Science.gov

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…

  3. South Cheshire Local Multi-disciplinary Evidence Centre: an evaluation.

    PubMed

    Howard, John C

    2002-07-01

    The South Cheshire Local Multidisciplinary Evidence Centre (LMEC) was a two-year project commenced in March 1998 and completed in April 2000. The project aimed to develop an information service to enable all primary and community care staff in South Cheshire to access high-quality evidence and thus to improve patient care. The LMEC gave access from the workplace to both physical and electronic resources to support clinical governance and lifelong learning, with a strong emphasis on evidence-based material. Automation of the library catalogue enabled its inclusion on the website. The project developed enquiry and document delivery services and provided training on using the LMEC and on critical appraisal. An evaluation carried out at the end of the project showed that over 120 primary and community care staff had used the LMEC and were positive about the service. As Clinical Governance, the NHSnet, and plans for continuing professional development are implemented, the LMEC is one model for a Local Health Information Service outlined in the NHS IT strategy.

  4. Reaction centres: the structure and evolution of biological solar power.

    PubMed

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

    2002-02-01

    Reaction centres are complexes of pigment and protein that convert the electromagnetic energy of sunlight into chemical potential energy. They are found in plants, algae and a variety of bacterial species, and vary greatly in their composition and complexity. New structural information has highlighted features that are common to the different types of reaction centre and has provided insights into some of the key differences between reaction centres from different sources. New ideas have also emerged on how contemporary reaction centres might have evolved and on the possible origin of the first chlorophyll-protein complexes to harness the power of sunlight.

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

    PubMed Central

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

    2003-01-01

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

  6. Lipids in photosynthetic reaction centres: structural roles and functional holes.

    PubMed

    Jones, Michael R

    2007-01-01

    Photosynthetic proteins power the biosphere. Reaction centres, light harvesting antenna proteins and cytochrome b(6)f (or bc(1)) complexes are expressed at high levels, have been subjected to an intensive spectroscopic, biochemical and mutagenic analysis, and several have been characterised to an informatively high resolution by X-ray crystallography. In addition to revealing the structural basis for the transduction of light energy, X-ray crystallography has brought molecular insights into the relationships between these multicomponent membrane proteins and their lipid environment. Lipids resolved in the X-ray crystal structures of photosynthetic proteins bind light harvesting cofactors, fill intra-protein cavities through which quinones can diffuse, form an important part of the monomer-monomer interface in multimeric structures and may facilitate structural flexibility in complexes that undergo partial disassembly and repair. It has been proposed that individual lipids influence the biophysical properties of reaction centre cofactors, and so affect the rate of electron transfer through the complex. Lipids have also been shown to be important for successful crystallisation of photosynthetic proteins. Comparison of the three types of reaction centre that have been structurally characterised reveals interesting similarities in the position of bound lipids that may point towards a generic requirement to reinforce the structure of the core electron transfer domain. The crystallographic data are also providing new opportunities to find molecular explanations for observed effects of different types of lipid on the structure, mechanism and organisation of reaction centres and other photosynthetic proteins.

  7. Magmatic Plumbing at an Incipient Oceanic Spreading Centre: Evidence From Local Earthquake Data in Northern Afar

    NASA Astrophysics Data System (ADS)

    Illsley-Kemp, F.; Keir, D.; Bull, J. M.; Ayele, A.; Hammond, J. O. S.; Kendal, M. J.; Gallacher, R. J.; Gernon, T.; Goitom, B.

    2015-12-01

    The transition from continental breakup to seafloor spreading is characterised by voluminous intrusive and extrusive magmatic activity, focused along narrow rift segments. The manner in which this magma is stored and transported within the crust is poorly constrained. It is difficult to answer these questions by studying previously rifted continental margins, as the area of transition is buried deep beneath volcanic and sedimentary sequences. Northern Afar presents a unique opportunity to resolve this problem, as it exposes subaerially the magma-rich transition from continental rifting to an oceanic spreading centre. The region therefore acts as a laboratory in which the geological signatures of continental breakup can be investigated unambiguously. For two years, between 2011 and 2013, a seismic network of 20 seismic stations was deployed in the area. Presented here are the hypocentral locations and local magnitudes of over 4500 earthquakes. Seismicity is focused along the western border fault and at active volcanic centres. Magma pathways beneath active volcanoes are clearly defined by seismicity spanning the entire crust. The data allows for the development of a calibrated local magnitude scale for northern Afar and provides an insight into the nature of seismic attenuation in the uppermost mantle. I discuss the implications that these results have on our understanding of the distribution of extension, melt storage and migration and upper mantle processes during the last stages of continental rifting.

  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

    2014-03-07

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

  9. 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

  10. Localized structures in convective experiments

    NASA Astrophysics Data System (ADS)

    Burguete, J.; Mancini, H.

    2014-01-01

    In this work we review localized structures appearing in thermo-convective experiments performed in extended (large "aspect ratio") fluid layers. After a brief general review (not exhaustive), we focus on some results obtained in pure fluids in a Bénard-Marangoni system with non-homogeneous heating where some structures of this kind appear. The experimental results are compared in reference to the most classical observed in binary mixtures experiments or simulations. In the Bénard-Marangoni experiment we present the stability diagram where localized structures appear and the typical situations where these local mechanisms have been studied experimentally. Some new experimental results are also included. The authors want to honor Prof. H. Brand in his 60th. birthday and to thank him for helpful discussions.

  11. Locally centred Mahalanobis distance: a new distance measure with salient features towards outlier detection.

    PubMed

    Todeschini, Roberto; Ballabio, Davide; Consonni, Viviana; Sahigara, Faizan; Filzmoser, Peter

    2013-07-17

    Outlier detection is a prerequisite to identify the presence of aberrant samples in a given set of data. The identification of such diverse data samples is significant particularly for multivariate data analysis where increasing data dimensionality can easily hinder the data exploration and such outliers often go undetected. This paper is aimed to introduce a novel Mahalanobis distance measure (namely, a pseudo-distance) termed as locally centred Mahalanobis distance, derived by centering the covariance matrix at each data sample rather than at the data centroid as in the classical covariance matrix. Two parameters, called as Remoteness and Isolation degree, were derived from the resulting pairwise distance matrix and their salient features facilitated a better identification of atypical samples isolated from the rest of the data, thus reflecting their potential application towards outlier detection. The Isolation degree demonstrated to be able to detect a new kind of outliers, that is, isolated samples within the data domain, thus resulting in a useful diagnostic tool to evaluate the reliability of predictions obtained by local models (e.g. k-NN models). To better understand the role of Remoteness and Isolation degree in identification of such aberrant data samples, some simulated and published data sets from literature were considered as case studies and the results were compared with those obtained by using Euclidean distance and classical Mahalanobis distance.

  12. Residential proximity to urban centres, local-area walkability and change in waist circumference among Australian adults.

    PubMed

    Sugiyama, Takemi; Niyonsenga, Theo; Howard, Natasha J; Coffee, Neil T; Paquet, Catherine; Taylor, Anne W; Daniel, Mark

    2016-12-01

    Consistent associations have been observed between macro-level urban sprawl and overweight/obesity, but whether residential proximity to urban centres predicts adiposity change over time has not been established. Further, studies of local-area walkability and overweight/obesity have generated mixed results. This study examined 4-year change in adults' waist circumference in relation to proximity to city centre, proximity to closest suburban centre, and local-area walkability. Data were from adult participants (n=2080) of a cohort study on chronic conditions and health risk factors in Adelaide, Australia. Baseline data were collected in 2000-03 with a follow-up in 2005-06. Multilevel regression models examined in 2015 the independent and joint associations of the three environmental measures with change in waist circumference, accounting for socio-demographic covariates. On average, waist circumference rose by 1.8cm over approximately 4years. Greater distance to city centre was associated with a greater increase in waist circumference. Participants living in distal areas (20km or further from city centre) had a greater increase in waist circumference (mean increase: 2.4cm) compared to those in proximal areas (9km or less, mean increase: 1.2cm). Counterintuitively, living in the vicinity of a suburban centre was associated with a greater increase in adiposity. Local-area walkability was not significantly associated with the outcome. Residential proximity to city centre appears to be protective against excessive increases in waist circumference. Controlled development and targeted interventions in the urban fringe may be needed to tackle obesity. Additional research needs to assess behaviours that mediate relationships between sprawl and obesity.

  13. 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…

  14. Quasi-local gravitational angular momentum and centre of mass from generalised Witten equations

    NASA Astrophysics Data System (ADS)

    Wieland, Wolfgang

    2017-03-01

    Witten's proof for the positivity of the ADM mass gives a definition of energy in terms of three-surface spinors. In this paper, we give a generalisation for the remaining six Poincaré charges at spacelike infinity, which are the angular momentum and centre of mass. The construction improves on certain three-surface spinor equations introduced by Shaw. We solve these equations asymptotically obtaining the ten Poincaré charges as integrals over the Nester-Witten two-form. We point out that the defining differential equations can be extended to three-surfaces of arbitrary signature and we study them on the entire boundary of a compact four-dimensional region of spacetime. The resulting quasi-local expressions for energy and angular momentum are integrals over a two-dimensional cross-section of the boundary. For any two consecutive such cross-sections, conservation laws are derived that determine the influx (outflow) of matter and gravitational radiation.

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

    ERIC Educational Resources Information Center

    Zarifis, George K.

    2008-01-01

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

  16. 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.

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

    ERIC Educational Resources Information Center

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

    2016-01-01

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

  18. 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…

  19. OPTICAL RECORDING AND COMMUNICATION: Optical recording of transient spatial structures in saturable three-level centres

    NASA Astrophysics Data System (ADS)

    Kucherenko, M. G.; Rusinov, A. P.

    2004-08-01

    Optical recording and decay of transient spatial structures is analysed in a system with a nonlinear response caused by incoherent saturation of three-level centres. The main attention is devoted to the thermal mechanism of phase recording in media with the temperature-independent heat conductivity. The relaxation of an inhomogeneous temperature field and the diffraction of a probe beam from the transient structure are studied.

  20. Spreading rate dependence of three-dimensional structure in oceanic spreading centres

    NASA Astrophysics Data System (ADS)

    Parmentier, E. M.; Morgant, Jason Phipps

    1990-11-01

    SEGMENTATION by transform faults and other types of along-axis discontinuity1 is a well described but poorly explained characteristic of oceanic spreading centres. Here we use numerical experiments to explore the dynamics of mantle flow and melting beneath a mid-ocean ridge. Buoyant upwelling, driven by compositional density variations resulting from the extraction of the melt that forms the ocean crust, exhibits a spreading-rate-dependent transition between two-dimensional and three-dimensional upwelling structures. For low spreading rates and mantle viscosities an initial two-dimensional structure transforms into a three-dimensional one; at high spreading rates, an initially two-dimensional structure remains two-dimensional. These results suggest that the origin of spreading-centre segmentation may be different at fast and slow spreading rates.

  1. Densest Local Structures of Uniaxial Ellipsoids

    NASA Astrophysics Data System (ADS)

    Schaller, Fabian M.; Weigel, Robert F. B.; Kapfer, Sebastian C.

    2016-10-01

    Connecting the collective behavior of disordered systems with local structure on the particle scale is an important challenge, for example, in granular and glassy systems. Compounding complexity, in many scientific and industrial applications, particles are polydisperse, aspherical, or even of varying shape. Here, we investigate a generalization of the classical kissing problem in order to understand the local building blocks of packings of aspherical grains. We numerically determine the densest local structures of uniaxial ellipsoids by minimizing the Set Voronoi cell volume around a given particle. Depending on the particle aspect ratio, different local structures are observed and classified by symmetry and Voronoi coordination number. In extended disordered packings of frictionless particles, knowledge of the densest structures allows us to rescale the Voronoi volume distributions onto the single-parameter family of k -Gamma distributions. Moreover, we find that approximate icosahedral clusters are found in random packings, while the optimal local structures for more aspherical particles are not formed.

  2. 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

  3. 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).

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

    PubMed

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

    2013-06-01

    Global surgery initiatives increasingly are focused on strengthening education and local health care systems to build surgical capacity. The goal of this education project was to support local health care providers in augmenting the surgical curriculum at a new medical school, thus promoting long-term local goals and involvement. Working with local surgeons, residents, and medical and assistant medical officer students, we identified the most common surgical conditions presenting to Weill Bugando Medical Centre in Mwanza, Tanzania, and the areas of greatest need in surgical education. We developed an 8-week teaching schedule for undergraduate students and an electronic database of clinical surgery topics. In addition, we started teaching basic surgical skills in the operating theatre, bridging to an official and recurring workshop through a supporting international surgery organization. The medical and assistant medical officer students reported increased satisfaction with their clinical surgery rotations and mastery of key educational subjects. The initiation of an Essential Surgical Skills workshop through the Canadian Network for International Surgery showed students had improved comfort with basic surgical techniques. Short-term surgical missions may appear to fill a void in the shortage of health care in the developing world. However, we conclude that global health resources are more appropriately used through projects giving ownership to local providers and promoting education as a foundation of development. This results in better coordination among local and visiting providers and greater impact on education and long-term growth of health care capacity.

  5. Local statistical interpretation for water structure

    NASA Astrophysics Data System (ADS)

    Sun, Qiang

    2013-05-01

    In this Letter, Raman spectroscopy is employed to study supercooled water down to a temperature of 248 K at ambient pressure. Based on our interpretation of the Raman OH stretching band, decreasing temperature mainly leads to a structural transition from the single donor-single acceptor (DA) to the double donor-double acceptor (DDAA) hydrogen bonding motif. Additionally, a local statistical interpretation of the water structure is proposed, which reveals that a water molecule interacts with molecules in the first shell through various local hydrogen-bonded networks. From this, a local structure order parameter is proposed to explain the short-range order and long-range disorder.

  6. Deterministic weak localization in periodic structures.

    PubMed

    Tian, C; Larkin, A

    2005-12-09

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

  7. 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.

  8. An observationally centred method to quantify local climate change as a distribution

    NASA Astrophysics Data System (ADS)

    Stainforth, David; Chapman, Sandra; Watkins, Nicholas

    2013-04-01

    For planning and adaptation, guidance on trends in local climate is needed at the specific thresholds relevant to particular impact or policy endeavours. This requires quantifying trends at specific quantiles in distributions of variables such as daily temperature or precipitation. These non-normal distributions vary both geographically and in time. The trends in the relevant quantiles may not simply follow the trend in the distribution mean. We present a method[1] for analysing local climatic timeseries data to assess which quantiles of the local climatic distribution show the greatest and most robust trends. We demonstrate this approach using E-OBS gridded data[2] timeseries of local daily temperature from specific locations across Europe over the last 60 years. Our method extracts the changing cumulative distribution function over time and uses a simple mathematical deconstruction of how the difference between two observations from two different time periods can be assigned to the combination of natural statistical variability and/or the consequences of secular climate change. This deconstruction facilitates an assessment of the sensitivity of different quantiles of the distributions to changing climate. Geographical location and temperature are treated as independent variables, we thus obtain as outputs how the trend or sensitivity varies with temperature (or occurrence likelihood), and with geographical location. These sensitivities are found to be geographically varying across Europe; as one would expect given the different influences on local climate between, say, Western Scotland and central Italy. We find as an output many regionally consistent patterns of response of potential value in adaptation planning. We discuss methods to quantify the robustness of these observed sensitivities and their statistical likelihood. This also quantifies the level of detail needed from climate models if they are to be used as tools to assess climate change impact. [1] S C

  9. An Observationally-Centred Method to Quantify the Changing Shape of Local Temperature Distributions

    NASA Astrophysics Data System (ADS)

    Chapman, S. C.; Stainforth, D. A.; Watkins, N. W.

    2014-12-01

    For climate sensitive decisions and adaptation planning, guidance on how local climate is changing is needed at the specific thresholds relevant to particular impacts or policy endeavours. This requires the quantification of how the distributions of variables, such as daily temperature, are changing at specific quantiles. These temperature distributions are non-normal and vary both geographically and in time. We present a method[1,2] for analysing local climatic time series data to assess which quantiles of the local climatic distribution show the greatest and most robust changes. We have demonstrated this approach using the E-OBS gridded dataset[3] which consists of time series of local daily temperature across Europe over the last 60 years. Our method extracts the changing cumulative distribution function over time and uses a simple mathematical deconstruction of how the difference between two observations from two different time periods can be assigned to the combination of natural statistical variability and/or the consequences of secular climate change. The change in temperature can be tracked at a temperature threshold, at a likelihood, or at a given return time, independently for each geographical location. Geographical correlations are thus an output of our method and reflect both climatic properties (local and synoptic), and spatial correlations inherent in the observation methodology. We find as an output many regionally consistent patterns of response of potential value in adaptation planning. For instance, in a band from Northern France to Denmark the hottest days in the summer temperature distribution have seen changes of at least 2°C over a 43 year period; over four times the global mean change over the same period. We discuss methods to quantify the robustness of these observed sensitivities and their statistical likelihood. This approach also quantifies the level of detail at which one might wish to see agreement between climate models and

  10. 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.

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

    PubMed

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

    2008-09-04

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

  12. On the influence of the local vibration on spectral and laser characteristics of F{sub 2}{sup -} colour centres in LiF crystals at low temperatures

    SciTech Connect

    Papashvili, A G; Smetanin, S N; Doroshenko, M E

    2015-12-31

    A study of spectral and laser properties of the LiF : F{sub 2}{sup -} crystal at low temperatures has revealed an electronic – vibrational interaction of electrons of the F{sub 2}{sup -} centre with the local vibration of the centre, which occurs against the background of coupling between electrons of F{sub 2}{sup -} centres and lattice phonons. The interaction of electrons with the local vibration manifests itself in spectra in the form of narrow lines superimposed on wide electron – phonon lines that are due to the electron – lattice interaction. An anomalous behaviour of spectral LiF : F{sub 2}{sup -} laser lines is also found at liquid nitrogen temperature upon selective excitation; this behaviour is explained by the difference in the probabilities of the lattice and local interactions. (active media)

  13. Polarization properties of localized structures in VCSELs

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  14. Survival and failure outcomes in locally advanced esthesioneuroblastoma: a single centre experience of 15 patients.

    PubMed

    Kumar, Ritesh; Ghoshal, Sushmita; Khosla, Divya; Bharti, Shreekant; Das, Ashim; Kumar, Narendra; Kapoor, Rakesh; Sharma, Suresh Chander

    2013-05-01

    Esthesioneuroblastoma (ENB) constitutes 3 % of all malignant intranasal tumors. As the tumor is very rare, the number of patients of ENB treated in individual departments is small. We present our institute's experience in combined modality management of 15 successive patients of ENB treated from 2006 to 2010. Clinical characteristics and treatment modality in form of surgery, radiotherapy and chemotherapy were noted. Kadish stage C was the most common stage (12 patients) followed by stage B (3 patients). Fourteen patients underwent primary surgery, of which nine had total excision and five had subtotal excision. One patient was treated with combination of chemotherapy (CT) and radiotherapy (RT). Median RT dose delivered was 54 Gy. Twelve patients received CT with cisplatin and etoposide. Overall, eight patients had complete response, five had partial response, while one had static disease and progressive disease each. Two patients had distant metastases. Four-year loco-regional control (LRC) was 25 % and 4-year overall survival (OS) was 45 %. Most common presentation in our series was locally advanced tumors. Most of these patients require adjuvant RT, which helps in significant LRC. Systemic CT benefits in inoperable, advanced and high risk tumors. Risk-adapted and multimodality approach is the need of hour to achieve good control rates while minimizing treatment related toxicity.

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

    PubMed

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

    2011-10-16

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

  16. 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...

  17. 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

  18. 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.

  19. Structure and binding efficiency relations of QB site inhibitors of photosynthetic reaction centres.

    PubMed

    Husu, Ivan; Magyar, Melinda; Szabó, Tibor; Fiser, Béla; Gómez-Bengoa, Enrique; Nagy, László

    2015-04-01

    Many herbicides employed in agriculture and also some antibiotics bind to a specific site of the reaction centre protein (RC) blocking the photosynthetic electron transport. Crystal structures showed that all these compounds bind at the secondary ubiquinone (QB) site albeit to slightly different places. Different herbicide molecules have different binding affinities (evaluated as inhibition constants, KI, and binding enthalpy values, ΔHbind). The action of inhibitors depends on the following parameters: (i) herbicide molecular structure; (ii) interactions between herbicide and quinone binding site; (iii) protein environment. In our investigations KI and ΔHbind were determined for several inhibitors. Bound herbicide structures were optimized and their intramolecular charge distributions were calculated. Experimental and calculated data were compared to those available from databank crystal structures. We can state that the herbicide inhibition efficiency depends on steric and electronic, i.e. geometry of binding with the protein and molecular charge distribution, respectively. Apolar bulky groups on N-7 atom of the inhibitor molecule (like t-buthyl in terbutryn) are preferable for establishing stronger interactions with QB site, while such substituents are not recommended on N-8. The N-4,7,8 nitrogen atoms maintain a larger electron density so that more effective H-bonds are formed between the inhibitor and the surrounding amino acids of the protein.

  20. Drifting localized structures in doubly diffusive convection

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

    We use numerical continuation to compute a multiplicity of spatially localized states in doubly diffusive convection in a vertical slot driven by imposed horizontal temperature and concentration differences. The calculations focus on the so-called opposing case, in which the resulting gradients are in balance. No-slip boundary conditions are used at the sides and periodic boundary conditions with large spatial period are used in the vertical direction. This system exhibits homoclinic snaking of stationary spatially localized structures with point symmetry. In this talk we demonstrate the existence, near threshold, of drifting pulses of spatially localized convection that appear when mixed concentration boundary conditions are used, and use homotopic continuation to identify similar states in the case of fixed concentration boundary conditions. We show that these states persist to large values of the Grasshof number and provide a detailed study of their properties.

  1. Automatic Tool for Local Assembly Structures

    SciTech Connect

    2016-10-11

    Whole community shotgun sequencing of total DNA (i.e. metagenomics) and total RNA (i.e. metatranscriptomics) has provided a wealth of information in the microbial community structure, predicted functions, metabolic networks, and is even able to reconstruct complete genomes directly. Here we present ATLAS (Automatic Tool for Local Assembly Structures) a comprehensive pipeline for assembly, annotation, genomic binning of metagenomic and metatranscriptomic data with an integrated framework for Multi-Omics. This will provide an open source tool for the Multi-Omic community at large.

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

    NASA Astrophysics Data System (ADS)

    Korger, Edith; Schlindwein, Vera

    2014-05-01

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

  3. Frequency based localization of structural discrepancies

    NASA Technical Reports Server (NTRS)

    Shepard, G. D.; Milani, J.

    1988-01-01

    The intent of modal analysis is to develop a reliable model of a structure by working with the analytical and experimental modal properties of frequency, damping and mode shape. In addition to identifying these modal properties, it would be desirable to determine spatially which parts of the structure are modelled poorly or well. It is shown how the pattern of discrepancies in the analytical and experimental test values for the pole and the driving point zero frequencies of a structure can be linked to discrepancies in the mass or stiffness of the structural elements. The success of the procedure depends on the numerical conditioning of a modal reference matrix. Strategies to insure adequate numerical conditioning require a formulation which avoids geometric and energy storage symmetries of the structure, and ignores structural elements which contribute negligibly small potential or kinetic energy to the excited modes. Physical insight into the numerical conditioning problem is provided by a numerical example and by localization of a mass discrepancy in a real structure based on lab tests.

  4. The ionized gas at the centre of IC 10: a possible localized chemical pollution by Wolf-Rayet stars

    NASA Astrophysics Data System (ADS)

    López-Sánchez, Á. R.; Mesa-Delgado, A.; López-Martín, L.; Esteban, C.

    2011-03-01

    We present results from integral field spectroscopy with the Potsdam Multi-Aperture Spectrograph at the 3.5-m telescope at Calar Alto Observatory of the intense star-forming region [HL90] 111 at the centre of the starburst galaxy IC 10. We have obtained maps with a spatial sampling of 1 × 1 arcsec2= 3.9× 3.9 pc2 of different emission lines and analysed the extinction, physical conditions, nature of the ionization and chemical abundances of the ionized gas, as well determined locally the age of the most recent star formation event. By defining several apertures, we study the main integrated properties of some regions within [HL90] 111. Two contiguous spaxels show an unambiguous detection of the broad He IIλ4686 emission line, this feature seems to be produced by a single late-type WN star. We also report a probable N and He enrichment in the precise spaxels where the Wolf-Rayet (WR) features are detected. The enrichment pattern is roughly consistent with that expected for the pollution of the ejecta of a single or a very small number of WR stars. Furthermore, this chemical pollution is very localized (˜2 arcsec ˜7.8 pc) and it should be difficult to detect in star-forming galaxies beyond the Local Volume. We also discuss the use of the most common empirical calibrations to estimate the oxygen abundances of the ionized gas in nearby galaxies from 2D spectroscopic data. The ionization degree of the gas plays an important role when applying these empirical methods, as they tend to give lower oxygen abundances with increasing ionization degree. Based on observations collected at the Centro Astrónomico Hispano Alemán (CAHA) at Calar Alto, operated jointly by the Max-Plank Institut für Astronomie and the Instituto de Astrofísica de Andalucía (CSIC).Visiting Astronomer at the Instituto de Astrofísica de Canarias.

  5. The Structure of the Local Hot Bubble

    NASA Astrophysics Data System (ADS)

    Liu, W.; Chiao, M.; Collier, M. R.; Cravens, T.; Galeazzi, M.; Koutroumpa, D.; Kuntz, K. D.; Lallement, R.; Lepri, S. T.; McCammon, D.; Morgan, K.; Porter, F. S.; Snowden, S. L.; Thomas, N. E.; Uprety, Y.; Ursino, E.; Walsh, B. M.

    2017-01-01

    Diffuse X-rays from the Local Galaxy (DXL) is a sounding rocket mission designed to quantify and characterize the contribution of Solar Wind Charge eXchange (SWCX) to the Diffuse X-ray Background and study the properties of the Local Hot Bubble (LHB). Based on the results from the DXL mission, we quantified and removed the contribution of SWCX to the diffuse X-ray background measured by the ROSAT All Sky Survey. The “cleaned” maps were used to investigate the physical properties of the LHB. Assuming thermal ionization equilibrium, we measured a highly uniform temperature distributed around kT = 0.097 keV ± 0.013 keV (FWHM) ± 0.006 keV (systematic). We also generated a thermal emission measure map and used it to characterize the three-dimensional (3D) structure of the LHB, which we found to be in good agreement with the structure of the local cavity measured from dust and gas.

  6. 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.

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

    SciTech Connect

    Shtern, A. I.

    2014-04-30

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

  8. 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

  9. Applied Research Centres at South African Universities. The Relationship between 'Base' Internal Structures and Network 'Superstructures'

    ERIC Educational Resources Information Center

    Cooper, David

    2005-01-01

    This article considers the way in which applied research centres and units at South African higher education institutions enhance their networks with industry, government and community organizations. The findings from 12 case studies of research groupings at higher education institutions in Cape Town support the author's argument for a more…

  10. The categorical structure of knowledge for famous people (and a novel application of Centre-Surround theory).

    PubMed

    Stone, Anna; Valentine, Tim

    2007-09-01

    Knowledge of familiar people is essential to guide social interaction, yet there is uncertainty about whether semantic knowledge for people is stored in a categorical structure as for objects. Four priming experiments using hard-to-perceive primes investigated whether occupation forms a category connecting famous persons in semantic memory. Primes were famous faces exposed for 17ms with masking, resulting in severely restricted awareness and thus precluding expectancy-based priming effects. Targets were consciously perceptible famous faces (Experiments 1-3), famous names (Experiment 3), or occupations (Experiment 4) representing either the same or different occupation to the prime. Significant priming demonstrated the operation of automatic processes, including spreading activation, among persons sharing a common occupation; this supports the categorical view. The direction of priming (faster/slower responses to same-occupation than different-occupation targets) was dependent on prime-target stimulus onset asynchrony (Experiments 1-3) and type of target (Experiment 4). This pattern of results is attributed to the Centre-Surround mechanism proposed by Carr and Dagenbach [Carr, T. H., & Dagenbach, D. (1990). Semantic priming and repetition priming from masked words: evidence for a centre-surround attentional mechanism in perceptual recognition. Journal of Experimental Psychology: Learning, Memory and Cognition, 16, 341-350]. These results support (a) the categorical structure of semantic knowledge for famous people and (b) the application of the Centre-Surround mechanism to the domain of person recognition.

  11. 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

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

    PubMed

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

    2013-09-20

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

  13. 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.

  14. High levels of diversity and population structure in the potato late blight pathogen at the Mexico centre of origin.

    PubMed

    Wang, Jianan; Fernández-Pavía, Sylvia P; Larsen, Meredith M; Garay-Serrano, Edith; Gregorio-Cipriano, Rosario; Rodríguez-Alvarado, Gerardo; Grünwald, Niklaus J; Goss, Erica M

    2017-02-01

    Globally destructive crop pathogens often emerge by migrating out of their native ranges. These pathogens are often diverse at their centre of origin and may exhibit adaptive variation in the invaded range via multiple introductions from different source populations. However, source populations are generally unidentified or poorly studied compared to invasive populations. Phytophthora infestans, the causal agent of late blight, is one of the most costly pathogens of potato and tomato worldwide. Mexico is the centre of origin and diversity of P. infestans and migration events out of Mexico have enormously impacted disease dynamics in North America and Europe. The debate over the origin of the pathogen, and population studies of P. infestans in Mexico, has focused on the Toluca Valley, whereas neighbouring regions have been little studied. We examined the population structure of P. infestans across central Mexico, including samples from Michoacán, Tlaxcala and Toluca. We found high levels of diversity consistent with sexual reproduction in Michoacán and Tlaxcala and population subdivision that was strongly associated with geographic region. We determined that population structure in central Mexico has contributed to diversity in introduced populations based on relatedness of U.S. clonal lineages to Mexican isolates from different regions. Our results suggest that P. infestans exists as a metapopulation in central Mexico, and this population structure could be contributing to the repeated re-emergence of P. infestans in the United States and elsewhere.

  15. Investigation of fine-structure dips in fission-fragment mass distribution: An asymmetric two centre shell model approach

    NASA Astrophysics Data System (ADS)

    Malik, Sham S.

    2017-04-01

    The fission fragment mass distribution followed by neutron emission is studied for the 208Pb (18O , f) reaction using the asymmetric two centre shell model. The measured mass distribution spectrum reveals new kind of systematics on shell structure and leads to an improved understanding of structure effects in nuclear fission. A detailed investigation of shell effects both in potential and cranking mass parameter has been carried out for explaining the observed fine structure dips (i.e., less probable distributions) corresponding to shell closure (Z = 50 and/or N = 82) of fission fragments and their complementary partners. The available energy states for the decay process are obtained by solving the Schrödinger equation and found that first-five eigenstates are sufficient in reproducing the observed mass distribution spectrum. An outcome of the asymmetric two centre shell model also completely favours the observed claim that ;the total number of emitted neutrons between correlated pairs of fission fragments should not exceed 6;. A complete observed spectrum is obtained by adding the mass distribution yields of all 6-neutron emission channels. This suggests a possible importance of extending these calculations to get new insight into an understanding of the dynamical behaviour of fragment formation in the fission process.

  16. 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.

  17. Rodlike localized structure in isotropic pattern-forming systems.

    PubMed

    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.

  18. Geometry motivated alternative view on local protein backbone structures.

    PubMed

    Zacharias, Jan; Knapp, Ernst Walter

    2013-11-01

    We present an alternative to the classical Ramachandran plot (R-plot) to display local protein backbone structure. Instead of the (φ, ψ)-backbone angles relating to the chemical architecture of polypeptides generic helical parameters are used. These are the rotation or twist angle ϑ and the helical rise parameter d. Plots with these parameters provide a different view on the nature of local protein backbone structures. It allows to display the local structures in polar (d, ϑ)-coordinates, which is not possible for an R-plot, where structural regimes connected by periodicity appear disconnected. But there are other advantages, like a clear discrimination of the handedness of a local structure, a larger spread of the different local structure domains--the latter can yield a better separation of different local secondary structure motives--and many more. Compared to the R-plot we are not aware of any major disadvantage to classify local polypeptide structures with the (d, ϑ)-plot, except that it requires some elementary computations. To facilitate usage of the new (d, ϑ)-plot for protein structures we provide a web application (http://agknapp.chemie.fu-berlin.de/secsass), which shows the (d, ϑ)-plot side-by-side with the R-plot.

  19. 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.

  20. Population structure with localized haplotype clusters.

    PubMed

    Browning, Sharon R; Weir, Bruce S

    2010-08-01

    We propose a multilocus version of F(ST) and a measure of haplotype diversity using localized haplotype clusters. Specifically, we use haplotype clusters identified with BEAGLE, which is a program implementing a hidden Markov model for localized haplotype clustering and performing several functions including inference of haplotype phase. We apply this methodology to HapMap phase 3 data. With this haplotype-cluster approach, African populations have highest diversity and lowest divergence from the ancestral population, East Asian populations have lowest diversity and highest divergence, and other populations (European, Indian, and Mexican) have intermediate levels of diversity and divergence. These relationships accord with expectation based on other studies and accepted models of human history. In contrast, the population-specific F(ST) estimates obtained directly from single-nucleotide polymorphisms (SNPs) do not reflect such expected relationships. We show that ascertainment bias of SNPs has less impact on the proposed haplotype-cluster-based F(ST) than on the SNP-based version, which provides a potential explanation for these results. Thus, these new measures of F(ST) and haplotype-cluster diversity provide an important new tool for population genetic analysis of high-density SNP data.

  1. 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.

  2. Local structural study of doped-ceria by EXAFS spectroscopy

    NASA Astrophysics Data System (ADS)

    Shirbhate, S. C.; Yadav, A. K.; Acharya, S. A.; Sagdeo, A. P.; Jha, S. N.

    2016-05-01

    In the present work, Structural and Local structural study of Sm, Gd doped and Sm-Gd co-doped ceria system has been studied by Extended X-ray Absorption Fine Structure Spectroscopy (EXAFS). These ceria based systems are synthesized by hydrothermal synthesis route. Fluorite structure is confirmed by X-ray diffraction (XRD) and data is well fitted using Rietveld refinement by Full-Prof suite. Local structural changes in terms of coordination with surrounding, inter atomic distances and Debye Waller factor of nearest neighbor and next nearest neighbor has been discussed.

  3. Band structures and localization properties of aperiodic layered phononic crystals

    NASA Astrophysics Data System (ADS)

    Yan, Zhi-Zhong; Zhang, Chuanzeng

    2012-03-01

    The band structures and localization properties of in-plane elastic waves with coupling of longitudinal and transverse modes oblique propagating in aperiodic phononic crystals based on Thue-Morse and Rudin-Shapiro sequences are studied. Using transfer matrix method, the concept of the localization factor is introduced and the correctness is testified through the Rytov dispersion relation. For comparison, the perfect periodic structure and the quasi-periodic Fibonacci system are also considered. In addition, the influences of the random disorder, local resonance, translational and/or mirror symmetries on the band structures of the aperiodic phononic crystals are analyzed in this paper.

  4. 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.

  5. Local Structure Around Te in Heavily Doped GaAs:Te using X-Ray Absorption Fine Structure

    SciTech Connect

    Pietnoczka, A.; Bacewicz, R.; Slupinski, T.; Antonowicz, J.; Wei, Su-Huai

    2012-04-01

    The annealing of heavily doped GaAs:Te can significantly change the free electron concentration in a reversible manner. These changes of electrical properties are accompanied by the structural changes of GaAs:Te solid solution. We used X-ray Absorption Fine Structure at K-edge of tellurium to determine local changes around Te atoms for different states of the GaAs:Te crystals caused by the annealing corresponding to different electron concentrations. The best EXAFS fit for the samples with high electron concentration was obtained for the substitutional Te{sub As} model with elongated Te-Ga bonds (as compared to the As-Ga distance). For the samples in the low concentration state the best fit was for the pairs of Te atoms forming a rhombohedral symmetry double-DX centre, with the proportional admixture of the substitutional tellurium.

  6. Local structural modeling for implementation of optimal active damping

    NASA Astrophysics Data System (ADS)

    Blaurock, Carl A.; Miller, David W.

    1993-09-01

    Local controllers are good candidates for active control of flexible structures. Local control generally consists of low order, frequency benign compensators using collocated hardware. Positive real compensators and plant transfer functions ensure that stability margins and performance robustness are high. The typical design consists of an experimentally chosen gain on a fixed form controller such as rate feedback. The resulting compensator performs some combination of damping (dissipating energy) and structural modification (changing the energy flow paths). Recent research into structural impedance matching has shown how to optimize dissipation based on the local behavior of the structure. This paper investigates the possibility of improving performance by influencing global energy flow, using local controllers designed using a global performance metric.

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

    PubMed

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

    2016-01-01

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

  8. Local Sparse Structure Denoising for Low-Light-Level Image.

    PubMed

    Han, Jing; Yue, Jiang; Zhang, Yi; Bai, Lianfa

    2015-12-01

    Sparse and redundant representations perform well in image denoising. However, sparsity-based methods fail to denoise low-light-level (LLL) images because of heavy and complex noise. They consider sparsity on image patches independently and tend to lose the texture structures. To suppress noises and maintain textures simultaneously, it is necessary to embed noise invariant features into the sparse decomposition process. We, therefore, used a local structure preserving sparse coding (LSPSc) formulation to explore the local sparse structures (both the sparsity and local structure) in image. It was found that, with the introduction of spatial local structure constraint into the general sparse coding algorithm, LSPSc could improve the robustness of sparse representation for patches in serious noise. We further used a kernel LSPSc (K-LSPSc) formulation, which extends LSPSc into the kernel space to weaken the influence of linear structure constraint in nonlinear data. Based on the robust LSPSc and K-LSPSc algorithms, we constructed a local sparse structure denoising (LSSD) model for LLL images, which was demonstrated to give high performance in the natural LLL images denoising, indicating that both the LSPSc- and K-LSPSc-based LSSD models have the stable property of noise inhibition and texture details preservation.

  9. Local structure preserving sparse coding for infrared target recognition

    PubMed Central

    Han, Jing; Yue, Jiang; Zhang, Yi; Bai, Lianfa

    2017-01-01

    Sparse coding performs well in image classification. However, robust target recognition requires a lot of comprehensive template images and the sparse learning process is complex. We incorporate sparsity into a template matching concept to construct a local sparse structure matching (LSSM) model for general infrared target recognition. A local structure preserving sparse coding (LSPSc) formulation is proposed to simultaneously preserve the local sparse and structural information of objects. By adding a spatial local structure constraint into the classical sparse coding algorithm, LSPSc can improve the stability of sparse representation for targets and inhibit background interference in infrared images. Furthermore, a kernel LSPSc (K-LSPSc) formulation is proposed, which extends LSPSc to the kernel space to weaken the influence of the linear structure constraint in nonlinear natural data. Because of the anti-interference and fault-tolerant capabilities, both LSPSc- and K-LSPSc-based LSSM can implement target identification based on a simple template set, which just needs several images containing enough local sparse structures to learn a sufficient sparse structure dictionary of a target class. Specifically, this LSSM approach has stable performance in the target detection with scene, shape and occlusions variations. High performance is demonstrated on several datasets, indicating robust infrared target recognition in diverse environments and imaging conditions. PMID:28323824

  10. Aluminum alloy material structure impact localization by using FBG sensors

    NASA Astrophysics Data System (ADS)

    Zhu, Xiubin

    2014-12-01

    The aluminum alloy structure impact localization system by using fiber Bragg grating (FBG) sensors and impact localization algorithm was investigated. A four-FBG sensing network was established. And the power intensity demodulation method was initialized employing the narrow-band tunable laser. The wavelet transform was used to weaken the impact signal noise. And the impact signal time difference was extracted to build the time difference localization algorithm. At last, a fiber Bragg grating impact localization system was established and experimentally verified. The experimental results showed that in the aluminum alloy plate with the 500 mm*500 mm*2 mm test area, the maximum and average impact abscissa localization errors were 11 mm and 6.25 mm, and the maximum and average impact ordinate localization errors were 9 mm and 4.25 mm, respectively. The fiber Bragg grating sensors and demodulation system are feasible to realize the aviation aluminum alloy material structure impact localization. The research results provide a reliable method for the aluminum alloy material structure impact localization.

  11. Two-dimensional localized structures in harmonically forced oscillatory systems

    NASA Astrophysics Data System (ADS)

    Ma, Y.-P.; Knobloch, E.

    2016-12-01

    Two-dimensional spatially localized structures in the complex Ginzburg-Landau equation with 1:1 resonance are studied near the simultaneous presence of a steady front between two spatially homogeneous equilibria and a supercritical Turing bifurcation on one of them. The bifurcation structures of steady circular fronts and localized target patterns are computed in the Turing-stable and Turing-unstable regimes. In particular, localized target patterns grow along the solution branch via ring insertion at the core in a process reminiscent of defect-mediated snaking in one spatial dimension. Stability of axisymmetric solutions on these branches with respect to axisymmetric and nonaxisymmetric perturbations is determined, and parameter regimes with stable axisymmetric oscillons are identified. Direct numerical simulations reveal novel depinning dynamics of localized target patterns in the radial direction, and of circular and planar localized hexagonal patterns in the fully two-dimensional system.

  12. Local structures around the substituted elements in mixed layered oxides

    PubMed Central

    Akama, Shota; Kobayashi, Wataru; Amaha, Kaoru; Niwa, Hideharu; Nitani, Hiroaki; Moritomo, Yutaka

    2017-01-01

    The chemical substitution of a transition metal (M) is an effective method to improve the functionality of a material, such as its electrochemical, magnetic, and dielectric properties. The substitution, however, causes local lattice distortion because the difference in the ionic radius (r) modifies the local interatomic distances. Here, we systematically investigated the local structures in the pure (x = 0.0) and mixed (x = 0.05 or 0.1) layered oxides, Na(M1−xM′x)O2 (M and M′ are the majority and minority transition metals, respectively), by means of extended X-ray absorption fine structure (EXAFS) analysis. We found that the local interatomic distance (dM-O) around the minority element approaches that around the majority element to reduces the local lattice distortion. We further found that the valence of the minority Mn changes so that its ionic radius approaches that of the majority M. PMID:28252008

  13. Local structures around the substituted elements in mixed layered oxides

    NASA Astrophysics Data System (ADS)

    Akama, Shota; Kobayashi, Wataru; Amaha, Kaoru; Niwa, Hideharu; Nitani, Hiroaki; Moritomo, Yutaka

    2017-03-01

    The chemical substitution of a transition metal (M) is an effective method to improve the functionality of a material, such as its electrochemical, magnetic, and dielectric properties. The substitution, however, causes local lattice distortion because the difference in the ionic radius (r) modifies the local interatomic distances. Here, we systematically investigated the local structures in the pure (x = 0.0) and mixed (x = 0.05 or 0.1) layered oxides, Na(M1‑xM‧x)O2 (M and M‧ are the majority and minority transition metals, respectively), by means of extended X-ray absorption fine structure (EXAFS) analysis. We found that the local interatomic distance (dM-O) around the minority element approaches that around the majority element to reduces the local lattice distortion. We further found that the valence of the minority Mn changes so that its ionic radius approaches that of the majority M.

  14. Local Factors Determine Plant Community Structure on Closely Neighbored Islands

    PubMed Central

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

    2011-01-01

    Despite the recent popularity of the metacommunity concept, ecologists have not evaluated the applicability of different metacommunity frameworks to insular organisms. We surveyed 50 closely spaced islands in the Thousand-Island Lake of China to examine the role of local (environmental) and regional (dispersal) factors in structuring woody plant assemblages (tree and shrub species) on these islands. By partitioning the variation in plant community structure into local and regional causes, we showed that local environmental conditions, specifically island morphometric characteristics, accounted for the majority of the variation in plant community structure among the studied islands. Spatial variables, representing the potential importance of species dispersal, explained little variation. We conclude that one metacommunity framework–species sorting–best characterizes these plant communities. This result reinforces the idea that the traditional approach of emphasizing the local perspective when studying ecological communities continues to hold its value. PMID:21572960

  15. 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.

  16. Fully automated localization of multiple pelvic bone structures on MRI.

    PubMed

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

    2014-01-01

    In this paper, we present a fully automated localization method for multiple pelvic bone structures on magnetic resonance images (MRI). Pelvic bone structures are currently identified manually on MRI to identify reference points for measurement and evaluation of pelvic organ prolapse (POP). Given that this is a time-consuming and subjective procedure, there is a need to localize pelvic bone structures without any user interaction. However, bone structures are not easily differentiable from soft tissue on MRI as their pixel intensities tend to be very similar. In this research, we present a model that automatically identifies the bounding boxes of the bone structures on MRI using support vector machines (SVM) based classification and non-linear regression model that captures global and local information. Based on the relative locations of pelvic bones and organs, and local information such as texture features, the model identifies the location of the pelvic bone structures by establishing the association between their locations. Results show that the proposed method is able to locate the bone structures of interest accurately. The pubic bone, sacral promontory, and coccyx were correctly detected (DSI > 0.75) in 92%, 90%, and 88% of the testing images. This research aims to enable accurate, consistent and fully automated identification of pelvic bone structures on MRI to facilitate and improve the diagnosis of female pelvic organ prolapse.

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

    PubMed

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

    2012-08-31

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

  18. Vortex emission accompanies the advection of optical localized structures.

    PubMed

    Haudin, F; Rojas, R G; Bortolozzo, U; Clerc, M G; Residori, S

    2011-02-11

    We show that the advection of optical localized structures is accompanied by the emission of vortices, with phase singularities appearing in the wake of the drifting structure. Localized structures are obtained in a light-valve experiment and made to drift by a mirror tilt in the feedback loop. Pairs of oppositely charged vortices are detected for small drifts, whereas for large drifts a vortex array develops. Observations are supported by numerical simulations and linear stability analysis of the system equations and are expected to be generic for a large class of translated optical patterns.

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

    SciTech Connect

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

    2014-10-20

    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.

  20. 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…

  1. Gamma-tubulin is required for the structure and function of the microtubule organizing centre in Drosophila neuroblasts.

    PubMed Central

    Sunkel, C E; Gomes, R; Sampaio, P; Perdigão, J; González, C

    1995-01-01

    We report that in Drosophila, gamma-tubulin is required for the structure as well as the function of microtubule organizing centres (MTOCs). This conclusion is based on the identification and phenotypic characterization of a mutant allele of the gamma-tubulin gene located at region 23C of the polytene chromosome map. This mutation, which we have called gamma-tub23CPl, is caused by the insertion of a P-element within the 5' untranslated leader of the gamma-tubulin transcript. Northern and Western analysis show that gamma-tub23CPl is either a null or a very severe hypomorph as no gamma-tubulin mRNA or protein can be detected in mutant individuals. Visualization of DNA, MTOCs and microtubules by confocal laser scanning microscopy of cells from individuals homozygous for gamma-tub23CPl reveals a series of phenotypic abnormalities. Some of these are similar to those observed after disruption of gamma-tubulin function in other organisms, including mitotic arrest and a dramatic decrease in the number of microtubules, but, in addition, we have observed that mutation in this gene also results in highly abnormal MTOCs which show a variety of shapes and sizes which we never observed in wild type cells. These results show that gamma-tubulin is required for both structural and functional roles in the MTOCs. Images PMID:7828594

  2. 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.

  3. 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

  4. Strain localization and percolation of stable structure in amorphous solids.

    PubMed

    Shi, Yunfeng; Falk, Michael L

    2005-08-26

    Spontaneous strain localization occurs during mechanical tests of a model amorphous solid simulated using molecular dynamics. The degree of localization depends upon the extent of structural relaxation prior to mechanical testing. In the most rapidly quenched samples higher strain rates lead to increased localization, while the more gradually quenched samples exhibit the opposite strain rate dependence. This transition coincides with the k-core percolation of atoms with quasi-crystal-like short range order. The authors infer the existence of a related microstructural length scale.

  5. 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

  6. Local function conservation in sequence and structure space.

    PubMed

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

    2008-07-04

    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).

  7. Stabilizing hierarchical compensation for locally controlled large flexible structures

    NASA Technical Reports Server (NTRS)

    Das, B.; Balas, M.

    1989-01-01

    A two-level hierarchical control strategy is proposed for large flexible space structures. The lower level consists of a set of local controllers. The higher level is a stabilizing compensator to account for any instabilities caused by controller-structure interaction with unmodeled dynamics. The advantage of this hierarchical strategy is that the lower level can be designed to meet the performance requirements, and the higher level can be designed independently to produce overall stability.

  8. Thyroïdectomies pratiquées sous anesthésie locale au Centre Hospitalier Universitaire d'Antananarivo

    PubMed Central

    Razafindrakoto, Rex Mario; Razafindranaivo, Mananjara Nandrianina; Valisoa, Herimalalaniaina Angelo; Schammirah, Mahamad Rojovolaarivony; Randriamboavonjy, Rado

    2015-01-01

    Menée le plus souvent sous anesthésie générale, la chirurgie thyroïdienne peut aussi être pratiquée sous anesthésie régionale ou sous anesthésie locale. Notre objectif a été de rapporter l'expérience du Centre Hospitalier Universitaire d'Antananarivo sur l'anesthésie locale dans les thyroïdectomies. La drogue employée dans notre protocole anesthésique a été le fentanyl, administré en intraveineuse directe, associé à une infiltration sous-cutanée de lidocaïne suivant la ligne d'incision. Le/la patient(e) n'a pas été intubé(e), l'oxygène étant délivré au niveau des cavités nasales. Ont été étudiés le type de chirurgie thyroïdienne, la durée de l'intervention, la satisfaction des patient(e)s vis-à-vis de la qualité de l'anesthésie, et le coût de l'intervention. Sur 567 thyroïdectomies effectuées, 51,68% (n= 293) ont été des lobo-isthmectomies gauches, 44,44% (n= 252) des lobo-isthmectomies droites, 2,82% (n= 16) des thyroïdectomies subtotales ou totales, 1,06% (n= six) des totalisations pour carcinomes thyroïdiens. La durée des interventions a varié de 30 à 90 minutes. Un total de 83,95% (n= 476) des patient(e)s a été très satisfait de la qualité de l'anesthésie et 15,87% autres (n= 90) satisfait. Les suites opératoires ont été bonnes dans la majorité des cas. Le coût d'une thyroïdectomie a été évalué à 100- 150 dollars américains. L'anesthésie locale utilisée dans les thyroïdectomies effectuées au Centre Hospitalier Universitaire d'Antananarivo est simple, rapide, d'un coût moyen, et permet d'alarmer précocement le chirurgien en cas de lésion d'un nerf laryngé inférieur. PMID:26587128

  9. 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.

  10. 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…

  11. 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.

  12. Wycheproof Education Centre.

    ERIC Educational Resources Information Center

    Sweetnam and Godfrey, Melbourne (Australia).

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

  13. OPEN PROBLEM: Spatially localized structures in dissipative systems: open problems

    NASA Astrophysics Data System (ADS)

    Knobloch, E.

    2008-04-01

    Stationary spatially localized structures, sometimes called dissipative solitons, arise in many interesting and important applications, including buckling of slender structures under compression, nonlinear optics, fluid flow, surface catalysis, neurobiology and many more. The recent resurgence in interest in these structures has led to significant advances in our understanding of the origin and properties of these states, and these in turn suggest new questions, both general and system-specific. This paper surveys these results focusing on open problems, both mathematical and computational, as well as on new applications.

  14. 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

  15. 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.

  16. Local magnetic structure determination using polarized neutron holography

    NASA Astrophysics Data System (ADS)

    Szakál, Alex; Markó, Márton; Cser, László

    2015-05-01

    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.

  17. 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

  18. 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.

  19. Functional implications of local DNA structures in regulatory motifs.

    PubMed

    Xiang, Qian

    2013-01-01

    The three-dimensional structure of DNA has been proposed to be a major determinant for functional transcription factors (TFs) and DNA interaction. Here, we use hydroxyl radical cleavage pattern as a measure of local DNA structure. We compared the conservation between DNA sequence and structure in terms of information content and attempted to assess the functional implications of DNA structures in regulatory motifs. We used statistical methods to evaluate the structural divergence of substituting a single position within a binding site and applied them to a collection of putative regulatory motifs. The following are our major observations: (i) we observed more information in structural alignment than in the corresponding sequence alignment for most of the transcriptional factors; (ii) for each TF, majority of positions have more information in the structural alignment as compared to the sequence alignment; (iii) we further defined a DNA structural divergence score (SD score) for each wild-type and mutant pair that is distinguished by single-base mutation. The SD score for benign mutations is significantly lower than that of switch mutations. This indicates structural conservation is also important for TFBS to be functional and DNA structures will provide previously unappreciated information for TF to realize the binding specificity.

  20. 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.

  1. Fluctuations and local ice structure in model supercooled water.

    PubMed

    Overduin, S D; Patey, G N

    2015-09-07

    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.

  2. Recognition of Local DNA Structures by p53 Protein.

    PubMed

    Brázda, Václav; Coufal, Jan

    2017-02-10

    p53 plays critical roles in regulating cell cycle, apoptosis, senescence and metabolism and is commonly mutated in human cancer. These roles are achieved by interaction with other proteins, but particularly by interaction with DNA. As a transcription factor, p53 is well known to bind consensus target sequences in linear B-DNA. Recent findings indicate that p53 binds with higher affinity to target sequences that form cruciform DNA structure. Moreover, p53 binds very tightly to non-B DNA structures and local DNA structures are increasingly recognized to influence the activity of wild-type and mutant p53. Apart from cruciform structures, p53 binds to quadruplex DNA, triplex DNA, DNA loops, bulged DNA and hemicatenane DNA. In this review, we describe local DNA structures and summarize information about interactions of p53 with these structural DNA motifs. These recent data provide important insights into the complexity of the p53 pathway and the functional consequences of wild-type and mutant p53 activation in normal and tumor cells.

  3. Recognition of Local DNA Structures by p53 Protein

    PubMed Central

    Brázda, Václav; Coufal, Jan

    2017-01-01

    p53 plays critical roles in regulating cell cycle, apoptosis, senescence and metabolism and is commonly mutated in human cancer. These roles are achieved by interaction with other proteins, but particularly by interaction with DNA. As a transcription factor, p53 is well known to bind consensus target sequences in linear B-DNA. Recent findings indicate that p53 binds with higher affinity to target sequences that form cruciform DNA structure. Moreover, p53 binds very tightly to non-B DNA structures and local DNA structures are increasingly recognized to influence the activity of wild-type and mutant p53. Apart from cruciform structures, p53 binds to quadruplex DNA, triplex DNA, DNA loops, bulged DNA and hemicatenane DNA. In this review, we describe local DNA structures and summarize information about interactions of p53 with these structural DNA motifs. These recent data provide important insights into the complexity of the p53 pathway and the functional consequences of wild-type and mutant p53 activation in normal and tumor cells. PMID:28208646

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

    PubMed

    Kim, Keonwook; Kim, Youngwoong

    2015-02-06

    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.

  5. 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

  6. 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

  7. 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.

  8. Electronic structure and localized states in a model amorphous silicon

    NASA Astrophysics Data System (ADS)

    Allan, G.; Delerue, C.; Lannoo, M.

    1998-03-01

    The electronic structure of a model amorphous silicon (a-Si) represented by a supercell of 4096 silicon atoms [B.R. Djordjevic, M.F. Thorpe, and F. Wooten, Phys. Rev. B 52, 5685 (1995)] and of a model hydrogenated amorphous silicon (a-Si:H) that we have built from the a-Si model are calculated in the tight-binding approximation. The band edges near the gap are characterized by exponential tails of localized states induced mainly by the variations in bond angles. The spatial localization of the states is compared between a-Si and a-Si:H. Comparison with experiments suggests that the structural models give good descriptions of the amorphous materials.

  9. Alfvénic localized structures in partially ionized plasmas

    NASA Astrophysics Data System (ADS)

    Borhanian, Jafar; Rezaei, Arash

    2017-02-01

    The existence and dynamics of Alfvénic localized structures are investigated in partially ionized plasmas. We have employed the Hall magnetohydrodynamics model for partially ionized plasmas and shown that the evolution of a weakly nonlinear and weakly dispersive Alfvén wave is governed by a derivative nonlinear Schrödinger (DNLS) type equation. In the Hall effect domination limit, this equation reduces to a standard DNLS equation that possesses localized solutions in the form of solitons and rogue waves. The dependence of the profile of these structures on the Hall parameter is addressed. When the ohmic and ambipolar effects are small but finite in comparison to the Hall effect, the evolution equation takes the form of a perturbed DNLS equation. In this limit, the dynamics of envelope soliton solution is examined by means of the soliton perturbation method, the moment method, to be precise.

  10. The local spiral structure of the Milky Way.

    PubMed

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

    2016-09-01

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

  11. The local spiral structure of the Milky Way

    PubMed Central

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

    2016-01-01

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

  12. 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

  13. Localized structural frustration for evaluating the impact of sequence variants

    PubMed Central

    Kumar, Sushant; Clarke, Declan; Gerstein, Mark

    2016-01-01

    Population-scale sequencing is increasingly uncovering large numbers of rare single-nucleotide variants (SNVs) in coding regions of the genome. The rarity of these variants makes it challenging to evaluate their deleteriousness with conventional phenotype–genotype associations. Protein structures provide a way of addressing this challenge. Previous efforts have focused on globally quantifying the impact of SNVs on protein stability. However, local perturbations may severely impact protein functionality without strongly disrupting global stability (e.g. in relation to catalysis or allostery). Here, we describe a workflow in which localized frustration, quantifying unfavorable local interactions, is employed as a metric to investigate such effects. Using this workflow on the Protein Databank, we find that frustration produces many immediately intuitive results: for instance, disease-related SNVs create stronger changes in localized frustration than non-disease related variants, and rare SNVs tend to disrupt local interactions to a larger extent than common variants. Less obviously, we observe that somatic SNVs associated with oncogenes and tumor suppressor genes (TSGs) induce very different changes in frustration. In particular, those associated with TSGs change the frustration more in the core than the surface (by introducing loss-of-function events), whereas those associated with oncogenes manifest the opposite pattern, creating gain-of-function events. PMID:27915290

  14. Distal chromatin structure influences local nucleosome positions and gene expression.

    PubMed

    Jansen, An; van der Zande, Elisa; Meert, Wim; Fink, Gerald R; Verstrepen, Kevin J

    2012-05-01

    The positions of nucleosomes across the genome influence several cellular processes, including gene transcription. However, our understanding of the factors dictating where nucleosomes are located and how this affects gene regulation is still limited. Here, we perform an extensive in vivo study to investigate the influence of the neighboring chromatin structure on local nucleosome positioning and gene expression. Using truncated versions of the Saccharomyces cerevisiae URA3 gene, we show that nucleosome positions in the URA3 promoter are at least partly determined by the local DNA sequence, with so-called 'anti-nucleosomal elements' like poly(dA:dT) tracts being key determinants of nucleosome positions. In addition, we show that changes in the nucleosome positions in the URA3 promoter strongly affect the promoter activity. Most interestingly, in addition to demonstrating the effect of the local DNA sequence, our study provides novel in vivo evidence that nucleosome positions are also affected by the position of neighboring nucleosomes. Nucleosome structure may therefore be an important selective force for conservation of gene order on a chromosome, because relocating a gene to another genomic position (where the positions of neighboring nucleosomes are different from the original locus) can have dramatic consequences for the gene's nucleosome structure and thus its expression.

  15. Cosmic structure and dynamics of the local Universe

    NASA Astrophysics Data System (ADS)

    Kitaura, Francisco-Shu; Erdoǧdu, Pirin; Nuza, Sebastián. E.; Khalatyan, Arman; Angulo, Raul E.; Hoffman, Yehuda; Gottlöber, Stefan

    2012-11-01

    We present a cosmography analysis of the local Universe based on the recently released Two-Micron All-Sky Redshift Survey catalogue. Our method is based on a Bayesian Networks Machine Learning algorithm (the KIGEN-code) which self-consistently samples the initial density fluctuations compatible with the observed galaxy distribution and a structure formation model given by second-order Lagrangian perturbation theory (2LPT). From the initial conditions we obtain an ensemble of reconstructed density and peculiar velocity fields which characterize the local cosmic structure with high accuracy unveiling non-linear structures like filaments and voids in detail. Coherent redshift-space distortions are consistently corrected within 2LPT. From the ensemble of cross-correlations between the reconstructions and the galaxy field and the variance of the recovered density fields, we find that our method is extremely accurate up to k˜ 1 h Mpc-1 and still yields reliable results down to scales of about 3-4 h-1 Mpc. The motion of the Local Group we obtain within ˜80 h-1 Mpc (vLG = 522 ± 86 km s-1, lLG = 291° ± 16°, bLG = 34° ± 8°) is in good agreement with measurements derived from the cosmic microwave background and from direct observations of peculiar motions and is consistent with the predictions of ΛCDM.

  16. Structural damage localization using wavelet-based silhouette statistics

    NASA Astrophysics Data System (ADS)

    Jung, Uk; Koh, Bong-Hwan

    2009-04-01

    This paper introduces a new methodology for classifying and localizing structural damage in a truss structure. The application of wavelet analysis along with signal classification techniques in engineering problems allows us to discover novel characteristics that can be used for the diagnosis and classification of structural defects. This study exploits the data discriminating capability of silhouette statistics, which is eventually combined with the wavelet-based vertical energy threshold technique for the purpose of extracting damage-sensitive features and clustering signals of the same class. This threshold technique allows us to first obtain a suitable subset of the extracted or modified features of our data, i.e. good predictor sets should contain features that are strongly correlated to the characteristics of the data without considering the classification method used, although each of these features should be as uncorrelated with each other as possible. The silhouette statistics have been used to assess the quality of clustering by measuring how well an object is assigned to its corresponding cluster. We use this concept for the discriminant power function used in this paper. The simulation results of damage detection in a truss structure show that the approach proposed in this study can be successfully applied for locating both open- and breathing-type damage even in the presence of a considerable amount of process and measurement noise. Finally, a typical data mining tool such as classification and regression tree (CART) quantitatively evaluates the performance of the damage localization results in terms of the misclassification error.

  17. 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.

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Weingartner, Nicholas B.; Nussinov, Zohar

    2016-09-01

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

  20. Localization and structure of carbonaceous deposits on reforming catalysts

    SciTech Connect

    Espinat, D.; Freund, E.; Martino, G. ); Dexpert, H. , Orsay )

    1990-12-01

    The aging of alumina-supported Pt-containing reforming catalysts by coke deposition has previously been extensively investigated. In the present work, a large number of techniques including optical and electron microscopy have been used to determine both the localization and the structure of the so-called coke (carbonaceous deposits) formed during the normal operation of these catalysts. The coke is not uniformly deposited on the surface of the catalysts. Its structure is not uniform for a given catalyst, and depends on the operating condition (especially the H{sub 2}/hydrocarbon ratio) as well as the composition of the metallic phase (pure platinum or multimetallic alloy). The structure is always rather well organized (pregraphitic) even at the onset of coke deposition.

  1. Electronic-structure calculation for metals by local optimization

    NASA Astrophysics Data System (ADS)

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

    1989-03-01

    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 Schlüter. 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.

  2. 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.

  3. The local electronic structure of alpha-Li3N.

    PubMed

    Fister, T T; Seidler, G T; Shirley, E L; Vila, F D; Rehr, J J; Nagle, K P; Linehan, J C; Cross, J O

    2008-07-28

    New theoretical and experimental investigations of the occupied and unoccupied local electronic densities of states (DOS) are reported for alpha-Li(3)N. Band-structure and density-functional theory calculations confirm the absence of covalent bonding character. However, real-space full-multiple-scattering (RSFMS) calculations of the occupied local DOS find less extreme nominal valences than have previously been proposed. Nonresonant inelastic x-ray scattering, RSFMS calculations, and calculations based on the Bethe-Salpeter equation are used to characterize the unoccupied electronic final states local to both the Li and N sites. There is a good agreement between experiment and theory. Throughout the Li 1s near-edge region, both experiment and theory find strong similarities in the s-and p-type components of the unoccupied local final DOS projected onto an orbital angular momentum basis (l-DOS). An unexpected, significant correspondence exists between the near-edge spectra for the Li 1s and N 1s initial states. We argue that both spectra are sampling essentially the same final DOS due to the combination of long core-hole lifetimes, long photoelectron lifetimes, and the fact that orbital angular momentum is the same for all relevant initial states. Such considerations may be generally applicable for low atomic number compounds.

  4. 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

  5. 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.

  6. Correlation Between Local Structure and Boson Peak in Metallic Glasses

    NASA Astrophysics Data System (ADS)

    Ahmad, Azkar Saeed; Zhao, Xiangnan; Xu, Mingxiang; Zhang, Dongxian; Hu, Junwen; Fecht, Hans J.; Wang, Xiaodong; Cao, Qingping; Jiang, J. Z.

    2017-01-01

    We made a systematic study of the boson peak for six different Zr-based metallic glasses and found a universal correlation between average local atomic structure and boson peak. It is found that the boson peak can be decomposed into six characteristic vibratory modes, i.e., Debye's vibratory mode and five Einstein's vibratory modes. By using the Ioffe-Regel condition over all studied Zr-based metallic glasses, we reveal that atomic pair correlation function exactly maps on the low-temperature dynamics and the origin of the boson peak, which is the sum of vibrations of local density fluctuation domains in the glasses. In addition, it is found that the Debye's type oscillators are the major contributors to the low-temperature specific heat capacities. This study opens a new way of understanding the relationship of the physical properties with the atomic arrangements in glasses.

  7. Reversible Boolean networks. II. Phase transitions, oscillations, and local structures

    NASA Astrophysics Data System (ADS)

    Coppersmith, S. N.; Kadanoff, Leo P.; Zhang, Zhitong

    2001-09-01

    We continue our consideration of a class of models describing the reversible dynamics of N Boolean variables, each with K inputs. We investigate in detail the behavior of the Hamming distance as well as of the distribution of orbit lengths as N and K are varied. We present numerical evidence for a phase transition in the behavior of the Hamming distance at a critical value Kc≈1.62 and also an analytic theory that yields the exact bounds 1.5< Kc<2. We also discuss the large oscillations that we observe in the Hamming distance for K< Kc as a function of time as well as in the distribution of cycle lengths as a function of cycle length for moderate K both greater than and less than Kc. We propose that local structures, or subsets of spins whose dynamics are not fully coupled to the other spins in the system, play a crucial role in generating these oscillations. The simplest of these structures are linear chains, called linkages, and rings, called circuits. We discuss the properties of the linkages in some detail, and sketch the properties of circuits. We argue that the observed oscillation phenomena can be largely understood in terms of these local structures.

  8. Local structure in hard-sphere chain-molecule fluids

    NASA Astrophysics Data System (ADS)

    Wasti, Sambid; Taylor, Mark

    2012-04-01

    The conformation of a polymer chain in solvent is coupled to the local structure of the solvent environment. For hard-sphere systems, a monomeric solvent acts to compress a flexible hard-sphere-solute chain and, for a dense system, the local solvent structure is imprinted onto the chain. Here we use Monte Carlo simulation, including bond-rebridging moves, to study the size and conformation of a hard sphere chain in a hard-sphere solvent as a function of both solvent density and solvent diameter. We also study the structure of a hard-sphere-chain solute in a hard-sphere-chain solvent. In the case of a 5-mer chain in 5-mer solvent we show that the effects of solvent can be mapped to a set of two-body solvation potentials. Following our previous work on hard-sphere chains in monomeric solvent [1], we explore the application of these short chain potentials to the study of longer chain-molecule fluids. [4pt] [1] M.P. Taylor and S. Ichida, J. Polym. Sci. B: Polym. Phys. 45, 3319 (2007).

  9. Local structure in hard-sphere chain-molecule fluids

    NASA Astrophysics Data System (ADS)

    Wasti, Sambid; Taylor, Mark

    2011-10-01

    The conformation of a polymer chain in solvent is coupled to the local structure of the solvent environment. For hard-sphere systems, a monomeric solvent acts to compress a flexible hard-sphere-solute chain and, for a dense system, the local solvent structure is imprinted onto the chain. Here we use Monte Carlo simulation, including bond-rebridging moves, to study the size and conformation of a hard sphere chain in a hard-sphere solvent as a function of both solvent density and solvent diameter. We also study the structure of a hard-sphere-chain solute in a hard-sphere-chain solvent. In the case of a 5-mer chain in 5-mer solvent we show that the effects of solvent can be mapped to a set of two-body solvation potentials. Following our previous work on hard-sphere chains in monomeric solvent [1], we explore the application of these short chain potentials to the study of longer chain-molecule fluids. [4pt] [1] M.P. Taylor and S. Ichida, J. Polym. Sci. B: Polym. Phys. 45, 3319 (2007).

  10. Local pulmonary structure classification for computer-aided nodule detection

    NASA Astrophysics Data System (ADS)

    Bahlmann, Claus; Li, Xianlin; Okada, Kazunori

    2006-03-01

    We propose a new method of classifying the local structure types, such as nodules, vessels, and junctions, in thoracic CT scans. This classification is important in the context of computer aided detection (CAD) of lung nodules. The proposed method can be used as a post-process component of any lung CAD system. In such a scenario, the classification results provide an effective means of removing false positives caused by vessels and junctions thus improving overall performance. As main advantage, the proposed solution transforms the complex problem of classifying various 3D topological structures into much simpler 2D data clustering problem, to which more generic and flexible solutions are available in literature, and which is better suited for visualization. Given a nodule candidate, first, our solution robustly fits an anisotropic Gaussian to the data. The resulting Gaussian center and spread parameters are used to affine-normalize the data domain so as to warp the fitted anisotropic ellipsoid into a fixed-size isotropic sphere. We propose an automatic method to extract a 3D spherical manifold, containing the appropriate bounding surface of the target structure. Scale selection is performed by a data driven entropy minimization approach. The manifold is analyzed for high intensity clusters, corresponding to protruding structures. Techniques involve EMclustering with automatic mode number estimation, directional statistics, and hierarchical clustering with a modified Bhattacharyya distance. The estimated number of high intensity clusters explicitly determines the type of pulmonary structures: nodule (0), attached nodule (1), vessel (2), junction (>3). We show accurate classification results for selected examples in thoracic CT scans. This local procedure is more flexible and efficient than current state of the art and will help to improve the accuracy of general lung CAD systems.

  11. Local structure probes of nanoscale heterogeneity in crystalline materials.

    PubMed

    Conradson, S; Espinosa, F; Villella, P

    2001-03-01

    In the conventional model of condensed matter increasing numbers of defects break down the order and ultimately convert perfect periodic crystals into aperiodic glasses. Local structure probes of a variety of materials with non-stoichiometric compositions, multiple degenerate ordering modes, or other symmetry breaking factors identify multiple ordered arrangements of atoms that render the materials heterogeneous on the nanometer scale. While exerting apparently negligible effects on bulk properties, this heterogeneity or phase separation does influence correlated or collective properties such as magnetism and phase stability.

  12. 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

  13. Structure and chromosomal localization of the human thrombospondin gene.

    PubMed

    Wolf, F W; Eddy, R L; Shows, T B; Dixit, V M

    1990-04-01

    Thrombospondin (THBS1) is a large modular glycoprotein component of the extracellular matrix and contains a variety of distinct domains, including three repeating subunits (types I, II, and III) that share homology to an assortment of other proteins. Determination of THBS1 gene structure has revealed that the type I repeat modules are encoded by symmetrical exons and that the heparin-binding domain is encoded by a single exon. To further elucidate the higher level organization of THBS1, the gene was localized to the q11-qter region of chromosome 15.

  14. Investigation of nanogap localized field enhancement in gold plasmonic structures

    NASA Astrophysics Data System (ADS)

    Debu, Desalegn Tadesse; Bauman, Stephen; Saylor, Cameron; Novak, Eric; French, David; Herzog, Joseph

    2015-03-01

    Nanogaps between plasmonic structures allow confining the localized electric field with moreenhancements. Based on previously implemented two-step lithography process, we introducea nano-masking technique to fabricate nanostructrues and nanogaps for various geometrical patterns. This new method can fabricate gold nanostructures as well as nanogaps that are less than 10nm, below the limiting scale of lithography. Simulation from finite element method (FEM) shows strong gap dependence of optical properties and peak enhancement of these devices. The fabricated plasmonic nanostructure provides wide range of potential future application including highly sensitive optical antenna, surface enhanced Raman spectroscopy and biosensing.

  15. 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

  16. Local structure and structural signature underlying properties in metallic glasses and supercooled liquids

    NASA Astrophysics Data System (ADS)

    Ding, Jun

    Metallic glasses (MGs), discovered five decades ago as a newcomer in the family of glasses, are of current interest because of their unique structures and properties. There are also many fundamental materials science issues that remain unresolved for metallic glasses, as well as their predecessor above glass transition temperature, the supercooled liquids. In particular, it is a major challenge to characterize the local structure and unveil the structure-property relationship for these amorphous materials. This thesis presents a systematic study of the local structure of metallic glasses as well as supercooled liquids via classical and ab initio molecular dynamics simulations. Three typical MG models are chosen as representative candidate, Cu64 Zr36, Pd82Si18 and Mg65Cu 25Y10 systems, while the former is dominant with full icosahedra short-range order and the prism-type short-range order dominate for latter two. Furthermore, we move to unravel the underlying structural signature among several properties in metallic glasses. Firstly, the temperature dependence of specific heat and liquid fragility between Cu-Zr and Mg-Cu-Y (also Pd-Si) in supercooled liquids are quite distinct: gradual versus fast evolution of specific heat and viscosity/relaxation time with undercooling. Their local structural ordering are found to relate with the temperature dependence of specific heat and relaxation time. Then elastic heterogeneity has been studied to correlate with local structure in Cu-Zr MGs. Specifically, this part covers how the degree of elastic deformation correlates with the internal structure at the atomic level, how to quantitatively evaluate the local solidity/liquidity in MGs and how the network of interpenetrating connection of icosahedra determine the corresponding shear modulus. Finally, we have illustrated the structure signature of quasi-localized low-frequency vibrational normal modes, which resides the intriguing vibrational properties in MGs. Specifically, the

  17. Single Posterior Approach for En-Bloc Resection and Stabilization for Locally Advanced Pancoast Tumors Involving the Spine: Single Centre Experience

    PubMed Central

    Sunna, Tarek; Liberman, Moishe; Boubez, Ghassan; Wang, Zhi; Shedid, Daniel

    2016-01-01

    Study Design Monocentric prospective study. Purpose To assess the safety and effectiveness of the posterior approach for resection of advanced Pancoast tumors. Overview of Literature In patients with advanced Pancoast tumors invading the spine, most surgical teams consider the combined approach to be necessary for “en-bloc” resection to control visceral, vascular, and neurological structures. We report our preliminary experience with a single-stage posterior approach. Methods We included all patients who underwent posterior en-bloc resection of advanced Pancoast tumors invading the spine in our institution between January 2014 and May 2015. All patients had locally advanced tumors without N2 nodes or distant metastases. All patients, except 1, benefited from induction treatment consisting of a combination of concomitant chemotherapy (cisplatin-VP16) and radiation. Results Five patients were included in this study. There were 2 men and 3 women with a mean age of 55 years (range, 46–61 years). The tumor involved 2 adjacent levels in 1 patient, 3 levels in 1 patient, and 4 levels in 3 patients. There were no intraoperative complications. The mean operative time was 9 hours (range, 8–12 hours), and the mean estimated blood loss was 3.2 L (range, 1.5–7 L). No patient had a worsened neurological condition at discharge. Four complications occurred in 4 patients. Three complications required reoperation and none was lethal. The mean follow-up was 15.5 months (range, 9–24 months). Four patients harbored microscopically negative margins (R0 resection) and remained disease free. One patient harbored a microscopically positive margin (R1 resection) and exhibited local recurrence at 8 months following radiation treatment. Conclusions The posterior approach was a valuable option that avoided the need for a second-stage operation. Induction chemoradiation is highly suitable for limiting the risk of local recurrence. PMID:27994780

  18. Local Tomography and the Jordan Structure of Quantum Theory

    NASA Astrophysics Data System (ADS)

    Barnum, Howard; Wilce, Alexander

    2014-02-01

    Using a result of H. Hanche-Olsen, we show that (subject to fairly natural constraints on what constitutes a system, and on what constitutes a composite system), orthodox finite-dimensional complex quantum mechanics with superselection rules is the only non-signaling probabilistic theory in which (i) individual systems are Jordan algebras (equivalently, their cones of unnormalized states are homogeneous and self-dual), (ii) composites are locally tomographic (meaning that states are determined by the joint probabilities they assign to measurement outcomes on the component systems) and (iii) at least one system has the structure of a qubit. Using this result, we also characterize finite dimensional quantum theory among probabilistic theories having the structure of a dagger-monoidal category.

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

    NASA Technical Reports Server (NTRS)

    Dong, Stanley B.

    1989-01-01

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

  20. Imaging biological structures with fluorescence photoactivation localization microscopy.

    PubMed

    Gould, Travis J; Verkhusha, Vladislav V; Hess, Samuel T

    2009-01-01

    Fluorescence photoactivation localization microscopy (FPALM) images biological structures with subdiffraction-limited resolution. With repeated cycles of activation, readout and bleaching, large numbers of photoactivatable probes can be precisely localized to obtain a map (image) of labeled molecules with an effective resolution of tens of nanometers. FPALM has been applied to a variety of biological imaging applications, including membrane, cytoskeletal and cytosolic proteins in fixed and living cells. Molecular motions can be quantified. FPALM can also be applied to nonbiological samples, which can be labeled with photoactivatable probes. With emphasis on cellular imaging, we describe here the adaptation of a conventional widefield fluorescence microscope for FPALM and present step-by-step procedures to successfully obtain and analyze FPALM images. The fundamentals of this protocol may also be applicable to users of similar imaging techniques that apply localization of photoactivatable probes to achieve super-resolution. Once alignment of the setup has been completed, data acquisitions can be obtained in approximately 1-30 min and analyzed in approximately 0.5-4 h.

  1. The local structure of topological charge fluctuations in QCD

    SciTech Connect

    I. Horvath; S.J. Dong; T. Draper; Frank Lee; K.F. Liu; J.B. Zhang; H.B. Thacker

    2002-06-01

    We introduce the Dirac eigenmode filtering of topological charge density associated with Ginsparg-Wilson fermions as a tool to investigate the local structure of topological charge fluctuations in QCD. The resulting framework is used to demonstrate that the bulk of topological charge in QCD does not appear in the form of unit quantized lumps. This means that the mixing of ''would-be'' zeromodes associated with such lumps is probably not the prevalent microscopic mechanism for spontaneous chiral symmetry breaking in QCD. To characterize the coherent local behavior in topological charge density at low energy, we compute the charges contained in maximal coherent spheres enclosing non-overlapping peaks. We find a continuous distribution essentially ending at {approx}0.5. Finally, we study, for the first time, the overlap-operator topological-charge-density correlators and find consistency with non-positivity at nonzero physical distance. This represents a non-trivial check on the locality (in gauge paths) of the overlap Dirac operator for realistic gauge backgrounds.

  2. 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.

  3. 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.

  4. 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.

  5. A local immunization strategy for networks with overlapping community structure

    NASA Astrophysics Data System (ADS)

    Taghavian, Fatemeh; Salehi, Mostafa; Teimouri, Mehdi

    2017-02-01

    Since full coverage treatment is not feasible due to limited resources, we need to utilize an immunization strategy to effectively distribute the available vaccines. On the other hand, the structure of contact network among people has a significant impact on epidemics of infectious diseases (such as SARS and influenza) in a population. Therefore, network-based immunization strategies aim to reduce the spreading rate by removing the vaccinated nodes from contact network. Such strategies try to identify more important nodes in epidemics spreading over a network. In this paper, we address the effect of overlapping nodes among communities on epidemics spreading. The proposed strategy is an optimized random-walk based selection of these nodes. The whole process is local, i.e. it requires contact network information in the level of nodes. Thus, it is applicable to large-scale and unknown networks in which the global methods usually are unrealizable. Our simulation results on different synthetic and real networks show that the proposed method outperforms the existing local methods in most cases. In particular, for networks with strong community structures, high overlapping membership of nodes or small size communities, the proposed method shows better performance.

  6. Mapping Milky Way and Local Volume Structure With LSST

    NASA Astrophysics Data System (ADS)

    Willman, Beth; Bochanski, J. J.; Bullock, J. S.; de Jong, R.; Debattista, V. P.; Finkbeiner, D.; Grillmair, C. J.; Henry, T. J.; Ivezić, Ž.; Johnston, K. V.; Jurić, M.; Kalirai, J.; McGehee, P. M.; Minniti, D.; Roškar, R.; Sarajedini, A.; Simon, J. D.; Strader, J.; Strauss, M. A.

    2010-01-01

    The last decade has seen a renaissance in the study of our own and other galaxies in the Local Volume, based in large part on the multi-dimensional maps provided by the vast numbers of stars cataloged by surveys such as 2MASS and SDSS. This renaissance has revolutionized our view of the Milky Way (MW) by facilitating tomographic studies of its global structure and by revealing a vast menagerie of substructures, including a new population of satellite galaxies with a millionth the luminosity of the MW and a halo replete with lumps and streams that betray the formation history of the MW. With LSST's 6 bands, 1000 epochs, and a final a limiting magnitude of r=27.6 (AB mag; 5-sigma), it will provide an excellent resource for mapping the structure and accretion history of the MW and beyond in a way that the present generation of surveys has only hinted at. LSST is anticipated to catalog 10 billion stars, including photometric abundances for the 200 million F/G stars within 100 kpc and proper motion/parallax measurements for stars brighter than r = 24 mag. Specific MW and Local Volume science to be enabled by LSST includes: mapping the 3D distribution of dust throughout the MW's disk, including variations in R_V; understanding the smooth distribution of stars in the MW and other nearby galaxies; understanding large-scale chemical gradients in the MW; discovering lumps and streams in metallicity and phase-space; inferring the mass distribution in the MW; discovering ultra-faint galaxies throughout the Local Volume as overdensities of resolved stars.

  7. Structure and local charging of electromigrated Au nanocontacts.

    PubMed

    Arnold, D; Marz, M; Schneider, S; Hoffmann-Vogel, R

    2017-02-03

    We study the structure and the electronic properties of Au nanocontacts created by controlled electromigration of thin film devices, a method frequently used to contact molecules. In contrast to electromigration testing, a current is applied in a cyclic fashion and during each cycle the resistance increase of the metal upon heating is used to avoid thermal runaway. In this way, nanometer sized-gaps are obtained. The thin film devices with an optimized structure at the origin of the electromigration process are made by shadow evaporation without contamination by organic materials. Defining rounded edges and a thinner area in the center of the device allow to pre-determine the location where the electromigration takes place. Scanning force microscopy images of the pristine Au film and electromigrated contact show its grainy structure. Through electromigration, a 1.5 μm-wide slit is formed, with extensions only on the anode side that had previously not been observed in narrower structures. It is discussed whether this could be explained by asymmetric heating of both electrodes. New grains are formed in the slit and on the extensions on both, the anode and the cathode side. The smaller structures inside the slit lead to an electrode distance below 150 nm. Kelvin probe force microscopy images show a local work function difference with fluctuations of 70 mV on the metal before electromigration. Between the electrodes, disconnected through electromigration, a work function difference of 3.2 V is observed due to charging. Some of the grains newly formed by electromigration are electrically disconnected from the electrodes.

  8. Structure and local charging of electromigrated Au nanocontacts

    NASA Astrophysics Data System (ADS)

    Arnold, D.; Marz, M.; Schneider, S.; Hoffmann-Vogel, R.

    2017-02-01

    We study the structure and the electronic properties of Au nanocontacts created by controlled electromigration of thin film devices, a method frequently used to contact molecules. In contrast to electromigration testing, a current is applied in a cyclic fashion and during each cycle the resistance increase of the metal upon heating is used to avoid thermal runaway. In this way, nanometer sized-gaps are obtained. The thin film devices with an optimized structure at the origin of the electromigration process are made by shadow evaporation without contamination by organic materials. Defining rounded edges and a thinner area in the center of the device allow to pre-determine the location where the electromigration takes place. Scanning force microscopy images of the pristine Au film and electromigrated contact show its grainy structure. Through electromigration, a 1.5 μm-wide slit is formed, with extensions only on the anode side that had previously not been observed in narrower structures. It is discussed whether this could be explained by asymmetric heating of both electrodes. New grains are formed in the slit and on the extensions on both, the anode and the cathode side. The smaller structures inside the slit lead to an electrode distance below 150 nm. Kelvin probe force microscopy images show a local work function difference with fluctuations of 70 mV on the metal before electromigration. Between the electrodes, disconnected through electromigration, a work function difference of 3.2 V is observed due to charging. Some of the grains newly formed by electromigration are electrically disconnected from the electrodes.

  9. Strain localization driven by structural relaxation in sheared amorphous solids.

    PubMed

    Jagla, E A

    2007-10-01

    A two dimensional amorphous material is modeled as an assembly of mesoscopic elemental pieces coupled together to form an elastically coherent structure. Plasticity is introduced as the existence of different minima in the energy landscape of the elemental constituents. Upon the application of an external strain rate, the material shears through the appearance of elemental slip events with quadrupolar symmetry. When the energy landscape of the elemental constituents is kept fixed, the slip events distribute uniformly throughout the sample, producing on average a uniform deformation. However, when the energy landscape at different spatial positions can be rearranged dynamically to account for structural relaxation, the system develops inhomogeneous deformation in the form of shear bands at low shear rates, and stick-slip-like motion at the shear bands for the lowest shear rates. The origin of strain localization is traced back to a region of negative correlation between strain rate and stress, which appears only if structural relaxation is present. The model also reproduces other well known effects in the rheology of amorphous materials, as a stress peak in a strain rate controlled experiment staring from rest, and the increase of the maximum of this peak with sample age.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Lim, Mikhiel; Hacihaliloglu, Ilker

    2016-03-01

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

  12. 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.

  13. Flexible structural protein alignment by a sequence of local transformations

    PubMed Central

    Rocha, Jairo; Segura, Joan; Wilson, Richard C.; Dasgupta, Swagata

    2009-01-01

    Motivation: Throughout evolution, homologous proteins have common regions that stay semi-rigid relative to each other and other parts that vary in a more noticeable way. In order to compare the increasing number of structures in the PDB, flexible geometrical alignments are needed, that are reliable and easy to use. Results: We present a protein structure alignment method whose main feature is the ability to consider different rigid transformations at different sites, allowing for deformations beyond a global rigid transformation. The performance of the method is comparable with that of the best ones from 10 aligners tested, regarding both the quality of the alignments with respect to hand curated ones, and the classification ability. An analysis of some structure pairs from the literature that need to be matched in a flexible fashion are shown. The use of a series of local transformations can be exported to other classifiers, and a future golden protein similarity measure could benefit from it. Availability: A public server for the program is available at http://dmi.uib.es/ProtDeform/. Contact: jairo@uib.es Supplementary information: All data used, results and examples are available at http://dmi.uib.es/people/jairo/bio/ProtDeform.Supplementary data are available at Bioinformatics online. PMID:19417057

  14. 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.

  15. Structure of the Ni(II) complex of Escherichia coli peptide deformylase and suggestions on deformylase activities depending on different metal(II) centres.

    PubMed

    Yen, Ngo Thi Hai; Bogdanović, Xenia; Palm, Gottfried J; Kühl, Olaf; Hinrichs, Winfried

    2010-02-01

    Crystal structures of polypeptide deformylase (PDF) of Escherichia coli with nickel(II) replacing the native iron(II) have been solved with chloride and formate as metal ligands. The chloro complex is a model for the correct protonation state of the hydrolytic hydroxo ligand and the protonated status of the Glu133 side chain as part of the hydrolytic mechanism. The ambiguity that recently some PDFs have been identified with Zn(2+) ion as the active-site centre whereas others are only active with Fe(2+) (or Co(2+), Ni(2+) is discussed with respect to Lewis acid criteria of the metal ion and substrate activation by the CD loop.

  16. 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.

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

    PubMed

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

    2013-07-15

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

  18. Characterization of localized transverse structures in wide-aperture lasers

    NASA Astrophysics Data System (ADS)

    Rosanov, N. N.; Fedorov, A. V.; Fedorov, S. V.; Khodova, G. V.

    The problem of characterization of spatio-temporal patterns is discussed for the case of wide-aperture lasers with nonlinear losses where variety of such patterns is especially rich. Laser autosolitons (LASs)-localized transverse structures representing “islands of lasing” on a background of the nonlasing mode on the laser aperture-are studied. Existence of stable single LASs which are motionless or moving in the transverse direction with constant linear velocity is shown. Described are also LASs with regular wavefronts, those with screw dislocations (defects) of wavefronts with different topological indices, and those with axially symmetric and asymmetric intensity distributions rotating with constant angular velocity around the LAS center. An approach is given for qualitative and quantitative characterization of a single LAS by its linear and angular velocities and frequency shift, based on a combination of analytical methods and computer simulations. Results of investigations of weak and strong interactions among the LASs are presented.

  19. 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).

  20. The local electronic structure of α-Li3N

    SciTech Connect

    Fister, Timothy T.; Siedler, Gerald T.; Shirley, E. L.; Vila, Fernando D.; Nagle, Kenneth P.; Rehr, John J.; Linehan, John C.; Cross, Julie O.

    2008-07-28

    We investigate the local electronic structure of α-Li3N by the combination of nonresonant inelastic x-ray scattering measurements and three independent ab initio theoretical treatments. Experimental determination of the local final density of states projected onto an orbital angular momentum basis (l-DOS) for Li 1s initial states finds strong similarities in the s- and p-DOS throughout the near-edge region, which we attribute to the 3-fold rotational symmetry about Li sites in the Li2N sheets of α-Li3N. We also find a significant correspondence between the near-edge spectra for the Li 1s and N 1s contributions to the NRIXS signal. This is unexpected, as such behavior is typically associated with covalent materials whereas α-Li3N is strongly ionic. We explain that such similarity in the DOS at different sites in either ionic or covalent systems may occur when the core-hole lifetimes are very long, so that the lifetime of the photoelectron is the dominant factor in cutting off high-order multiple scattering in the near-edge regime. This work was supported by the U.S. Department of Energy's Office of Basic Energy Sciences. The Pacific Northwest National Laboratory is operated by Battelle for DOE.

  1. 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.

  2. 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.

  3. 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.

  4. Identification of Ligand Templates using Local Structure Alignment for Structure-based Drug Design

    PubMed Central

    Lee, Hui Sun; Im, Wonpil

    2012-01-01

    With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. Based on the fact that the structurally similar binding sites share information about their ligands, we have developed a local structure alignment tool, G-LoSA (Graph-based Local Structure Alignment). In G-LoSA, the known protein-ligand binding-site structure library is searched to detect binding-site structures with similar geometry and physicochemical properties to a query binding-site structure regardless of sequence continuity and protein fold. Then, the ligands in the identified complexes are used as templates (i.e., template ligands) to predict/design a ligand for the target protein. The performance of G-LoSA is validated against 76 benchmark targets from the Astex diverse set. Using the currently available protein-ligand structure library, G-LoSA is able to identify a single template ligand (from a non-homologous protein complex) that is highly similar to the target ligand in more than half of the benchmark targets. In addition, our benchmark analyses show that an assembly of structural fragments from multiple template ligands with partial similarity to the target ligand can be used to design novel ligand structures specific to the target protein. This study clearly indicates that a template-based ligand modeling has potential for de novo ligand design and can be a complementary approach to the receptor structure based methods. PMID:22978550

  5. Localized and chaotic folding: the role of axial plane structures.

    PubMed

    Hobbs, Bruce E; Ord, Alison

    2012-04-28

    Most natural fold systems are not sinusoidal in profile. A widely held view is that such irregularity derives solely from inherited initial geometrical perturbations. Although, undoubtedly, initial perturbations can contribute to irregularity, we explore a different (but complementary) view in which the irregular geometry results from some material or system softening process. This arises because the buckling response of a layer (or layers) embedded in a weaker matrix is controlled in a sensitive manner by the nature of the reaction forces exerted by the deforming matrix on the layer. In many theoretical treatments of the folding problem, this reaction force is assumed to be a linear function of some measure of the deformation or deformation rate. This paper is concerned with the influence of nonlinear reaction forces such as arise from nonlinear elasticity or viscosity. Localized folds arising from nonlinearity form in a fundamentally different way than the Biot wavelength selection process. As a particular example of nonlinear behaviour, we examine the influence of axial plane structures made up of layers of different mineralogy formed by chemical differentiation processes accompanying the deformation; they are referred to as metamorphic layering. The alternating mineralogical composition in the metamorphic layers means that the embedding matrix exerts a reaction force on the folded layers that varies not only with the deflection or the velocity of deflection of the layer, but also in a periodic manner along the length of the folded layers. The influence of this spatially periodic reaction force on the development of localized and chaotic folding is explored numerically.

  6. Probing the band structure and local electronic properties of low-dimensional semiconductor structures

    NASA Astrophysics Data System (ADS)

    Walrath, Jenna Cherie

    Low-dimensional semiconductor structures are important for a wide variety of applications, and recent advances in nanoscale fabrication are paving the way for increasingly precise nano-engineering of a wide range of materials. It is therefore essential that the physics of materials at the nanoscale are thoroughly understood to unleash the full potential of nanotechnology, requiring the development of increasingly sophisticated instrumentation and modeling. Of particular interest is the relationship between the local density of states (LDOS) of low-dimensional structures and the band structure and local electronic properties. This dissertation presents the investigation of the band structure, LDOS, and local electronic properties of nanostructures ranging from zero-dimensional (0D) quantum dots (QDs) to two-dimensional (2D) thin films, synthesizing computational and experimental approaches including Poisson-Schrodinger band structure calculations, scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and scanning thermoelectric microscopy (SThEM). A method is presented for quantifying the local Seebeck coefficient (S) with SThEM, using a quasi-3D conversion matrix approach to directly convert temperature gradient-induced voltages S. For a GaAs p-n junction, the resulting S-profile is consistent with that computed using the free carrier concentration profile. This combined computational-experimental approach is expected to enable nanoscale measurements of S across a wide variety of heterostructure interfaces. The local carrier concentration, n, is profiled across epitaxial InAs/GaAs QDs, where SThEM is used to profile the temperature gradient-induced voltage, which is converted to a profile of the local S and finally to an n profile. The S profile is converted to a conduction band-edge profile and compared with Poisson-Schrodinger band-edge simulations. The combined computational-experimental approach suggests a reduced n in the QD center in

  7. Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction.

    PubMed

    Faraggi, Eshel; Yang, Yuedong; Zhang, Shesheng; Zhou, Yaoqi

    2009-11-11

    Local structures predicted from protein sequences are used extensively in every aspect of modeling and prediction of protein structure and function. For more than 50 years, they have been predicted at a low-resolution coarse-grained level (e.g., three-state secondary structure). Here, we combine a two-state classifier with real-value predictor to predict local structure in continuous representation by backbone torsion angles. The accuracy of the angles predicted by this approach is close to that derived from NMR chemical shifts. Their substitution for predicted secondary structure as restraints for ab initio structure prediction doubles the success rate. This result demonstrates the potential of predicted local structure for fragment-free tertiary-structure prediction. It further implies potentially significant benefits from using predicted real-valued torsion angles as a replacement for or supplement to the secondary-structure prediction tools used almost exclusively in many computational methods ranging from sequence alignment to function prediction.

  8. 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

    2012-07-27

    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.

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

    PubMed

    Rey, Arnaud; Perruchet, Pierre; Fagot, Joël

    2012-04-01

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

  10. 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

  11. Local Structural Distortion Induced Uniaxial Negative Thermal Expansion in Nanosized Semimetal Bismuth.

    PubMed

    Li, Qiang; Zhu, He; Zheng, Lirong; Fan, Longlong; Ren, Yang; Chen, Jun; Deng, Jinxia; Xing, Xianran

    2016-11-01

    The corrugated layer structure bismuth has been successfully tailored into negative thermal expansion along c axis by size effect. Pair distribution function and extended X-ray absorption fine structure are combined to reveal the local structural distortion for nanosized bismuth. The comprehensive method to identify the local structure of nanomaterials can benefit the regulating and controlling of thermal expansion in nanodivices.

  12. 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.

  13. Historic timber skeleton structures and the local seismic culture

    NASA Astrophysics Data System (ADS)

    Bostenaru, M.

    2009-04-01

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

  14. Crustal structure beneath the southern Korean Peninsula from local earthquakes

    NASA Astrophysics Data System (ADS)

    Kim, Kwang-Hee; Park, Jung-Ho; Park, Yongcheol; Hao, Tian-Yao; Kim, Han-Joon

    2017-02-01

    The three-dimensional subsurface structure beneath the southern Korean Peninsula is poorly known, even though such information could be key in verifying or rejecting several competing models of the tectonic evolution of East Asia. We constructed a three-dimensional velocity model of the upper crust beneath the southern Korean Peninsula using 19,935 P-wave arrivals from 747 earthquakes recorded by high-density local seismic networks. Results show significant lateral and vertical variations: velocity increases from northwest to southeast at shallow depths, and significant velocity variations are observed across the South Korea Tectonic Line between the Okcheon Fold Belt and the Youngnam Massif. Collision between the North China and South China blocks during the Early Cretaceous might have caused extensive deformation and the observed negative velocity anomalies in the region. The results of the tomographic inversion, combined with the findings of previous studies of Bouguer and isostatic gravity anomalies, indicate the presence of high-density material in the upper and middle crust beneath the Gyeongsang Basin in the southeastern Korean Peninsula. Although our results partially support the indentation tectonic model, it is still premature to discard other tectonic evolution models because our study only covers the southern half of the peninsula.

  15. Local structure analysis of materials for increased energy efficiency

    NASA Astrophysics Data System (ADS)

    Medling, Scott

    In this dissertation, a wide range of materials which exhibit interesting properties with potential for energy efficiency applications are investigated. The bulk of the research was conducted using the Extended X-ray Absorption Fine Structure (EXAFS) technique. EXAFS is a powerful tool for elucidating the local structure of novel materials, and it's advantages are presented in Chapter 2. In Chapter 3, I present details on two new techniques which are used in studies later in this dissertation, but are also promising for other, unrelated studies and, therefore, warrant being discussed generally. I explain the presence of and present a method for subtracting the X-ray Raman background in the fluorescence window when collecting fluorescence EXAFS data of a dilute dopant Z in a Z+1 host. I introduce X-ray magnetic circular dichroism (XMCD) and discuss the process to reduce XMCD data, including the self-absorption corrections for low energy K-edges. In Chapter 4, I present a series of investigations on ZnS:Cu electroluminescent phosphors. Optical microscopy indicates that the emission centers do not degrade uniformly or monotonically, but rather, most of the emission centers blink on and off during degradation. The effect of this on various proposed degradation mechanisms is discussed. EXAFS data of ZnS:Cu phosphors ground to enable thinner, lower-voltage devices indicate that grinding preferentially causes damage to the CuS nanoprecipitates, quenching electroluminescence (EL) and concluding that smaller particles must be built up from nanoparticles instead. EXAFS data of nanoparticles show that adding a ZnS shell outside a ZnS:Cu core provides significant additional encapsulation of the Cu, increasing photoluminescence and indicating that this may increase EL if devices can be fabricated. Data from extremely dilute (0.02% Cu) ZnS:Cu nanoparticles is presented in order to specifically study the non-precipitate and suggests that the Cu dopant substitutes for Zn and is

  16. Expectation and Locality Effects in German Verb-final Structures.

    PubMed

    Levy, Roger P; Keller, Frank

    2013-02-01

    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.

  17. 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.

  18. Superpose3D: A Local Structural Comparison Program That Allows for User-Defined Structure Representations

    PubMed Central

    Gherardini, Pier Federico; Ausiello, Gabriele; Helmer-Citterich, Manuela

    2010-01-01

    Local structural comparison methods can be used to find structural similarities involving functional protein patches such as enzyme active sites and ligand binding sites. The outcome of such analyses is critically dependent on the representation used to describe the structure. Indeed different categories of functional sites may require the comparison program to focus on different characteristics of the protein residues. We have therefore developed superpose3D, a novel structural comparison software that lets users specify, with a powerful and flexible syntax, the structure description most suited to the requirements of their analysis. Input proteins are processed according to the user's directives and the program identifies sets of residues (or groups of atoms) that have a similar 3D position in the two structures. The advantages of using such a general purpose program are demonstrated with several examples. These test cases show that no single representation is appropriate for every analysis, hence the usefulness of having a flexible program that can be tailored to different needs. Moreover we also discuss how to interpret the results of a database screening where a known structural motif is searched against a large ensemble of structures. The software is written in C++ and is released under the open source GPL license. Superpose3D does not require any external library, runs on Linux, Mac OSX, Windows and is available at http://cbm.bio.uniroma2.it/superpose3D. PMID:20700534

  19. 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

  20. 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.

  1. Information content of the Centre d'Etude du Polymorphisme Humain (CEPH) family structures for linkage studies.

    PubMed

    Chakravarti, A

    1991-10-01

    This paper derives theoretical values for joint polymorphism information content for two markers from a family structure consisting of four grandparents, two parents, and many offspring. These data determine the efficiency of linkage map construction.

  2. Homeland Security: What Are the Advantages and Disadvantages of Different Local Homeland Security Organizational Structures?

    DTIC Science & Technology

    2015-06-01

    WHAT ARE THE ADVANTAGES AND DISADVANTAGES OF DIFFERENT LOCAL HOMELAND SECURITY ORGANIZATIONAL STRUCTURES? by William Mark Fitzpatrick...ADVANTAGES AND DISADVANTAGES OF DIFFERENT LOCAL HOMELAND SECURITY ORGANIZATIONAL STRUCTURES? 5. FUNDING NUMBERS 6. AUTHOR(S) William Mark Fitzpatrick 7...analyzed three homeland security organizational structures located within the Metro Atlanta, GA, area to find their advantages and disadvantages

  3. Hen Egg-White Lysozyme Crystallisation: Protein Stacking and Structure Stability Enhanced by a Tellurium(VI)-Centred Polyoxotungstate

    PubMed Central

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

    2015-01-01

    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[TeW6O24]⋅22 H2O (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

  4. The Categorical Structure of Knowledge for Famous People (And a Novel Application of Centre-Surround Theory)

    ERIC Educational Resources Information Center

    Stone, Anna; Valentine, Tim

    2007-01-01

    Knowledge of familiar people is essential to guide social interaction, yet there is uncertainty about whether semantic knowledge for people is stored in a categorical structure as for objects. Four priming experiments using hard-to-perceive primes investigated whether occupation forms a category connecting famous persons in semantic memory. Primes…

  5. 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.

  6. Structural alteration of the metal-organic pyrogallol[4]arene nano-capsule motif by incorporation of large metal centres.

    PubMed

    Jin, Ping; Kumari, Harshita; Kennedy, Stuart; Barnes, Charles L; Teat, Simon J; Dalgarno, Scott J; Atwood, Jerry L

    2014-05-04

    Addition of cadmium(II) nitrate to gallium-coordinated metal-organic C-alkylpyrogallol[4]arene nano-capsules affords a variation of the near spherical hexamer motif, structural changes in which are induced by the markedly different nature of the secondary incorporated metal.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  8. Effect of local structures on structural evolution during crystallization in undercooled metallic glass-forming liquids.

    PubMed

    Wu, Z W; Li, M Z; Wang, W H; Song, W J; Liu, K X

    2013-02-21

    The effect of local structures on structural evolution during the crystallization of undercooled ZrCu metallic glass-forming liquid was studied via molecular dynamics simulations. It is found that body-centered-cubic (bcc)-like clusters play a key role in structural evolution during crystallization. In contrast to previous speculations, the number of bcc-like crystal nuclei does not change much before the onset of crystallization. Instead, the development of a bcc-like critical nucleus during annealing leads to a strong spatial correlation with other nuclei in its surroundings, forming a crystalline structure template. It is also found that the size distribution of bcc-like nuclei follows a power-law form with an exponential cutoff in the early stage of annealing, but changes to a pure power-law behavior just before the onset of crystallization. This implies that the crystalline structure template has fractal feature and the undercooled liquids evolve to a self-organized critical state before the onset of crystallization, which might trigger the subsequent rapid crystallization. According to the graph theory analysis, it is also found that the observed large scatter of the onset time of crystallization in different liquid samples results from the connectivity of the bcc-like clusters.

  9. The Manitoba Centre for Health Policy: A Case Study

    PubMed Central

    Marchessault, Gail

    2011-01-01

    Context: The Manitoba Centre for Health Policy (MCHP) is a university research centre with a long-standing contractual arrangement with government. Objective: The purpose of this project was to examine the facilitators and challenges in the development, establishment and continuation of MCHP. Methods: In-depth, semi-structured interviews with 28 participants selected purposefully and a document review were conducted and analyzed using qualitative methods. Results: Although a unique confluence of factors facilitated MCHP's establishment, participants viewed safeguards to credibility (arm's-length from government; guaranteed academic freedom) along with powerful advocates as key to longevity. Other factors that participants discussed as important to sustainability included excellence in scholarship; thorough protection of privacy; stable funding; incremental growth; teamwork; leadership; nurturing of relationships; and authentic partnerships. Conclusions: MCHP has demonstrated that using local administrative data to address policy-related research questions is of enduring value to local and provincial communities, and also has national and international relevance. PMID:24933371

  10. Local structure studies of some cobalt (II) complexes using extended X-ray absorption fine structure

    NASA Astrophysics Data System (ADS)

    Mishra, Ashutosh; Ninama, Samrath; Trivedi, Apurva

    2014-09-01

    Extended X-ray Absorption Fine Structure (EXAFS) analysis of Cobalt (II) complex as a ligand of 2 -methyl-3-[(bis-aniline(R) phenyl]-3H-l,5 benzodiazepine for finding local structure using conventional method .The Co(II) complexes were prepared by chemical root method. The EXAFS spectra were recorded at Cobalt K-edge i.e.; 7709 eV using Dispersive EXFAS beam line at 2.5GeV Indus-2 Synchrotron Radiation Source(SRS) at RRCAT, Indore, India. The recorded EXAFS data were analysed using the computer software Athena for determine the nearest neighbouring distances (bond lengths) of these complexes with conventional methods and it compared with Fourier transform(FT) analysis. The Fourier Transform convert EXAFS data signal into r-space or k-space. This is useful for visualizing the major contributions to the EXAFS spectrum.

  11. Expectation and Locality Effects in German Verb-Final Structures

    ERIC Educational Resources Information Center

    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 having more dependents…

  12. Complex haplotype structure of the human GNAS gene identifies a recombination hotspot centred on a single nucleotide polymorphism widely used in association studies.

    PubMed

    Yang, Wanling; White, Brook; Spicer, Eleanor K; Weinstein, Benjamin L; Hildebrandt, John D

    2004-11-01

    The alpha subunit of the heterotrimeric G protein Gs (Gsalpha) is involved in numerous physiological processes and is a primary determinant of cellular responses to extracellular signals. Genetic variations in the Gsalpha gene may play an important role in complex diseases and drug responses. To characterize the genetic diversity in this locus, we resequenced exons and flanking introns of the gene in 44 genomic samples and analysed the haplotype structure of the gene in an additional 50 African-Americans and 50 Caucasians. Significant differences in allele frequency for nearly all the genotyped single nucleotide polymorphism (SNPs) were detected between the two ethnic groups. Linkage disequilibrium (LD) analysis of this locus revealed two haplotype blocks characterized by strong LD and reduced haplotype diversity, especially in Caucasians. Between the two blocks is a narrow (approximately 3 kb) recombination hotspot centred on exons 4 and 5, and a widely used genetic marker in association studies in this region (rs7121) was in linkage equilibrium with the rest of the gene. The haplotype structure of the GNAS locus warrants reevaluation of previous association studies that used marker rs7121 and affects choice of SNP markers to be used in future studies of this locus.

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

    PubMed

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

    2013-01-01

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

  14. Spatial Variation in the Population Structure and Reproductive Biology of Rimicaris hybisae (Caridea: Alvinocarididae) at Hydrothermal Vents on the Mid-Cayman Spreading Centre

    PubMed Central

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

    2013-01-01

    The dynamics and microdistribution of faunal assemblages at hydrothermal vents often reflect the fine-scale spatial and temporal heterogeneity of the vent environment. This study examined the reproductive development and population structure of the caridean shrimp Rimicaris hybisae at the Beebe and Von Damm Vent Fields (Mid-Cayman Spreading Centre, Caribbean) using spatially discrete samples collected in January 2012. Rimicaris hybisae is gonochoric and exhibits iteroparous reproduction. Oocyte size-frequency distributions (21-823 µm feret diameters) varied significantly among samples. Embryo development was asynchronous among females, which may result in asynchronous larval release for the populations. Specimens of R. hybisae from the Von Damm Vent Field (2294 m) were significantly larger than specimens from the Beebe Vent Field. Brooding females at Von Damm exhibited greater size-specific fecundity, possibly as a consequence of a non-linear relationship between fecundity and body size that was consistent across both vent fields. Samples collected from several locations at the Beebe Vent Field (4944–4972 m) revealed spatial variability in the sex ratios, population structure, size, and development of oocytes and embryos of this mobile species. Samples from the Von Damm Vent Field and sample J2-613-24 from Beebe Woods exhibited the highest frequencies of ovigerous females and significantly female-biased sex ratios. Environmental variables within shrimp aggregations may influence the distribution of ovigerous females, resulting in a spatially heterogeneous pattern of reproductive development in R. hybisae, as found in other vent taxa. PMID:23555955

  15. 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.

  16. Oscillation structure of localized perturbations in modulationally unstable media.

    PubMed

    Biondini, Gino; Li, Sitai; Mantzavinos, Dionyssios

    2016-12-01

    We characterize the properties of the asymptotic stage of modulational instability arising from localized perturbations of a constant background, including the number and location of the individual peaks in the oscillation region. We show that, for long times, the solution tends to an ensemble of classical (i.e., sech-shaped) solitons of the focusing nonlinear Schrödinger equation (as opposed to the various breatherlike solutions of the same equation with a nonzero background). We also confirm the robustness of the theoretical results by comparing the analytical predictions with careful numerical simulations with a variety of initial conditions, which confirm that the evolution of modulationally unstable media in the presence of localized initial perturbations is indeed described by the same asymptotic state.

  17. Oscillation structure of localized perturbations in modulationally unstable media

    NASA Astrophysics Data System (ADS)

    Biondini, Gino; Li, Sitai; Mantzavinos, Dionyssios

    2016-12-01

    We characterize the properties of the asymptotic stage of modulational instability arising from localized perturbations of a constant background, including the number and location of the individual peaks in the oscillation region. We show that, for long times, the solution tends to an ensemble of classical (i.e., sech-shaped) solitons of the focusing nonlinear Schrödinger equation (as opposed to the various breatherlike solutions of the same equation with a nonzero background). We also confirm the robustness of the theoretical results by comparing the analytical predictions with careful numerical simulations with a variety of initial conditions, which confirm that the evolution of modulationally unstable media in the presence of localized initial perturbations is indeed described by the same asymptotic state.

  18. Structural biomechanics modulate intramuscular distribution of locally delivered drugs.

    PubMed

    Wu, Peter I-Kung; Edelman, Elazer R

    2008-09-18

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

  19. The role of local structure in dynamical arrest

    NASA Astrophysics Data System (ADS)

    Royall, C. Patrick; Williams, Stephen R.

    2015-02-01

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

  20. Remote sensing image segmentation using local sparse structure constrained latent low rank representation

    NASA Astrophysics Data System (ADS)

    Tian, Shu; Zhang, Ye; Yan, Yimin; Su, Nan; Zhang, Junping

    2016-09-01

    Latent low-rank representation (LatLRR) has been attached considerable attention in the field of remote sensing image segmentation, due to its effectiveness in exploring the multiple subspace structures of data. However, the increasingly heterogeneous texture information in the high spatial resolution remote sensing images, leads to more severe interference of pixels in local neighborhood, and the LatLRR fails to capture the local complex structure information. Therefore, we present a local sparse structure constrainted latent low-rank representation (LSSLatLRR) segmentation method, which explicitly imposes the local sparse structure constraint on LatLRR to capture the intrinsic local structure in manifold structure feature subspaces. The whole segmentation framework can be viewed as two stages in cascade. In the first stage, we use the local histogram transform to extract the texture local histogram features (LHOG) at each pixel, which can efficiently capture the complex and micro-texture pattern. In the second stage, a local sparse structure (LSS) formulation is established on LHOG, which aims to preserve the local intrinsic structure and enhance the relationship between pixels having similar local characteristics. Meanwhile, by integrating the LSS and the LatLRR, we can efficiently capture the local sparse and low-rank structure in the mixture of feature subspace, and we adopt the subspace segmentation method to improve the segmentation accuracy. Experimental results on the remote sensing images with different spatial resolution show that, compared with three state-of-the-art image segmentation methods, the proposed method achieves more accurate segmentation results.

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

    PubMed

    Narushima, Tetsuya; Hashiyada, Shun; Okamoto, Hiromi

    2016-07-01

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

  2. Local Crystalline Structure in an Amorphous Protein Dense Phase.

    PubMed

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

    2015-10-20

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

  3. Local Crystalline Structure in an Amorphous Protein Dense Phase

    PubMed Central

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

    2015-01-01

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

  4. 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.

  5. 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

  6. 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…

  7. 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

  8. Molecular modeling of phosphorylation sites in proteins using a database of local structure segments.

    PubMed

    Plewczynski, Dariusz; Jaroszewski, Lukasz; Godzik, Adam; Kloczkowski, Andrzej; Rychlewski, Leszek

    2005-11-01

    A new bioinformatics tool for molecular modeling of the local structure around phosphorylation sites in proteins has been developed. Our method is based on a library of short sequence and structure motifs. The basic structural elements to be predicted are local structure segments (LSSs). This enables us to avoid the problem of non-exact local description of structures, caused by either diversity in the structural context, or uncertainties in prediction methods. We have developed a library of LSSs and a profile--profile-matching algorithm that predicts local structures of proteins from their sequence information. Our fragment library prediction method is publicly available on a server (FRAGlib), at http://ffas.ljcrf.edu/Servers/frag.html . The algorithm has been applied successfully to the characterization of local structure around phosphorylation sites in proteins. Our computational predictions of sequence and structure preferences around phosphorylated residues have been confirmed by phosphorylation experiments for PKA and PKC kinases. The quality of predictions has been evaluated with several independent statistical tests. We have observed a significant improvement in the accuracy of predictions by incorporating structural information into the description of the neighborhood of the phosphorylated site. Our results strongly suggest that sequence information ought to be supplemented with additional structural context information (predicted with our segment similarity method) for more successful predictions of phosphorylation sites in proteins.

  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. Deformed relativity symmetries and the local structure of spacetime

    NASA Astrophysics Data System (ADS)

    Letizia, Marco; Liberati, Stefano

    2017-02-01

    A spacetime interpretation of deformed relativity symmetry groups was recently proposed by resorting to Finslerian geometries, seen as the outcome of a continuous limit endowed with first-order corrections from the quantum gravity regime. In this work, we further investigate such connections between deformed algebras and Finslerian geometries by showing that the Finsler geometries associated with the generalization of the Poincaré group (the so-called κ -Poincaré Hopf algebra) are maximally symmetric spacetimes which are also of the Berwald type: Finslerian spacetimes for which the connections are substantially Riemannian, belonging to the unique class for which the weak equivalence principle still holds. We also extend this analysis by considering a generalization of the de Sitter group (the so-called q -de Sitter group) and showing that its associated Finslerian geometry reproduces locally the one from the κ -Poincaré group, and that it itself can be recast in a Berwald form in an appropriate limit.

  11. Light Localization by Defects in Optically Induced Photonic Structures

    NASA Astrophysics Data System (ADS)

    Yang, Jianke; Wang, Xiaosheng; Wang, Jiandong; Chen, Zhigang

    In the past ten years, there has blossomed an interest in the study of collective behavior of wave propagation in periodic waveguide arrays and photonic lattices [1-3]. The unique bandgap structures of these periodic media, coupled with nonlinear effects, give rise to many types of novel soliton structures [1- 26]. On the other hand, it is well known that one of the unique and most interesting features of photonic band-gap structures is a fundamentally different way of waveguiding by defects in otherwise uniformly periodic structures. Such waveguiding has been demonstrated with an "air-hole" in photonic crystal fibers (PCF) for optical waves [27, 28], in an isolated defect in two-dimensional arrays of dielectric cylinders for microwaves [29-31], and recently in all-solid PCF with a lower-index core [32, 33]. In addition, laser emission based on photonic defect modes has been realized in a number of experiments [34-38]. In one-dimensional (1D) fabricated semiconductor waveguide arrays, previous experiments have investigated nonlinearity-induced escape from a defect state [39] and interactions of discrete solitons with structural defects [40] (see also [41]). Despite the above efforts, theoretical understanding on defect guiding was still limited, and experimental demonstrations of defect guiding was still scarce. In addition, when nonlinear effects are significant, how defect guiding is affected by nonlinearity is largely an open issue. Recently, in a series of theoretical and experimental studies, we optically induced 1D, 2D and ringlike photonic lattices with single-site negative defects in photorefractive crystals, and investigated their linear and nonlinear light guiding properties [42-48]. This work will be reviewed in this Chapter. In addition, we present the first experimental demonstration of nonlinear defect modes which undergoes nonlinear propagation through the defects. Our work not only has a direct link to technologically important systems of periodic

  12. 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.

  13. Local structures in computer-generated liquids and glasses: Classification of three-dimensional patterns

    NASA Astrophysics Data System (ADS)

    Gades, Heinrich; Mitus, Antoni C.

    1991-08-01

    Using probabilistic methods we work out mathematical tools for an identification of local close-packed structures (fcc, hcp, icosahedron) in a configuration of atoms undergoing (thermal) fluctuations. A structure is described by invariants constructed from standard and generalized local bond-order parameters and by laws of their fluctuations. We provide a detailed analysis of fluctuations of 13-atom close-packed clusters, find the most informative invariants for each of them and calculate the metric which quantifies a concept of similarity of fluctuating structures. A simple algorithm for an identification of close-packed clusters is proposed. As an example, we analyze local structures in hot fcc solid. We discuss the origin of the difficulties encountered by a classification of local structures in liquids and glasses (Voronoi-like or standard bond-order analysis) and suggest how they can be avoided.

  14. 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.

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

    DOE PAGES

    Timoshenko, J.; Shivhare, A.; Scott, R. W.; ...

    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.

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

    PubMed

    Timoshenko, Janis; Shivhare, Atal; Scott, Robert W J; Lu, Deyu; Frenkel, Anatoly I

    2016-07-20

    We adopted ab initio X-ray absorption near edge structure (XANES) modeling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modeling, where the candidate structures are known, and the inverse modeling, 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 revealing the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

  17. Dynamics of galaxy structures in the Local Volume

    NASA Astrophysics Data System (ADS)

    Karachentsev, I. D.

    2016-10-01

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

  18. Structural Damage Detection Using Frequency Domain Error Localization.

    DTIC Science & Technology

    1994-12-01

    113 rn ~l-,I T X ~oy Ul C 114 APPENDIX D. FE MODEL / COMPUTER CODES The following is a brief description of MATLAB routines employed in this thesis...R.R., Structural Dynamics, An Introduction to Computer Methods , pp. 383-387, John Wiley and Sons, Inc., 1981. 8. Guyan , R.J., "Reduction of Stiffness...official policy or position of the Department of Defense or the U.S. Government. 12a. DISTRIBUTION/AVAILABILITY STATEMENT 12b. DISTRIBUTION CODE

  19. 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

  20. 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.

  1. Laser-induced periodic surface structures: Fingerprints of light localization

    NASA Astrophysics Data System (ADS)

    Skolski, J. Z. P.; Römer, G. R. B. E.; Obona, J. V.; Ocelik, V.; Huis in't Veld, A. J.; de Hosson, J. Th. M.

    2012-02-01

    The finite-difference time-domain (FDTD) method is used to study the inhomogeneous absorption of linearly polarized laser radiation below a rough surface. The results are first analyzed in the frequency domain and compared to the efficacy factor theory of Sipe and coworkers. Both approaches show that the absorbed energy shows a periodic nature, not only in the direction orthogonal to the laser polarization, but also in the direction parallel to it. It is shown that the periodicity is not always close to the laser wavelength for the perpendicular direction. In the parallel direction, the periodicity is about λ/Re(ñ), with ñ being the complex refractive index of the medium. The space-domain FDTD results show a periodicity in the inhomogeneous energy absorption similar to the periodicity of the low- and high-spatial-frequency laser-induced periodic surface structures depending on the material's excitation.

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    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.

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

    PubMed

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

    2015-08-19

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

  5. The influence of the local sequence environment on RNA loop structures.

    PubMed

    Schudoma, Christian; Larhlimi, Abdelhalim; Walther, Dirk

    2011-07-01

    RNA folding is assumed to be a hierarchical process. The secondary structure of an RNA molecule, signified by base-pairing and stacking interactions between the paired bases, is formed first. Subsequently, the RNA molecule adopts an energetically favorable three-dimensional conformation in the structural space determined mainly by the rotational degrees of freedom associated with the backbone of regions of unpaired nucleotides (loops). To what extent the backbone conformation of RNA loops also results from interactions within the local sequence context or rather follows global optimization constraints alone has not been addressed yet. Because the majority of base stacking interactions are exerted locally, a critical influence of local sequence on local structure appears plausible. Thus, local loop structure ought to be predictable, at least in part, from the local sequence context alone. To test this hypothesis, we used Random Forests on a nonredundant data set of unpaired nucleotides extracted from 97 X-ray structures from the Protein Data Bank (PDB) to predict discrete backbone angle conformations given by the discretized η/θ-pseudo-torsional space. Predictions on balanced sets with four to six conformational classes using local sequence information yielded average accuracies of up to 55%, thus significantly better than expected by chance (17%-25%). Bases close to the central nucleotide appear to be most tightly linked to its conformation. Our results suggest that RNA loop structure does not only depend on long-range base-pairing interactions; instead, it appears that local sequence context exerts a significant influence on the formation of the local loop structure.

  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. 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…

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

    SciTech Connect

    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.

  9. ConvNet-Based Localization of Anatomical Structures in 3D Medical Images.

    PubMed

    de Vos, Bob; Wolterink, Jelmer; de Jong, Pim; Leiner, Tim; Viergever, Max; Isgum, Ivana

    2017-02-23

    Localization of anatomical structures is a prerequisite for many tasks in medical image analysis. We propose a method for automatic localization of one or more anatomical structures in 3D medical images through detection of their presence in 2D image slices using a convolutional neural network (ConvNet). A single ConvNet is trained to detect presence of the anatomical structure of interest in axial, coronal, and sagittal slices extracted from a 3D image. To allow the ConvNet to analyze slices of different sizes, spatial pyramid pooling is applied. After detection, 3D bounding boxes are created by combining the output of the ConvNet in all slices. In the experiments 200 chest CT, 100 cardiac CT angiography (CTA), and 100 abdomen CT scans were used. The heart, ascending aorta, aortic arch, and descending aorta were localized in chest CT scans, the left cardiac ventricle in cardiac CTA scans, and the liver in abdomen CT scans. Localization was evaluated using the distances between automatically and manually defined reference bounding box centroids and walls. The best results were achieved in localization of structures with clearly defined boundaries (e.g. aortic arch) and the worst when the structure boundary was not clearly visible (e.g. liver). The method was more robust and accurate in localization multiple structures.

  10. Parameters Affecting Loads on Buried Structures Subjected to Localized Blast Effects

    DTIC Science & Technology

    1992-04-01

    Structures Laboratory DEPARTMENT OF THE ARMY Waterways Experiment Station, Corps of Engineers 3909 Halls Ferry Road, Vicksburg, Mississippi 39180-6199...ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NUMBER US Army Engineer Waterways Experiment Station, Structures Laboratory, Technical Report SL-92-9...Loads on Buried Structures Subjected to Localized Blast Effects." These analyses were performed in the Structures Laboratory (SL), U.S. Army Engineer

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

    NASA Astrophysics Data System (ADS)

    Havu, Vile; Blum, Volker; Scheffler, Matthias

    2007-03-01

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

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

    PubMed

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

    2010-01-05

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

  13. Resolving the Sedimentary Basin Structure from Oklahoma with Local Receiver Function

    NASA Astrophysics Data System (ADS)

    Zheng, D.; Ni, S.

    2015-12-01

    The teleseismic receiver function is defined as the radial component of P wave being deconvoluted from the vertical component of the earthquakes with magnitude larger than 5.5 at teleseismic distances. It has successfully been applied in resolving the structure of the crust and upper mantle in many regions. The receiver function can also be used to determine the thickness of sedimentary basin. However the corner frequency of the P waves from the teleseismic events (M>5.5) is relatively low and the high frequency content in the teleseismic P waves is attenuated, thus, the teleseismic receiver function is usually not sufficient to reveal details of sedimentary basin structure. Instead, local small earthquake (~ M3) generates P waves of short duration waveforms with high frequency content, which can be used to calculate receiver functions (called local receiver function). As a case study, we study waveform data from local earthquakes in Oklahoma. We first explore feasibility of local receiver function for different magnitude, focal depth, epicentral distance, filtering band and time window length. After local receiver functions are computed, we search the best velocity model to fit the local receiver function waveforms with the Differential Evolution (DE) algorithm which is a global optimization method. We invert the sedimentary basin structure in Oklahoma and find that this method is suitable for other area for the sedimentary basin structure where local seismic waveforms are available.

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

    PubMed Central

    Davie, Stuart J; Di Pasquale, Nicodemo

    2016-01-01

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

  15. 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.

  16. Origin of the phase transition in IrTe2: structural modulation and local bonding instability

    SciTech Connect

    Cao, Huibo; Chakoumakos, Bryan C; Yan, Jiaqiang; Zhou, Haidong; Custelcean, Radu; Mandrus, D.; McGuire, Michael A; Singh, David J; Chen, Xin; Yang, Hui

    2013-01-01

    We used X-ray/neutron diffraction to determine the low temperature (LT) structure of IrTe2. A structural modulation was observed with a wavevector of k =(1/5, 0, 1/5) below Ts285 K, accompanied by a structural transition from a trigonal to a triclinic lattice. We also performed the first principles calculations for high temperature (HT) and LT structures, which elucidate the nature of the phase transition and the LT structure. A local bonding instability associated with the Te 5p states is likely the origin of the structural phase transition in IrTe2.

  17. Local reversibility and entanglement structure of many-body ground states

    NASA Astrophysics Data System (ADS)

    Kuwahara, Tomotaka; Arad, Itai; Amico, Luigi; Vedral, Vlatko

    2017-03-01

    The low-temperature physics of quantum many-body systems is largely governed by the structure of their ground states. Minimizing the energy of local interactions, ground states often reflect strong properties of locality such as the area law for entanglement entropy and the exponential decay of correlations between spatially separated observables. Here, we present a novel characterization of quantum states, which we call ‘local reversibility’. It characterizes the type of operations that are needed to reverse the action of a general disturbance on the state. We prove that unique ground states of gapped local Hamiltonian are locally reversible. This way, we identify new universal features of many-body ground states, which cannot be derived from the aforementioned properties. We use local reversibility to distinguish between states enjoying microscopic and macroscopic quantum phenomena. To demonstrate the potential of our approach, we prove specific properties of ground states, which are relevant both to critical and non-critical theories.

  18. Ultrahigh resolution imaging of local structural distortions in intergrowth tungsten bronzes.

    PubMed

    Kirkland, A I; Sloan, J; Haigh, S

    2007-01-01

    Details of the local structure of a complex tungsten bronze, K(x)WO(3) have been determined using focal series exit wave reconstruction. Octahedral rotations in different structural regions of the same crystal have been directly measured from the exit wave phase and correlated with variations in cation occupancy determined from the exit wave modulus.

  19. 33 CFR 208.10 - Local flood protection works; maintenance and operation of structures and facilities.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...; maintenance and operation of structures and facilities. 208.10 Section 208.10 Navigation and Navigable Waters... Local flood protection works; maintenance and operation of structures and facilities. (a) General. (1... responsible for the development and maintenance of, and directly in charge of, an organization responsible...

  20. 33 CFR 208.10 - Local flood protection works; maintenance and operation of structures and facilities.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...; maintenance and operation of structures and facilities. 208.10 Section 208.10 Navigation and Navigable Waters... Local flood protection works; maintenance and operation of structures and facilities. (a) General. (1... responsible for the development and maintenance of, and directly in charge of, an organization responsible...

  1. 33 CFR 208.10 - Local flood protection works; maintenance and operation of structures and facilities.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...; maintenance and operation of structures and facilities. 208.10 Section 208.10 Navigation and Navigable Waters... Local flood protection works; maintenance and operation of structures and facilities. (a) General. (1... responsible for the development and maintenance of, and directly in charge of, an organization responsible...

  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. Simulation of NMR data reveals that proteins' local structures are stabilized by electronic polarization.

    PubMed

    Tong, Yan; Ji, Chang G; Mei, Ye; Zhang, John Z H

    2009-06-24

    Molecular dynamics simulations of NMR backbone relaxation order parameters have been carried out to investigate the polarization effect on the protein's local structure and dynamics for five benchmark proteins (bovine pancreatic trypsin inhibitor, immunoglobulin-binding domain (B1) of streptococcal protein G, bovine apo-calbindin D9K, human interleukin-4 R88Q mutant, and hen egg white lysozyme). In order to isolate the polarization effect from other interaction effects, our study employed both the standard AMBER force field (AMBER03) and polarized protein-specific charges (PPCs) in the MD simulations. The simulated order parameters, employing both the standard nonpolarizable and polarized force fields, are directly compared with experimental data. Our results show that residue-specific order parameters at some specific loop and turn regions are significantly underestimated by the MD simulations using the standard AMBER force field, indicating hyperflexibility of these local structures. Detailed analysis of the structures and dynamic motions of individual residues reveals that the hyperflexibility of these local structures is largely related to the breaking or weakening of relevant hydrogen bonds. In contrast, the agreement with the experimental results is significantly improved and more stable local structures are observed in the MD simulations using the polarized force field. The comparison between theory and experiment provides convincing evidence that intraprotein hydrogen bonds in these regions are stabilized by electronic polarization, which is critical to the dynamical stability of these local structures in proteins.

  4. Defect-mediated snaking: A new growth mechanism for localized structures

    NASA Astrophysics Data System (ADS)

    Ma, Y.-P.; Burke, J.; Knobloch, E.

    2010-10-01

    Stationary spatially localized patterns in parametrically driven systems are studied, focusing on the 2:1 and 1:1 resonance tongues as described by the forced complex Ginzburg-Landau equation. Homoclinic snaking is identified in both cases and the nature of the growth of the localized structures along the snaking branches is described. The structures grow from a central defect that inserts new rolls on either side, while pushing existing rolls outwards. This growth mechanism differs fundamentally from that found in other systems exhibiting homoclinic snaking in which new rolls are added at the fronts that connect the structure to the background homogeneous state.

  5. Quantitative Characterization of Local Protein Solvation To Predict Solvent Effects on Protein Structure

    PubMed Central

    Vagenende, Vincent; Trout, Bernhardt L.

    2012-01-01

    Characterization of solvent preferences of proteins is essential to the understanding of solvent effects on protein structure and stability. Although it is generally believed that solvent preferences at distinct loci of a protein surface may differ, quantitative characterization of local protein solvation has remained elusive. In this study, we show that local solvation preferences can be quantified over the entire protein surface from extended molecular dynamics simulations. By subjecting microsecond trajectories of two proteins (lysozyme and antibody fragment D1.3) in 4 M glycerol to rigorous statistical analyses, solvent preferences of individual protein residues are quantified by local preferential interaction coefficients. Local solvent preferences for glycerol vary widely from residue to residue and may change as a result of protein side-chain motions that are slower than the longest intrinsic solvation timescale of ∼10 ns. Differences of local solvent preferences between distinct protein side-chain conformations predict solvent effects on local protein structure in good agreement with experiment. This study extends the application scope of preferential interaction theory and enables molecular understanding of solvent effects on protein structure through comprehensive characterization of local protein solvation. PMID:22995508

  6. Enhanced damage localization for complex structures through statistical modeling and sensor fusion

    NASA Astrophysics Data System (ADS)

    Haynes, Colin; Todd, Michael

    2015-03-01

    Ultrasonic guided waves represent a promising technique for detecting and localizing structural damage, but their application to realistic structures has been hampered by the complicated interference patterns produced by scattering from geometric features. This work presents a new damage localization paradigm based on a statistical approach to dealing with uncertainty in the guided wave signals. A bolted frame and a section of a fuselage rib are tested with different simulated damage conditions and used to conduct a detailed comparison between the proposed solution and other sparse-array localization approaches. After establishing the superiority of the statistical approach, two novel innovations to the localization procedure are proposed: an approach to sensor fusion based on the Neyman-Pearson criterion, and a method of constructing simple models of geometrical features. Including the sensor fusion and geometrical models produces a substantial improvement in the system's localization accuracy. The final result is a robust and accurate framework for single-site damage localization that moves structural health monitoring towards practical implementation on a much broader range of structures.

  7. 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.

  8. Seismicity and structure of the 85°E volcanic complex at the ultraslow spreading Gakkel Ridge from local earthquake tomography

    NASA Astrophysics Data System (ADS)

    Korger, E. I. M.; Schlindwein, V.

    2014-01-01

    Accretion mechanisms at ultraslow spreading ridges are still only poorly understood due to difficult survey conditions for seismic experiments at these ridges. Melts gets focused in distinct magmatic centres, with thin crust in between. At the 85°E/85°N volcanic complex at Gakkel Ridge, Arctic Ocean, where a recent spreading episode has been observed, perennial sea ice cover challenges traditional investigations of seismic structure and microseismicity. We used an unusual survey set-up to gather seismological data during 16 d in 2007 July, using seismometer arrays mounted on ice floes. Despite only 12 stations, the drift of the ice floes over the survey area resulted in a multitude of crossing rays in the rift valley. The data included 303 microearthquakes of which 248 events could be confidently located. We compiled a 1-D velocity model by localizing a subset of these earthquakes with a suite of randomly created velocity models. In this model, the Moho is placed at 7 km depth below seafloor, inferring a thick, basaltic crust. Using 124 events which were recorded by at least two arrays, we inverted for P-wave velocity structure in a local earthquake tomography. Resolution tests indicate reliable results in the central rift valley, illuminating the thermal structure underneath the Asgard volcanic chain in the aftermath of its most recent spreading episode. Our results show microearthquake activity down to 16 km beneath seafloor, inferring a cold lithosphere. Most hypocentres cluster at the centre of the rift valley at the site of the Asgard volcanic chain. This may mean that existing thermal models for this class of ridges have to be refined. An area of decreased seismic velocities crosses the rift valley at this location and microearthquake activity is located at its eastern fringe where the velocity gradient is highest. We therefore speculate that the reduced velocities may be caused by warm intruded material and that the observed seismicity predominatly

  9. 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.

  10. Cryogenic optical localization provides 3D protein structure data with Angstrom resolution.

    PubMed

    Weisenburger, Siegfried; Boening, Daniel; Schomburg, Benjamin; Giller, Karin; Becker, Stefan; Griesinger, Christian; Sandoghdar, Vahid

    2017-02-01

    We introduce Cryogenic Optical Localization in 3D (COLD), a method to localize multiple fluorescent sites within a single small protein with Angstrom resolution. We demonstrate COLD by determining the conformational state of the cytosolic Per-ARNT-Sim domain from the histidine kinase CitA of Geobacillus thermodenitrificans and resolving the four biotin sites of streptavidin. COLD provides quantitative 3D information about small- to medium-sized biomolecules on the Angstrom scale and complements other techniques in structural biology.

  11. Effect of structural distortion and polarization in localization of electronic excitations in organic semiconductor materials

    NASA Astrophysics Data System (ADS)

    Nayyar, Iffat; Batista, Enrique; Tretiak, Sergei; Saxena, Avadh; Smith, Darryl; Martin, Richard

    2012-02-01

    Organic polymers find varied applications in optoelectronic devices such as solar cells, light emitting diodes and lasers. Detailed understanding of charge carrier transport by polarons and excitonic energy transfer producing singlet and triplet excitations is critical to improve their efficiency. We benchmarked the ability of current functional models to describe the spatial extent of self-trapped neutral and charged excitations for MEH-PPV owing to its superior luminescence and experimental evidence. Now we are interested in distinguishing between two distinct origins leading to localization; spatial localization of the wavefunction by itself on the undistorted geometry and localization of the wavefunction assured by distortion of the structure during its relaxation. We suggest localization is produced by electronic rearrangements and character of the functional. We also observe that different functionals place the highest occupied and lowest virtual orbitals at different positions in the energy band diagram based on their ability to predict the extent of localization of these states.

  12. 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

  13. Effect of eddy current damping on phononic band gaps generated by locally resonant periodic structures

    NASA Astrophysics Data System (ADS)

    Ozkaya, Efe; Yilmaz, Cetin

    2017-02-01

    The effect of eddy current damping on a novel locally resonant periodic structure is investigated. The frequency response characteristics are obtained by using a lumped parameter and a finite element model. In order to obtain wide band gaps at low frequencies, the periodic structure is optimized according to certain constraints, such as mass distribution in the unit cell, lower limit of the band gap, stiffness between the components in the unit cell, the size of magnets used for eddy current damping, and the number of unit cells in the periodic structure. Then, the locally resonant periodic structure with eddy current damping is manufactured and its experimental frequency response is obtained. The frequency response results obtained analytically, numerically and experimentally match quite well. The inclusion of eddy current damping to the periodic structure decreases amplitudes of resonance peaks without disturbing stop band width.

  14. Chalcogenide centred gold complexes.

    PubMed

    Gimeno, M Concepción; Laguna, Antonio

    2008-09-01

    Chalcogenide-centred gold complexes are an important class of compounds in which a central chalcogen is surrounded by several gold atoms or gold and other metals. They have special characteristics such as unusual geometries, electron deficiency and properties such as luminescence or non-linear optical properties. The best known species are the trinuclear [E(AuPR3)3]+, 'oxonium' type species, that have high synthetic applicability, not only in other chalcogen-centred species, but in many other organometallic derivatives. The aurophilic interactions play an important role in the stability, preference for a particular geometry and luminescence properties in this type of derivatives (critical review, 117 references).

  15. Lidar Calibration Centre

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  16. Prediction of Local Quality of Protein Structure Models Considering Spatial Neighbors in Graphical Models

    PubMed Central

    Shin, Woong-Hee; Kang, Xuejiao; Zhang, Jian; Kihara, Daisuke

    2017-01-01

    Protein tertiary structure prediction methods have matured in recent years. However, some proteins defy accurate prediction due to factors such as inadequate template structures. While existing model quality assessment methods predict global model quality relatively well, there is substantial room for improvement in local quality assessment, i.e. assessment of the error at each residue position in a model. Local quality is a very important information for practical applications of structure models such as interpreting/designing site-directed mutagenesis of proteins. We have developed a novel local quality assessment method for protein tertiary structure models. The method, named Graph-based Model Quality assessment method (GMQ), explicitly considers the predicted quality of spatially neighboring residues using a graph representation of a query protein structure model. GMQ uses conditional random field as its core of the algorithm, and performs a binary prediction of the quality of each residue in a model, indicating if a residue position is likely to be within an error cutoff or not. The accuracy of GMQ was improved by considering larger graphs to include quality information of more surrounding residues. Moreover, we found that using different edge weights in graphs reflecting different secondary structures further improves the accuracy. GMQ showed competitive performance on a benchmark for quality assessment of structure models from the Critical Assessment of Techniques for Protein Structure Prediction (CASP). PMID:28074879

  17. Prediction of Local Quality of Protein Structure Models Considering Spatial Neighbors in Graphical Models.

    PubMed

    Shin, Woong-Hee; Kang, Xuejiao; Zhang, Jian; Kihara, Daisuke

    2017-01-11

    Protein tertiary structure prediction methods have matured in recent years. However, some proteins defy accurate prediction due to factors such as inadequate template structures. While existing model quality assessment methods predict global model quality relatively well, there is substantial room for improvement in local quality assessment, i.e. assessment of the error at each residue position in a model. Local quality is a very important information for practical applications of structure models such as interpreting/designing site-directed mutagenesis of proteins. We have developed a novel local quality assessment method for protein tertiary structure models. The method, named Graph-based Model Quality assessment method (GMQ), explicitly considers the predicted quality of spatially neighboring residues using a graph representation of a query protein structure model. GMQ uses conditional random field as its core of the algorithm, and performs a binary prediction of the quality of each residue in a model, indicating if a residue position is likely to be within an error cutoff or not. The accuracy of GMQ was improved by considering larger graphs to include quality information of more surrounding residues. Moreover, we found that using different edge weights in graphs reflecting different secondary structures further improves the accuracy. GMQ showed competitive performance on a benchmark for quality assessment of structure models from the Critical Assessment of Techniques for Protein Structure Prediction (CASP).

  18. 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.

  19. Robust extraction of local structures by the minimum beta-divergence method.

    PubMed

    Mollah, Md Nurul Haque; Sultana, Nayeema; Minami, Mihoko; Eguchi, Shinto

    2010-03-01

    This paper discusses a new highly robust learning algorithm for exploring local principal component analysis (PCA) structures in which an observed data follow one of several heterogeneous PCA models. The proposed method is formulated by minimizing beta-divergence. It searches a local PCA structure based on an initial location of the shifting parameter and a value for the tuning parameter beta. If the initial choice of the shifting parameter belongs to a data cluster, then the proposed method detects the local PCA structure of that data cluster, ignoring data in other clusters as outliers. We discuss the selection procedures for the tuning parameter beta and the initial value of the shifting parameter mu in this article. We demonstrate the performance of the proposed method by simulation. Finally, we compare the proposed method with a method based on a finite mixture model.

  20. 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.

  1. 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…

  2. 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.

  3. 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.

  4. 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.

  5. Functional classification of protein 3D structures from predicted local interaction sites.

    PubMed

    Parasuram, Ramya; Lee, Joslynn S; Yin, Pengcheng; Somarowthu, Srinivas; Ondrechen, Mary Jo

    2010-12-01

    A new approach to the functional classification of protein 3D structures is described with application to some examples from structural genomics. This approach is based on functional site prediction with THEMATICS and POOL. THEMATICS employs calculated electrostatic potentials of the query structure. POOL is a machine learning method that utilizes THEMATICS features and has been shown to predict accurate, precise, highly localized interaction sites. Extension to the functional classification of structural genomics proteins is now described. Predicted functionally important residues are structurally aligned with those of proteins with previously characterized biochemical functions. A 3D structure match at the predicted local functional site then serves as a more reliable predictor of biochemical function than an overall structure match. Annotation is confirmed for a structural genomics protein with the ribulose phosphate binding barrel (RPBB) fold. A putative glucoamylase from Bacteroides fragilis (PDB ID 3eu8) is shown to be in fact probably not a glucoamylase. Finally a structural genomics protein from Streptomyces coelicolor annotated as an enoyl-CoA hydratase (PDB ID 3g64) is shown to be misannotated. Its predicted active site does not match the well-characterized enoyl-CoA hydratases of similar structure but rather bears closer resemblance to those of a dehalogenase with similar fold.

  6. Coordination Analysis Using Global Structural Constraints and Alignment-based Local Features

    NASA Astrophysics Data System (ADS)

    Hara, Kazuo; Shimbo, Masashi; Matsumoto, Yuji

    We propose a hybrid approach to coordinate structure analysis that combines a simple grammar to ensure consistent global structure of coordinations in a sentence, and features based on sequence alignment to capture local symmetry of conjuncts. The weight of the alignment-based features, which in turn determines the score of coordinate structures, is optimized by perceptron training on a given corpus. A bottom-up chart parsing algorithm efficiently finds the best scoring structure, taking both nested or non-overlapping flat coordinations into account. We demonstrate that our approach outperforms existing parsers in coordination scope detection on the Genia corpus.

  7. RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs

    PubMed Central

    Sabarinathan, Radhakrishnan; Tafer, Hakim; Seemann, Stefan E; Hofacker, Ivo L; Stadler, Peter F; Gorodkin, Jan

    2013-01-01

    Structural characteristics are essential for the functioning of many noncoding RNAs and cis-regulatory elements of mRNAs. SNPs may disrupt these structures, interfere with their molecular function, and hence cause a phenotypic effect. RNA folding algorithms can provide detailed insights into structural effects of SNPs. The global measures employed so far suffer from limited accuracy of folding programs on large RNAs and are computationally too demanding for genome-wide applications. Here, we present a strategy that focuses on the local regions of maximal structural change between mutant and wild-type. These local regions are approximated in a “screening mode” that is intended for genome-wide applications. Furthermore, localized regions are identified as those with maximal discrepancy. The mutation effects are quantified in terms of empirical P values. To this end, the RNAsnp software uses extensive precomputed tables of the distribution of SNP effects as function of length and GC content. RNAsnp thus achieves both a noise reduction and speed-up of several orders of magnitude over shuffling-based approaches. On a data set comprising 501 SNPs associated with human-inherited diseases, we predict 54 to have significant local structural effect in the untranslated region of mRNAs. RNAsnp is available at http://rth.dk/resources/rnasnp. PMID:23315997

  8. Local structures in a computer-generated liquid. Two-dimensional Lennard-Jones liquid

    NASA Astrophysics Data System (ADS)

    Mitus, Antoni C.; Patashinskii, Alexander Z.; Sokolowski, Stefan

    1991-06-01

    We study the local structures in a 2D Lennard-Jones liquid of 2500 atoms near the melting line ( ϱ ∗ = 0.76 , T ∗ = 0.47 ) with the help of methods of mathematical statistics based on an earlier proposed probabilistic approach. We analyze the local structures in individual configurations and study the time evolution of patterns of matter which is close to the solid hexagonal structure. We conclude that the model liquid displays two types of local structure: hexagonal and “chaotic”. The first one corresponds to the fluctuations of the hexagon with root-mean-square fluctuations ξ of atoms equal to ξ = 0.14-0.16 while the second one can be represented by a strongly fluctuating (ξ = 0.25-0.30) “defect” pattern. We discuss the consequences of the physical picture of the liquid as a locally ordered two-structure system for the methodology of computer simulations and for theories of the 2D liquid phase.

  9. 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…

  10. 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…

  11. Discovering a Discovery Centre

    ERIC Educational Resources Information Center

    McCullagh, John; Stewart, James; Greenwood, Julian

    2007-01-01

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

  12. The Iranian Documentation Centre.

    ERIC Educational Resources Information Center

    Harvey, John F.

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

  13. 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…

  14. 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.

  15. Molecular dynamics simulations on local structure and diffusion in liquid Ti x Al 1- x alloys

    NASA Astrophysics Data System (ADS)

    Xia, J. H.; Liu, C. S.; Cheng, Z. F.; Shi, D. P.

    2011-10-01

    The microscopic structure and dynamics of liquid Ti xAl 1- x alloys together with pure liquid Ti and Al metals were investigated by means of molecular dynamics simulations. This work gives the structural properties, including pair-correlation function, bond-angle distribution function, HA and Voronoi indices, and their composition dependence. The dynamical properties have also been studied. The calculated pair-correlation function, bond-angle distribution function, and HA and Voronoi indices suggest that the stoichiometric composition Ti 0.75Al 0.25 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum diffusion coefficient at this composition. These results indicate that the mobility of atoms strongly depends on their atomic local structure.

  16. Local modulation and trapping of energetic particles by coherent magnetic structures

    NASA Astrophysics Data System (ADS)

    Tessein, Jeffrey A.; Ruffolo, David; Matthaeus, William H.; Wan, Minping

    2016-04-01

    Recent observational studies show strong statistical associations between features of interplanetary suprathermal energetic particle (EP) data and rapid changes in the interplanetary vector magnetic field. The latter are connected to intermittency and coherent magnetic structures, including classical discontinuities. Here we discuss these observations in the context of two appealing theoretical ideas: First, magnetic structures bounding flux tubes can cause local or temporary topological trapping, thus influencing EP transport. Second, charged particles may be accelerated by interacting with dynamic flux tubes, either through reconnection, trapping in secondary islands, or a betatron mechanism. We present observations that support interpretation in terms of trapping boundaries associated with changes in EP flux and also find a case in which an EP peak lies near a coherent magnetic structure that is not a shock, with changing particle anisotropy consistent with outflow from the structure, suggestive of local particle acceleration.

  17. Pressure-Induced Local Structural Changes in Heavy Fermion β-YbAlB4

    NASA Astrophysics Data System (ADS)

    Sakaguchi, Yui; Ikeda, Shugo; Kuga, Kentaro; Suzuki, Shintaro; Nakatsuji, Satoru; Hirao, Naohisa; Ohishi, Yasuo; Kobayashi, Hisao

    2016-02-01

    The structural properties of β-YbAlB4 with an orthorhombic Cmmm symmetry have been investigated by powder X-ray diffraction analysis using synchrotron radiation under high pressure (up to ˜20 GPa) at 7 K. Although the refined lattice parameters exhibit no discontinuity and the pressure dependence of the volume was well reproduced by the Murnaghan's equation of state up to ˜20 GPa, detailed analyses of the observed X-ray diffraction patterns reveal local structure changes in B layers at 3.5(2) and 5.8(1) GPa. The changes in the local structure strongly affect the bonding structures in the B layers among the conduction electrons of β-YbAlB4 under pressure at 7 K.

  18. 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.

  19. Genetic Structure and Potential Environmental Determinants of Local Genetic Diversity in Japanese Honeybees (Apis cerana japonica)

    PubMed Central

    Nagamitsu, Teruyoshi; Yasuda, Mika; Saito-Morooka, Fuki; Inoue, Maki N.; Nishiyama, Mio; Goka, Koichi; Sugiura, Shinji; Maeto, Kaoru; Okabe, Kimiko; Taki, Hisatomo

    2016-01-01

    Declines in honeybee populations have been a recent concern. Although causes of the declines remain unclear, environmental factors may be responsible. We focused on the potential environmental determinants of local populations of wild honeybees, Apis cerana japonica, in Japan. This subspecies has little genetic variation in terms of its mitochondrial DNA sequences, and genetic variations at nuclear loci are as yet unknown. We estimated the genetic structure and environmental determinants of local genetic diversity in nuclear microsatellite genotypes of fathers and mothers, inferred from workers collected at 139 sites. The genotypes of fathers and mothers showed weak isolation by distance and negligible genetic structure. The local genetic diversity was high in central Japan, decreasing toward the peripheries, and depended on the climate and land use characteristics of the sites. The local genetic diversity decreased as the annual precipitation increased, and increased as the proportion of urban and paddy field areas increased. Positive effects of natural forest area, which have also been observed in terms of forager abundance in farms, were not detected with respect to the local genetic diversity. The findings suggest that A. cerana japonica forms a single population connected by gene flow in its main distributional range, and that climate and landscape properties potentially affect its local genetic diversity. PMID:27898704

  20. 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.

  1. 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.

  2. 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.

  3. Structure and luminescence of intrinsic localized states in sodium silicate glasses

    NASA Astrophysics Data System (ADS)

    Konstantinou, Konstantinos; Duffy, Dorothy M.; Shluger, Alexander L.

    2016-11-01

    Sodium silicate glasses exhibit a characteristic luminescence with a maximum at about 3.4 eV, which is thought to be determined by optical excitation of local glass structures, called L centers. To investigate the atomic and electronic structures of these centers, we calculated the electronic properties of the ground and excited states of a sodium silicate glass using classical and ab initio methods. Classical molecular dynamics was used to generate glass models of Na2O -3 SiO2 molar composition, and the density functional theory (DFT), with hybrid functionals, was used to identify and characterize the geometric and electronic structures of L centers. The ground and excited L* center states are studied, and their calculated excitation and luminescence transition energies are in good agreement with experimental data. The results confirm that the lowest triplet excited states in sodium silicate glass are associated with small clusters of Na ions and nonbridging oxygen atoms. These clusters serve as structural precursors for the localization of the excited states, and the broad distribution of the luminescence energies is correlated with the short-range order of the Na cations. The atomic and electronic structures of the electron E1- and hole H1+ centers are also studied. These results provide a more detailed insight into the atomistic structure of localized states in these important glasses.

  4. Limits of slow sound propagation and transparency in lossy, locally resonant periodic structures

    NASA Astrophysics Data System (ADS)

    Theocharis, G.; Richoux, O.; Romero García, V.; Merkel, A.; Tournat, V.

    2014-09-01

    We investigate sound propagation in lossy, locally resonant periodic structures by studying an air-filled tube periodically loaded with Helmholtz resonators and taking into account the intrinsic viscothermal losses. In particular, by tuning the resonator with the Bragg gap in this prototypical locally resonant structure, we study the limits and various characteristics of slow sound propagation. While in the lossless case the overlapping of the gaps results in slow-sound-induced transparency of a narrow frequency band surrounded by a strong and broadband gap, the inclusion of the unavoidable losses imposes limits to the slowdown factor and the maximum transmission. Experiments, theory, and finite element simulations have been used for the characterization of acoustic wave propagation by tuning the Helmholtz/Bragg frequencies and the total amount of loss both for infinite and finite lattices. This study contributes to the field of locally resonant acoustic metamaterials and slow sound applications.

  5. Strong nonlocal coupling stabilizes localized structures: an analysis based on front dynamics.

    PubMed

    Fernandez-Oto, C; Clerc, M G; Escaff, D; Tlidi, M

    2013-04-26

    We investigate the effect of strong nonlocal coupling in bistable spatially extended systems by using a Lorentzian-like kernel. This effect through front interaction drastically alters the space-time dynamics of bistable systems by stabilizing localized structures in one and two dimensions, and by affecting the kinetics law governing their behavior with respect to weak nonlocal and local coupling. We derive an analytical formula for the front interaction law and show that the kinetics governing the formation of localized structures obeys a law inversely proportional to their size to some power. To illustrate this mechanism, we consider two systems, the Nagumo model describing population dynamics and nonlinear optics model describing a ring cavity filled with a left-handed material. Numerical solutions of the governing equations are in close agreement with analytical predictions.

  6. Testing the relationship between local cue-response patterns and the global structure of communication behaviour.

    PubMed

    Taylor, Paul J; Donald, Ian

    2007-06-01

    A central assumption of negotiation research is that organized sequences of cues and responses underlie the dimensions and constructs found to structure interaction. We empirically tested this assumption using a new 'proximity' coefficient, which measures the global interrelationships among behaviours based on their intrinsic local organization within an interaction sequence. An analysis of sequences from 21 hostage negotiations showed that local cue-response dependencies are organized in a way that corresponds with an established structural model of communication. Further analysis of case-specific coefficients showed that criminal, political and domestic incidents involve very different cue-response dynamics, with criminal incidents dividing into two distinct types of interaction. The importance of the proximity concept for unifying local and global accounts of negotiation behaviour, and the avenues of research made possible by the proximity coefficient, are discussed.

  7. 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.

  8. 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…

  9. 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.

  10. Influence of static habitat attributes on local and regional Rocky intertidal community structure

    USGS Publications Warehouse

    Konar, B.; Iken, K.; Coletti, H.; Monson, Daniel H.; Weitzman, Ben P.

    2016-01-01

    Rocky intertidal communities are structured by local environmental drivers, which can be dynamic, fluctuating on various temporal scales, or static and not greatly varying across years. We examined the role of six static drivers (distance to freshwater, tidewater glacial presence, wave exposure, fetch, beach slope, and substrate composition) on intertidal community structure across the northern Gulf of Alaska. We hypothesized that community structure is less similar at the local scale compared with the regional scale, coinciding with static drivers being less similar on smaller than larger scales. We also hypothesized that static attributes mainly drive local biological community structure. For this, we surveyed five to six sites in each of the six regions in the mid and low intertidal strata. Across regions, static attributes were not consistently different and only small clusters of sites had similar attributes. Additionally, intertidal communities were less similar on the site compared with the region level. These results suggest that these biological communities are not strongly influenced by the local static attributes measured in this study. An alternative explanation is that static attributes among our regions are not different enough to influence the biological communities. This lack of evidence for a strong static driver may be a result of our site selection, which targeted rocky sheltered communities. This suggests that this habitat may be ideal to examine the influence of dynamic drivers. We recommend that future analyses of dynamic attributes may best be performed after analyses have demonstrated that sites do not differ in static attributes.

  11. 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

  12. 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.

  13. An Integrated Program Structure and System of Account Codes for PPBS in Local School Districts.

    ERIC Educational Resources Information Center

    Miller, Donald R.

    This monograph presents a comprehensive but tentative matrix program structure and system of account codes that have been integrated to facilitate the implementation of PPB systems in local school districts. It is based on the results of an extensive analysis of K-12 public school district programs and management practices. In its entirety, the…

  14. Types and concentrations of metal ions affect local structure and dynamics of RNA

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Xiao, Yi

    2016-10-01

    The roles that metal ions play in the structure and dynamics of RNA molecules are long-standing problems that have been studied extensively but are still not well understood. Here we show that metal ions have distributions around RNA molecules that strongly depend on the types and concentrations of the metal ions and also the electrostatic surface of the molecule. In particular, the ion distributions may not balance all the local electronegativity of the molecule. These ion distributions do not only greatly affect local structures but also lead to different local dynamics of RNA. We studied the effects of different ion solutions on the structure and dynamics of RNA by taking the pre Q1 riboswitch aptamer domain as an illustrative example and using molecular dynamics simulations. Since the local structures and dynamics of RNAs are important to their functions, our results also indicate that the selection of proper ion conditions is necessary to model them correctly, in contrast to the use of diverse ion solutions in current molecular dynamics simulations.

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

    PubMed

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

    2013-11-13

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

  16. Decoupling local mechanics from large-scale structure in modular metamaterials.

    PubMed

    Yang, Nan; Silverberg, Jesse L

    2017-04-04

    A defining feature of mechanical metamaterials is that their properties are determined by the organization of internal structure instead of the raw fabrication materials. This shift of attention to engineering internal degrees of freedom has coaxed relatively simple materials into exhibiting a wide range of remarkable mechanical properties. For practical applications to be realized, however, this nascent understanding of metamaterial design must be translated into a capacity for engineering large-scale structures with prescribed mechanical functionality. Thus, the challenge is to systematically map desired functionality of large-scale structures backward into a design scheme while using finite parameter domains. Such "inverse design" is often complicated by the deep coupling between large-scale structure and local mechanical function, which limits the available design space. Here, we introduce a design strategy for constructing 1D, 2D, and 3D mechanical metamaterials inspired by modular origami and kirigami. Our approach is to assemble a number of modules into a voxelized large-scale structure, where the module's design has a greater number of mechanical design parameters than the number of constraints imposed by bulk assembly. This inequality allows each voxel in the bulk structure to be uniquely assigned mechanical properties independent from its ability to connect and deform with its neighbors. In studying specific examples of large-scale metamaterial structures we show that a decoupling of global structure from local mechanical function allows for a variety of mechanically and topologically complex designs.

  17. 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.

  18. Local structural investigation of SmFeAsO₁₋xF(x) high temperature superconductors.

    PubMed

    Malavasi, Lorenzo; Artioli, Gianluca A; Kim, Hyunjeong; Maroni, Beatrice; Joseph, Boby; Ren, Yang; Proffen, Thomas; Billinge, Simon J L

    2011-07-13

    A strong revitalization of the field of high temperature superconductivity (HTSC) has been induced recently by the discovery of T(C) around 26 K in F-doped LaFeAsO iron pnictides. Starting from this discovery, a huge amount of experimental data have been accumulated. This important corpus of results will allow the development of suitable theoretical models aimed at describing the basic electronic structure properties and nature of superconducting states in these fascinating new systems. A close correlation between structural features and physical properties of the normal and superconducting states has already been demonstrated in the current literature. Advanced theoretical models are also based on the close correlation with structural properties and in particular with the Fe-As tetrahedral array. As for other complex materials, a deeper understanding of their structure-properties correlation requires a full knowledge of the atomic arrangement within the structure. Here we report an investigation of the local structure in the SmFeAsO₁₋ xF(x) system carried out by means of x-ray total scattering measurements and pair distribution function analysis. The results presented indicate that the local structure of these HTSC significantly differs from the average structure determined by means of traditional diffraction techniques, in particular the distribution of Fe-As bond lengths. In addition, a model for describing the observed discrepancies is presented.

  19. Local structural investigation of SmFeAsO1 - xFx high temperature superconductors

    NASA Astrophysics Data System (ADS)

    Malavasi, Lorenzo; Artioli, Gianluca A.; Kim, Hyunjeong; Maroni, Beatrice; Joseph, Boby; Ren, Yang; Proffen, Thomas; Billinge, Simon J. L.

    2011-07-01

    A strong revitalization of the field of high temperature superconductivity (HTSC) has been induced recently by the discovery of TC around 26 K in F-doped LaFeAsO iron pnictides. Starting from this discovery, a huge amount of experimental data have been accumulated. This important corpus of results will allow the development of suitable theoretical models aimed at describing the basic electronic structure properties and nature of superconducting states in these fascinating new systems. A close correlation between structural features and physical properties of the normal and superconducting states has already been demonstrated in the current literature. Advanced theoretical models are also based on the close correlation with structural properties and in particular with the Fe-As tetrahedral array. As for other complex materials, a deeper understanding of their structure-properties correlation requires a full knowledge of the atomic arrangement within the structure. Here we report an investigation of the local structure in the SmFeAsO1 - xFx system carried out by means of x-ray total scattering measurements and pair distribution function analysis. The results presented indicate that the local structure of these HTSC significantly differs from the average structure determined by means of traditional diffraction techniques, in particular the distribution of Fe-As bond lengths. In addition, a model for describing the observed discrepancies is presented.

  20. Propagation and localization of electromagnetic waves in quasiperiodic serial loop structures

    NASA Astrophysics Data System (ADS)

    Aynaou, H.; El Boudouti, E. H.; El Hassouani, Y.; Akjouj, A.; Djafari-Rouhani, B.; Vasseur, J.; Benomar, A.; Velasco, V. R.

    2005-11-01

    We study the propagation of electromagnetic waves in one-dimensional quasiperiodic photonic band gap structures made of serial loop structures separated by segments. Different quasiperiodic structures such as Fibonacci, Thue-Morse, Rudin-Shapiro, and double period are investigated with special focus on the Fibonacci structure. Depending on the lengths of the two arms constituting the loops, one can distinguish two particular cases. (i) There are symmetric loop structures, which are shown to be equivalent to impedance-modulated mediums. In this case, it is found that besides the existence of extended and forbidden modes, some narrow frequency bands appear as defect modes in the transmission spectrum inside the gaps. These modes are shown to be localized within only one of the two types of blocks constituting the structure. An analysis of the transmission phase time enables us to derive the group velocity as well as the density of states in these structures. In particular, the stop bands (localized modes) may give rise to unusual (strong normal) dispersion in the gaps, yielding fast (slow) group velocities above (below) the velocity of light. (ii) There are also asymmetric loop structures, where the loops play the role of resonators that may introduce transmission zeros and hence additional gaps unnoticed in the case of simple impedance-modulated mediums. A comparison of the transmission amplitude and phase time of Fibonacci systems with those of other quasiperiodic systems is also outlined. In particular, it was shown that these structures present similar behaviors in the transmission spectra inside the regions of extended modes, whereas they present different localized modes inside the gaps. Experiments and numerical calculations are in very good agreement.

  1. 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.

  2. The green emission and local structure of the scintillator PbWO 4

    NASA Astrophysics Data System (ADS)

    Qi, Zeming; Shi, Chaoshu; Zhou, Dongfang; Tang, Honggao; Liu, Tao; Hu, Tiandou

    2001-12-01

    The green emission of lead tungstate (PbWO 4 ) is closely related to structure defects. For studying the mechanism of the green emission, the local structure of PbWO 4 has been first investigated by extended X-ray absorption fine structure using synchrotron radiation. The results indicate that the excess oxygen in air-annealed PbWO 4 exists and forms “WO 4+O i” centers. The green emission of PbWO 4 is not caused by (WO 3+F) centers, but probably originates from the centers of “WO 4+O i”.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Quantitative characterizations of phasic structure developments by local measurement methods in two-phase flow

    SciTech Connect

    Eberle, C.S.; Leung, W.H.; Wu, Q.; Ueno, T.; Ishii, M.

    1995-06-01

    An experimental study on the internal structure an a out in a 25.4 mm ID pipe. The local void fraction and interfacial area concentration were measured by a double-sensor probe. The flow structure development was visualized by measuring the radial distribution of these two parameters at three axial, locations (L/D = 12, 62, and 112). A more detailed study on the fully developed flow structure was conducted at L/D = 120. The interfacial structure were measured by the double- and four-sensor probes. A bubbly to-=slug transition region was defined according to the local data.The area-averaged void fraction measurements were given by a gamma densitometer. Other parameters such as the Taylor bubble film thickness, bubble length and slug unit length in slug flow were measured by a film robe. The redundant measurements were made to calibrate the local probe measurements. The quantitative representation of the phasic structure can then be used for modeling.

  8. Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity

    PubMed Central

    Lee, Hui Sun; Im, Wonpil

    2013-01-01

    Accurate determination of potential ligand binding sites (BS) is a key step for protein function characterization and structure-based drug design. Despite promising results of template-based BS prediction methods using global structure alignment (GSA), there is a room to improve the performance by properly incorporating local structure alignment (LSA) because BS are local structures and often similar for proteins with dissimilar global folds. We present a template-based ligand BS prediction method using G-LoSA, our LSA tool. A large benchmark set validation shows that G-LoSA predicts drug-like ligands’ positions in single-chain protein targets more precisely than TM-align, a GSA-based method, while the overall success rate of TM-align is better. G-LoSA is particularly efficient for accurate detection of local structures conserved across proteins with diverse global topologies. Recognizing the performance complementarity of G-LoSA to TM-align and a non-template geometry-based method, fpocket, a robust consensus scoring method, CMCS-BSP (Complementary Methods and Consensus Scoring for ligand Binding Site Prediction), is developed and shows improvement on prediction accuracy. The G-LoSA source code is freely available at http://im.bioinformatics.ku.edu/GLoSA. PMID:23957286

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

    PubMed

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

    2010-07-01

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

  10. 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

  11. Local structural investigation of buried InAs(x)P(1-x)/InP interfaces

    NASA Astrophysics Data System (ADS)

    Lamberti, C.; Bordiga, S.; Boscherini, F.; Pascarelli, S.; Schiavini, G. M.; Ferari, C.; Lazzarini, L.; Salviati, G.

    1994-10-01

    A local structural investigation has been carried out on the 10 A InAs(x)P(1-x) layer in ad hoc grown InAs(x)P(1-x)/InP epitaxal multistructures deposited by low pressure metallorganic chemical vapor deposition by means of extended x-ray absorption fine structure spectroscopy, high resolution transmission electron microscopy, and high resolution x-ray diffraction analyses. The goal was to characterize the local structure of the unwanted, strained, interface layers of InAs(x)P(1-x) produced by the exposure of the InP surface to AsH3 as occurs during the growth of InP/In(0.53)Ga(0.47)As heterostructures optimized for photonics. High resolution x-ray diffraction and high resolution transmission electron microscopy confirm the high crystalline perfection of the investigated interfaces. As K-edge extended x-ray absorption fine structure analysis shows, the first shell environment of As at these interfaces is similar to that found in bulk InAs(x)P(1-X) alloys of similar composition, as determined experimentally and by comparison with recent theories of bond lengths in semiconductor alloys. In particular we measure an As-In bond length which varies at most 0.02 A with As concentration at the interface; this implies that epitaxy with InP is accompanied by local structural distortions, such as bond angle variations, which accommodate the nearly constant As-In bond length.

  12. Damage localization in linear-form structures based on sensitivity investigation for principal component analysis

    NASA Astrophysics Data System (ADS)

    Viet Ha, Nguyen; Golinval, Jean-Claude

    2010-10-01

    This paper addresses the problem of damage detection and localization in linear-form structures. Principal component analysis (PCA) is a popular technique for dynamic system investigation. The aim of the paper is to present a damage diagnosis method based on sensitivities of PCA results in the frequency domain. Starting from frequency response functions (FRFs) measured at different locations on the structure; PCA is performed to determine the main features of the signals. Sensitivities of principal directions obtained from PCA to structural parameters are then computed and inspected according to the location of sensors; their variation from the healthy state to the damaged state indicates damage locations. It is worth noting that damage localization is performed without the need of modal identification. Influences of some features as noise, choice of parameter and number of sensors are discussed. The efficiency and limitations of the proposed method are illustrated using numerical and real-world examples.

  13. Localization and fractal spectra of optical phonon modes in quasiperiodic structures

    NASA Astrophysics Data System (ADS)

    Anselmo, D. H. A. L.; Dantas, A. L.; Medeiros, S. K.; Albuquerque, E. L.; Freire, V. N.

    2005-04-01

    The dispersion relation and localization profile of confined optical phonon modes in quasiperiodic structures, made up of nitride semiconductor materials, are analyzed through a transfer-matrix approach. The quasiperiodic structures are characterized by the nature of their Fourier spectrum, which can be dense pure point (Fibonacci sequences) or singular continuous (Thue-Morse and Double-period sequences). These substitutional sequences are described in terms of a series of generations that obey peculiar recursion relations and/or inflation rules. We present a quantitative analysis of the localization and magnitude of the allowed band widths in the optical phonons spectra of these quasiperiodic structures, as well as how they scale as a function of the number of generations of the sequences.

  14. On the influence of ion exchange on the local structure of the titanosilicate ETS-10.

    PubMed

    Pavel, Claudiu C; Zibrowius, Bodo; Löffler, Elke; Schmidt, Wolfgang

    2007-07-14

    The effect of ion exchange with different monovalent cations (NH(4)(+), K(+), Na(+) and Cs(+)) on the local structure of the titanosilicate ETS-10 has been studied by (29)Si MAS NMR and Raman spectroscopy. Although X-ray diffraction shows no significant influence of ion exchange on the long range order, ammonium exchange is found to result in substantial damage to the local structure. Ion exchange experiments with alkali cations under significantly more acidic conditions clearly show that the structural damage brought about by ammonium exchange is not caused by the low pH of the exchange solution. The exchange with potassium and caesium ions also leads to significant changes in the (29)Si NMR and Raman spectra. However, these changes can largely be reversed by sodium back-exchange.

  15. Effective 3D protein structure prediction with local adjustment genetic-annealing algorithm.

    PubMed

    Zhang, Xiao-Long; Lin, Xiao-Li

    2010-09-01

    The protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing the energy function. The protein folding structure prediction is computationally challenging and has been shown to be NP-hard problem when the 3D off-lattice AB model is employed. In this paper, the local adjustment genetic-annealing (LAGA) algorithm was used to search the ground state of 3D offlattice AB model for protein folding structure. The algorithm included an improved crossover strategy and an improved mutation strategy, where a local adjustment strategy was also used to enhance the searching ability. The experiments were carried out with the Fibonacci sequences. The experimental results demonstrate that the LAGA algorithm appears to have better performance and accuracy compared to the previous methods.

  16. Forced snaking: Localized structures in the real Ginzburg-Landau equation with spatially periodic parametric forcing

    NASA Astrophysics Data System (ADS)

    Ponedel, Benjamin C.; Knobloch, Edgar

    2016-11-01

    We study spatial localization in the real subcritical Ginzburg-Landau equation ut = m0u + Q(x)u + uxx + d|u|2u -|u|4u with spatially periodic forcing Q(x). When d>0 and Q ≡ 0 this equation exhibits bistability between the trivial state u = 0 and a homogeneous nontrivial state u = u0 with stationary localized structures which accumulate at the Maxwell point m0 = -3d2/16. When spatial forcing is included its wavelength is imprinted on u0 creating conditions favorable to front pinning and hence spatial localization. We use numerical continuation to show that under appropriate conditions such forcing generates a sequence of localized states organized within a snakes-and-ladders structure centered on the Maxwell point, and refer to this phenomenon as forced snaking. We determine the stability properties of these states and show that longer lengthscale forcing leads to stationary trains consisting of a finite number of strongly localized, weakly interacting pulses exhibiting foliated snaking.

  17. Local structure and La L1 and L3-edge XANES spectra of lanthanum complex oxides.

    PubMed

    Asakura, Hiroyuki; Shishido, Tetsuya; Teramura, Kentaro; Tanaka, Tsunehiro

    2014-06-16

    La L1 and L3-edge X-ray absorption near-edge structure (XANES) of various La oxides were classified according to the local configuration of La. We found a correlation between both of the areas of the pre-edge peaks of the La L1-edge XANES spectra and the full width at half-maximum of white line of La L3-edge XANES spectra and the local configuration of La. Theoretical calculation of the XANES spectra and local density of states reveals the difference of La L1 and L3-edge XANES spectra of various La compounds is related to the p-d hybridization of the unoccupied band and broadening of the d band of La induced by the difference of local configuration. In addition, simplified bond angle analysis parameters defined by the angles of the La atom and the two adjacent oxygen atoms are correlated to the pre-edge peak intensity of the La L1-edge XANES spectra. These results indicate that quantitative analysis of La L1 and L3-edge XANES spectra could be an indicator of the local structure of La materials.

  18. Emergence of Coherent Localized Structures in Shear Deformations of Temperature Dependent Fluids

    NASA Astrophysics Data System (ADS)

    Katsaounis, Theodoros; Olivier, Julien; Tzavaras, Athanasios E.

    2016-12-01

    Shear localization occurs in various instances of material instability in solid mechanics and is typically associated with Hadamard-instability for an underlying model. While Hadamard instability indicates the catastrophic growth of oscillations around a mean state, it does not by itself explain the formation of coherent structures typically observed in localization. The latter is a nonlinear effect and its analysis is the main objective of this article. We consider a model that captures the main mechanisms observed in high strain-rate deformation of metals, and describes shear motions of temperature dependent non-Newtonian fluids. For a special dependence of the viscosity on the temperature, we carry out a linearized stability analysis around a base state of uniform shearing solutions, and quantitatively assess the effects of the various mechanisms affecting the problem: thermal softening, momentum diffusion and thermal diffusion. Then, we turn to the nonlinear model, and construct localized states—in the form of similarity solutions—that emerge as coherent structures in the localization process. This justifies a scenario for localization that is proposed on the basis of asymptotic analysis in uc(Katsaounis) and uc(Tzavaras) (SIAM J Appl Math 69:1618-1643, 2009).

  19. Emergence of Coherent Localized Structures in Shear Deformations of Temperature Dependent Fluids

    NASA Astrophysics Data System (ADS)

    Katsaounis, Theodoros; Olivier, Julien; Tzavaras, Athanasios E.

    2017-04-01

    Shear localization occurs in various instances of material instability in solid mechanics and is typically associated with Hadamard-instability for an underlying model. While Hadamard instability indicates the catastrophic growth of oscillations around a mean state, it does not by itself explain the formation of coherent structures typically observed in localization. The latter is a nonlinear effect and its analysis is the main objective of this article. We consider a model that captures the main mechanisms observed in high strain-rate deformation of metals, and describes shear motions of temperature dependent non-Newtonian fluids. For a special dependence of the viscosity on the temperature, we carry out a linearized stability analysis around a base state of uniform shearing solutions, and quantitatively assess the effects of the various mechanisms affecting the problem: thermal softening, momentum diffusion and thermal diffusion. Then, we turn to the nonlinear model, and construct localized states—in the form of similarity solutions—that emerge as coherent structures in the localization process. This justifies a scenario for localization that is proposed on the basis of asymptotic analysis in Katsaounis and Tzavaras (SIAM J Appl Math 69:1618-1643, 2009).

  20. 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

  1. Structural and functional characterization of human telomerase RNA processing and cajal body localization signals.

    PubMed

    Theimer, Carla A; Jády, Beáta E; Chim, Nicholas; Richard, Patricia; Breece, Katherine E; Kiss, Tamás; Feigon, Juli

    2007-09-21

    The RNA component of human telomerase (hTR) includes H/ACA and CR7 domains required for 3' end processing, localization, and accumulation. The terminal loop of the CR7 domain contains the CAB box (ugAG) required for targeting of scaRNAs to Cajal bodies (CB) and an uncharacterized sequence required for accumulation and processing. To dissect out the contributions of the CR7 stem loop to hTR processing and localization, we solved the solution structures of the 3' terminal stem loops of hTR CR7 and U64 H/ACA snoRNA, and the 5' terminal stem loop of U85 C/D-H/ACA scaRNA. These structures, together with analysis of localization, processing, and accumulation of hTRs containing nucleotide substitutions in the CR7 domain, identified the sequence and structural requirements of the hTR processing and CB localization signals and showed that these signals are functionally independent. Further, 3' end processing was found to be a prerequisite for translocation of hTR to CBs.

  2. 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

  3. 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.

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

    DOE PAGES

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

    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

  5. 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

  6. Probing Local Structures in ZrO2 Nanocrystals Using EXAFS

    NASA Astrophysics Data System (ADS)

    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.; Lee, J. F.; Cheung, C. L.; Sabirianov, R. F.; Namavar, F.; Mei, W. N.

    2008-03-01

    Extended x-ray absorption fine structure (EXAFS) has been employed to investigate the local structures surrounding Zr in cubic zirconia thin films prepared by an ion beam assisted deposition technique. These materials have demonstrated promising mechanical properties such as improved hardness and lubricant wettability compared to yttria-stabilized zirconia. To verify the cubic structure of zirconia in films prepared under different growth conditions and to fully understand the mechanism leading to their unique physical properties, the structural information is a required prerequisite. Since zirconia is in the form of nanosized crystallets, conventional x-ray diffraction method is not useful for this purpose. Our x-ray results reveal cubic-like structure with O vacancies around Zr in several nanocrystal samples. Powders of cubic zirconia prepared using chemical methods were also measured for comparison.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. Local structure, composition, and crystallization mechanism of a model two-phase “composite nanoglass”

    SciTech Connect

    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.

  13. Local structure, composition, and crystallization mechanism of a model two-phase “composite nanoglass”

    SciTech Connect

    Chattopadhyay, Soma; Shibata, Tomohiro; Kelly, S. D.; 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 Cu{sub 55}Nb{sub 45}. 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.

  14. 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

  15. 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.

  16. Delay-induced depinning of localized structures in a spatially inhomogeneous Swift-Hohenberg model

    NASA Astrophysics Data System (ADS)

    Tabbert, Felix; Schelte, Christian; Tlidi, Mustapha; Gurevich, Svetlana V.

    2017-03-01

    We report on the dynamics of localized structures in an inhomogeneous Swift-Hohenberg model describing pattern formation in the transverse plane of an optical cavity. This real order parameter equation is valid close to the second-order critical point associated with bistability. The optical cavity is illuminated by an inhomogeneous spatial Gaussian pumping beam and subjected to time-delayed feedback. The Gaussian injection beam breaks the translational symmetry of the system by exerting an attracting force on the localized structure. We show that the localized structure can be pinned to the center of the inhomogeneity, suppressing the delay-induced drift bifurcation that has been reported in the particular case where the injection is homogeneous, assuming a continuous wave operation. Under an inhomogeneous spatial pumping beam, we perform the stability analysis of localized solutions to identify different instability regimes induced by time-delayed feedback. In particular, we predict the formation of two-arm spirals, as well as oscillating and depinning dynamics caused by the interplay of an attracting inhomogeneity and destabilizing time-delayed feedback. The transition from oscillating to depinning solutions is investigated by means of numerical continuation techniques. Analytically, we use an order parameter approach to derive a normal form of the delay-induced Hopf bifurcation leading to an oscillating solution. Additionally we model the interplay of an attracting inhomogeneity and destabilizing time delay by describing the localized solution as an overdamped particle in a potential well generated by the inhomogeneity. In this case, the time-delayed feedback acts as a driving force. Comparing results from the later approach with the full Swift-Hohenberg model, we show that the approach not only provides an instructive description of the depinning dynamics, but also is numerically accurate throughout most of the parameter regime.

  17. Direct probe of interplay between local structure and superconductivity in FeTe₀.₅₅Se₀.₄₅.

    PubMed

    Lin, Wenzhi; Li, Qing; Sales, Brian C; Jesse, Stephen; Sefat, Athena S; Kalinin, Sergei V; Pan, Minghu

    2013-03-26

    The relationship between atomically defined structures and physical properties in functional materials remains a subject of constant interest. We explore the interplay between local crystallographic structure, composition, and local superconductive properties in iron chalcogenide superconductors. Direct structural analysis of scanning tunneling microscopy data allows local lattice distortions and structural defects across an FeTe0.55Se0.45 surface to be explored on a single unit-cell level. Concurrent superconducting gap (SG) mapping reveals suppression of the SG at well-defined structural defects, identified as a local structural distortion. The strong structural distortion causes the vanishing of the superconducting state. This study provides insight into the origins of superconductivity in iron chalcogenides by providing an example of atomic-level studies of the structure-property relationship.

  18. The phase diagram of molybdenum at extreme conditions and the role of local liquid structures

    SciTech Connect

    Ross, M

    2008-08-15

    Recent DAC measurements made of the Mo melting curve by the x-ray diffraction studies confirms that, up to at least 110 GPa (3300K) melting is directly from bcc to liquid, evidence that there is no basis for a speculated bcc-hcp or fcc transition. An examination of the Poisson Ratio, obtained from shock sound speed measurements, provides evidence that the 210 GPa (4100K) transition detected from shock experiments is a continuation of the bcc-liquid melting, but is from a bcc-to a solid-like mixed phase rather than to liquid. Calculations, modeled to include the free energy of liquid local structures, predict that the transition from the liquid to the mixed phase is near 150 GPa(3500K). The presence of local structures provides the simplest and most direct explanation for the Mo phase diagram, and the low melting slopes.

  19. 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.

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  2. 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.

  3. Effects of Local Structure on Seafloor Ambient Noise at the Hawaii-2 Observatory

    NASA Astrophysics Data System (ADS)

    Bromirski, P. D.; Stephen, R.; Duennebier, F. K.

    2006-12-01

    Long time series of broadband (0.001-60Hz) seismometer and hydrophone data collected at the Hawaii-2 Observatory reveal many time independent characteristics in power spectral density and coherence that persist regardless of the type or location of the noise sources. These characteristics can be attributed to the water depth, sediment thickness, igneous crustal structure, and other geological features local to the observatory. It is important to recognize that these characteristics are due to local structure so that they do not confuse the interpretation of noise generated by storms and earthquakes in terms of other physical processes such as infra-gravity wave excitation and propagation, wave-wave interaction, breaking waves, Rayleigh/Stoneley/Scholte wave effects, and propagation and leakage from the ocean wave guide. Locally controlled signal characteristics include: 1) shear wave resonances (modes) in sediments (Godin and Chapman, 1999), 2) water multiples (organ pipe modes) in the ocean (Bradner et al, BSSA, 1970), and 3) secondary scattering of Scholte waves from local seafloor heterogeneities (Dorman et al, in Natural Physical Sources of Underwater Sound, Kerman et al (ed.), Kluwer, 1993). Sediment resonances particularly can act as an amplifier for excitation by natural and controlled sources.

  4. 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.

  5. 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…

  6. 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.

  7. 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.

  8. Correlating local structure with inhomogeneous elastic deformation in a metallic glass

    NASA Astrophysics Data System (ADS)

    Ding, J.; Cheng, Y. Q.; Ma, E.

    2012-09-01

    The elastic response of metallic glasses (MGs) is inhomogeneous, due to the wide variation of local structural arrangements. Here, we present molecular dynamics simulations on a one-million-atoms sample of a Cu64Zr36 model MG, correlating the atomic strain and non-affine displacement with short-range order. Cu atoms in full icosahedra experience less atomic relaxation and behave stiffer, while the rest of Cu atoms contribute more to anelasticity on the timescale of simulation.

  9. 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.

  10. Cavity light bullets: three-dimensional localized structures in a nonlinear optical resonator.

    PubMed

    Brambilla, Massimo; Maggipinto, Tommaso; Patera, Giuseppe; Columbo, Lorenzo

    2004-11-12

    We consider the paraxial model for a nonlinear resonator with a saturable absorber beyond the mean-field limit. For accessible parametric domains we observe total radiation confinement and the formation of 3D localized bright structures. Different from freely propagating light bullets, here the self-organization proceeds from the resonator feedback, combined with diffraction and nonlinearity. Such "cavity" light bullets can be independently excited and erased by appropriate pulses, and once created, they endlessly travel the cavity round-trip.

  11. Nonlinear Localized Dissipative Structures for Long-Time Solution of Wave Equation

    DTIC Science & Technology

    2009-07-01

    Fatemi, E., Engquist, B., and Osher, S., " Numerical Solution of the High Frequency Asymptotic Expansion for the Scalar Wave Equation ", Journal of...FINAL REPORT Grant Title: Nonlinear Localized Dissipative Structures for Long-Time Solution of Wave Equation By Dr. John Steinhoff Grant number... numerical method, "Wave Confinement" (WC), is developed to efficiently solve the linear wave equation . This is similar to the originally developed

  12. 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.

  13. Local structure and magnetism of Co3 + in wurtzite Co:ZnO

    NASA Astrophysics Data System (ADS)

    Henne, Bastian; Ney, Verena; Lumetzberger, Julia; Ollefs, Katharina; Wilhelm, Fabrice; Rogalev, Andrei; Ney, Andreas

    2017-02-01

    The structural and magnetic properties of 30% and 50% Co-doped ZnO have been investigated in order to determine the influence of the presence of Co3 + as a potential p -type dopant. For 30% doping, Co3 + could be stabilized in the wurtzite lattice of ZnO without phase separation by providing high oxygen partial pressures during growth. At 50% Co concentration, the crystal lattice destabilizes. X-ray absorption spectroscopy and simulations are used to substantiate the valence and local structure of Co3 +. Integral and element selective magnetometry reveals uncompensated antiferromagnetism of the Co atoms irrespective of being present as Co2 + or Co3 +.

  14. Protein ranking: From local to global structure in the protein similarity network

    PubMed Central

    Weston, Jason; Elisseeff, Andre; Zhou, Dengyong; Leslie, Christina S.; Noble, William Stafford

    2004-01-01

    Biologists regularly search databases of DNA or protein sequences for evolutionary or functional relationships to a given query sequence. We describe a ranking algorithm that exploits the entire network structure of similarity relationships among proteins in a sequence database by performing a diffusion operation on a precomputed, weighted network. The resulting ranking algorithm, evaluated by using a human-curated database of protein structures, is efficient and provides significantly better rankings than a local network search algorithm such as psi-blast. PMID:15087500

  15. 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.

  16. 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.

  17. 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.

  18. 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.

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

    SciTech Connect

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

    2007-12-19

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

  20. 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.

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

    PubMed Central

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

    2012-01-01

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

  2. 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.

  3. 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…

  4. Disruption of thermally-stable nanoscale grain structures by strain localization.

    PubMed

    Khalajhedayati, Amirhossein; Rupert, Timothy J

    2015-06-01

    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.

  5. 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.

  6. 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

  7. 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

  8. Effect of oxygen deficiency on electronic properties and local structure of amorphous tantalum oxide thin films

    SciTech Connect

    Denny, Yus Rama; Firmansyah, Teguh; Oh, Suhk Kun; Kang, Hee Jae; Yang, Dong-Seok; Heo, Sung; Chung, JaeGwan; Lee, Jae Cheol

    2016-10-15

    Highlights: • The effect of oxygen flow rate on electronic properties and local structure of tantalum oxide thin films was studied. • The oxygen deficiency induced the nonstoichiometric state a-TaOx. • A small peak at 1.97 eV above the valence band side appeared on nonstoichiometric Ta{sub 2}O{sub 5} thin films. • The oxygen flow rate can change the local electronic structure of tantalum oxide thin films. - Abstract: The dependence of electronic properties and local structure of tantalum oxide thin film on oxygen deficiency have been investigated by means of X-ray photoelectron spectroscopy (XPS), Reflection Electron Energy Loss Spectroscopy (REELS), and X-ray absorption spectroscopy (XAS). The XPS results showed that the oxygen flow rate change results in the appearance of features in the Ta 4f at the binding energies of 23.2 eV, 24.4 eV, 25.8, and 27.3 eV whose peaks are attributed to Ta{sup 1+}, Ta{sup 2+}, Ta{sup 3+}/Ta{sup 4+}, and Ta{sup 5+}, respectively. The presence of nonstoichiometric state from tantalum oxide (TaOx) thin films could be generated by the oxygen vacancies. In addition, XAS spectra manifested both the increase of coordination number of the first Ta-O shell and a considerable reduction of the Ta-O bond distance with the decrease of oxygen deficiency.

  9. 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

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

    SciTech Connect

    Peng, Jamy C.

    2007-01-01

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

  11. Impact of aquifer heterogeneity structure and local-scale dispersion on solute concentration uncertainty

    NASA Astrophysics Data System (ADS)

    Srzic, Veljko; Cvetkovic, Vladimir; Andricevic, Roko; Gotovac, Hrvoje

    2013-06-01

    In this paper, we study the influence of high log-conductivity variance (σY2) and local-scale dispersion on the first two concentration moments as well as on higher-order moments, skewness, and kurtosis, in a 2-D heterogeneous aquifer. Three different heterogeneity structures are considered, defined with one and the same global isotropic Gaussian variogram. The three structures differ in terms of spatial connectivity patterns at extreme log-conductivity values. Our numerical approach to simulate contaminant transport through heterogeneous porous media is based on the Lagrangian framework with a reverse tracking formulation. Advection and local-scale dispersion are two competing and controlling mechanisms, with a relative ratio defined by the Peclet number (Pe); hydraulic log-conductivity variance σY2 in the simulations is assumed to be one or eight. The term local-scale dispersion is used as a combined effect of molecular diffusion and mechanical dispersion. Uncertainty of the concentration field is quantified by the second-order moment, or the coefficient of variation (CVC) as a function of the sampling position along a centerline, Peclet number, and σY2, as well as by higher-order moments, i.e., skewness and kurtosis. The parameter σY2 shows a strong influence on the concentration statistics, while the three different structures have a minor impact in the case of low heterogeneity. The results also indicate that for σY2=8, the influence of local-scale dispersion is significant after five integral scales (IY) from the source for the connected (CN) field, while in case of a disconnected field, the local-scale dispersion effect is observed after 20IY from the source. In the case of unit σY2, local-scale dispersion acts very slowly affecting concentration uncertainty at distances higher than 20IY from the source. Our inspection of Monte Carlo concentration skewness and kurtosis with the ones obtained from the Beta distribution show the discrepancies for high

  12. 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.

  13. 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.

  14. 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

  15. Modeling Structural and Mechanical Responses to Localized Erosional Processes on a Bivergent Orogenic Wedge

    NASA Astrophysics Data System (ADS)

    Marzen, R.; Morgan, J. K.

    2014-12-01

    Critical Coulomb wedge theory established that orogenic and accretionary wedges should develop self-similarly and maintain a critical taper that reflects the balance of strength of the wedge material and a basal décollement. However, a variety of geological processes can perturb that balance, forcing readjustment of the wedge. For example, glacial erosion and landsliding can concentrate erosion on a localized portion of the wedge slope, leaving that portion of the wedge with an out-of-equilibrium slope that would need to re-develop for the wedge to resume self-similar growth. We use the discrete element method to analyze how growing bivergent wedges with different cohesive strengths respond structurally and mechanically to erosional events localized along upper, middle, and lower segments of the pro-wedge. Mechanically, pro-wedge erosion results in a sudden decrease followed by a quick recovery of the mean stress and maximum shear stress throughout the pro-wedge. However, when erosion is localized in the mid- to lower portions of the pro-wedge, a zone of increased mean stress develops where the wedge is concentrating deformation to recover its taper. In contrast, when erosion is localized in the upper axial zone, there is almost no recovery of the wedge taper, reflecting the fact that the material at the top of the wedge is being carried passively in a transition zone between the pro-wedge and retro-wedge. Structurally, wedges composed of lower cohesion material recover their critical taper almost immediately through distributed deformation, while wedges of higher-cohesion material recover more slowly, and incompletely, by concentrating deformation along existing fault surfaces. As a result, localized erosional episodes can have a lasting effect on the wedge morphology when the wedge is composed of higher cohesion material.

  16. 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.

  17. Measuring local flow velocities and biofilm structure in biofilm systems with magnetic resonance imaging (MRI).

    PubMed

    Manz, Bertram; Volke, Frank; Goll, Danile; Horn, Harald

    2003-11-20

    The characterization of substrate transport in the bulk phase and in the biofilm matrix is one of the problems which has to be solved for the verification of biofilm models. Additionally, the surface structure of biofilms has to be described with appropriate parameters. Magnetic resonance imaging (MRI) is one of the promising methods for the investigation of transport phenomena and structure in biofilm systems. The MRI technique allows the noninvasive determination of flow velocities and biofilm structures with a high resolution on the sub-millimeter scale. The presented investigations were carried out for defined heterotrophic biofilms which were cultivated in a tube reactor at a Reynolds number of 2000 and 8000 and a substrate load of 6 and 4 g/m2d glucose. Magnetic resonance imaging provides both structure data of the biofilm surface and flow velocities in the bulk phase and at the bulk/biofilm interface. It is shown that the surface roughness of the biofilms can be determined in one experiment for the complete cross section of the test tubes both under flow and stagnant conditions. Furthermore, the local shear stress was calculated from the measured velocity profiles. In the investigated biofilm systems the local shear stress at the biofilm surface was up to 3 times higher compared to the mean wall shear stress calculated on the base of the mean flow velocity.

  18. 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.

  19. Locally preferred structures and many-body static correlations in viscous liquids

    NASA Astrophysics Data System (ADS)

    Coslovich, Daniele

    2011-05-01

    The influence of static correlations beyond the pair level on the dynamics of selected model glass formers is investigated. The pair structure, angular distribution functions, and statistics of Voronoi polyhedra of two well-known Lennard-Jones mixtures as well as of the corresponding Weeks-Chandler-Andersen variants, in which the attractive part of the potential is truncated, are compared. By means of the Voronoi construction, the atomic arrangements corresponding to the locally preferred structures of the models are identified. It is found that the growth of domains formed by interconnected locally preferred structures signals the onset of the slow-dynamics regime and allows the rationalization of the different dynamic behaviors of the models. At low temperature, the spatial extension of the structurally correlated domains, evaluated at fixed relaxation time, increases with the fragility of the models and is systematically reduced by truncating the attractions. In view of these results, proper inclusion of many-body static correlations in theories of the glass transition appears crucial for the description of the dynamics of fragile glass formers.

  20. Local structure in magnetostrictive melt-spun Fe80Ga20 alloys

    NASA Astrophysics Data System (ADS)

    Pascarelli, S.; Ruffoni, M. P.; Sato Turtelli, R.; Kubel, F.; Grössinger, R.

    2008-05-01

    We perform a detailed investigation of the local atomic structure in highly magnetostrictive α-FeGa melt-spun ribbons. By using extended x-ray absorption fine structure (EXAFS) analysis at the Fe and GaK edges coupled to x-ray diffraction (XRD) and to ab initio full multiple scattering calculations of the x-ray absorption near edge structure (XANES), we test for the presence of different local defect structures proposed in literature as being responsible for the large magnetostriction in these alloys. XRD shows that the ribbons crystallize in the A2 phase. Invisible by XRD, the presence of small Ga clusters is excluded by both EXAFS and XANES since no first shell Ga-Ga bonds are detected. However, EXAFS analysis of the second coordination shell around Ga clearly provides evidence for the presence of one highly strained (+4%) Ga-Ga pair and five Ga-Fe pairs, among the six crystallographically equivalent ⟨001⟩ atomic pairs. This conclusion supports recent total energy calculations that assign the large magnetostriction in these alloys to the strain caused by the rotation of the magnetization in the vicinity of such defects.

  1. 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.

  2. 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.

  3. Correlative infrared-electron nanoscopy reveals the local structure-conductivity relationship in zinc oxide nanowires

    NASA Astrophysics Data System (ADS)

    Stiegler, J. M.; Tena-Zaera, R.; Idigoras, O.; Chuvilin, A.; Hillenbrand, R.

    2012-10-01

    High-resolution characterization methods play a key role in the development, analysis and optimization of nanoscale materials and devices. Because of the various material properties, only a combination of different characterization techniques provides a comprehensive understanding of complex functional materials. Here we introduce correlative infrared-electron nanoscopy, a novel method yielding transmission electron microscope and infrared near-field images of one and the same nanostructure. While transmission electron microscopy provides structural information up to the atomic level, infrared near-field imaging yields nanoscale maps of chemical composition and conductivity. We demonstrate the method's potential by studying the relation between conductivity and crystal structure in ZnO nanowire cross-sections. The combination of infrared conductivity maps and the local crystal structure reveals a radial free-carrier gradient, which inversely correlates to the density of extended crystalline defects. Our method opens new avenues for studying the local interplay between structure, conductivity and chemical composition in widely different material systems.

  4. Protein Dynamics from NMR: The Slowly Relaxing Local Structure Analysis Compared with Model-Free Analysis

    PubMed Central

    Meirovitch, Eva; Shapiro, Yury E.; Polimeno, Antonino; Freed, Jack H.

    2009-01-01

    15N-1H spin relaxation is a powerful method for deriving information on protein dynamics. The traditional method of data analysis is model-free (MF), where the global and local N-H motions are independent and the local geometry is simplified. The common MF analysis consists of fitting single-field data. The results are typically field-dependent, and multi-field data cannot be fit with standard fitting schemes. Cases where known functional dynamics has not been detected by MF were identified by us and others. Recently we applied to spin relaxation in proteins the Slowly Relaxing Local Structure (SRLS) approach which accounts rigorously for mode-mixing and general features of local geometry. SRLS was shown to yield MF in appropriate asymptotic limits. We found that the experimental spectral density corresponds quite well to the SRLS spectral density. The MF formulae are often used outside of their validity ranges, allowing small data sets to be force-fitted with good statistics but inaccurate best-fit parameters. This paper focuses on the mechanism of force-fitting and its implications. It is shown that MF force-fits the experimental data because mode-mixing, the rhombic symmetry of the local ordering and general features of local geometry are not accounted for. Combined multi-field multi-temperature data analyzed by MF may lead to the detection of incorrect phenomena, while conformational entropy derived from MF order parameters may be highly inaccurate. On the other hand, fitting to more appropriate models can yield consistent physically insightful information. This requires that the complexity of the theoretical spectral densities matches the integrity of the experimental data. As shown herein, the SRLS densities comply with this requirement. PMID:16821820

  5. 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

  6. 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/.

  7. 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.

  8. Locally favoured structures and dynamic length scales in a simple glass-former

    NASA Astrophysics Data System (ADS)

    Royall, C. Patrick; Kob, Walter

    2017-02-01

    We investigate the static and dynamic properties of a weakly polydisperse hard sphere system in the deeply supercooled state, i.e. at densities higher than that corresponding to the mode-coupling transition. The structural analysis reveals the emergence of icosahedral locally favoured structures, previously only found in trace quantities. We present a new approach to probe the shape of dynamically heterogeneous regions, which is insensitive to particle packing effects that can hamper such analysis. Our results indicate that the shape of the dynamically heterogeneous regions changes only weakly and moreover hint that the often-used four-point correlation length may exhibit a growth in excess of that which our method identifies. The growth of the size of the dynamically heterogeneous regions appears instead to be in line with the one of structural and dynamic propensity correlations.

  9. 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.

  10. Local structures of ions at ion-exchange resin/solution interface.

    PubMed

    Harada, Makoto; Okada, Tetsuo

    2005-08-26

    The local structures of Cl- and Br- in anion-exchange resins have been studied by X-ray absorption fine structure (XAFS), and separation selectivity is discussed on the basis of results. When two different anion-exchange resins having trimethylammonium and dimethylammonium groups as anion-exchange groups are employed for ion-exchange experiments, slightly higher Br- selectivity has been obtained with the former. XAFS has indicated that the average hydration numbers for a given anion is not affected by the structure of the ion-exchange group, but that the extent of ion-association between the anion and the ion-exchange groups depends on the type of the ion-exchange group. Shorter interaction distance (and in turn stronger ion-association) has been confirmed for the dimethylammonium-type resin, and is consistent with lower Br- selectivity of this resin.

  11. 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.

  12. Fusion of multichannel local and global structural cues for photo aesthetics evaluation.

    PubMed

    Luming Zhang; Yue Gao; Zimmermann, Roger; Qi Tian; Xuelong Li

    2014-03-01

    Photo aesthetic quality evaluation is a fundamental yet under addressed task in computer vision and image processing fields. Conventional approaches are frustrated by the following two drawbacks. First, both the local and global spatial arrangements of image regions play an important role in photo aesthetics. However, existing rules, e.g., visual balance, heuristically define which spatial distribution among the salient regions of a photo is aesthetically pleasing. Second, it is difficult to adjust visual cues from multiple channels automatically in photo aesthetics assessment. To solve these problems, we propose a new photo aesthetics evaluation framework, focusing on learning the image descriptors that characterize local and global structural aesthetics from multiple visual channels. In particular, to describe the spatial structure of the image local regions, we construct graphlets small-sized connected graphs by connecting spatially adjacent atomic regions. Since spatially adjacent graphlets distribute closely in their feature space, we project them onto a manifold and subsequently propose an embedding algorithm. The embedding algorithm encodes the photo global spatial layout into graphlets. Simultaneously, the importance of graphlets from multiple visual channels are dynamically adjusted. Finally, these post-embedding graphlets are integrated for photo aesthetics evaluation using a probabilistic model. Experimental results show that: 1) the visualized graphlets explicitly capture the aesthetically arranged atomic regions; 2) the proposed approach generalizes and improves four prominent aesthetic rules; and 3) our approach significantly outperforms state-of-the-art algorithms in photo aesthetics prediction.

  13. The growth of aspherical structure in the universe - Is the Local Supercluster an unusual system

    NASA Technical Reports Server (NTRS)

    White, S. D. M.; Silk, J.

    1979-01-01

    The growth and subsequent collapse of homogeneous ellipsoidal perturbations in a uniform expanding background is considered as a simple model for the formation of large-scale aspherical structures in the observed universe. Numerical calculations of the evolution of such perturbations turn out to be well described by an approximate analytic solution of the equations of motion, and simple relationships are found between the initial shape of a perturbation and its shape and kinematic properties at the time of collapse. Perturbations do not change their shape significantly until they reach a density contrast of order unity. As a result, structures with the kinematic properties of the Local Supercluster should form much more commonly in a low-density universe than in a flat universe. The homogeneity of the local Hubble flow, the motion of the Milky Way with respect to the microwave background, and the flattening of the Local Supercluster can be successfully accounted for by these models, provided that the initial perturbation is sufficiently flattened. Viable models are obtained only if the ratio of the lengths of the two smaller axes of the initial perturbation is at least 3:1 in an Einstein-de Sitter universe or at least 1.8:1 in a universe for which the density parameter (Omega) is of order 0.1, when the protocluster pancakes.

  14. Automated foveola localization in retinal 3D-OCT images using structural support vector machine prediction.

    PubMed

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

    2012-01-01

    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.

  15. Local and global responses of insect motion detectors to the spatial structure of natural scenes.

    PubMed

    O'Carroll, David C; Barnett, Paul D; Nordström, Karin

    2011-12-27

    As a consequence of the non-linear correlation mechanism underlying motion detection, the variability in local pattern structure and contrast inherent within natural scenes profoundly influences local motion responses. To accurately interpret optic flow induced by self-motion, neurons in many dipteran flies smooth this "pattern noise" by wide-field spatial integration. We investigated the role that size and shape of the receptive field plays in smoothing out pattern noise in two unusual hoverfly optic flow neurons: one (HSN) with an exceptionally small receptive field and one (HSNE) with a larger receptive field. We compared the local and global responses to a sequence of panoramic natural images in these two neurons with a parsimonious model for elementary motion detection weighted for their spatial receptive fields. Combined with manipulation of size and contrast of the stimulus images, this allowed us to separate spatial integration properties arising from the receptive field, from other local and global non-linearities, such as motion adaptation and dendritic gain control. We show that receptive field properties alone are poor predictors of the response to natural scenes. If anything, additional non-linearity enhances the pattern dependence of HSN's response, particularly to vertically elongated features, suggesting that it may serve a role in forward fixation during hovering.

  16. 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.

  17. Kinetic model of electric potentials in localized collisionless plasma structures under steady quasi-gyrotropic conditions

    SciTech Connect

    Schindler, K.; Birn, J.; Hesse, M.

    2012-08-15

    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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

    2013-03-07

    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.

  2. [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.

  3. A sensitive method based on fluorescence-detected circular dichroism for protein local structure analysis.

    PubMed

    Nehira, Tatsuo; Ishihara, Kaoru; Matsuo, Koichi; Izumi, Shunsuke; Yamazaki, Takeshi; Ishida, Atsuhiko

    2012-11-15

    We report an improved fluorescence-detected circular dichroism (FDCD)-based analytical method that is useful for probing protein three-dimensional structures. The method uses a novel FDCD device with an ellipsoidal mirror that functions on a standard circular dichroism (CD) spectrometer and eliminates all artifacts. Our experiments demonstrated three important findings. First, the method is applicable to any proteins either by using intrinsic fluorescence derived from tryptophan residues or by introducing a fluorescent label onto nonfluorescent proteins. Second, by using intrinsic fluorescence, FDCD spectroscopy can detect a structural change in the tertiary structure of metmyoglobin due to stepwise denaturation on a change in pH. Such changes could not be detected by conventional CD spectroscopy. Third, based on the typical advantages of fluorescence-based analyses, FDCD measurements enable observation of only the target proteins in a solution even in the presence of other peptides. Using our ellipsoidal mirror FDCD device, we could observe structural changes of fluorescently labeled calmodulin on binding with Ca(2+) and/or interacting with binding peptides. Because FDCD appears to reflect the protein's local structure around the fluorophore, it may provide a useful means for "pinpoint analysis" of protein structures.

  4. 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.

  5. Local electronic structures in electron-doped cuprates with coexisting orders

    NASA Astrophysics Data System (ADS)

    Liu, Bin; Hu, Xiao

    2010-12-01

    Motivated by the observation of a so-called non-monotonic gap in recent angle-resolved photoemission spectroscopy measurement, we study the local electronic structure near impurities in electron-doped cuprates by considering the influence of antiferromagnetic (AF) spin-density-wave (SDW) order. We find that the evolution of density of states (DOS) with AF SDW order clearly indicates the non-monotonic d-wave gap behavior. More interestingly, the local DOS for spin-up is much different from that for spin-down with increasing AF SDW order. As a result, the impurity induced resonance state near the Fermi energy exhibits a spin-polarized feature. These features can be detected by spin-polarized scanning tunneling microscopy experiments.

  6. Stromal networking: cellular connections in the germinal centre.

    PubMed

    Denton, Alice E; Linterman, Michelle A

    2017-03-17

    Secondary lymphoid organs are organized into distinct zones, governed by different types of mesenchymal stromal cells. These stromal cell subsets are critical for the generation of protective humoral immunity because they direct the migration of, and interaction between, multiple immune cell types to form the germinal centre. The germinal centre response generates long-lived antibody-secreting plasma cells and memory B cells which can provide long-term protection against re-infection. Stromal cell subsets mediate this response through control of immune cell trafficking, activation, localization and antigen access within the secondary lymphoid organ. Further, distinct populations of stromal cells underpin the delicate spatial organization of immune cells within the germinal centre. Because of this, the interactions between immune cells and stromal cells in secondary lymphoid organs are fundamental to the germinal centre response. Herein we review how this unique relationship leads to effective germinal centre responses.

  7. 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.

  8. The road not taken: retreat and diverge in local search for simplified protein structure prediction

    PubMed Central

    2013-01-01

    Background Given a protein's amino acid sequence, the protein structure prediction problem is to find a three dimensional structure that has the native energy level. For many decades, it has been one of the most challenging problems in computational biology. A simplified version of the problem is to find an on-lattice self-avoiding walk that minimizes the interaction energy among the amino acids. Local search methods have been preferably used in solving the protein structure prediction problem for their efficiency in finding very good solutions quickly. However, they suffer mainly from two problems: re-visitation and stagnancy. Results In this paper, we present an efficient local search algorithm that deals with these two problems. During search, we select the best candidate at each iteration, but store the unexplored second best candidates in a set of elite conformations, and explore them whenever the search faces stagnation. Moreover, we propose a new non-isomorphic encoding for the protein conformations to store the conformations and to check similarity when applied with a memory based search. This new encoding helps eliminate conformations that are equivalent under rotation and translation, and thus results in better prevention of re-visitation. Conclusion On standard benchmark proteins, our algorithm significantly outperforms the state-of-the art approaches for Hydrophobic-Polar energy models and Face Centered Cubic Lattice. PMID:23368768

  9. 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.

  10. Protein Secondary Structure Prediction Using Local Adaptive Techniques in Training Neural Networks

    NASA Astrophysics Data System (ADS)

    Aik, Lim Eng; Zainuddin, Zarita; Joseph, Annie

    2008-01-01

    One of the most significant problems in computer molecular biology today is how to predict a protein's three-dimensional structure from its one-dimensional amino acid sequence or generally call the protein folding problem and difficult to determine the corresponding protein functions. Thus, this paper involves protein secondary structure prediction using neural network in order to solve the protein folding problem. The neural network used for protein secondary structure prediction is multilayer perceptron (MLP) of the feed-forward variety. The training set are taken from the protein data bank which are 120 proteins while 60 testing set is the proteins which were chosen randomly from the protein data bank. Multiple sequence alignment (MSA) is used to get the protein similar sequence and Position Specific Scoring matrix (PSSM) is used for network input. The training process of the neural network involves local adaptive techniques. Local adaptive techniques used in this paper comprises Learning rate by sign changes, SuperSAB, Quickprop and RPROP. From the simulation, the performance for learning rate by Rprop and Quickprop are superior to all other algorithms with respect to the convergence time. However, the best result was obtained using Rprop algorithm.

  11. Crystal structure of rice importin-α and structural basis of its interaction with plant-specific nuclear localization signals.

    PubMed

    Chang, Chiung-Wen; Couñago, Rafael Lemos Miguez; Williams, Simon J; Bodén, Mikael; Kobe, Boštjan

    2012-12-01

    In the classical nucleocytoplasmic import pathway, nuclear localization signals (NLSs) in cargo proteins are recognized by the import receptor importin-α. Importin-α has two separate NLS binding sites (the major and the minor site), both of which recognize positively charged amino acid clusters in NLSs. Little is known about the molecular basis of the unique features of the classical nuclear import pathway in plants. We determined the crystal structure of rice (Oryza sativa) importin-α1a at 2-Å resolution. The structure reveals that the autoinhibitory mechanism mediated by the importin-β binding domain of importin-α operates in plants, with NLS-mimicking sequences binding to both minor and major NLS binding sites. Consistent with yeast and mammalian proteins, rice importin-α binds the prototypical NLS from simian virus 40 large T-antigen preferentially at the major NLS binding site. We show that two NLSs, previously described as plant specific, bind to and are functional with plant, mammalian, and yeast importin-α proteins but interact with rice importin-α more strongly. The crystal structures of their complexes with rice importin-α show that they bind to the minor NLS binding site. By contrast, the crystal structures of their complexes with mouse (Mus musculus) importin-α show preferential binding to the major NLS binding site. Our results reveal the molecular basis of a number of features of the classical nuclear transport pathway specific to plants.

  12. 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

  13. Local scale structures in Earth's thermospheric winds and their consequences for wind driven transport

    NASA Astrophysics Data System (ADS)

    Dhadly, Manbharat Singh

    In the traditional picture of Earth's upper thermosphere (~190--300 km), it is widely presumed that its convective stability and enormous kinematic viscosity attenuate wind gradients, and hence smooth out any structure present in the wind over scale size of several hundreds of kilometers. However, several independent experimental studies have shown that observed upper thermospheric wind fields at high latitudes contain stronger than expected local-scale spatial structures. The motivation of this dissertation is to investigate how the resulting local-scale gradients would distort neutral air masses and complicate thermospheric wind transport. To achieve this goal, we examined the behavior of a simple parameter that we refer to as the "distortion gradient". It incorporates all of the wind field's departures from uniformity, and is thus capable of representing all resulting contributions to the distortion or mixing of air masses. Climatological analysis of the distortion gradient using 2010, 2011, and 2012 wind data from the All-sky Scanning Doppler Imager (SDI) located at Poker Flat (65.12N, 147.47W) revealed the diurnal and seasonal trends in distortion of thermospheric masses. Distortion was observed to be dependent on geomagnetic activity and orientation of the interplanetary magnetic field. To understand the time-cumulative influence of these local-scale non-uniformities on thermospheric wind driven transport, time-resolved two-dimensional maps of the thermospheric vector wind fields were used to infer forward and backward air parcel trajectories. Tracing air parcel trajectories through a given geographic location indicates where they came from previously, and where they will go in the future. Results show that wind driven transport is very sensitive to small-scale details of the wind field. Any local-scale spatial wind gradients can significantly complicate air parcel trajectories. Transport of thermospheric neutral species in the presence of the local

  14. Local population structure of Plasmodium: impact on malaria control and elimination

    PubMed Central

    2012-01-01

    Background Regardless of the growing interest in detecting population structures in malarial parasites, there have been limited discussions on how to use this concept in control programmes. In such context, the effects of the parasite population structures will depend on interventions’ spatial or temporal scales. This investigation explores the problem of identifying genetic markers, in this case microsatellites, to unveil Plasmodium genetic structures that could affect decisions in the context of elimination. The study was performed in a low-transmission area, which offers a good proxy to better understand problems associated with surveillance at the final stages of malaria elimination. Methods Plasmodium vivax samples collected in Tumeremo, Venezuela, between March 2003 and November 2004 were analysed. Since Plasmodium falciparum also circulates in many low endemic areas, P. falciparum samples from the same locality and time period were included for comparison. Plasmodium vivax samples were assayed for an original set of 25 microsatellites and P. falciparum samples were assayed for 12 microsatellites. Results Not all microsatellite loci assayed offered reliable local data. A complex temporal-cluster dynamics is found in both P. vivax and P. falciparum. Such dynamics affect the numbers and the type of microsatellites required for identifying individual parasites or parasite clusters when performing cross-sectional studies. The minimum number of microsatellites required to differentiate circulating P. vivax clusters differs from the minimum number of hyper-variable microsatellites required to distinguish individuals within these clusters. Regardless the extended number of microsatellites used in P. vivax, it was not possible to separate all individual infections. Conclusions Molecular surveillance has great potential; however, it requires preliminary local studies in order to properly interpret the emerging patterns in the context of elimination. Clonal

  15. Electronic structure and local magnetism of 3d-5d impurity substituted CeFe2

    NASA Astrophysics Data System (ADS)

    Das, Rakesh; Das, G. P.; Srivastava, S. K.

    2016-04-01

    We present here a systematic first-principles study of electronic structure and local magnetic properties of Ce[Fe0.75M0.25]2 compounds, where M is a 3d, 4d or 5d transition or post-transition element, using the generalized gradient approximation of the density functional theory. The d-f band hybridizations existing in CeFe2 get modified by the impurity M in an orderly manner across a period for each impurity series: the hybridization is strongest for the Mn group impurity in the period and gets diminished on either side of it. The weakening of the d-f hybridization strength is also associated with a relative localization of the Ce 4f states with respect to the delocalized 4f states in CeFe2. The above effects are most prominent for 3d impurity series, while for 4d and 5d impurities, the hybridizations and relocalizations are relatively weak due primarily to the relatively extended nature of 4d and 5d wavefunctions. The Ce local moment is found to decrease from the CeFe2 value in proportion to the strength of relocalization, thus following almost the same orderly trend as obeyed by the d-f hybridization. Further, depending on the way the spin-up and spin-down densities of states of an impurity shift relative to the Fermi energy, the impurity local moments are highest for Mn or Fe group, reduce on either side, become zero for Ni to Ga, and are small but negative for V and Ti. The Ce hyperfine field is found to follow the M local moment in a linear fashion, and vice-versa.

  16. Probing local structure of pyrochlore lead zinc niobate with synchrotron x-ray absorption spectroscopy technique

    NASA Astrophysics Data System (ADS)

    Kanchiang, Kanokwan; Pramchu, Sittichain; Yimnirun, Rattikorn; Pakawanit, Phakkhananan; Ananta, Supon; Laosiritaworn, Yongyut

    2013-08-01

    Local structure of lead zinc niobate (PZN) ceramic, synthesized via B-site oxide precursor route in atmospheric pressure, was investigated using synchrotron x-ray absorption spectroscopy (XAS) technique. The x-ray absorption near-edge structure (XANES) simulation was first carried out. The XANES simulation results indicate that the PZN ceramic is in pyrochlore phase having Zn2+ substituted on Nb5+ site. Afterwards, the extended x-ray absorption fine structure (EXAFS) analysis was performed to extract the bond length information between Zn2+ and its neighboring atoms. From the EXAFS fitting, the bond length between Zn2+ and Pb2+ in the pyrochlore phase was found to be longer than the previously reported bond length in the perovskite phase. Further, with the radial distribution information of Zn2+'s neighboring atoms, the formation energies along the precursor-to-pyrochlore and precursor-to-perovskite reaction paths were calculated using the density functional theory (DFT). The calculated results show that the formation energy of the perovskite phase is noticeably higher than that of the pyrochlore phase, which is influenced by the presence of energetic Pb2+ lone pair, as the perovskite phase has shorter Zn2+ to Pb2+ bonding. This therefore suggests the steric hindrance of Pb2+ lone pair and the mutual interactions between Pb2+ lone pair and Zn2+ are main causes of the instability of lead zinc niobate in the perovskite structure and confirm the efficacy of XAS and DFT analysis in revealing local structural details of complex pyrochlore materials.

  17. The Local Atomic Structure and Chemical Bonding in Sodium Tin Phases

    DOE PAGES

    Baggetto, Loic; Bridges, Craig A.; Jumas, Dr. Jean-Claude; ...

    2014-01-01

    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

  18. 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.

    2014-01-01

    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.

  19. Local and transient structural changes in stratum corneum at high electric fields: contribution of Joule heating.

    PubMed

    Pliquett, U; Gallo, S; Hui, S W; Gusbeth, Ch; Neumann, E

    2005-09-01

    Electroporation of skin is accompanied by local heating, such that thermally induced structural changes of the stratum corneum (SC) accompany the field effect. Comparing on the time scale, the local changes in structure, temperature and conductance of the SC, during and after the pulse, it is seen that Joule heating also facilitates the subsequent molecular transport. It is found that the transport of medium-sized, ionic molecules occurs through localized transport regions (LTR). The size of a LTR increases with the pulse length, whereas the density of the LTRs increases with increasing voltage, for instance at U(SC=)80 V, the LTR cover approximately 0.02--1% of the surface area. The state of low resistance within the LTR is long-lived. During high voltage application, the center of the LTR is heated above the phase transition temperature of the SC lipids (70 degrees C) and the heat front propagates outwards. Inside the SC, the pulse causes aggregates of small-sized vesicles. At a higher temperature, the aggregate formation and their disappearance are delayed. Multiple pulses with the applied voltage of U(appl)=80 V induce the formation of long-lasting vesicle aggregates with a diameter of slashed circle=1--30 microm, covering 0.05--0.5% of the total sample area. The electric energy dissipated within the LTR during high voltage application is apparently sufficient to raise the temperature well above the phase transition temperature of the lipids of the SC, accounting for the conformational changes from the multi-lamella to the vesicular structures.

  20. TiO2 nanotube arrays for photocatalysis: Effects of crystallinity, local order, and electronic structure

    DOE PAGES

    Liu, Jing; Hosseinpour, Pegah M.; Luo, Si; ...

    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

  1. 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.

  2. Magnetic Structure of the Local-moment Antiferromagnet CeCuSn

    SciTech Connect

    Chang, S.; Janssen, Y.; Garlea, Vasile O; Zarestky, Jerel L; Nakotte, H.; McQueeney, R. J.

    2005-01-01

    We report on single-crystal neutron diffraction studies of the local-moment antiferromagnet CeCuSn. The ground-state magnetic structure is characterized by a magnetic wave vector k = (0.115,0,0). The onset of antiferromagnetic order occurs around 12 K with an inflection in the temperature dependence of the magnetic intensities at about 8 K. This is in contrast to bulk measurements, which only show broad features at 8--10 K. The ordered moments are likely reduced from the free-ion moment for Ce.

  3. Formation of Si clusters in AlGaN: A study of local structure

    SciTech Connect

    Somogyi, A.; Martinez-Criado, G.; Homs, A.; Hernandez-Fenollosa, M. A.; Vantelon, D.; Ambacher, O.

    2007-04-30

    In this study, the authors report on the application of synchrotron radiation x-ray microprobe to the study of Si impurities in plasma-induced molecular beam epitaxy grown Al{sub 0.32}Ga{sub 0.68}N. Elemental maps obtained by {mu}-x-ray fluorescence spectrometry show inhomogeneous distributions of Si, Al, and Ga on the micron scale. X-ray absorption near-edge structure spectra taken at the Si and Al K edges provided information about their local chemical environment and revealed the change of the spectral features as depending on the position compared to the sample surface and on the concentration of Si.

  4. Local duality in spin structure functions g1(p) and g1(d)

    SciTech Connect

    Yelena Prok

    2006-02-01

    Inclusive double spin asymmetries obtained by scattering polarized electrons off polarized protons and deuterons have been analyzed to address the issue of quark hadron duality in the polarized spin structure functions gp 1 and gd 1. A polarized electron beam, solid polarized NH3 and ND3 targets and the CEBAF Large Acceptance Spectrometer (CLAS) in Hall B were used to collect the data. The resulting gp 1 and gd 1 were averaged over the nucleon resonance energy region (M local duality.

  5. Should "Teacher Centred Teaching" Replace "Student Centred Learning"?

    ERIC Educational Resources Information Center

    Bailey, Patrick D.

    2008-01-01

    Mission statements of most HEIs across the UK support "student centred learning". In this paper, it is suggested that "teacher centred teaching" should also have a major role to play, improving the quality of the learning experience in higher education. Students are extremely diverse in their skills, weaknesses, and learning…

  6. On-line structural damage localization and quantification using wireless sensors

    NASA Astrophysics Data System (ADS)

    Hsu, Ting-Yu; Huang, Shieh-Kung; Lu, Kung-Chung; Loh, Chin-Hsiung; Wang, Yang; Lynch, Jerome Peter

    2011-10-01

    In this paper, a wireless sensing system is designed to realize on-line damage localization and quantification of a structure using a frequency response function change method (FRFCM). Data interrogation algorithms are embedded in the computational core of the wireless sensing units to extract the necessary structural features, i.e. the frequency spectrum segments around eigenfrequencies, automatically from measured structural response for the FRFCM. Instead of the raw time history of the structural response, the extracted compact structural features are transmitted to the host computer. As a result, with less data transmitted from the wireless sensors, the energy consumed by the wireless transmission is reduced. To validate the performance of the proposed wireless sensing system, a six-story steel building with replaceable bracings in each story is instrumented with the wireless sensors for on-line damage detection during shaking table tests. The accuracy of the damage detection results using the wireless sensing system is verified through comparison with the results calculated from data recorded of a traditional wired monitoring system. The results demonstrate that, by taking advantage of collocated computing resources in wireless sensors, the proposed wireless sensing system can locate and quantify damage with acceptable accuracy and moderate energy efficiency.

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

    PubMed

    Baldeck, Claire A; Harms, Kyle E; Yavitt, Joseph B; John, Robert; Turner, Benjamin L; Valencia, Renato; Navarrete, Hugo; Davies, Stuart J; Chuyong, George B; Kenfack, David; Thomas, Duncan W; Madawala, Sumedha; Gunatilleke, Nimal; Gunatilleke, Savitri; Bunyavejchewin, Sarayudh; Kiratiprayoon, Somboon; Yaacob, Adzmi; Supardi, Mohd N Nur; Dalling, James W

    2013-02-22

    Both habitat filtering and dispersal limitation influence the compositional structure of forest communities, but previous studies examining the relative contributions of these processes with variation partitioning have primarily used topography to represent the influence of the environment. Here, we bring together data on both topography and soil resource variation within eight large (24-50 ha) tropical forest plots, and use variation partitioning to decompose community compositional variation into fractions explained by spatial, soil resource and topographic variables. Both soil resources and topography account for significant and approximately equal variation in tree community composition (9-34% and 5-29%, respectively), and all environmental variables together explain 13-39% of compositional variation within a plot. A large fraction of variation (19-37%) was spatially structured, yet unexplained by the environment, suggesting an important role for dispersal processes and unmeasured environmental variables. For the majority of sites, adding soil resource variables to topography nearly doubled the inferred role of habitat filtering, accounting for variation in compositional structure that would previously have been attributable to dispersal. Our results, illustrated using a new graphical depiction of community structure within these plots, demonstrate the importance of small-scale environmental variation in shaping local community structure in diverse tropical forests around the globe.

  8. The action of local anesthetics on myelin structure and nerve conduction in toad sciatic nerve.

    PubMed

    Mateu, L; Morán, O; Padrón, R; Borgo, M; Vonasek, E; Márquez, G; Luzzati, V

    1997-06-01

    X-ray scattering and electrophysiological experiments were performed on toad sciatic nerves in the presence of local anesthetics. In vitro experiments were performed on dissected nerves superfused with Ringer's solutions containing procaine, lidocaine, tetracaine, or dibucaine. In vivo experiments were performed on nerves dissected from animals anesthesized by targeted injections of tetracaine-containing solutions. In all cases the anesthetics were found to have the same effects on the x-ray scattering spectra: the intensity ratio of the even-order to the odd-order reflections increases and the lattice parameter increases. These changes are reversible upon removal of the anesthetic. The magnitude of the structural changes varies with the duration of the superfusion and with the nature and concentration of the anesthetic molecule. A striking quantitative correlation was observed between the structural effects and the potency of the anesthetic. Electron density profiles, which hardly showed any structural alteration of the unit membrane, clearly indicated that the anesthetics have the effect of moving the pairs of membranes apart by increasing the thickness of the cytoplasmic space. Electrophysiological measurements performed on the very samples used in the x-ray scattering experiments showed that the amplitude of the compound action potential is affected earlier than the structure of myelin (as revealed by the x-ray scattering experiments), whereas conduction velocity closely follows the structural alterations.

  9. 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.

  10. The brain differentiates human and non-human grammars: functional localization and structural connectivity.

    PubMed

    Friederici, Angela D; Bahlmann, Jörg; Heim, Stefan; Schubotz, Ricarda I; Anwander, Alfred

    2006-02-14

    The human language faculty has been claimed to be grounded in the ability to process hierarchically structured sequences. This human ability goes beyond the capacity to process sequences with simple transitional probabilities of adjacent elements observable in non-human primates. Here we show that the processing of these two sequence types is supported by different areas in the human brain. Processing of local transitions is subserved by the left frontal operculum, a region that is phylogenetically older than Broca's area, which specifically holds responsible the computation of hierarchical dependencies. Tractography data revealing differential structural connectivity signatures for these two brain areas provide additional evidence for a segregation of two areas in the left inferior frontal cortex.

  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. The structure of filled skutterudites and the local vibration behavior of the filling atom

    NASA Astrophysics Data System (ADS)

    Zhou, Xiaojuan; Zong, Peng-an; Chen, Xihong; Tao, Juzhou; Lin, He

    2017-02-01

    Both of atomic pair distribution function (PDF) and extended x-ray absorption fine structure (EXAFS) experiments have been carried out on unfilled and Yb-filled skutterudites YbxCo4Sb12 (x=0, 0.15, 0.2 and 0.25) samples. The structure refinements on PDF data confirm the large amplitude vibration of Yb atom and the dependence of Yb vibration amplitude on the filling content. Temperature dependent EXAFS experiment on filled skutterudites have been carried out at Yb LⅢ-edge in order to explore the local vibration behavior of filled atom. EXAFS experiments show that the Einstein temperature of the filled atom is very low (70.9 K) which agrees with the rattling behavior.

  13. 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.

  14. 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.

  15. 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.

  16. Local structural evidence for strong electronic correlations in spinel LiRh2O4

    NASA Astrophysics Data System (ADS)

    Knox, K. R.; Abeykoon, A. M. M.; Zheng, H.; Yin, W.-G.; Tsvelik, A. M.; Mitchell, J. F.; Billinge, S. J. L.; Bozin, E. S.

    2013-11-01

    The local structure of the spinel LiRh2O4 has been studied using atomic-pair distribution function analysis of powder x-ray diffraction data. This measurement is sensitive to the presence of short Rh-Rh bonds that form due to dimerization of Rh4+ ions on the pyrochlore sublattice, independent of the existence of long-range order. We show that structural dimers exist in the low-temperature phase, as previously supposed, with a bond shortening of Δr˜0.15 Å. The dimers persist up to 350 K, well above the insulator-metal transition, with Δr decreasing in magnitude on warming. Such behavior is inconsistent with the Fermi-surface nesting-driven Peierls transition model. Instead, we argue that LiRh2O4 should properly be described as a strongly correlated system.

  17. Local structure study of Fe dopants in Ni-deficit Ni3Al alloys

    DOE PAGES

    V. N. Ivanovski; Umicevic, A.; Belosevic-Cavor, J.; ...

    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

  18. 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.

  19. Robust object tracking based on structural local sparsity via a global L2 norm constraint

    NASA Astrophysics Data System (ADS)

    Li, Meihui; Peng, Zhenming; Zhang, Ping

    2016-10-01

    In the structural local sparse model, every candidate derived from the particle filter framework is divided into several overlapping image patches. However, in the tracking process, the structural characteristics of the target may change due to alterations in appearance, resulting in unstable pooled features and therefore drifting and false tracking. We propose a method to correct the changed part of the target using atoms in the patched dictionary by adding a global constraint. If the target is corrupted, this constraint term will weaken the influence of variation and strengthen the stability of the pooled features. Otherwise, the method is based on the whole target and will protect its spatial continuity. Both qualitative and quantitative evaluations on challenging benchmark image sequences demonstrate that the proposed algorithm has excellent tracking behavior, displaying robustness and stability with little drifting on a target with altering appearance and partial occlusion.

  20. 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.

  1. Magnetic Doppler imaging considering atmospheric structure modifications due to local abundances: a luxury or a necessity?

    NASA Astrophysics Data System (ADS)

    Kochukhov, O.; Wade, G. A.; Shulyak, D.

    2012-04-01

    Magnetic Doppler imaging is currently the most powerful method of interpreting high-resolution spectropolarimetric observations of stars. This technique has provided the very first maps of stellar magnetic field topologies reconstructed from time series of full Stokes vector spectra, revealing the presence of small-scale magnetic fields on the surfaces of Ap stars. These studies were recently criticised by Stift et al., who claimed that magnetic inversions are not robust and are seriously undermined by neglecting a feedback on the Stokes line profiles from the local atmospheric structure in the regions of enhanced metal abundance. We show that Stift et al. misinterpreted published magnetic Doppler imaging results and consistently neglected some of the most fundamental principles behind magnetic mapping. Using state-of-the-art opacity sampling model atmosphere and polarized radiative transfer codes, we demonstrate that the variation of atmospheric structure across the surface of a star with chemical spots affects the local continuum intensity but is negligible for the normalized local Stokes profiles except for the rare situation of a very strong line in an extremely Fe-rich atmosphere. For the disc-integrated spectra of an Ap star with extreme abundance variations, we find that the assumption of a mean model atmosphere leads to moderate errors in Stokes I but is negligible for the circular and linear polarization spectra. Employing a new magnetic inversion code, which incorporates the horizontal variation of atmospheric structure induced by chemical spots, we reconstructed new maps of magnetic field and Fe abundance for the bright Ap star α2 CVn. The resulting distribution of chemical spots changes insignificantly compared to the previous modelling based on a single model atmosphere, while the magnetic field geometry does not change at all. This shows that the assertions by Stift et al. are exaggerated as a consequence of unreasonable assumptions and

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

    SciTech Connect

    Kageyama, Shota; Matsuki, Nobuyuki; Fujiwara, Hiroyuki

    2013-12-21

    The microscopic disordered structures of hydrogenated amorphous silicon carbide (a-Si{sub 1−x}C{sub x}:H) layers with different carbon contents have been determined based on the correlations between the dielectric function in the ultraviolet/visible region and the local bonding states studied by high-sensitivity infrared attenuated total reflection spectroscopy. We find that the microscopic structure of the a-Si{sub 1−x}C{sub x}:H layers fabricated by plasma-enhanced chemical vapor deposition shows a sharp structural transition at a boundary of x = 6.3 at. %. In the regime of x ≤ 6.3 at. %, (i) the amplitude of the a-SiC:H dielectric function reduces and (ii) the SiH{sub 2} content increases drastically with x, even though most of the C atoms are introduced into the tetrahedral sites without bonding with H. In the regime of x > 6.3 at. %, on the other hand, (i) the amplitude of the dielectric function reduces further and (ii) the concentration of the sp{sup 3} CH{sub n} (n = 2,3) groups increases. Moreover, we obtained the direct evidence that the sp{sup 2} C bonding state in the a-SiC matrix exists in the configuration of C = CH{sub 2} and the generation of the graphite-like C = CH{sub 2} unit suppresses the band gap widening significantly. At high C contents of x > 6.3 at. %, the a-SiC:H layers show quite porous structures due to the formation of microvoids terminated with the SiH{sub 2}/CH{sub n} groups. By taking the SiH{sub 2}/CH{sub n} microvoid generation in the network and the high-energy shift of the dielectric function by the local bonding states into account, the a-SiC:H dielectric function model has been established. From the analysis using this model, we have confirmed that the a-SiC:H optical properties in the ultraviolet/visible region are determined almost completely by the local network structures.

  3. 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.

  4. Local Climate Heterogeneity Shapes Population Genetic Structure of Two Undifferentiated Insular Scutellaria Species.

    PubMed

    Hsiung, Huan-Yi; Huang, Bing-Hong; Chang, Jui-Tse; Huang, Yao-Moan; Huang, Chih-Wei; Liao, Pei-Chun

    2017-01-01

    Spatial climate heterogeneity may not only affect adaptive gene frequencies but could also indirectly shape the genetic structure of neutral loci by impacting demographic dynamics. In this study, the effect of local climate on population genetic variation was tested in two phylogenetically close Scutellaria species in Taiwan. Scutellaria taipeiensis, which was originally assumed to be an endemic species of Taiwan Island, is shown to be part of the widespread species S. barbata based on the overlapping ranges of genetic variation and climatic niches as well as their morphological similarity. Rejection of the scenario of "early divergence with secondary contact" and the support for multiple origins of populations of S. taipeiensis from S. barbata provide strong evolutionary evidence for a taxonomic revision of the species combination. Further tests of a climatic effect on genetic variation were conducted. Regression analyses show nonlinear correlations among any pair of geographic, climatic, and genetic distances. However, significantly, the bioclimatic variables that represent the precipitation from late summer to early autumn explain roughly 13% of the genetic variation of our sampled populations. These results indicate that spatial differences of precipitation in the typhoon season may influence the regeneration rate and colonization rate of local populations. The periodic typhoon episodes explain the significant but nonlinear influence of climatic variables on population genetic differentiation. Although, the climatic difference does not lead to species divergence, the local climate variability indeed impacts the spatial genetic distribution at the population level.

  5. Sparse Codebook Model of Local Structures for Retrieval of Focal Liver Lesions Using Multiphase Medical Images

    PubMed Central

    Han, Xian-Hua; Xu, Yingying; Lin, Lanfen; Hu, Hongjie; Jin, Chongwu

    2017-01-01

    Characterization and individual trait analysis of the focal liver lesions (FLL) is a challenging task in medical image processing and clinical site. The character analysis of a unconfirmed FLL case would be expected to benefit greatly from the accumulated FLL cases with experts' analysis, which can be achieved by content-based medical image retrieval (CBMIR). CBMIR mainly includes discriminated feature extraction and similarity calculation procedures. Bag-of-Visual-Words (BoVW) (codebook-based model) has been proven to be effective for different classification and retrieval tasks. This study investigates an improved codebook model for the fined-grained medical image representation with the following three advantages: (1) instead of SIFT, we exploit the local patch (structure) as the local descriptor, which can retain all detailed information and is more suitable for the fine-grained medical image applications; (2) in order to more accurately approximate any local descriptor in coding procedure, the sparse coding method, instead of K-means algorithm, is employed for codebook learning and coded vector calculation; (3) we evaluate retrieval performance of focal liver lesions (FLL) using multiphase computed tomography (CT) scans, in which the proposed codebook model is separately learned for each phase. The effectiveness of the proposed method is confirmed by our experiments on FLL retrieval. PMID:28293255

  6. Local swirl chamber heat transfer and flow structure at different Reynolds numbers

    SciTech Connect

    Hedlung, C.R.; Ligrani, P.M.

    2000-04-01

    Local flow behavior and heat transfer results are presented from two swirl chambers, which model passages used to cool the leading edges of turbine blades in gas turbine engines. Flow results are obtained in an isothermal swirl chamber. Surface Nusselt number distributions are measured in a second swirl chamber (with a constant wall heat flux boundary condition) using infrared thermography in conjunction with thermocouples, energy balances, and in situ calibration procedures. In both cases, Reynolds numbers Re based on inlet duct characteristics range from 6,000 to about 20,000. Bulk helical flow is produced in each chamber by two inlets, which are tangent to the swirl chamber circumference. Important changes to local and globally averaged surface Nusselt numbers, instantaneous flow structure from flow visualizations, and distributions of static pressure, total pressure, and circumferential velocity are observed throughout the swirl chambers as the Reynolds number increases. Of particular importance are increases of local surface Nusselt numbers (as well as ones globally averaged over the entire swirl chamber surface) with increasing Reynolds number. These are tied to increased advection, as well as important changes to vortex characteristics near the concave surfaces of the swirl chambers. Higher Re also give larger axial components of velocity, and increased turning of the flow from each inlet, which gives Goertler vortex pair trajectories greater skewness as they are advected downstream of each inlet.

  7. Local Climate Heterogeneity Shapes Population Genetic Structure of Two Undifferentiated Insular Scutellaria Species

    PubMed Central

    Hsiung, Huan-Yi; Huang, Bing-Hong; Chang, Jui-Tse; Huang, Yao-Moan; Huang, Chih-Wei; Liao, Pei-Chun

    2017-01-01

    Spatial climate heterogeneity may not only affect adaptive gene frequencies but could also indirectly shape the genetic structure of neutral loci by impacting demographic dynamics. In this study, the effect of local climate on population genetic variation was tested in two phylogenetically close Scutellaria species in Taiwan. Scutellaria taipeiensis, which was originally assumed to be an endemic species of Taiwan Island, is shown to be part of the widespread species S. barbata based on the overlapping ranges of genetic variation and climatic niches as well as their morphological similarity. Rejection of the scenario of “early divergence with secondary contact” and the support for multiple origins of populations of S. taipeiensis from S. barbata provide strong evolutionary evidence for a taxonomic revision of the species combination. Further tests of a climatic effect on genetic variation were conducted. Regression analyses show nonlinear correlations among any pair of geographic, climatic, and genetic distances. However, significantly, the bioclimatic variables that represent the precipitation from late summer to early autumn explain roughly 13% of the genetic variation of our sampled populations. These results indicate that spatial differences of precipitation in the typhoon season may influence the regeneration rate and colonization rate of local populations. The periodic typhoon episodes explain the significant but nonlinear influence of climatic variables on population genetic differentiation. Although, the climatic difference does not lead to species divergence, the local climate variability indeed impacts the spatial genetic distribution at the population level. PMID:28239386

  8. 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.

  9. Dynamical properties and instability of local fluorite BaF(2) structure around doped Mn(2+) ions-EPR and electron spin echo studies.

    PubMed

    Lijewski, S; Hoffmann, S K; Goslar, J; Wencka, M; Ulanov, V A

    2008-09-24

    The electron paramagnetic resonance (EPR) and electron spin echo (ESE) were measured at the X-band for Mn(2+) in a BaF(2) crystal in the temperature range 4.2-300 K. In addition to the cubic symmetry centre, two other lower concentration tetragonal centres were identified. Temperature variations and computer simulation of the EPR spectrum confirm that the cubic symmetry of the MnF(8) centre is deformed to two T(d) tetrahedra of different dimensions at around 45 K. Electron spin relaxation was measured in the temperature range 4.2-35 K, where the ESE signal was detectable. For higher temperature the Mn(2+) dynamics produces homogeneously broadened EPR lines. At the lowest temperatures the spin-lattice relaxation is governed by ordinary phonon processes with 1/T(1)∼T(5). The efficiency of these processes rapidly decreases and at about 11 K a local mode of energy 17 cm(-1) becomes the relaxation mechanism. Phase relaxation observed as ESE signal dephasing indicates that after the local deformation jumps (tunnelling with frequency 4 × 10(8) s(-1)) between the two tetrahedral configurations appear, with the energy barrier being the local mode energy. This motion is directly visible as a resonance-type enhancement of the ESE dephasing rate 1/T(M) around 11 K. Only the cubic centre displays the above dynamics.

  10. The Canadian Astronomy Data Centre

    NASA Astrophysics Data System (ADS)

    Ball, Nicholas M.; Schade, D.; Astronomy Data Centre, Canadian

    2011-01-01

    The Canadian Astronomy Data Centre (CADC) is the world's largest astronomical data center, holding over 0.5 Petabytes of information, and serving nearly 3000 astronomers worldwide. Its current data collections include BLAST, CFHT, CGPS, FUSE, Gemini, HST, JCMT, MACHO, MOST, and numerous other archives and services. It provides extensive data archiving, curation, and processing expertise, via projects such as MegaPipe, and enables substantial day-to-day collaboration between resident astronomers and computer specialists. It is a stable, powerful, persistent, and properly supported environment for the storage and processing of large volumes of data, a condition that is now absolutely vital for their science potential to be exploited by the community. Through initiatives such as the Common Archive Observation Model (CAOM), the Canadian Virtual Observatory (CVO), and the Canadian Advanced Network for Astronomical Research (CANFAR), the CADC is at the global forefront of advancing astronomical research through improved data services. The CAOM aims to provide homogeneous data access, and hence viable interoperability between a potentially unlimited number of different data collections, at many wavelengths. It is active in the definition of numerous emerging standards within the International Virtual Observatory, and several datasets are already available. The CANFAR project is an initiative to make cloud computing for storage and data-intensive processing available to the community. It does this via a Virtual Machine environment that is equivalent to managing a local desktop. Several groups are already processing science data. CADC is also at the forefront of advanced astronomical data analysis, driven by the science requirements of astronomers both locally and further afield. The emergence of 'Astroinformatics' promises to provide not only utility items like object classifications, but to directly enable new science by accessing previously undiscovered or intractable

  11. 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

  12. 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

  13. Extracting structural information from the OH and CH stretch spectral regions with a local mode approach

    NASA Astrophysics Data System (ADS)

    Tabor, Daniel P.

    This thesis focuses on the development and application of a reduced-dimensional local mode approach to the calculation of the infrared spectra of molecules and clusters. The basic properties of infrared spectra can often be understood in the context of the harmonic oscillator/linear dipole approximation. However, the spectra of the molecules and clusters of interest in this study contain additional complications due to stretch-bend Fermi resonances. The presence of these resonances makes the assignment of vibrational spectra to particular isomers or conformers much more difficult. By using a reduced-dimensional local mode approach, we are able to incorporate the important anharmonic terms in an efficient manner and accurately model the spectra with only modest additional costs. The first part of this thesis is a detailed study on the CH stretch region vibrational spectroscopy of a series of molecules with alkyl and alkoxy groups. The conclusions of this study formed the foundation for the construction of the model for the rest of the molecules in this thesis. The approach is shown to model all of the major features of short alkylbenzenes. The second part investigates the interaction of a benzene molecule with a cluster of water molecules in the gas phase. An understanding of these structures provides a framework for understanding the solvation structure of benzene in water. Using the model Hamiltonian, we are able to make definitive assignments of the structures of benzene complexed with both six and seven water molecules based on their infrared spectra in the OH stretch region. For both clusters, the assigned structures show a fundamental change in the structure of the water network, illustrating the strong impact that a benzene molecule can have on the structure of water. Finally, we employ the model to investigate the structure and spectroscopy of longer alkylbenzene chains, alkylbenzyl radicals, and water clusters solvated with other molecules. This series of

  14. Damage localization in beam-like structures using changes in modal strain energy

    NASA Astrophysics Data System (ADS)

    Ouali, M.; Mellel, N.; Dougdag, M.

    2017-02-01

    This paper investigates the application and reliability of using modal strain energy in damage localization estimation of beam-like structures. This is based on the fact that damage often cause a loss of stiffness that increase the modal displacement of two ends of beam element containing the damage, So the modal strain energy after damage will be increased and Modal Strain Energy Change Ratio (MSECR) in this element is larger than other elements and the location of damage is detected by finding the element with higher MSECR. To conduct this investigation, an experimental modal analysis program was carried out on a cantilever beam subjected to a controlled crack levels and the first seven mode shapes were extracted and used to calculate the modal strain energy change. The experimental MSECR was computed and the location of the damage was accurately identified especially for crack sizing as small as 10% of the beam height. Finally, finite elements models were built and validated, MSE change method was applied and the results demonstrate that the method is capable of localizing the damage for beam structure.

  15. Universal properties from a local geometric structure of a Killing horizon

    NASA Astrophysics Data System (ADS)

    Koga, Jun-ichirou

    2007-06-01

    We consider universal properties that arise from a local geometric structure of a Killing horizon, and analyse whether such universal properties give rise to degeneracy of classical configurations. We first introduce a non-perturbative definition of such a local geometric structure, which we call an asymptotic Killing horizon. It is then shown that infinitely many asymptotic Killing horizons reside on a common null hypersurface, once there exists one asymptotic Killing horizon, which is thus considered as degeneracy. In order to see how this degeneracy is physically meaningful, we analyse also the acceleration of the orbits of the vector that generates an asymptotic Killing horizon. It is shown that there exists the diff(S1) or diff(R1) sub-algebra on an asymptotic Killing horizon universally, which is picked out naturally, based on the behaviour of the acceleration. We argue that the discrepancy between string theory and the Euclidean approach in the entropy of an extreme black hole may be resolved, if the microscopic states responsible for black hole thermodynamics are connected with asymptotic Killing horizons.

  16. Structure and functionalization of mesoporous bioceramics for bone tissue regeneration and local drug delivery.

    PubMed

    Vallet-Regí, María; Izquierdo-Barba, Isabel; Colilla, Montserrat

    2012-03-28

    This review article describes the importance of structure and functionalization in the performance of mesoporous silica bioceramics for bone tissue regeneration and local drug delivery purposes. Herein, we summarize the pivotal features of mesoporous bioactive glasses, also known as 'templated glasses' (TGs), which present chemical compositions similar to those of conventional bioactive sol-gel glasses and the added value of an ordered mesopore arrangement. An in-depth study concerning the possibility of tailoring the structural and textural characteristics of TGs at the nanometric scale and their influence on bioactive behaviour is discussed. The highly ordered mesoporous arrangement of cavities allows these materials to confine drugs to be subsequently released, acting as drug delivery devices. The functionalization of mesoporous silica walls has been revealed as the cornerstone in the performance of these materials as controlled release systems. The synergy between the improved bioactive behaviour and local sustained drug release capability of mesostructured materials makes them suitable to manufacture three-dimensional macroporous scaffolds for bone tissue engineering. Finally, this review tackles the possibility of covalently grafting different osteoinductive agents to the scaffold surface that act as attracting signals for bone cells to promote the bone regeneration process.

  17. 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

    2013-10-09

    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.

  18. 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.

  19. 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.

  20. Capturing ultrafast photoinduced local structural distortions of BiFeO3

    DOE PAGES

    Wen, Haidan; Sassi, Michel JPC; Luo, Zhenlin; ...

    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

  1. Structure of the pilus assembly protein TadZ from Eubacterium rectale: Implications for polar localization

    PubMed Central

    Xu, Qingping; Christen, Beat; Chiu, Hsiu-Ju; Jaroszewski, Lukasz; Klock, Heath E.; Knuth, Mark W.; Miller, Mitchell D.; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Figurski, David H.; Shapiro, Lucy; Wilson, Ian A.

    2011-01-01

    Summary The tad (tight adherence) locus encodes a protein translocation system that produces a novel variant of type IV pili. The pilus assembly protein TadZ (called CpaE in Caulobacter crescentus) is ubiquitous in tad loci, but is absent in other type IV pilus biogenesis systems. The crystal structure of TadZ from E. rectale (ErTadZ), in complex with ATP and Mg2+, was determined to 2.1 Å resolution. ErTadZ contains an atypical ATPase domain with a variant of a deviant Walker-A motif that retains ATP binding capacity while displaying only low intrinsic ATPase activity. The bound ATP plays an important role in dimerization of ErTadZ. The N-terminal atypical receiver domain resembles the canonical receiver domain of response regulators, but has a degenerate, stripped-down “active site”. Homology modeling of the N-terminal atypical receiver domain of CpaE indicates that it has a conserved protein-protein binding surface similar to that of the polar localization module of the social mobility protein FrzS, suggesting a similar function. Our structural results also suggest that TadZ localizes to the pole through the atypical receiver domain during early stage of pili biogenesis, and functions as a hub for recruiting other pili components, thus providing insights into the Tad pilus assembly process. PMID:22211578

  2. 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).

  3. 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.

  4. “SP-G”, a Putative New Surfactant Protein – Tissue Localization and 3D Structure

    PubMed Central

    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

  5. 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).

  6. Structure of the pilus assembly protein TadZ from Eubacterium rectale: implications for polar localization.

    PubMed

    Xu, Qingping; Christen, Beat; Chiu, Hsiu-Ju; Jaroszewski, Lukasz; Klock, Heath E; Knuth, Mark W; Miller, Mitchell D; Elsliger, Marc-André; Deacon, Ashley M; Godzik, Adam; Lesley, Scott A; Figurski, David H; Shapiro, Lucy; Wilson, Ian A

    2012-02-01

    The tad (tight adherence) locus encodes a protein translocation system that produces a novel variant of type IV pili. The pilus assembly protein TadZ (called CpaE in Caulobacter crescentus) is ubiquitous in tad loci, but is absent in other type IV pilus biogenesis systems. The crystal structure of TadZ from Eubacterium rectale (ErTadZ), in complex with ATP and Mg(2+) , was determined to 2.1 Å resolution. ErTadZ contains an atypical ATPase domain with a variant of a deviant Walker-A motif that retains ATP binding capacity while displaying only low intrinsic ATPase activity. The bound ATP plays an important role in dimerization of ErTadZ. The N-terminal atypical receiver domain resembles the canonical receiver domain of response regulators, but has a degenerate, stripped-down 'active site'. Homology modelling of the N-terminal atypical receiver domain of CpaE indicates that it has a conserved protein-protein binding surface similar to that of the polar localization module of the social mobility protein FrzS, suggesting a similar function. Our structural results also suggest that TadZ localizes to the pole through the atypical receiver domain during an early stage of pili biogenesis, and functions as a hub for recruiting other pili components, thus providing insights into the Tad pilus assembly process.

  7. 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.

  8. "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.

  9. Probing the local structure of dilute Cu dopants in fluorescent ZnS nanocrystals using EXAFS.

    PubMed

    Car, Brad; Medling, Scott; Corrado, Carley; Bridges, Frank; Zhang, Jin Z

    2011-10-05

    A local structure study of ZnS nanocrystals, doped with very low concentrations of Cu, was carried out using the EXAFS technique to better understand how Cu substitutes into the host lattice and forms Cu luminescence centers. We show that a large fraction of the Cu have three nearest neighbor S atoms and the Cu-S bond is significantly shortened compared to Zn-S, by ∼0.08 Å. In addition, the second neighbor Cu-Cu peak is extremely small. We propose that Cu occupies an interior site next to a S(2-) vacancy, with the Cu displaced towards the remaining S(2-) and away from the vacancy; such a displacement immediately explains the lack of a significant Cu-Cu peak in the data. There is no evidence for interstitial Cu sites (Cu(i)), indicating that no more than 2% of the Cu are Cu(i.) This study provides new insights into the local structure of the Cu dopant in ZnS without the presence of CuS nanoprecipitates that are present at higher Cu doping levels.

  10. Probing the local structure of dilute Cu dopants in fluorescent ZnS nanocrystals using EXAFS

    NASA Astrophysics Data System (ADS)

    Car, Brad; Medling, Scott; Corrado, Carley; Bridges, Frank; Zhang, Jin Z.

    2011-10-01

    A local structure study of ZnS nanocrystals, doped with very low concentrations of Cu, was carried out using the EXAFS technique to better understand how Cu substitutes into the host lattice and forms Cu luminescence centers. We show that a large fraction of the Cu have three nearest neighbor S atoms and the Cu-S bond is significantly shortened compared to Zn-S, by ~0.08 Å. In addition, the second neighbor Cu-Cu peak is extremely small. We propose that Cu occupies an interior site next to a S2- vacancy, with the Cu displaced towards the remaining S2- and away from the vacancy; such a displacement immediately explains the lack of a significant Cu-Cu peak in the data. There is no evidence for interstitial Cu sites (Cui), indicating that no more than 2% of the Cu are Cui. This study provides new insights into the local structure of the Cu dopant in ZnS without the presence of CuS nanoprecipitates that are present at higher Cu doping levels.

  11. 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.

  12. Robust structural damage detection and localization based on joint approximate diagonalization technique in frequency domain

    NASA Astrophysics Data System (ADS)

    Cao, Shancheng; Ouyang, Huajiang

    2017-01-01

    The structural characteristic deflection shapes (CDS’s) such as mode shapes and operational deflection shapes are highly sensitive to structural damage in beam- or plate-type structures. Nevertheless, they are vulnerable to measurement noise and could result in unacceptable identification errors. In order to increase the accuracy and noise robustness of damage identification based on CDS’s using vibration responses of random excitation, joint approximate diagonalization (JAD) technique and gapped smoothing method (GSM) are combined to form a sensitive and robust damage index (DI), which can simultaneously detect the existence of damage and localize its position. In addition, it is possible to apply this approach to damage identification of structures under ambient excitation. First, JAD method which is an essential technique of blind source separation is investigated to simultaneously diagonalize a set of power spectral density matrices corresponding to frequencies near a certain natural frequency to estimate a joint unitary diagonalizer. The columns of this joint diagonalizer contain dominant CDS’s. With the identified dominant CDS’s around different natural frequencies, GSM is used to extract damage features and a robust damage identification index is then proposed. Numerical and experimental examples of beams with cracks are used to verify the validity and noise robustness of JAD based CDS estimation and the proposed DI. Furthermore, damage identification using dominant CDS’s estimated by JAD method is demonstrated to be more accurate and noise robust than by the commonly used singular value decomposition method.

  13. Local electronic structure and nanolevel hierarchical organization of bone tissue: theory and NEXAFS study

    NASA Astrophysics Data System (ADS)

    Pavlychev, A. A.; Avrunin, A. S.; Vinogradov, A. S.; Filatova, E. O.; Doctorov, A. A.; Krivosenko, Yu S.; Samoilenko, D. O.; Svirskiy, G. I.; Konashuk, A. S.; Rostov, D. A.

    2016-12-01

    Theoretical and experimental investigations of native bone are carried out to understand relationships between its hierarchical organization and local electronic and atomic structure of the mineralized phase. The 3D superlattice model of a coplanar assembly of the hydroxyapatite (HAP) nanocrystallites separated by the hydrated nanolayers is introduced to account the interplay of short-, long- and super-range order parameters in bone tissue. The model is applied to (i) predict and rationalize the HAP-to-bone spectral changes in the electronic structure and (ii) describe the mechanisms ensuring the link of the hierarchical organization with the electronic structure of the mineralized phase in bone. To check the predictions the near-edge x-ray absorption fine structure (NEXAFS) at the Ca 2p, P 2p and O 1s thresholds is measured for native bone and compared with NEXAFS for reference compounds. The NEXAFS analysis has demonstrated the essential hierarchy induced HAP-to-bone red shifts of the Ca and P 2p-to-valence transitions. The lowest O 1s excitation line at 532.2 eV in bone is assigned with superposition of core transitions in the hydroxide OH-(H2O) m anions, Ca2+(H2O) n cations, the carboxyl groups inside the collagen and [PO4]2- and [PO4]- anions with unsaturated P-O bonds.

  14. Local structure and optical absorption characteristic investigation on Fe doped TiO2 nanoparticles

    NASA Astrophysics Data System (ADS)

    Zhao, Tian-Xing; Feng, Ya-Juan; Huang, Jun-Heng; He, Jin-Fu; Liu, Qing-Hua; Pan, Zhi-Yun; Wu, Zi-Yu

    2015-02-01

    The local structures and optical absorption characteristics of Fe doped TiO2 nanoparticles synthesized by the sol-gel method were characterized by X-ray diffraction (XRD), X-ray absorption fine structure spectroscopy (XAFS) and ultraviolet-visible absorption spectroscopy (UV-Vis). XRD patterns show that all Fe-doped TiO2 samples have the characteristic anatase structure. Accurate Fe and Ti K-edge EXAFS analysis further reveal that all Fe atoms replace Ti atoms in the anatase lattice. The analysis of UV-Vis data shows a red shift to the visible range. According to the above results, we claim that substitutional Fe atoms lead to the formation of structural defects and new intermediate energy levels appear, narrowing the band gap and extending the optical absorption edge towards the visible region. Supported by National Basic Research Program of China (2012CB825801), Science Fund for Creative Research Groups of NSFC (11321503), National Natural Science Foundation of China (11321503, 11179004) and Guangdong Natural Science Foundation (S2011040003985)

  15. Clinal resistance structure and pathogen local adaptation in a serpentine flax-flax rust interaction.

    PubMed

    Springer, Yuri P

    2007-08-01

    Because disease resistance is a hallmark signature of pathogen-mediated selection pressure on hosts, studies of resistance structure (the spatial distribution of disease resistance genes among conspecific host populations) can provide valuable insights into the influence of pathogens on host evolution and spatial variation in the magnitude of their effects. To date few studies of wild plant-pathogen interactions have characterized resistance structure by sampling across the host's biogeographic range, and only a handful have paired such investigations with studies of disease levels under natural conditions. I used a greenhouse cross-inoculation experiment to characterize genetic resistance of 16 populations of California dwarf flax (Hesperolinon californicum) to attack by multiple samples of the rust fungus Melampsora lini. I documented a latitudinal cline in resistance structure, manifest across the host's biogeographic range, which mirrored almost identically a cline in infection prevalence documented through field surveys of disease in study populations. These results provide empirical evidence for clinal patterns of antagonistic selection pressure, demonstrate that such patterns can be manifest across broad biogeographic scales, and suggest that rates of disease prevalence in wild plant populations may be tightly linked to the distribution of host resistance genes. Tests for local adaptation of the fungus revealed evidence of the phenomenon (significantly greater infection in sympatric plant-fungal pairings) as well as the potential for substantial bias to be introduced into statistical analyses by spatial patterns of host resistance structure.

  16. Sure Start Children's Centres: time to make them better known.

    PubMed

    Thompson, Christine

    2010-01-01

    Health services have traditionally been available to local communities through general practices, health visitors and midwives. Since the introduction of the Sure Start Local programme in 1997 and Sure Start Children's Centres in 2004, an increasing number of children's centres are working with their local NHS to provide health services for the under fives, and improve the accessibility of these services to local families. Sure Start Children's Centres were set up in England as part of the Department for Children, Schools and Families' Children's Plan to improve outcomes for children and their families and contribute to the strategic objectives of Every Child Matters. Children's centres offer a range of integrated services from child health and maternity services to parenting and childcare provisions. They also deliver key health promotion activities and programmes that contribute to the public health priorities of Primary Care Trusts, e.g. breast-feeding, smoking in pregnancy, physical activity and healthy eating. There are now 3,500 children's centres offering easily accessible services to more than 2.4 million children and families across England. Health professionals are asked work proactively together to raise awareness of these among local communities so that more families can benefit from the services they offer.

  17. The local and long-range structural order of the spin-glass pyrochlore, Tb2Mo2O7

    SciTech Connect

    Ehlers, Georg; Jiang, Yu; Booth, Corwin H; Greedan, John E; Gardner, Jason; Huq, Ashfia

    2011-01-01

    To understand the origin of the spin-glass state in molybdate pyrochlores, the structure of Tb2Mo2O7 is investigated using two techniques: the long-range lattice structure was measured using neutron powder diffraction (NPD), and the local structure information was obtained from extended x-ray absorption fine structure (EXAFS) measurements. While the long-range structure appears well ordered, apart from some enhanced mean-squared site displacements, the local structure measurements indicate nearest-neighbor disorder exists, similar to that found in the related spinglass pyrochlore, Y2Mo2O7. Although the freezing temperature in Tb2Mo2O7, 25 K, is slightly higher than in Y2Mo2O7, 22 K, the degree of local bond disorder is actually less in Tb2Mo2O7. This apparaent contradiction is considered in light of the interactions involved in the freezing process.

  18. Solution structure of the cytoplasmic domain of phopholamban: phosphorylation leads to a local perturbation in secondary structure.

    PubMed

    Mortishire-Smith, R J; Pitzenberger, S M; Burke, C J; Middaugh, C R; Garsky, V M; Johnson, R G

    1995-06-13

    Peptides representing the N-terminal domain (Ia) of the cardiac sarcoplasmic reticulum protein phospholamban (residues 1-25 [PLB(1-25)] and a phosphorylated form [pPLB(1-25)]) were synthesized and their conformations examined using circular dichroism and nuclear magnetic resonance spectroscopy. In aqueous solution, both PLB(1-25) and pPLB(1-25) adopt a primarily disordered conformation. In 30% trifluoroethanol/10 mM phosphate, PLB(1-25) exhibits a CD spectrum consistent with 60% helical structure. This value decreases to 27% for the phosphorylated peptide. CD spectra in 2% SDS indicate 40% alpha-helix for PLB(1-25) and 20% for pPLB(1-25). Full chemical shift assignments were obtained by conventional homonuclear NMR methodologies for both PLB(1-25) and pPLB(1-25) in 30% trifluoroethanol/water and 300 mM SDS. The solution structure of PLB(1-25) in 30% TFE/water was determined from distance geometry calculations using 54 NOE distance constraints and 17 torsion angle constraints. In the family of 20 calculated conformers, the root mean square deviation from the mean structure is 0.79 A for backbone heavy atoms of residues 1-17. The structure comprises a regular alpha-helix extending from M1 to S16 with the remaining C-terminal residues disordered. The calculated structure is supported by analysis of C alpha H secondary shifts which are significantly negative for residues 1-16. Chemical shift degeneracy is substantially more extensive in the phospho form and precludes a direct comparison of calculated structures. However, the magnitudes of upfield secondary shifts are decreased by 20% in residues 1-11 and are not significantly helical for residues 12-16 according to the criteria of Wishart et al. [(1992) Biochemistry 31, 1647-1651]. 3JHN alpha coupling constants measured for I12, R13, A15, and S16 also suggest that residues 12-16 undergo a local unwinding of the helix upon phosphorylation. Similar results are obtained for PLB(1-25) and pPLB(1-25) in 300 mM perdeuterated

  19. 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

  20. Li-Ion Localization and Energetics as a Function of Anode Structure.

    PubMed

    McNutt, Nicholas W; McDonnell, Marshall; Rios, Orlando; Keffer, David J

    2017-03-01

    In this work, we study the effect of carbon composite anode structure on the localization and energetics of Li-ions. A computational molecular dynamics study is combined with experimental results from neutron scattering experiments to understand the effect of composite density, crystallite size, volume fraction of crystalline carbon, and ion loading on the nature of ion storage in novel, lignin-derived composite materials. In a recent work, we demonstrated that these carbon composites display a fundamentally different mechanism for Li-ion storage than traditional graphitic anodes. The edges of the crystalline and amorphous fragments of aromatic carbon that exist in these composites are terminated by hydrogen atoms, which play a crucial role in adsorption. In this work, we demonstrate how differences in composite structure due to changes in the processing conditions alter the type and extent of the interface between the amorphous and crystalline domains, thus impacting the nature of Li-ion storage. The effects of structural properties are evaluated using a suite of pair distribution functions as well as an original technique to extract archetypal structures, in the form of three-dimensional atomic density distributions, from highly disordered systems. The energetics of Li-ion binding are understood by relating changes in the energy and charge distributions to changes in structural properties. The distribution of Li-ion energies reveals that some structures lead to greater chemisorption, while others have greater physisorption. Carbon composites with a high volume fraction of small crystallites demonstrate the highest ion storage capacity because of the high interfacial area between the crystalline and amorphous domains. At these interfaces, stable H atoms, terminating the graphitic crystallites, provide favorable sites for reversible Li adsorption.

  1. 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

  2. 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

  3. 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

  4. Local structure investigation of oxide ion and proton defects in Ge-apatites by pair distribution function analysis.

    PubMed

    Malavasi, Lorenzo; Orera, Alodia; Slater, Peter R; Panchmatia, Pooja M; Islam, M Saiful; Siewenie, Joan

    2011-01-07

    In this communication we provide a direct insight into the local structure and defects of oxygen excess Ge-apatites, in both dry and deuterated states, by means of pair distribution function analysis.

  5. Comparative analysis of local and consensus quantitative structure-activity relationship approaches for the prediction of bioconcentration factor.

    PubMed

    Piir, G; Sild, S; Maran, U

    2013-01-01

    Quantitative structure-activity relationships (QSARs) are broadly classified as global or local, depending on their molecular constitution. Global models use large and diverse training sets covering a wide range of chemical space. Local models focus on smaller structurally or chemically similar subsets that are conventionally selected by human experts or alternatively using clustering analysis. The current study focuses on the comparative analysis of different clustering algorithms (expectation-maximization, K-means and hierarchical) for seven different descriptor sets as structural characteristics and two rule-based approaches to select subsets for designing local QSAR models. A total of 111 local QSAR models are developed for predicting bioconcentration factor. Predictions from local models were compared with corresponding predictions from the global model. The comparison of coefficients of determination (r(2)) and standard deviations for local models with similar subsets from the global model show improved prediction quality in 97% of cases. The descriptor content of derived QSARs is discussed and analyzed. Local QSAR models were further consolidated within the framework of consensus approach. All different consensus approaches increased performance over the global and local models. The consensus approach reduced the number of strongly deviating predictions by evening out prediction errors, which were produced by some local QSARs.

  6. 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.

  7. 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

  8. 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

  9. CMCC Data Distribution Centre

    NASA Astrophysics Data System (ADS)

    Aloisio, Giovanni; Fiore, Sandro; Negro, A.

    2010-05-01

    The CMCC Data Distribution Centre (DDC) is the primary entry point (web gateway) to the CMCC. It is a Data Grid Portal providing a ubiquitous and pervasive way to ease data publishing, climate metadata search, datasets discovery, metadata annotation, data access, data aggregation, sub-setting, etc. The grid portal security model includes the use of HTTPS protocol for secure communication with the client (based on X509v3 certificates that must be loaded into the browser) and secure cookies to establish and maintain user sessions. The CMCC DDC is now in a pre-production phase and it is currently used only by internal users (CMCC researchers and climate scientists). The most important component already available in the CMCC DDC is the Search Engine which allows users to perform, through web interfaces, distributed search and discovery activities by introducing one or more of the following search criteria: horizontal extent (which can be specified by interacting with a geographic map), vertical extent, temporal extent, keywords, topics, creation date, etc. By means of this page the user submits the first step of the query process on the metadata DB, then, she can choose one or more datasets retrieving and displaying the complete XML metadata description (from the browser). This way, the second step of the query process is carried out by accessing to a specific XML document of the metadata DB. Finally, through the web interface, the user can access to and download (partially or totally) the data stored on the storage device accessing to OPeNDAP servers and to other available grid storage interfaces. Requests concerning datasets stored in deep storage will be served asynchronously.

  10. 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

  11. Magnetic structure and local lattice distortion in giant negative thermal expansion material Mn3Cu1-xGexN

    NASA Astrophysics Data System (ADS)

    Iikubo, S.; Kodama, K.; Takenaka, K.; Takagi, H.; Shamoto, S.

    2010-11-01

    Magnetic and local structures in an antiperovskite system, Mn3Cu1-xGexN, with a giant negative thermal expansion have been studied by neutron powder diffraction measurement. We discuss (1) an importance of an averaged cubic crystal structure and a ΓG5g antiferromagnetic spin structure for the large magneto-volume effect (MVE) in this itinerant electron system, (2) an unique role of a local lattice distortion well described by the low temperature tetragonal structure of Mn3GeN for the broadening of MVE.

  12. 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

  13. 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.

  14. 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.

  15. 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