the exact nature of these sites nor the degree of medium range order has been fully determined. In this paper, we present the first results for the local structure, from a combined study using angular correlation of positron annihilation radiation (ACAR) and synchrotron radiation diffraction. Reciprocal space information is obtained directly, for the mesoscale structure and the local defect structure, from the orientation dependent diffraction and 2D-ACAR patterns, respectively. Furthermore, inversion of both patterns yields a comparison of real space information through maps of the silicon-silicon pair correlation function and the electron-positron autocorrelation function B2 γ( r). From this information, it is possible to identify the dominant structural defect as a vacancy-size dangling bond cluster, around which the network strain is fully relaxed.

  16. 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.

  17. 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

  18. Global- and local-scale characterisation of bed surface structure in coarse-grained alluvial rivers

    NASA Astrophysics Data System (ADS)

    Powell, Mark; Ockelford, Annie; Nguyen, Thao; Wood, Jo; Rice, Steve; Reid, Ian; Tate, Nick

    2013-04-01

    It is widely recognised that adjustments in bed surface grain size (texture) and grain arrangement (structure) exert significant controls on the stability of coarse-grained alluvial rivers. Modifications to bed surface texture and structure occur during active sediment transport and are mediated by the process of mobile armouring which concentrates coarser-than-average particles on the surface and organises them into a variety of grain- and bedform-scale configurations. Textural aspects of surface armouring are well understood to the extent that sediment transport models can be used to predict the size distribution of armours that develop under different sediment supply regimes and shear stresses. Research has also found that the adjustment of bed surface grain size is often patchy and that the development of finer-grained and coarser-grained areas of the bed has important implications for both the rate and grain size of transported sediment. The structural aspects of stream-bed armouring, however, are less well understood, largely because of the difficulty of recognising and characterising bedforms and bed-structures that have dimensions similar to their constituent particles. Moreover, bed structure is generally parameterised using global scale descriptors of the bed surface such that information on the spatial heterogeneity of the structure is lost. The aim of this poster is to characterise the structural characteristics of water-worked river gravels, paying particular attention to quantifying the spatial heterogeneity of those characteristics using local scale descriptors. Results reported from a number of flume experiments designed to simulate the spatio-temporal evolution of bed configurations (surface texture and structure) as the system adjusts to a condition of equilibrium transport are used to evaluate the spatial variability of bed surface structure and explore its significance for modelling sediment transport rates in gravel-bed rivers. Keywords: bed

  19. 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

  20. Cluster Ion Beam Induced Nano Metallic Rippled Structures for Localized Surface Plasmon Resonance (LSPR) Based Sensors

    NASA Astrophysics Data System (ADS)

    Saleem, Iram; Tilakaratne, Buddhi; He, Yanzhi; Nzumbe, Epie; Wijesundera, Dharshana; Chen, Quark; Chu, Wei-Kan

    2015-03-01

    Localized surface plasmon resonance (LSPR) based bio sensors have a high sensitivity and exploit a label free real time analytical detection mechanism. We have produced plasmonic nano-structured substrates by cluster ion beam irradiation of thin gold films and have studied their effectiveness as potential plasmonic sensors. By adsorbing a mono-layer of thiolated organic compounds on the surface of these substrates we identified the shift in the LSPR peaks triggered by the change of dielectric function in the neighborhood of the structures. These plasmonic nano-metallic structures can be utilized to observe the change of LSPR resonance frequency due to adsorption, re-adsorption and reactions taking place on the surface that can potentially be mapped to reaction mechanics

  1. 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.

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

    NASA Technical Reports Server (NTRS)

    Li, Chung-Chi Jim; Chen, Paul Peichuan; Fuchs, W. Kent

    1989-01-01

    A new technique, based on virtual backpointers, for local concurrent error detection and correction in linked data strutures 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 database of Virtual Double Linked Lists.

  3. 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.

  4. Analysis of local structure of Ru1-xNixO2 electrocatalytic materials

    NASA Astrophysics Data System (ADS)

    Petrykin, V.; Macounova, K.; Okube, M.; Franc, J.; Krtil, P.

    2009-11-01

    Nanocrystalline Ru1-xNixO2 materials were synthesized by a solution method. Local structure around doped Ni atoms was characterized by extended X-ray absorption fine structure (EXAFS) functions obtained from X-ray absorption spectra acquired at Ni-K edge (8333eV). It was found that Ni ions are confined to the Ru site in the RuO2 rutile-type crystal structure, and Ni atoms tend to group by entering neighbouring sites along the body diagonal of rutile lattice. Such a neighbourhood of two Ni atoms may act as an active site for oxygen evolution by promoting simultaneous two electron transfer from the absorbed molecule of water. The refined Ni-O bond distances suggest that oxidation state of Ni ions is between +2 and +3.

  5. Temporal localized structures in photonic crystal fibre resonators and their spontaneous symmetry-breaking instability.

    PubMed

    Bahloul, L; Cherbi, L; Hariz, A; Tlidi, M

    2014-10-28

    We investigate analytically and numerically the formation of temporal localized structures (TLSs) in an all photonic crystal fibre resonator. These dissipative structures consist of isolated or randomly distributed peaks in a uniform background of the intensity profile. The number of peaks and their temporal distribution are determined solely by the initial conditions. They exhibit multistability behaviour for a finite range of parameters. A weakly nonlinear analysis is performed in the neighbourhood of the first threshold associated with the modulational instability. We consider the regime where the instability is not degenerate. We show that fourth-order dispersion affects the threshold associated with the formation of bright TLSs. We estimate both analytically and numerically the linear and nonlinear corrections to the velocity of moving temporal structures induced by spontaneous broken reflection symmetry mediated by third-order dispersion. Finally, we show that third-order dispersion affects the threshold associated with the moving TLSs. PMID:25246684

  6. Local structure analysis of magnetic transparent conducting films by x-ray spectroscopy

    NASA Astrophysics Data System (ADS)

    Nakamura, Toshihiro

    2016-02-01

    We prepared Mn-doped indium-tin oxide (ITO) films on glass substrates by radio-frequency magnetron sputtering and investigated local structures surrounding Mn ions in the films by x-ray absorption spectroscopy. The Fourier transform of the extended x-ray absorption fine structure (EXAFS) spectrum indicated that the Mn ions preferably substitute the In ions at the b sites of the In2O3 lattice. According to the threshold energy obtained from the inflection point of the edge in the x-ray absorption near edge structure (XANES) spectrum, the valence of the Mn ions was evaluated to range from  +2 to  +3. These x-ray absorption spectroscopic data are useful for revealing the origin of the magnetism of the Mn-doped ITO films.

  7. Local Structure of Cu in Cs8Na16Cu5Ge131 Type II Clathrate

    SciTech Connect

    Mansour, A.; Beekman, M; Wong-Ng, W; Nolas, G

    2008-01-01

    We have used X-ray absorption spectroscopy (XAS) to investigate the local structure of Cu and Ge in the Cs8Na16Cu5Ge131 type II clathrate. We show that the local structure parameters for Ge (coordination number and distances) are consistent with those derived on the basis of XRD investigation of Cs8Na16Ge136. The EXAFS data suggest that Cu either randomly substitutes for Ge on the clathrate framework or preferentially on the 96g site but not preferentially on the 32e or 8a sites (Wyckoff notation). Furthermore, we find that the Cu-Ge distance is smaller than the Ge-Ge distance by 0.13 Angstroms, indicating a local distortion around the Cu atoms. The estimated degrees of disorder for Cu-Ge and Ge-Ge interactions indicate the Cu-Ge clathrate framework to be relatively stiff, while those for Na-Ge and Cs-Ge interactions corroborate previous observations of strong thermal disorder of the alkali guests in these materials. Our XAS results offer insight into the site substitution of Cu in this material, information unattainable from X-ray diffraction due to the lack of scattering contrast between Cu and Ge.

  8. 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.

  9. Trends in the properties and structures of the simple metals from a universal local pseudopotential

    NASA Astrophysics Data System (ADS)

    Nogueira, Fernando; Fiolhais, Carlos; Perdew, John P.

    1999-01-01

    The properties of simple metals are fixed primarily by the equilibrium average valence-electron density parameter rs, and secondarily by the valence z. The simplest level of theory that can account quantitatively for these trends invokes a ``universal'' local electron-ion pseudopotential, defined for each pair (rs,z) and treated as a second-order perturbation. We construct this pseudopotential from two conditions: (1) The total energy should minimize at the equilibrium Wigner-Seitz radius z1/3rs. (2) The bulk modulus should equal the realistic rs-dependent prediction of the stabilized jellium model with effective valence z*=1. These conditions can be satisfied by an analytic local pseudopotential depending upon two parameters other than z; we show that the choice of the two-parameter form (evanescent core vs Heine-Abarenkov) is not important. Our universal local pseudopotential is applied to calculate realistic bulk binding energies, pressure derivatives of bulk moduli, Voigt shear moduli, and interstitial electron numbers, revealing their trends as functions of rs and z. Equilibrium crystal structures are mapped in the rs-z plane, where the Hume-Rothery rules for substitutional alloys are manifest. The effect of pressure on crystal structure is also examined.

  10. 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.

  11. 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.

  12. Automated Foveola Localization in Retinal 3D-OCT Images Using Structural Support Vector Machine Prediction

    PubMed Central

    Liu, Yu-Ying; Ishikawa, Hiroshi; Chen, Mei; Wollstein, Gadi; Schuman, Joel S.; Rehg, James M.

    2013-01-01

    We develop an automated method to determine the foveola location in macular 3D-OCT images in either healthy or pathological conditions. Structural Support Vector Machine (S-SVM) is trained to directly predict the location of the foveola, such that the score at the ground truth position is higher than that at any other position by a margin scaling with the associated localization loss. This S-SVM formulation directly minimizes the empirical risk of localization error, and makes efficient use of all available training data. It deals with the localization problem in a more principled way compared to the conventional binary classifier learning that uses zero-one loss and random sampling of negative examples. A total of 170 scans were collected for the experiment. Our method localized 95.1% of testing scans within the anatomical area of the foveola. Our experimental results show that the proposed method can effectively identify the location of the foveola, facilitating diagnosis around this important landmark. PMID:23285565

  13. Connectivity structures local population dynamics: a long-term empirical test in a large metapopulation system.

    PubMed

    Castorani, Max C N; Reed, Daniel C; Alberto, Filipe; Bell, Tom W; Simons, Rachel D; Cavanaugh, Kyle C; Siegel, David A; Raimondi, Peter T

    2015-12-01

    Ecological theory predicts that demographic connectivity structures the dynamics of local populations within metapopulation systems, but empirical support has been constrained by major limitations in data and methodology. We tested this prediction for giant kelp Macrocystis pyrifera, a key habitat-forming species in temperate coastal ecosystems worldwide, in southern California, USA. We combined a long-term (22 years), large-scale (~500 km coastline), high-resolution census of abundance with novel patch delineation methods and an innovative connectivity measure incorporating oceanographic transport and source fecundity. Connectivity strongly predicted local dynamics (well-connected patches had lower probabilities of extinction and higher probabilities of colonization, leading to greater likelihoods of occupancy) but this relationship was mediated by patch size. Moreover, the relationship between connectivity and local population dynamics varied over time, possibly due to temporal variation in oceanographic transport processes. Surprisingly, connectivity had a smaller influence on colonization relative to extinction, possibly because local ecological factors differ greatly between extinct and extant patches. Our results provide the first comprehensive evidence that southern California giant kelp populations function as a metapopulation system, challenging the view that populations of this important foundation species are governed exclusively by self-replenishment. PMID:26909421

  14. Structural phase-dependent hole localization and transport in bismuth vanadate

    NASA Astrophysics Data System (ADS)

    Kweon, Kyoung E.; Hwang, Gyeong S.

    2013-05-01

    We present theoretical evidence for the phase dependence of hole localization and transport in bismuth vanadate (BiVO4). Our hybrid density-functional theory calculations predict that, in the tetragonal phase [tetragonal scheelite BiVO4 (ts-BiVO4)], an excess hole tends to localize around a BiO8 polyhedron with strong lattice distortion, whereas, in the monoclinic phase [monoclinic scheelite BiVO4 (ms-BiVO4)], it spreads over many lattice sites. The phase-dependent behavior is likely related to the higher structural stability of ms-BiVO4 than ts-BiVO4, which may suppress hole-induced lattice distortions. Our study also demonstrates that the relatively weakly localized hole in ms-BiVO4 undergoes faster diffusion compared to the case of ts-BiVO4, irrespective of the fact that the degrees of localization and mobility vary depending on the choice of exchange-correlation functional. The mobility difference may provide an explanation for the enhanced photocatalytic activity of ms-BiVO4 over ts-BiVO4 for water oxidation, considering that the increased mobility would lead to an increase in the hole current to the catalyst surface.

  15. Hierarchical pictorial structures for simultaneously localizing multiple organs in volumetric pre-scan CT

    NASA Astrophysics Data System (ADS)

    Montillo, Albert; Song, Qi; Das, Bipul; Yin, Zhye

    2015-03-01

    Parsing volumetric computed tomography (CT) into 10 or more salient organs simultaneously is a challenging task with many applications such as personalized scan planning and dose reporting. In the clinic, pre-scan data can come in the form of very low dose volumes acquired just prior to the primary scan or from an existing primary scan. To localize organs in such diverse data, we propose a new learning based framework that we call hierarchical pictorial structures (HPS) which builds multiple levels of models in a tree-like hierarchy that mirrors the natural decomposition of human anatomy from gross structures to finer structures. Each node of our hierarchical model learns (1) the local appearance and shape of structures, and (2) a generative global model that learns probabilistic, structural arrangement. Our main contribution is twofold. First we embed the pictorial structures approach in a hierarchical framework which reduces test time image interpretation and allows for the incorporation of additional geometric constraints that robustly guide model fitting in the presence of noise. Second we guide our HPS framework with the probabilistic cost maps extracted using random decision forests using volumetric 3D HOG features which makes our model fast to train and fast to apply to novel test data and posses a high degree of invariance to shape distortion and imaging artifacts. All steps require approximate 3 mins to compute and all organs are located with suitably high accuracy for our clinical applications such as personalized scan planning for radiation dose reduction. We assess our method using a database of volumetric CT scans from 81 subjects with widely varying age and pathology and with simulated ultra-low dose cadaver pre-scan data.

  16. Person-Centred (Deictic) Expressions and Autism

    ERIC Educational Resources Information Center

    Hobson, R. Peter; Garcia-Perez, Rosa M.; Lee, Anthony

    2010-01-01

    We employed semi-structured tests to determine whether children with autism produce and comprehend deictic (person-centred) expressions such as "this"/"tilde" "here"/"there" and "come"/"go", and whether they understand atypical non-verbal gestural deixis in the form of directed head-nods to indicate location. In Study 1, most participants…

  17. MEMS Biomimetic Acoustic Pressure Gradient Sensitive Structure for Sound Source Localization

    PubMed Central

    An, Peng; Yuan, Weizheng; Ren, Sen

    2009-01-01

    The parasitoid fly Ormia ochracea shows an astonishing localization ability with its tiny hearing organ. A novel MEMS biomimetic acoustic pressure gradient sensitive structure was designed and fabricated by mimicking the mechanically coupled tympana of the fly. Firstly, the analytic representation formulas of the resultant force and resultant moment of the incoming plane wave acting on the structure were derived. After that, structure modal analysis was performed and the results show that the structure has out-of-phase and in-phase vibration modes, and the corresponding eigenfrequency is decided by the stiffness of vertical torsional beam and horizontal beam respectively. Acoustic-structural coupled analysis was performed and the results show that phase difference and amplitude difference between the responses of the two square diaphragms of the sensitive structure are effectively enlarged through mechanical coupling beam. The phase difference and amplitude difference increase with increasing incident angle and can be used to distinguish the direction of sound arrival. At last, the fabrication process and results of the device is also presented. PMID:22346718

  18. Studies of Element-Specific Local Structures in Compound Materials Using X-Ray Absorption Spectroscopy

    NASA Astrophysics Data System (ADS)

    Soo, Yun-Liang

    1995-01-01

    The x-ray absorption spectroscopy techniques have been used to study a variety of semiconductor and superconductor materials. In such experiments, synchrotron radiation harnessed by a delicate beamline electronic and control system are used to obtain data with analyzable quality in a reasonable time scale. The element-selectivity is achieved by selecting an energy-scan range close to a characteristic "absorption edge" of the selected element. Peak structures below the absorption edge (pre-edge structures) reflect the local unoccupied states of the selected atomic species. The position of absorption edge (part of the near-edge x-ray absorption fine structure, NEXAFS) provides some qualitative information of the effective valency of the selected element. And, most importantly, the modulation in the spectrum some 40 eV above the absorption edge (extended x-ray absorption fine structure, EXAFS) gives quantitative information of the local structure around the selected atomic species. The selected atomic species such as magnetic Mn ions in III-V diluted magnetic semiconductors (DMS) rm In_{1-x}Mn_{x}As, Mn as the luminescent centers in nanocrystals of ZnS, O in the CuO_2 planes which host the carriers in high-T_{rm c} superconductors, and F as the electron reservoir in the n-type high-T_{rm c} superconductors rm Nd_2CuO _{4-x}F_{x} all play an important role in the novel mechanism of these new materials. Along with other detailed information, our EXAFS results have revealed (i) III-V DMS can indeed be prepared by substitutional doping of magnetic impurities under proper processing conditions. (ii) Mn ions substitute for the Zn sites in the nanocrystals of ZnS with significant size-dependent local structural changes. (iii) Only ~6% of O in the CuO_2 planes in rm Nd_2CuO_{4 -x}F_{x} are substituted by F. The rest of F atoms substitute for O atoms in the NdO layers and serve as electron reservoirs. The NEXAFS results have shown that the effective valency of Mn in Zn

  19. High-order spoof localized surface plasmons supported on a complementary metallic spiral structure.

    PubMed

    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

  20. 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.

  1. Local structure modification in lithium rich layered Li-Mn-O cathode material

    NASA Astrophysics Data System (ADS)

    Giorgetti, Marco; Wang, Diandian; Aquilanti, Giuliana; Buchholz, Daniel; Passerini, Stefano

    2016-05-01

    X-ray absorption spectroscopy (XAS) is applied to study the local geometry of Co, Ni, and Mn sites in a new high voltage cathode for lithium batteries. The material is a solid solution between Li2MnO3 and Li(x)Mn0.4Ni0.4Co0.2O2. The XAS technique has permitted to check the local atomic structure and charge associated with the metals in a series of electrodes with different lithium concentration x, obtained during the first charge operation, and compared to the first discharge and a successive charge. The ex-situ XAS investigation on the initial activation of the cathode material (first charge) can be described by two separated reaction of LiMO2 (M = Ni and Co) and Li2MnO3. The strength and limitations of the ExAFS approach in these materials is underlined.

  2. 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

  3. An Efficient Algorithm for Stiffness Identification of Truss Structures Through Distributed Local Computation

    NASA Astrophysics Data System (ADS)

    Zhang, G.; Burgueño, R.; Elvin, N. G.

    2010-02-01

    This paper presents an efficient stiffness identification technique for truss structures based on distributed local computation. Sensor nodes on each element are assumed to collect strain data and communicate only with sensors on neighboring elements. This can significantly reduce the energy demand for data transmission and the complexity of transmission protocols, thus enabling a simplified wireless implementation. Element stiffness parameters are identified by simple low order matrix inversion at a local level, which reduces the computational energy, allows for distributed computation and makes parallel data processing possible. The proposed method also permits addressing the problem of missing data or faulty sensors. Numerical examples, with and without missing data, are presented and the element stiffness parameters are accurately identified. The computation efficiency of the proposed method is n2 times higher than previously proposed global damage identification methods.

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Classification of trabeculae into three-dimensional rodlike and platelike structures via local inertial anisotropy

    PubMed Central

    Vasilić, Branimir; Rajapakse, Chamith S.; Wehrli, Felix W.

    2009-01-01

    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. PMID:19673224

  10. Local-global interaction and the emergence of scale-free networks with community structures.

    PubMed

    Liu, Jing; Abbass, Hussein A; Zhong, Weicai; Green, David G

    2011-01-01

    Understanding complex networks in the real world is a nontrivial task. In the study of community structures we normally encounter several examples of these networks, which makes any statistical inferencing a challenging endeavor. Researchers resort to computer-generated networks that resemble networks encountered in the real world as a means to generate many networks with different sizes, while maintaining the real-world characteristics of interest. The generation of networks that resemble the real world turns out in itself to be a complex search problem. We present a new rewiring algorithm for the generation of networks with unique characteristics that combine the scale-free effects and community structures encountered in the real world. The algorithm is inspired by social interactions in the real world, whereby people tend to connect locally while occasionally they connect globally. This local-global coupling turns out to be a powerful characteristics that is required for our proposed rewiring algorithm to generate networks with community structures, power law distributions both in degree and in community size, positive assortative mixing by degree, and the rich-club phenomenon. PMID:21762023

  11. Stochastic reduced order computational model of structures having numerous local elastic modes in low frequency dynamics

    NASA Astrophysics Data System (ADS)

    Arnoux, A.; Batou, A.; Soize, C.; Gagliardini, L.

    2013-08-01

    This paper is devoted to the construction of a stochastic reduced order computational model of structures having numerous local elastic modes in low frequency dynamics. We are particularly interested in automotive vehicles which are made up of stiff parts and flexible components. This type of structure is characterized by the fact that it exhibits, in the low frequency range, not only the classical global elastic modes but also numerous local elastic modes which cannot easily be separated from the global elastic modes. To solve this difficult problem, an innovative method has recently been proposed for constructing a reduced order computational dynamical model adapted to this particular situation for the low frequency range. Then a new adapted generalized eigenvalue problem is introduced and allows a global vector basis to be constructed for the global displacements space. This method requires to decompose the domain of the structure into sub-domains. Such a decomposition is carried out using the Fast Marching Method. This global vector basis is then used to construct the reduced order computational model. Since there are model uncertainties induced by modeling errors in the computational model, the nonparametric probabilistic approach of uncertainties is used and implemented in the reduced order computational model. The methodology is applied to a complex computational model of an automotive vehicle.

  12. 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.

  13. Local structural investigation of Eu3+-doped BaTiO3 nanocrystals

    NASA Astrophysics Data System (ADS)

    Rabuffetti, Federico A.; Culver, Sean P.; Lee, John S.; Brutchey, Richard L.

    2014-02-01

    A structural investigation of sub-15 nm xEu:BaTiO3 nanocrystals (x = 0-5 mol%) was conducted to determine the distribution of the Eu3+ ion in the BaTiO3 lattice. Pair distribution function analysis of X-ray total scattering data (PDF), steady-state photoluminescence, and X-ray absorption spectroscopy (XANES/EXAFS) were employed to interrogate the crystal structure of the nanocrystals and the local atomic environment of the Eu3+ ion. The solubility limit of the Eu3+ ion in the nanocrystalline BaTiO3 host synthesized via the vapor diffusion sol-gel method was estimated to be ~4 mol%. A contraction of the perovskite unit cell volume was observed upon incorporation of 1 mol% of europium, while an expansion was observed for nominal concentrations between 1 and 3 mol%. The average Eu-O distance and europium coordination number decreased from 2.46 Å and 9.9 to 2.42 Å and 8.6 for europium concentrations of 1 and 5 mol%, respectively. Structural trends were found to be consistent with the substitution of Eu3+ for Ba2+via creation of a Ti4+ vacancy at low europium concentrations (<1 mol%), and with the substitution of Eu3+ for both Ba2+ and Ti4+ at high europium concentrations (1-3 mol%). The significance of accounting for local structural distortions to rationalize the distribution of lanthanide ions in the perovskite host is highlighted.A structural investigation of sub-15 nm xEu:BaTiO3 nanocrystals (x = 0-5 mol%) was conducted to determine the distribution of the Eu3+ ion in the BaTiO3 lattice. Pair distribution function analysis of X-ray total scattering data (PDF), steady-state photoluminescence, and X-ray absorption spectroscopy (XANES/EXAFS) were employed to interrogate the crystal structure of the nanocrystals and the local atomic environment of the Eu3+ ion. The solubility limit of the Eu3+ ion in the nanocrystalline BaTiO3 host synthesized via the vapor diffusion sol-gel method was estimated to be ~4 mol%. A contraction of the perovskite unit cell volume was

  14. Dynamic behavior of acoustic metamaterials and metaconfigured structures with local oscillators

    NASA Astrophysics Data System (ADS)

    Manimala, James Mathew

    Dynamic behavior of acoustic metamaterials (AM) and metaconfigured structures (MCS) with various oscillator-type microstructures or local attachments was investigated. AM derive their unusual elastic wave manipulation capabilities not just from material constituents but more so from engineered microstructural configurations. Depending on the scale of implementation, these "microstructures" may be deployed as microscopic inclusions in metacomposites or even as complex endo-structures within load-bearing exo-structures in MCS. The frequency-dependent negative effective-mass exhibited by locally resonant microstructures when considered as a single degree of freedom system was experimentally verified using a structure with an internal mass-spring resonator. AM constructed by incorporating resonators in a host material display spatial attenuation of harmonic stress waves within a tunable bandgap frequency range. An apparent damping coefficient was derived to compare the degree of attenuation achieved in these wholly elastic AM to equivalent conventionally damped models illustrating their feasibility as stiff structures that simultaneously act as effective damping elements. Parametric studies were performed using simulations to design and construct MCS with attached resonators for dynamic load mitigation applications. 98% payload isolation at resonance (7 Hz) was experimentally attained using a low-frequency vibration isolator with tip-loaded cantilever beam resonators. Pendulum impact tests on a resonator stack substantiated a peak transmitted stress reduction of about 60% and filtering of the resonator frequencies in the transmitted spectrum. Drop-tower tests were done to gauge the shock mitigation performance of an AM-inspired infrastructural building-block with internal resonators. Proof-of-concept experiments using an array of multifunctional resonators demonstrate the possibility of integrating energy harvesting and transducer capabilities. Stress wave attenuation

  15. 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. PMID:21545358

  16. 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.

  17. Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport

    PubMed Central

    2013-01-01

    Background To study the chemical determinants of small molecule transport inside cells, it is crucial to visualize relationships between the chemical structure of small molecules and their associated subcellular distribution patterns. For this purpose, we experimented with cells incubated with a synthetic combinatorial library of fluorescent, membrane-permeant small molecule chemical agents. With an automated high content screening instrument, the intracellular distribution patterns of these chemical agents were microscopically captured in image data sets, and analyzed off-line with machine vision and cheminformatics algorithms. Nevertheless, it remained challenging to interpret correlations linking the structure and properties of chemical agents to their subcellular localization patterns in large numbers of cells, captured across large number of images. Results To address this challenge, we constructed a Multidimensional Online Virtual Image Display (MOVID) visualization platform using off-the-shelf hardware and software components. For analysis, the image data set acquired from cells incubated with a combinatorial library of fluorescent molecular probes was sorted based on quantitative relationships between the chemical structures, physicochemical properties or predicted subcellular distribution patterns. MOVID enabled visual inspection of the sorted, multidimensional image arrays: Using a multipanel desktop liquid crystal display (LCD) and an avatar as a graphical user interface, the resolution of the images was automatically adjusted to the avatar’s distance, allowing the viewer to rapidly navigate through high resolution image arrays, zooming in and out of the images to inspect and annotate individual cells exhibiting interesting staining patterns. In this manner, MOVID facilitated visualization and interpretation of quantitative structure-localization relationship studies. MOVID also facilitated direct, intuitive exploration of the relationship between the

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. Surface structure and hole localization in bismuth vanadate: A first principles study

    NASA Astrophysics Data System (ADS)

    Kweon, Kyoung E.; Hwang, Gyeong S.

    2013-09-01

    The monoclinic and tetragonal phases of bismuth vanadate (BiVO4) 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 BiVO4 (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 BiVO4 are discussed.

  4. 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

  5. Soil resources and topography shape local tree community structure in tropical forests

    PubMed Central

    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.

    2013-01-01

    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. PMID:23256196

  6. 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

  7. 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.

  8. The Mott State and Superconductivity in Face-Centred Cubic Structured Cs3C60: A 133Cs-Nuclear Magnetic Resonance Study under Pressure

    NASA Astrophysics Data System (ADS)

    Kawasaki, Shinji; Fukui, Junji; Motoyama, Takeshi; Suzuki, Yuta; Shibasaki, Seiji; Zheng, Guo-qing

    2013-01-01

    Over the past 20 years, fullerides have been studied as the source of high-transition-temperature (Tc) superconductivity except for copper oxides. The recent finding of the Mott insulating state right beside superconductivity in Cs3C60 has suggested that magnetism helps raise Tc even in fullerides as in heavy-fermion compounds, high-Tc copper oxides, two-dimensional organic conductors, and iron pnictides. Namely, one tends to think that the link between Mott insulator and superconductivity takes place in fullerides, which can give rise to the mechanism beyond the Bardeen--Cooper--Schrieffer framework. However, the relationship between the Mott state and the superconductivity in Cs3C60 is still under debate. By nuclear magnetic resonance measurements under pressure, we find that the magnetism and superconductivity in Cs3C60 are competing orders. Different from previous reports, the phase separation of Cs3C60 crystals into the Mott and metallic states allows us to systematically study the evolution of the ground state under pressure. Our careful experiments have found that the prevention of a magnetic order is rather essential for the superconductivity in face-centred cubic Cs3C60, which presents a basic strategy for finding still higher Tc in this system.

  9. LETTER TO THE EDITOR: Metal (M) dopant centred local structures, high-pressure synthesis and bulk superconductivity in ?: M = Fe, Co, Ni

    NASA Astrophysics Data System (ADS)

    Shi, F.; Harris, R.; Bresser, W. J.; McDaniel, D.; Boolchand, P.

    1997-05-01

    Depression of 0953-8984/9/21/001/img9 by the dopants Fe or Co, but not Ni, is spectacularly reversed by synthesis of the titled cuprates at high P instead of ambient P of oxygen with 0953-8984/9/21/001/img9 enhanced from 32 to 82 K for M = Fe at x = 0.10. With Fe dopant, Mössbauer spectroscopy reveals a conversion of a tetrahedral (A) into a trigonal bipyramidal coordinated (C) Fe chain site by oxygen addition in the chains upon high-P processing. The A 0953-8984/9/21/001/img11 C site transformation is elucidated and extended to the case of Co dopant, and its consequences for superconducting behaviour discussed.

  10. 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. PMID:23160484

  11. 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.

  12. 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.

  13. Local Structures around Si, Al and Na in Hydrated Silicate Glasses

    SciTech Connect

    Farges, Francois; Wispelaere, Sidoine de; Rossano, Stephanie; Munos, Manuel; Wilke, Max; Flank, Anne-Marie; Lagarde, Pierre

    2007-02-02

    XANES spectra were collected at the Si-, Al-, and Na K-edge in hydrous silicate glasses to understand the effect of water on the local structure around these cations. Around network forming Si and Al, no drastic changes are observed. Around Na, the dissolution of water creates more ordered environments in Al-bearing glasses and less ordered environment in Al-free glasses. Ab-initio XANES calculations were undertaken to understand the structural origins for these features. Based on these results, a bond valence model was refined that considers not only the present XANES experiments and models but also NMR information. The double percolation model refined explains, among others, the explosive properties of water-bearing hydrous melts, at the origin of a number of cataclysmic eruptions in subduction zones.

  14. Local vibrational properties of GaAs studied by extended X-ray absorption fine structure.

    PubMed

    Ahmed, S I; Aquilanti, G; Novello, N; Olivi, L; Grisenti, R; Fornasini, P

    2013-10-28

    Extended X-ray absorption fine structure (EXAFS) has been measured at both the K edges of gallium and arsenic in GaAs, from 14 to 300 K, to investigate the local vibrational and thermodynamic behaviour in terms of bond expansion, parallel, and perpendicular mean square relative displacements and third cumulant. The separate analysis of the two edges allows a self-consistent check of the results and suggests that a residual influence of Ga EXAFS at the As edge cannot be excluded. The relation between bond expansion, lattice expansion, and expansion due to anharmonicity of the effective potential is quantitatively clarified. The comparison with previous EXAFS results on other crystals with the diamond or zincblende structure shows that the values of a number of parameters determined from EXAFS are clearly correlated with the fractional ionicity and with the strength and temperature interval of the lattice negative expansion. PMID:24182054

  15. Localization of structural proteins in African swine fever virus particles by immunoelectron microscopy.

    PubMed Central

    Carrascosa, J L; González, P; Carrascosa, A L; Garciá-Barreno, B; Enjuanes, L; Viñuela, E

    1986-01-01

    Seven African swine fever virus structural proteins were localized in the virion by immunoelectron microscopy. African swine fever virus-infected cells were incubated, before or after embedding and thin sectioning, with monoclonal antibodies specific for different structural proteins, and after labeling with protein A-gold complexes, the samples were examined in the electron microscope. Proteins p14 and p24 were found in the external region of the virion, proteins p12, p72, p17, and p37 were found in the intermediate layers, and protein p150 was found in the nucleoid and in one vertex. A monoclonal antibody that recognized protein p150 as well as p220, a virus-induced, nonstructural protein, could also bind to a component present in the nucleus of both uninfected and virus-infected cells. Images PMID:3517383

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. Aggregate colour centres in impurity LiF crystals

    SciTech Connect

    Basiev, Tasoltan T; Karasik, Aleksandr Ya; Konyushkin, V A; Papashvili, A G; Pukhov, K K; Ermakov, I V; Gellermann, V

    2002-08-31

    LiF crystals with colour centres exhibiting a zero-phonon line (ZPL) at 1080 nm in absorption and luminescence are studied. The decay time of luminescence of colour centres at 10 K is 260 - 280 ns, the ZPL half-width is 4.7 cm{sup -1}, and colour centres are characterised by a weak electron - phonon interaction (the Huang - Rhys factor is S < 0.11). The polarisation analysis of luminescence showed that the transition dipole moments of colour centres are oriented along the crystal axes [100], [010], and [001]. The model of aggregate F{sub 4} colour centres having a spatial structure with three symmetry axes C{sub 2} may correspond to the colour centres studied in the paper. (active media. lasers)

  3. Local network structure of a-SiC:H and its correlation with dielectric function

    NASA Astrophysics Data System (ADS)

    Kageyama, Shota; Matsuki, Nobuyuki; Fujiwara, Hiroyuki

    2013-12-01

    The microscopic disordered structures of hydrogenated amorphous silicon carbide (a-Si1-xCx: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-Si1-xCx: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 SiH2 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 sp3 CHn (n = 2,3) groups increases. Moreover, we obtained the direct evidence that the sp2 C bonding state in the a-SiC matrix exists in the configuration of C = CH2 and the generation of the graphite-like C = CH2 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 SiH2/CHn groups. By taking the SiH2/CHn 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.

  4. 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.

  5. 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. PMID:27095512

  6. The effect of amorphization on the local structure of arsenic chalcogenides

    SciTech Connect

    Bordovsky, G. A.; Marchenko, A. V.; Seregin, P. P. Terukov, E. I.

    2009-01-15

    The effect of amorphization on the symmetry of the local environment of chalcogen atoms in As{sub 2}S{sub 3}, As{sub 2}Se{sub 3}, and As{sub 2}Te{sub 3} compounds has been investigated by {sup 129}Te({sup 129}I) Moessbauer spectroscopy. Three states of triply coordinated tellurium atoms are indistinguishable in the Moessbauer spectra of crystalline As{sub 2}Te{sub 3}. Amorphization of As{sub 2}Te{sub 3} decreases the local symmetry of triply coordinated states of Te atoms and leads to the formation of doubly coordinated states in -As-Te-Te-As- chains. In the structure of crystalline As{sub 2}S{sub 3} and As{sub 2}Se{sub 3}, two states of doubly coordinated chalcogen atoms X in -As-X-As- chains manifest themselves in the broadening of the Moessbauer spectra. Amorphization of As{sub 2}S{sub 3} and As{sub 2}Se{sub 3} is not accompanied by a change in the local symmetry of doubly coordinated chalcogen atoms in -As-X-As- chains; however, doubly coordinated states of S and Se atoms in -As-X-X-As chains are formed in the amorphous material.

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. [The primary healthcare centres].

    PubMed

    Brambilla, Antonio; Maciocco, Gavino

    2014-04-01

    The central attributes of primary care are: first contact (accessibility), longitudinality (person- focused preventive and curative care overtime), patient-oriented comprehensiveness and coordination (including navigation towards secondary and tertiary care). Besides taking care of the needs of the individuals, primary health care teams are also looking at the community, especially when addressing social determinants of health. The rationale for the benefits for primary care for health has been found in: 1) greater access to needed services; 2) better quality of care; 3) a greater focus on prevention; 4) early management of health problems; 5) organizing and delivering high quality care for chronic non-communicable diseases. This paper describes the role of primary healthcare centres in strengthening community primary services and in reducing health inequalities. Furthemore, the experiences of Regional Health Services from Tuscany and Emilia-Romagna are discussed, with a brief overview of the literature. PMID:24770539

  12. 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

  13. 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.

  14. 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

  15. The human BARX2 gene: genomic structure, chromosomal localization, and single nucleotide polymorphisms.

    PubMed

    Hjalt, T A; Murray, J C

    1999-12-15

    The BARX genes 1 and 2 are Bar class homeobox genes expressed in craniofacial structures during development. In this report, we present the genomic structure, chromosomal localization, and polymorphic markers in BARX2. The gene has four exons, ranging in size from 85 to 1099 bp. BARX2 is localized on human chromosome 11q25, as determined by radiation hybrid mapping. In the mouse, Barx2 is coexpressed with Pitx2 in several tissues. Based on the coexpression, BARX2 was assumed to be a candidate gene for those cases of Rieger syndrome that cannot be associated with mutations of PITX2. Mutations in PITX2 cause some cases of Rieger syndrome, an autosomal dominant disorder affecting eyes, teeth, and umbilicus. DNA from Rieger patients was subjected to single-strand conformation polymorphism screening of the BARX2 coding region. Three single nucleotide polymorphisms were found in a normal population, although no etiologic mutations were detectable in over 100 cases of Rieger syndrome or in individuals with related ocular disorders. PMID:10644443

  16. 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).

  17. 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.

  18. Capturing ultrafast photoinduced local structural distortions of BiFeO3.

    PubMed

    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

  19. Local atomic and electronic structure of boron chemical doping in monolayer graphene.

    PubMed

    Zhao, Liuyan; Levendorf, Mark; Goncher, Scott; Schiros, Theanne; Pálová, Lucia; Zabet-Khosousi, Amir; Rim, Kwang Taeg; Gutiérrez, Christopher; Nordlund, Dennis; Jaye, Cherno; Hybertsen, Mark; Reichman, David; Flynn, George W; Park, Jiwoong; Pasupathy, Abhay N

    2013-10-01

    We use scanning tunneling microscopy and X-ray spectroscopy to characterize the atomic and electronic structure of boron-doped and nitrogen-doped graphene created by chemical vapor deposition on copper substrates. Microscopic measurements show that boron, like nitrogen, incorporates into the carbon lattice primarily in the graphitic form and contributes ~0.5 carriers into the graphene sheet per dopant. Density functional theory calculations indicate that boron dopants interact strongly with the underlying copper substrate while nitrogen dopants do not. The local bonding differences between graphitic boron and nitrogen dopants lead to large scale differences in dopant distribution. The distribution of dopants is observed to be completely random in the case of boron, while nitrogen displays strong sublattice clustering. Structurally, nitrogen-doped graphene is relatively defect-free while boron-doped graphene films show a large number of Stone-Wales defects. These defects create local electronic resonances and cause electronic scattering, but do not electronically dope the graphene film. PMID:24032458

  20. 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.

  1. Visual Tracking via Coarse and Fine Structural Local Sparse Appearance Models.

    PubMed

    Jia, Xu; Lu, Huchuan; Yang, Ming-Hsuan

    2016-10-01

    Sparse representation has been successfully applied to visual tracking by finding the best candidate with a minimal reconstruction error using target templates. However, most sparse representation-based tracking methods only consider holistic rather than local appearance to discriminate between target and background regions, and hence may not perform well when target objects are heavily occluded. In this paper, we develop a simple yet robust tracking algorithm based on a coarse and fine structural local sparse appearance model. The proposed method exploits both partial and structural information of a target object based on sparse coding using the dictionary composed of patches from multiple target templates. The likelihood obtained by averaging and pooling operations exploits consistent appearance of object parts, thereby helping not only locate targets accurately but also handle partial occlusion. To update templates more accurately without introducing occluding regions, we introduce an occlusion detection scheme to account for pixels belonging to the target objects. The proposed method is evaluated on a large benchmark data set with three evaluation metrics. Experimental results demonstrate that the proposed tracking algorithm performs favorably against several state-of-the-art methods. PMID:27448350

  2. 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.

  3. "SP-G", a putative new surfactant protein--tissue localization and 3D structure.

    PubMed

    Rausch, Felix; Schicht, Martin; Paulsen, Friedrich; Ngueya, Ivan; Bräuer, Lars; Brandt, Wolfgang

    2012-01-01

    Surfactant proteins (SP) are well known from human lung. These proteins assist the formation of a monolayer of surface-active phospholipids at the liquid-air interface of the alveolar lining, play a major role in lowering the surface tension of interfaces, and have functions in innate and adaptive immune defense. During recent years it became obvious that SPs are also part of other tissues and fluids such as tear fluid, gingiva, saliva, the nasolacrimal system, and kidney. Recently, a putative new surfactant protein (SFTA2 or SP-G) was identified, which has no sequence or structural identity to the already know surfactant proteins. In this work, computational chemistry and molecular-biological methods were combined to localize and characterize SP-G. With the help of a protein structure model, specific antibodies were obtained which allowed the detection of SP-G not only on mRNA but also on protein level. The localization of this protein in different human tissues, sequence based prediction tools for posttranslational modifications and molecular dynamic simulations reveal that SP-G has physicochemical properties similar to the already known surfactant proteins B and C. This includes also the possibility of interactions with lipid systems and with that, a potential surface-regulatory feature of SP-G. In conclusion, the results indicate SP-G as a new surfactant protein which represents an until now unknown surfactant protein class. PMID:23094088

  4. 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.

  5. 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).

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. Critiquing Child-Centred Pedagogy to Bring Children and Early Childhood Educators into the Centre of a Democratic Pedagogy

    ERIC Educational Resources Information Center

    Langford, Rachel

    2010-01-01

    Child-centred pedagogy is both an enduring approach and a revered concept in Western-based teacher preparation. This article weaves together major critiques of child-centred pedagogy that draw on critical feminist, postmodernist and post-structural theories. These critiques have particular relevance for conceptualizing what it can mean to be, and…

  11. Non-local physics: Applications from the universe evolution to the atom structure in the frame of the unified theory

    NASA Astrophysics Data System (ADS)

    Alexeev, B. V.

    2013-10-01

    The main principles of the non-local physics are delivered. The unified theory of transport processes is applicable to the physical systems in tremendous diapason of scales - from atom structures to the Universe evolution. The origin of difficulties connected with the hypothetical dark matter and dark energy consists in the total Oversimplification following from the principles of local physics and reflects the general shortcomings of the local kinetic transport theory.

  12. Self-organization of local magnetoplasma structures in the upper layers of the solar convection zone

    SciTech Connect

    Chumak, O. V.

    2013-08-15

    Self-organization and evolution of magnetoplasma structures in the upper layers of the solar convection zone are discussed as a process of diffuse aggregation of magnetic flux tubes. Equations describing the tube motion under the action of magnetic interaction forces, hydrodynamic forces, and random forces are written explicitly. The process of aggregation of magnetic flux tubes into magnetic flux clusters of different shapes and dimensions is simulated numerically. The obtained structures are compared with the observed morphological types of sunspot groups. The quantitative comparison with the observational data was performed by comparing the fractal dimensions of the photospheric magnetic structures observed in solar active regions with those of structures obtained in the numerical experiment. The model has the following free parameters: the numbers of magnetic flux tubes with opposite polarities on the considered area element (Nn and Ns), the average radius of the cross section of the magnetic flux tube (a), its effective length (l), the twist factor of the tube field (k), and the absolute value of the average velocity of chaotic tube displacements (d). Variations in these parameters in physically reasonable limits leads to the formation of structures (tube clusters of different morphological types) having different fractal dimensions. Using the NOAA 10488 active region, which appeared and developed into a complicated configuration near the central meridian, as an example, it is shown that good quantitative agreement between the fractal dimensions is achieved at the following parameters of the model: Nn = Ns = 250 ± 50; a = 150 ± 50 km; l ∼ 5000 km, and d = 80 ± 10 m/s. These results do not contradict the observational data and theoretical estimates obtained in the framework of the Parker “spaghetti” model and provide new information on the physical processes resulting in the origin and evolution of local magnetic plasma structures in the near

  13. Self-organization of local magnetoplasma structures in the upper layers of the solar convection zone

    NASA Astrophysics Data System (ADS)

    Chumak, O. V.

    2013-08-01

    Self-organization and evolution of magnetoplasma structures in the upper layers of the solar convection zone are discussed as a process of diffuse aggregation of magnetic flux tubes. Equations describing the tube motion under the action of magnetic interaction forces, hydrodynamic forces, and random forces are written explicitly. The process of aggregation of magnetic flux tubes into magnetic flux clusters of different shapes and dimensions is simulated numerically. The obtained structures are compared with the observed morphological types of sunspot groups. The quantitative comparison with the observational data was performed by comparing the fractal dimensions of the photospheric magnetic structures observed in solar active regions with those of structures obtained in the numerical experiment. The model has the following free parameters: the numbers of magnetic flux tubes with opposite polarities on the considered area element ( Nn and Ns), the average radius of the cross section of the magnetic flux tube ( a), its effective length ( l), the twist factor of the tube field ( k), and the absolute value of the average velocity of chaotic tube displacements ( d). Variations in these parameters in physically reasonable limits leads to the formation of structures (tube clusters of different morphological types) having different fractal dimensions. Using the NOAA 10488 active region, which appeared and developed into a complicated configuration near the central meridian, as an example, it is shown that good quantitative agreement between the fractal dimensions is achieved at the following parameters of the model: Nn = Ns = 250 ± 50; a = 150 ± 50 km; l ˜ 5000 km, and d = 80 ± 10 m/s. These results do not contradict the observational data and theoretical estimates obtained in the framework of the Parker "spaghetti" model and provide new information on the physical processes resulting in the origin and evolution of local magnetic plasma structures in the near

  14. 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

  15. 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

  16. 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

  17. Coupling and simulation of acoustic fluid-structure interaction systems using localized Lagrange multipliers

    NASA Astrophysics Data System (ADS)

    Ross, Mike R.

    This thesis presents a new coupling method for treating the interaction of an acoustic fluid with a flexible structure, with emphasis on handling spatially non-matching meshes. It is based on the Localized Lagrange Multiplier (LLM) method. A frame is introduced as a "mediator" or "information relay" device between the fluid and the structure at the interaction surface. The frame is discretized in terms of kinematic variables. A Lagrange multiplier field is introduced between the frame and the structure, and another one between the frame and the fluid. The function of the multiplier pair is weak enforcement of kinematic continuity. This configuration completely decouples the structure and fluid models, because each model communicates to the frame through node collocated multipliers and not directly to each other. In order to assure proper communication, energy formulations of the fluid and structure models are in terms of displacements and associated time derivatives. A novel transformation of the fluid displacement model into a fluid displacement potential model enforces the irrotational condition of the acoustic fluid. This transformation reduces the number of degrees of freedom in two and three-dimensions and is suitable for both vibration and transient analyses. The LLM method facilitates the construction of separate discretizations using different mesh generation programs, as well as use of customized time integration methods. To advance the solution in time, the LLM coupling method is combined with a partitioned solution procedure. The time-stepping computations are organized in a way that eliminates the traditional prediction step characteristic of staggered solution procedures. This is accomplished by solving for the interface variables: Lagrange multipliers and frame states, and then feeding this solution back to the coupled components. This sequence forestalls the well-known stability degradation caused by prediction, yet it retains the desirable

  18. 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

    2016-07-01

    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

  19. Evidence of local structural order and spin-lattice coupling in the frustrated pyrochlore Y2Ru2O7

    NASA Astrophysics Data System (ADS)

    Castellano, C.; Berti, G.; Sanna, S.; Ruiz-Bustos, R.; van Duijn, J.; Brambilla, A.; Muñoz-Noval, Á.; Carretta, P.; Duò, L.; Demartin, F.

    2015-06-01

    We present an extended x-ray absorption fine structure study of the pyrochlore Y2Ru2O7 (8-298 K). We find evidence, on a local scale, of a significant magnetoelastic coupling at the Néel temperature TN˜77 K pointed out by a huge Debye-Waller σ2 factor deviation from a correlated temperature dependent Debye-like local order behavior plus a temperature independent static contribution. Moreover, we notice the occurrence of a potential local order-disorder structural phase transition at T*=150 K. This anomalous behavior is consistent with the pyrochlore's predisposition towards structural disorder and with a strong spin-phonon correlation. Remarkably the low-temperature order competes with the tendency of magnetic frustration to induce a less symmetric local structure.

  20. Policies for control of communicable disease in day care centres.

    PubMed Central

    Chouillet, A; Maguire, H; Kurtz, Z

    1992-01-01

    A survey was carried out to identify the availability and quality of guidelines for the prevention and control of communicable disease and procedures in use in child day care centres within the South West Thames Regional Health Authority. A sample of 50 day care centres was investigated including those funded by social services and privately funded day care centres. Policies for the prevention and control of communicable disease for children and staff showed a wide variation between different centres. Exclusion criteria were unclear especially in relation to carriers of the hepatitis B virus and HIV positive children. Channels for reporting and seeking advice were inconsistent. It is recommended that clear and up to date written guidelines on the prevention and control of communicable diseases should be available in all day care centres with clear indications of good practice and channels for reporting and advice. It is desirable that guidelines are agreed by the different health and local authorities throughout the region. PMID:1417054

  1. 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.

  2. 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

  3. 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

  4. Crustal Structure of Northeastern Sicily, South Italy, From Tomographic Inversion of Local Earthquake Arrival-times

    NASA Astrophysics Data System (ADS)

    Orecchio, B.; Aloisi, M.; Barberi, G.; Neri, G.

    After integrating the databases of the local and national seismic networks relative to lithospheric seismicity that occurred in and around Northeastern Sicily bet ween 1978 and 2001, we selected 932 events for 3D local tomography of P- and S-wave velocity. A dataset of 10241 P and 5597 S arrival times was inverted for Vp, Vs and hypocenter distributions using the SIMULPS12 algorithm. Analysis of the Derivative Weight Sum and Spread Function detected a rather good level of constraint of velocity at nodes of a grid with horizontal and vertical spacing of 10 and 6 km respectively, spanning the upper 30 Km beneath the area including Central and Northeastern Sicily, Southern Calabria and the Southeasternmost Tyrrhenian Sea. Standard deviation of arrival-time residuals after 3D inversion was about 20% lower than obtained by locating the same earthquakes using the minimum 1D model. Four main spatial domains can be distinguished in the obtained velocity structure: i) a high-velocity domain corresponding to Tyrrhenian structural units; ii) low-velocity domain corresponding to Sicilian units; iii) a domain corresponding to the Calabrian Arc characterized by positive velocity anomalies at shallow depth (nodes in the range 0-12 Km) and by negative velocity ones below (18-30 Km); iv) positive anomalies at deep nodes (18-30 Km) and negative anomalies above, in the area including the Etna volcano and the Ionian coast of Sicily near the volcanic edifice. Velocity distributions were analyzed jointly with the geophysical and geological information available in the literature in order to improve our knowledge of the crustal structure in the study area. Furthermore, comparisons were made with the most recent regional geodynamic models and led us to state that the crustal features evidenced in the present investigation match well with the model assuming gravity- induced southeastward roll-back of an Ionian lithospheric slab subducting beneath the Tyrrhenian sea.

  5. 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

  6. 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

  7. Engineering characterization of ground motion. Task II. Effects of ground motion characteristics on structural response considering localized structural nonlinearities and soil-structure interaction effects. Volume 2

    SciTech Connect

    Kennedy, R.P.; Kincaid, R.H.; Short, S.A.

    1985-03-01

    This report presents the results of part of a two-task study on the engineering characterization of earthquake ground motion for nuclear power plant design. Task I of the study, which is presented in NUREG/CR-3805, Vol. 1, developed a basis for selecting design response spectra taking into account the characteristics of free-field ground motion found to be significant in causing structural damage. Task II incorporates additional considerations of effects of spatial variations of ground motions and soil-structure interaction on foundation motions and structural response. The results of Task II are presented in four parts: (1) effects of ground motion characteristics on structural response of a typical PWR reactor building with localized nonlinearities and soil-structure interaction effects; (2) empirical data on spatial variations of earthquake ground motion; (3) soil-structure interaction effects on structural response; and (4) summary of conclusions and recommendations based on Tasks I and II studies. This report presents the results of the first part of Task II. The results of the other parts will be presented in NUREG/CR-3805, Vols. 3 to 5.

  8. 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

  9. 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.

  10. 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

  11. Probing the Impact of Local Structural Dynamics of Conformational Epitopes on Antibody Recognition.

    PubMed

    Liang, Yu; Guttman, Miklos; Davenport, Thaddeus M; Hu, Shiu-Lok; Lee, Kelly K

    2016-04-19

    Antibody-antigen interactions are governed by recognition of specific residues and structural complementarity between the antigen epitope and antibody paratope. While X-ray crystallography has provided detailed insights into static conformations of antibody-antigen complexes, factors such as conformational flexibility and dynamics, which are not readily apparent in the structures, can also have an impact on the binding event. Here we investigate the contribution of dynamics in the HIV-1 gp120 glycoprotein to antibody recognition of conserved conformational epitopes, including the CD4- and coreceptor-binding sites, and an inner domain site that is targeted by ADCC-active antibodies. Hydrogen/deuterium-exchange mass spectrometry (HDX-MS) was used to measure local structural dynamics across a panel of variable loop truncation mutants of HIV-1 gp120, including full-length gp120, ΔV3, ΔV1/V2, and extended core, which includes ΔV1/V2 and V3 loop truncations. CD4-bound full-length gp120 was also examined as a reference state. HDX-MS revealed a clear trend toward an increased level of order of the conserved subunit core resulting from loop truncation. Combined with biolayer interferometry and enzyme-linked immunosorbent assay measurements of antibody-antigen binding, we demonstrate that an increased level of ordering of the subunit core was associated with better recognition by an array of antibodies targeting complex conformational epitopes. These results provide detailed insight into the influence of structural dynamics on antibody-antigen interactions and suggest the importance of characterizing the structural stability of vaccine candidates to improve antibody recognition of complex epitopes. PMID:27003615

  12. Dynamic morphometric characterization of local connective tissue network structure in humans using ultrasound

    PubMed Central

    Langevin, Helene M; Rizzo, Donna M; Fox, James R; Badger, Gary J; Wu, Junru; Konofagou, Elisa E; Stevens-Tuttle, Debbie; Bouffard, Nicole A; Krag, Martin H

    2007-01-01

    Background In humans, connective tissue forms a complex, interconnected network throughout the body that may have mechanosensory, regulatory and signaling functions. Understanding these potentially important phenomena requires non-invasive measurements of collagen network structure that can be performed in live animals or humans. The goal of this study was to show that ultrasound can be used to quantify dynamic changes in local connective tissue structure in vivo. We first performed combined ultrasound and histology examinations of the same tissue in two subjects undergoing surgery: in one subject, we examined the relationship of ultrasound to histological images in three dimensions; in the other, we examined the effect of a localized tissue perturbation using a previously developed robotic acupuncture needling technique. In ten additional non-surgical subjects, we quantified changes in tissue spatial organization over time during needle rotation vs. no rotation using ultrasound and semi-variogram analyses. Results 3-D renditions of ultrasound images showed longitudinal echogenic sheets that matched with collagenous sheets seen in histological preparations. Rank correlations between serial 2-D ultrasound and corresponding histology images resulted in high positive correlations for semi-variogram ranges computed parallel (r = 0.79, p < 0.001) and perpendicular (r = 0.63, p < 0.001) to the surface of the skin, indicating concordance in spatial structure between the two data sets. Needle rotation caused tissue displacement in the area surrounding the needle that was mapped spatially with ultrasound elastography and corresponded to collagen bundles winding around the needle on histological sections. In semi-variograms computed for each ultrasound frame, there was a greater change in the area under the semi-variogram curve across successive frames during needle rotation compared with no rotation. The direction of this change was heterogeneous across subjects. The frame

  13. 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

  14. Electrical conductivity and local structure of lithium tin iron vanadate glass

    NASA Astrophysics Data System (ADS)

    Kubuki, Shiro; Masuda, Hitomi; Akiyama, Kazuhiko; Homonnay, Zoltán; Kuzmann, Ernő; Nishida, Tetsuaki

    2013-04-01

    A relationship between electrical conductivity ( σ) and local structure of 15Li2O·10Fe2O3· xSnO2·(70- x)V2O5·5P2O5 glass ( x = 0-20 mol%), abbreviated as xLFSVP glass, was investigated by 57Fe- and 119Sn-Mössbauer spectroscopies, differential thermal analysis (DTA) and dc-four probe method. A small increase in quadrupole splitting ( Δ) for FeIII was observed from 0.70 to 0.74± 0.02 mm s - 1 with an increase of " x", whereas isomer shift ( Δ) values of 0.40±0.01 mm s - 1 were independent of " x". This result suggests that local distortion of FeIIIO4 tetrahedra was slightly increased in SnO2-containing vanadate glasses, which was reflected as an increase in glass transition temperature (Tg) from 266 to 285±5 °C. A slope of 675 K / (mm s - 1) obtained in `Tg vs. Δ plot' proved that FeIII occupied the site of network former (NWF). An isothermal annealing of 10LFSVP glass at 500 °C for 100 min resulted in a marked decrease of Δ from 0.72 to 0.56±0.02 mm s - 1, indicating that local distortion of FeO4 tetrahedra was reduced by the structural relaxation of 3D-network. In contrast, identical δ and Δ values of 0.07±0.01 and 0.53±0.02 mms - 1, respectively, were observed in 119Sn-Mössbauer spectra of 10LFSVP glass before and after the annealing. These results indicate that SnIVO6 octahedra are loosely bound in the glass matrix as a network modifier (NWM). A marked increase in σ from 7.4 × 10 - 7 to 9.1 × 10 - 3 S cm - 1 was observed in 20LFSVP glass after the isothermal annealing, indicating that structural relaxation of 3D-network evidently causes a marked increase in σ.

  15. 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. PMID:22931378

  16. 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

  17. ODS steel raw material local structure analysis using X-ray absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Cintins, A.; Anspoks, A.; Purans, J.; Kuzmin, A.; Timoshenko, J.; Vladimirov, P.; Gräning, T.; Hoffmann, J.

    2015-03-01

    Oxide dispersion strengthened (ODS) steels are promising materials for fusion power reactors, concentrated solar power plants, jet engines, chemical reactors as well as for hydrogen production from thermolysis of water. In this study we used X-ray absorption spectroscopy at the Fe and Cr K-edges as a tool to get insight into the local structure of ferritic and austenitic ODS steels around Fe and Cr atoms and its transformation during mechanical alloying process. Using the analysis of X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) we found that for austenitic samples a transformation of ferritic steel to austenitic steel is detectable after 10 hours of milling and proceeds till 40 hours of milling; only small amount of a-phase remains after 80 hours of milling. We found that the Cr K-edge EXAFS can be used to observe distortions inside the material and to get an impression on the formation of chromium clusters. In-situ EXAFS experiments offer a reliable method to investigate the ferritic to austenitic transformation.

  18. 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.

  19. Local structural properties of Co-ion-implanted ZnO nanorods

    NASA Astrophysics Data System (ADS)

    Park, C. I.; Jin, Zhenlan; Jeong, E. S.; Hwang, I. H.; Han, S. W.

    2013-12-01

    We examined the local structural properties around Co and Zn ions in Co-ion-implanted ZnO nanorods by using an X-ray absorption fine structure (XAFS) analysis. Vertically-aligned ZnO nanorods were synthesized on Al2O3 substrates by using a catalyst-free metal-organic chemicalvapor deposition. Co ions (Co+ and Co2+) with energies of 50 and 100 keV and fluxes of 1013 and 1015 particles/cm2 were implanted in the ZnO nanorods, and the ion-implanted ZnO nanorods were annealed at 400-650°C. X-ray absorption near edge structure (XANES) analyses demonstrated that the chemical valence state of the Co ions were mostly 2+. An extended XAFS (EXAFS) analysis revealed that the Co ions were mostly substituted at the Zn sites of ZnO nanorods at a Coion flux of 1015 particles/cm2. However, at a flux of 1013 particles/cm2, Co ions formed Co-O and Co-Co clusters. These results were in contrast to the Co distribution in Co-added ZnO predicted by using a Monte Carlo method.

  20. Structural Propensities of Human Ubiquitination Sites: Accessibility, Centrality and Local Conformation

    PubMed Central

    Song, Jiangning; Zhang, Ziding

    2013-01-01

    The existence and function of most proteins in the human proteome are regulated by the ubiquitination process. To date, tens of thousands human ubiquitination sites have been identified from high-throughput proteomic studies. However, the mechanism of ubiquitination site selection remains elusive because of the complicated sequence pattern flanking the ubiquitination sites. In this study, we perform a systematic analysis of 1,330 ubiquitination sites in 505 protein structures and quantify the significantly high accessibility and unexpectedly high centrality of human ubiquitination sites. Further analysis suggests that the higher centrality of ubiquitination sites is associated with the multi-functionality of ubiquitination sites, among which protein-protein interaction sites are common targets of ubiquitination. Moreover, we demonstrate that ubiquitination sites are flanked by residues with non-random local conformation. Finally, we provide quantitative and unambiguous evidence that most of the structural propensities contain specific information about ubiquitination site selection that is not represented by the sequence pattern. Therefore, the hypothesis about the structural level of the ubiquitination site selection mechanism has been substantially approved. PMID:24349449