Science.gov

Sample records for local structural bias

  1. Locally Biased Galaxy Formation and Large-Scale Structure

    NASA Astrophysics Data System (ADS)

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

    2000-01-01

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

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

    ERIC Educational Resources Information Center

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

    2006-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  4. Bias structure to efficiently package a magnetic bubble domain device

    NASA Technical Reports Server (NTRS)

    Chen, Thomas T. (Inventor)

    1978-01-01

    A single, compact bias structure to efficiently package a plurality of magnetic bubble domain device chips having different bias requirements. The vertical magnetic field distribution within the bias structure air gap is selectively controlled by a magnetically soft field adjusting assembly suitably attached within the bias structure. The size and configuration of the field adjusting assembly tailors local field variations within the air gap to correspond with the bias requirements of the bubble domain chips disposed therein.

  5. Local gravitational redshifts can bias cosmological measurements

    SciTech Connect

    Wojtak, Radosław; Davis, Tamara M.; Wiis, Jophiel E-mail: tamarad@physics.uq.edu.au

    2015-07-01

    Measurements of cosmological parameters via the distance-redshift relation usually rely on models that assume a homogenous universe. It is commonly presumed that the large-scale structure evident in our Universe has a negligible impact on the measurement if distances probed in observations are sufficiently large (compared to the scale of inhomogeneities) and are averaged over different directions on the sky. This presumption does not hold when considering the effect of the gravitational redshift caused by our local gravitational potential, which alters light coming from all distances and directions in the same way. Despite its small magnitude, this local gravitational redshift gives rise to noticeable effects in cosmological inference using SN Ia data. Assuming conservative prior knowledge of the local potential given by sampling a range of gravitational potentials at locations of Milky-Way-like galaxies identified in cosmological simulations, we show that ignoring the gravitational redshift effect in a standard data analysis leads to an additional systematic error of ∼1% in the determination of density parameters and the dark energy equation of state. We conclude that our local gravitational field affects our cosmological inference at a level that is important in future observations aiming to achieve percent-level accuracy.

  6. Do local and global perceptual biases tell us anything about local and global selective attention?

    PubMed

    Caparos, Serge; Linnell, Karina J; Bremner, Andrew J; de Fockert, Jan W; Davidoff, Jules

    2013-02-01

    Local, as opposed to global, perceptual bias has been linked to a lesser ability to attend globally. We examined this proposed link in Himba observers, members of a remote Namibian population who have demonstrated a strong local bias compared with British observers. If local perceptual bias is related to a lesser ability to attend globally, Himba observers, relative to British observers, should be less distracted by global information when performing a local-selection task but more distracted by local information when performing a global-selection task. However, Himba observers performed better than British observers did on both a local-selection task and a global-selection task (both of which used local/global hierarchical figures as stimuli), which suggests that they possessed greater control over attentional selection in response to task demands. We conclude that local and global perceptual biases must be distinguished from local and global selective attention.

  7. Auditory local bias and reduced global interference in autism.

    PubMed

    Bouvet, Lucie; Simard-Meilleur, Andrée-Anne; Paignon, Adeline; Mottron, Laurent; Donnadieu, Sophie

    2014-06-01

    Processing local elements of hierarchical patterns at a superior level and independently from an intact global influence is a well-established characteristic of autistic visual perception. However, whether this confirmed finding has an equivalent in the auditory modality is still unknown. To fill this gap, 18 autistics and 18 typical participants completed a melodic decision task where global and local level information can be congruent or incongruent. While focusing either on the global (melody) or local level (group of notes) of hierarchical auditory stimuli, participants have to decide whether the focused level is rising or falling. Autistics showed intact global processing, a superior performance when processing local elements and a reduced global-to-local interference compared to typical participants. These results are the first to demonstrate that autistic processing of auditory hierarchical stimuli closely parallels processing of visual hierarchical stimuli. When analyzing complex auditory information, autistic participants present a local bias and a more autonomous local processing, but not to the detriment of global processing.

  8. OPTIMIZATION BIAS IN ENERGY-BASED STRUCTURE PREDICTION

    PubMed Central

    Petrella, Robert J.

    2014-01-01

    Physics-based computational approaches to predicting the structure of macromolecules such as proteins are gaining increased use, but there are remaining challenges. In the current work, it is demonstrated that in energy-based prediction methods, the degree of optimization of the sampled structures can influence the prediction results. In particular, discrepancies in the degree of local sampling can bias the predictions in favor of the oversampled structures by shifting the local probability distributions of the minimum sampled energies. In simple systems, it is shown that the magnitude of the errors can be calculated from the energy surface, and for certain model systems, derived analytically. Further, it is shown that for energy wells whose forms differ only by a randomly assigned energy shift, the optimal accuracy of prediction is achieved when the sampling around each structure is equal. Energy correction terms can be used in cases of unequal sampling to reproduce the total probabilities that would occur under equal sampling, but optimal corrections only partially restore the prediction accuracy lost to unequal sampling. For multiwell systems, the determination of the correction terms is a multibody problem; it is shown that the involved cross-correlation multiple integrals can be reduced to simpler integrals. The possible implications of the current analysis for macromolecular structure prediction are discussed. PMID:25552783

  9. Bias in the effective field theory of large scale structures

    SciTech Connect

    Senatore, Leonardo

    2015-11-01

    We study how to describe collapsed objects, such as galaxies, in the context of the Effective Field Theory of Large Scale Structures. The overdensity of galaxies at a given location and time is determined by the initial tidal tensor, velocity gradients and spatial derivatives of the regions of dark matter that, during the evolution of the universe, ended up at that given location. Similarly to what was recently done for dark matter, we show how this Lagrangian space description can be recovered by upgrading simpler Eulerian calculations. We describe the Eulerian theory. We show that it is perturbatively local in space, but non-local in time, and we explain the observational consequences of this fact. We give an argument for why to a certain degree of accuracy the theory can be considered as quasi time-local and explain what the operator structure is in this case. We describe renormalization of the bias coefficients so that, after this and after upgrading the Eulerian calculation to a Lagrangian one, the perturbative series for galaxies correlation functions results in a manifestly convergent expansion in powers of k/k{sub NL} and k/k{sub M}, where k is the wavenumber of interest, k{sub NL} is the wavenumber associated to the non-linear scale, and k{sub M} is the comoving wavenumber enclosing the mass of a galaxy.

  10. Bias in the effective field theory of large scale structures

    SciTech Connect

    Senatore, Leonardo

    2015-11-05

    We study how to describe collapsed objects, such as galaxies, in the context of the Effective Field Theory of Large Scale Structures. The overdensity of galaxies at a given location and time is determined by the initial tidal tensor, velocity gradients and spatial derivatives of the regions of dark matter that, during the evolution of the universe, ended up at that given location. Similarly to what was recently done for dark matter, we show how this Lagrangian space description can be recovered by upgrading simpler Eulerian calculations. We describe the Eulerian theory. We show that it is perturbatively local in space, but non-local in time, and we explain the observational consequences of this fact. We give an argument for why to a certain degree of accuracy the theory can be considered as quasi time-local and explain what the operator structure is in this case. Furthermore, we describe renormalization of the bias coefficients so that, after this and after upgrading the Eulerian calculation to a Lagrangian one, the perturbative series for galaxies correlation functions results in a manifestly convergent expansion in powers of k/kNL and k/kM, where k is the wavenumber of interest, kNL is the wavenumber associated to the non-linear scale, and kM is the comoving wavenumber enclosing the mass of a galaxy.

  11. Bias in the effective field theory of large scale structures

    DOE PAGES

    Senatore, Leonardo

    2015-11-05

    We study how to describe collapsed objects, such as galaxies, in the context of the Effective Field Theory of Large Scale Structures. The overdensity of galaxies at a given location and time is determined by the initial tidal tensor, velocity gradients and spatial derivatives of the regions of dark matter that, during the evolution of the universe, ended up at that given location. Similarly to what was recently done for dark matter, we show how this Lagrangian space description can be recovered by upgrading simpler Eulerian calculations. We describe the Eulerian theory. We show that it is perturbatively local inmore » space, but non-local in time, and we explain the observational consequences of this fact. We give an argument for why to a certain degree of accuracy the theory can be considered as quasi time-local and explain what the operator structure is in this case. Furthermore, we describe renormalization of the bias coefficients so that, after this and after upgrading the Eulerian calculation to a Lagrangian one, the perturbative series for galaxies correlation functions results in a manifestly convergent expansion in powers of k/kNL and k/kM, where k is the wavenumber of interest, kNL is the wavenumber associated to the non-linear scale, and kM is the comoving wavenumber enclosing the mass of a galaxy.« less

  12. When being narrow minded is a good thing: locally biased people show stronger contextual cueing.

    PubMed

    Bellaera, Lauren; von Mühlenen, Adrian; Watson, Derrick G

    2014-01-01

    Repeated contexts allow us to find relevant information more easily. Learning such contexts has been proposed to depend upon either global processing of the repeated contexts, or alternatively processing of the local region surrounding the target information. In this study, we measured the extent to which observers were by default biased to process towards a more global or local level. The findings showed that the ability to use context to help guide their search was strongly related to an observer's local/global processing bias. Locally biased people could use context to help improve their search better than globally biased people. The results suggest that the extent to which context can be used depends crucially on the observer's attentional bias and thus also to factors and influences that can change this bias. PMID:24313265

  13. Local bias induced ferroelectricity in manganites with competing charge and orbital order states.

    PubMed

    Figueiras, Fábio G N; Bdikin, Igor K; Amaral, Vitor B S; Kholkin, Andrei L

    2014-03-14

    Perovskite-type manganites, such as Pr1-xCaxMnO3, La1-xCaxMnO3 and La1-xSrxMnO3 solid solutions, are set forth as a case study of ferroelectricity formation mechanisms associated with the appearance of site- and bond-centered orbital ordering which breaks structural inversion symmetry. Even though the observation of macroscopic ferroelectricity may be hindered by the finite conductivity of manganites, polarization can still exist in nanoscale volumes. We use Piezoresponse Force Microscopy to probe local bias induced modifications of electrical and electromechanical properties at the manganite surface. Clear bias-induced piezocontrast and local hysteresis loops are observed for La0.89Sr0.11MnO3 and Pr0.60Ca0.40MnO3 compounds providing convincing evidence of the existence of locally induced polar states well above the transition temperature of the CO phase, while the reference samples without CO behavior show no ferroelectric-like response. Such coexistence of ferroelectricity and magnetism in manganites due to the charge ordering (CO) under locally applied electric field opens up a new pathway to expand the phase diagrams of such systems and to achieve spatially localized multiferroic effects with a potential to be used in a new generation of memory cells and data processing circuits. PMID:24477353

  14. Non-local bias contribution to third-order galaxy correlations

    NASA Astrophysics Data System (ADS)

    Bel, J.; Hoffmann, K.; Gaztañaga, E.

    2015-10-01

    We study halo clustering bias with second- and third-order statistics of halo and matter density fields in the Marenostrum Institut de Ciències de l'Espai (MICE) Grand Challenge simulation. We verify that two-point correlations deliver reliable estimates of the linear bias parameters at large scales, while estimations from the variance can be significantly affected by non-linear and possibly non-local contributions to the bias function. Combining three-point auto- and cross-correlations we find, for the first time in configuration space, evidence for the presence of such non-local contributions. These contributions are consistent with predicted second-order non-local effects on the bias functions originating from the dark matter tidal field. Samples of massive haloes show indications of bias (local or non-local) beyond second order. Ignoring non-local bias causes 20-30 and 5-10 per cent overestimation of the linear bias from three-point auto- and cross-correlations, respectively. We study two third-order bias estimators that are not affected by second-order non-local contributions. One is a combination of three-point auto- and cross-correlations. The other is a combination of third-order one- and two-point cumulants. Both methods deliver accurate estimations of the linear bias. Ignoring non-local bias causes higher values of the second-order bias from three-point correlations. Our results demonstrate that third-order statistics can be employed for breaking the growth-bias degeneracy.

  15. Estimating the Bias of Local Polynomial Approximations Using the Peano Kernel

    SciTech Connect

    Blair, J., and Machorro, E.

    2012-03-22

    These presentation visuals define local polynomial approximations, give formulas for bias and random components of the error, and express bias error in terms of the Peano kernel. They further derive constants that give figures of merit, and show the figures of merit for 3 common weighting functions. The Peano kernel theorem yields estimates for the bias error for local-polynomial-approximation smoothing that are superior in several ways to the error estimates in the current literature.

  16. Exposure to an Urban Environment Alters the Local Bias of a Remote Culture

    ERIC Educational Resources Information Center

    Caparos, Serge; Ahmed, Lubna; Bremner, Andrew J.; de Fockert, Jan W.; Linnell, Karina J.; Davidoff, Jules

    2012-01-01

    There is substantial evidence that populations in the Western world exhibit a local bias compared to East Asian populations that is widely ascribed to a difference between individualistic and collectivist societies. However, we report that traditional Himba--a remote interdependent society--exhibit a strong local bias compared to both Japanese and…

  17. Exchange bias training effect in coupled all ferromagnetic bilayer structures.

    PubMed

    Binek, Ch; Polisetty, S; He, Xi; Berger, A

    2006-02-17

    Exchange coupled bilayers of soft and hard ferromagnetic thin films show remarkable analogies to conventional antiferromagnetic/ferromagnetic exchange bias heterostructures. Not only do all these ferromagnetic bilayers exhibit a tunable exchange bias effect, they also show a distinct training behavior upon cycling the soft layer through consecutive hysteresis loops. In contrast with conventional exchange bias systems, such all ferromagnetic bilayer structures allow the observation of training induced changes in the bias-setting hardmagnetic layer by means of simple magnetometry. Our experiments show unambiguously that the exchange bias training effect is driven by deviations from equilibrium in the pinning layer. A comparison of our experimental data with predictions from a theory based upon triggered relaxation phenomena shows excellent agreement.

  18. Asymmetric bias in user guided segmentations of brain structures.

    PubMed

    Maltbie, Eric; Bhatt, Kshamta; Paniagua, Beatriz; Smith, Rachel G; Graves, Michael M; Mosconi, Matthew W; Peterson, Sarah; White, Scott; Blocher, Joseph; El-Sayed, Mohammed; Hazlett, Heather C; Styner, Martin A

    2012-01-16

    Brain morphometric studies often incorporate comparative hemispheric asymmetry analyses of segmented brain structures. In this work, we present evidence that common user guided structural segmentation techniques exhibit strong left-right asymmetric biases and thus fundamentally influence any left-right asymmetry analyses. In this study, MRI scans from ten pediatric subjects were employed for studying segmentations of amygdala, globus pallidus, putamen, caudate, and lateral ventricle. Additionally, two pediatric and three adult scans were used for studying hippocampus segmentation. Segmentations of the sub-cortical structures were performed by skilled raters using standard manual and semi-automated methods. The left-right mirrored versions of each image were included in the data and segmented in a random order to assess potential left-right asymmetric bias. Using shape analysis we further assessed whether the asymmetric bias is consistent across subjects and raters with the focus on the hippocampus. The user guided segmentation techniques on the sub-cortical structures exhibited left-right asymmetric volume bias with the hippocampus displaying the most significant asymmetry values (p<0.01). The hippocampal shape analysis revealed the bias to be strongest on the lateral side of the body and medial side of the head and tail. The origin of this asymmetric bias is considered to be based in laterality of visual perception; therefore segmentations with any degree of user interaction contain an asymmetric bias. The aim of our study is to raise awareness in the neuroimaging community regarding the presence of the asymmetric bias and its influence on any left-right hemispheric analyses. We also recommend reexamining previous research results in the light of this new finding. PMID:21889995

  19. A new configurational bias scheme for sampling supramolecular structures.

    PubMed

    De Gernier, Robin; Curk, Tine; Dubacheva, Galina V; Richter, Ralf P; Mognetti, Bortolo M

    2014-12-28

    We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias scheme of Siepmann and Frenkel and is powered by the possibility of changing the topology of the supramolecular network by a non-local Monte Carlo algorithm. Such a plan is accomplished by a multi-scale modelling that merges coarse-grained simulations, describing the typical polymer conformations, with experimental results accounting for free energy terms involved in the reactions of the active sites. We test the new algorithm for a system of DNA coated colloids for which we compute the hybridisation free energy cost associated to the binding of tethered single stranded DNAs terminated by short sequences of complementary nucleotides. In order to demonstrate the versatility of our method, we also consider polymers functionalized by receptors that bind a surface decorated by ligands. In particular, we compute the density of states of adsorbed polymers as a function of the number of ligand-receptor complexes formed. Such a quantity can be used to study the conformational properties of adsorbed polymers useful when engineering adsorption with tailored properties. We successfully compare the results with the predictions of a mean field theory. We believe that the proposed method will be a useful tool to investigate supramolecular structures resulting from direct interactions between functionalized polymers for which efficient numerical methodologies of investigation are still lacking. PMID:25554182

  20. A new configurational bias scheme for sampling supramolecular structures

    SciTech Connect

    De Gernier, Robin; Mognetti, Bortolo M.; Curk, Tine; Dubacheva, Galina V.; Richter, Ralf P.

    2014-12-28

    We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias scheme of Siepmann and Frenkel and is powered by the possibility of changing the topology of the supramolecular network by a non-local Monte Carlo algorithm. Such a plan is accomplished by a multi-scale modelling that merges coarse-grained simulations, describing the typical polymer conformations, with experimental results accounting for free energy terms involved in the reactions of the active sites. We test the new algorithm for a system of DNA coated colloids for which we compute the hybridisation free energy cost associated to the binding of tethered single stranded DNAs terminated by short sequences of complementary nucleotides. In order to demonstrate the versatility of our method, we also consider polymers functionalized by receptors that bind a surface decorated by ligands. In particular, we compute the density of states of adsorbed polymers as a function of the number of ligand–receptor complexes formed. Such a quantity can be used to study the conformational properties of adsorbed polymers useful when engineering adsorption with tailored properties. We successfully compare the results with the predictions of a mean field theory. We believe that the proposed method will be a useful tool to investigate supramolecular structures resulting from direct interactions between functionalized polymers for which efficient numerical methodologies of investigation are still lacking.

  1. Local Scrape-Off Layer Control Using Biased electrodes in NSTX

    SciTech Connect

    Zweben, S J; Maqueda, R J; Roquemore, A L; Bush, C E; Kaita, R; Marsala, R J; Raitses, Y; Cohen, R H; Ryutov, D D

    2009-06-23

    An experiment was designed to test the theory that biased electrodes can affect the local scrape-off layer (SOL) width by creating a strong radial ExB drift [Cohen, R.H. and Ryutov, D.D, Nucl. Fusion 37, 621 (1997)]. These electrodes were located near the outer midplane in the SOL of the National Spherical Torus Experiment (NSTX). The electrodes were biased at up to {+-} 100 Volts, and the radial profile of the plasma between them was measured by an array of Langmuir probes. The biasing caused large changes in the local SOL profiles at least qualitatively consistent with this theory.

  2. Local scrape-off layer control using biased electrodes in NSTX

    SciTech Connect

    Zweben, S. J.; Maqueda, R. J.; Roquemore, A. L.; Bush, C. E.; Kaita, R.; Marsala, R. J.; Raitses, Y.; Cohen, R. H.; Ryutov, D. D.

    2009-04-01

    An experiment was designed to test the theory that biased electrodes can affect the local scrape-off layer (SOL) width by creating a strong radial ExB drift [Cohen, R.H. and Ryutov, D.D, Nucl. Fusion 37, 621 (1997)]. These electrodes were located near the outer midplane in the SOL of the National Spherical Torus Experiment (NSTX). The electrodes were biased at up to 100 Volts, and the radial profile of the plasma between them was measured by an array of Langmuir probes. The biasing caused large changes in the local SOL profiles at least qualitatively consistent with this theory.

  3. Spontaneous local variations in ongoing neural activity bias perceptual decisions

    PubMed Central

    Hesselmann, Guido; Kell, Christian A.; Eger, Evelyn; Kleinschmidt, Andreas

    2008-01-01

    Neural variability in responding to identical repeated stimuli has been related to trial-by-trial fluctuations in ongoing activity, yet the neural and perceptual consequences of these fluctuations remain poorly understood. Using functional neuroimaging, we recorded brain activity in subjects who reported perceptual decisions on an ambiguous figure, Rubin's vase-faces picture, which was briefly presented at variable intervals of ≥20 s. Prestimulus activity in the fusiform face area, a cortical region preferentially responding to faces, was higher when subjects subsequently perceived faces instead of the vase. This finding suggests that endogenous variations in prestimulus neuronal activity biased subsequent perceptual inference. Furnishing evidence that evoked sensory responses, we then went on to show that the pre- and poststimulus activity interact in a nonlinear way and the ensuing perceptual decisions depend upon the prestimulus context in which they occur. PMID:18664576

  4. "Autistic" Local Processing Bias Also Found in Children Gifted in Realistic Drawing

    ERIC Educational Resources Information Center

    Drake, Jennifer E.; Redash, Amanda; Coleman, Katelyn; Haimson, Jennifer; Winner, Ellen

    2010-01-01

    We investigated whether typically-developing children with a gift for drawing realistically show the local processing bias seen in individuals with autism spectrum disorder (ASD). Twenty-seven 6-12 year-olds made an observational drawing (scored for level of realism) and completed three local processing tasks, and parents completed the Childhood…

  5. Interloper bias in future large-scale structure surveys

    NASA Astrophysics Data System (ADS)

    Pullen, Anthony R.; Hirata, Christopher M.; Doré, Olivier; Raccanelli, Alvise

    2016-02-01

    Next-generation spectroscopic surveys will map the large-scale structure of the observable universe, using emission line galaxies as tracers. While each survey will map the sky with a specific emission line, interloping emission lines can masquerade as the survey's intended emission line at different redshifts. Interloping lines from galaxies that are not removed can contaminate the power spectrum measurement, mixing correlations from various redshifts and diluting the true signal. We assess the potential for power spectrum contamination, finding that an interloper fraction worse than 0.2% could bias power spectrum measurements for future surveys by more than 10% of statistical errors, while also biasing power spectrum inferences. We also construct a formalism for predicting cosmological parameter measurement bias, demonstrating that a 0.15%-0.3% interloper fraction could bias the growth rate by more than 10% of the error, which can affect constraints on gravity from upcoming surveys. We use the COSMOS Mock Catalog (CMC), with the emission lines rescaled to better reproduce recent data, to predict potential interloper fractions for the Prime Focus Spectrograph (PFS) and the Wide-Field InfraRed Survey Telescope (WFIRST). We find that secondary line identification, or confirming galaxy redshifts by finding correlated emission lines, can remove interlopers for PFS. For WFIRST, we use the CMC to predict that the 0.2% target can be reached for the WFIRST Hα survey, but sensitive optical and near-infrared photometry will be required. For the WFIRST [O III] survey, the predicted interloper fractions reach several percent and their effects will have to be estimated and removed statistically (e.g., with deep training samples). These results are optimistic as the CMC does not capture the full set of correlations of galaxy properties in the real Universe, and they do not include blending effects. Mitigating interloper contamination will be crucial to the next generation of

  6. Local magnetoresistance through Si and its bias voltage dependence in ferromagnet/MgO/silicon-on-insulator lateral spin valves

    SciTech Connect

    Saito, Y. Tanamoto, T.; Ishikawa, M.; Sugiyama, H.; Inokuchi, T.; Hamaya, K.; Tezuka, N.

    2014-05-07

    Local magnetoresistance (MR) through silicon (Si) and its bias voltage (V{sub bias}) (bias current (I{sub bias})) dependence in ferromagnet (FM)/MgO/silicon-on-insulator lateral spin valves are investigated. From the experimental measurements, we find that the local-MR through Si increases with increasing V{sub bias}. This anomalous increase of local-MR as a function of V{sub bias} can be understood by considering the standard drift-diffusion theory improved by taking into account the difference in the interface resistances and first order quantum effect between FM/MgO/Si (source) and Si/MgO/FM (drain) interfaces. The interface resistance dependence on experimentally obtained local-MR ratios also agrees with the improved standard spin diffusion theory. These results indicate that experimentally observed local-MR is certainly related to the spin signal through the Si bulk band.

  7. Dy-V magnetic interaction and local structure bias on the complex spin and orbital ordering in Dy₁₋xTbxVO₃ (x=0 and 0.2)

    DOE PAGES

    Yan, J.-Q.; Cao, H. B.; McGuire, M. A.; Ren, Y.; Sales, B. C.; Mandrus, D. G.

    2013-06-10

    The spin and orbital ordering in Dy₁₋xTbxVO₃ (x=0 and 0.2) was studied by measuring x-ray powder diffraction, magnetization, specific heat, and neutron single-crystal diffraction. The results show that G-OO/C-AF and C-OO/G-AF phases coexist in Dy0.8Tb0.20VO3 in the temperature range 2–60 K, and the volume fraction of each phase is temperature and field dependent. The ordering of Dy moments at T* = 12 K induces a transition from G-OO/C-AF to a C-OO/G-AF phase. Magnetic fields suppress the long-range order of Dy moments and thus the C-OO/G-AF phase below T*. The polarized moments induced at the Dy sublattice by external magnetic fieldsmore » couple to the V 3d moments, and this coupling favors the G-OO/C-AF state. Also discussed is the effect of the Dy-V magnetic interaction and local structure distortion on the spin and orbital ordering in Dy₁₋xTbxVO₃.« less

  8. Dy-V magnetic interaction and local structure bias on the complex spin and orbital ordering in Dy₁₋xTbxVO₃ (x=0 and 0.2)

    SciTech Connect

    Yan, J.-Q.; Cao, H. B.; McGuire, M. A.; Ren, Y.; Sales, B. C.; Mandrus, D. G.

    2013-06-10

    The spin and orbital ordering in Dy₁₋xTbxVO₃ (x=0 and 0.2) was studied by measuring x-ray powder diffraction, magnetization, specific heat, and neutron single-crystal diffraction. The results show that G-OO/C-AF and C-OO/G-AF phases coexist in Dy0.8Tb0.20VO3 in the temperature range 2–60 K, and the volume fraction of each phase is temperature and field dependent. The ordering of Dy moments at T* = 12 K induces a transition from G-OO/C-AF to a C-OO/G-AF phase. Magnetic fields suppress the long-range order of Dy moments and thus the C-OO/G-AF phase below T*. The polarized moments induced at the Dy sublattice by external magnetic fields couple to the V 3d moments, and this coupling favors the G-OO/C-AF state. Also discussed is the effect of the Dy-V magnetic interaction and local structure distortion on the spin and orbital ordering in Dy₁₋xTbxVO₃.

  9. Local heating in noble metal nanocontacts under high biases at 77 K

    NASA Astrophysics Data System (ADS)

    Tsutsui, Makusu; Teramae, Yumi; Kurokawa, Shu; Sakai, Akira

    2006-10-01

    Effects of local heating of noble metal nanocontacts under high biases at 77 K are investigated by measuring the bias dependence of the two-level fluctuation (TLF) frequency of the contact conductance. The TLF frequency increases exponentially in a bias range from 0.2 to 0.6 V for Au and Cu nanocontacts. This result indicates that the effective contact temperature of these contacts remains unchanged up to 0.6 V, in accordance with the theoretical prediction by Todorov et al. [T.N. Todorov, J. Hoekstra, A.P. Sutton, Phys. Rev. Lett. 86 (2001) 3606]. In contrast, the TLF frequency of Ag nanocontacts starts to increase more rapidly above 0.45 V than that of Au and Cu nanocontacts. The steep rise in the TLF frequency is possibly attributed to a poor heat transfer to the bulk part of the contact and a resulting rapid increase in the effective temperature.

  10. ASSEMBLY BIAS AND THE DYNAMICAL STRUCTURE OF DARK MATTER HALOS

    SciTech Connect

    Faltenbacher, Andreas; White, Simon D. M.

    2010-01-01

    Based on the Millennium Simulation we examine assembly bias for the halo properties: shape, triaxiality, concentration, spin, shape of the velocity ellipsoid, and velocity anisotropy. For consistency, we determine all these properties using the same set of particles, namely all gravitationally self-bound particles belonging to the most massive substructure of a given friends-of-friends halo. We confirm that near-spherical and high-spin halos show enhanced clustering. The opposite is true for strongly aspherical and low-spin halos. Further, below the typical collapse mass, M{sub *}, more concentrated halos show stronger clustering, whereas less concentrated halos are less clustered which is reversed for masses above M{sub *}. Going beyond earlier work we show that: (1) oblate halos are more strongly clustered than prolate ones; (2) the dependence of clustering on the shape of the velocity ellipsoid coincides with that of the real-space shape, although the signal is stronger; (3) halos with weak velocity anisotropy are more clustered, whereas radially anisotropic halos are more weakly clustered; (4) for all highly clustered subsets we find systematically less radially biased velocity anisotropy profiles. These findings indicate that the velocity structure of halos is tightly correlated with environment.

  11. A Modified Brain MR Image Segmentation and Bias Field Estimation Model Based on Local and Global Information

    PubMed Central

    Cong, Wang; Luan, Kuan; Liang, Hong; Ma, Xingcheng

    2016-01-01

    Because of the poor radio frequency coil uniformity and gradient-driven eddy currents, there is much noise and intensity inhomogeneity (bias) in brain magnetic resonance (MR) image, and it severely affects the segmentation accuracy. Better segmentation results are difficult to achieve by traditional methods; therefore, in this paper, a modified brain MR image segmentation and bias field estimation model based on local and global information is proposed. We first construct local constraints including image neighborhood information in Gaussian kernel mapping space, and then the complete regularization is established by introducing nonlocal spatial information of MR image. The weighting between local and global information is automatically adjusted according to image local information. At the same time, bias field information is coupled with the model, and it makes the model reduce noise interference but also can effectively estimate the bias field information. Experimental results demonstrate that the proposed algorithm has strong robustness to noise and bias field is well corrected. PMID:27660649

  12. A Modified Brain MR Image Segmentation and Bias Field Estimation Model Based on Local and Global Information

    PubMed Central

    Cong, Wang; Luan, Kuan; Liang, Hong; Ma, Xingcheng

    2016-01-01

    Because of the poor radio frequency coil uniformity and gradient-driven eddy currents, there is much noise and intensity inhomogeneity (bias) in brain magnetic resonance (MR) image, and it severely affects the segmentation accuracy. Better segmentation results are difficult to achieve by traditional methods; therefore, in this paper, a modified brain MR image segmentation and bias field estimation model based on local and global information is proposed. We first construct local constraints including image neighborhood information in Gaussian kernel mapping space, and then the complete regularization is established by introducing nonlocal spatial information of MR image. The weighting between local and global information is automatically adjusted according to image local information. At the same time, bias field information is coupled with the model, and it makes the model reduce noise interference but also can effectively estimate the bias field information. Experimental results demonstrate that the proposed algorithm has strong robustness to noise and bias field is well corrected.

  13. Alerting enhances attentional bias for salient stimuli: evidence from a global/local processing task.

    PubMed

    Weinbach, Noam; Henik, Avishai

    2014-11-01

    The present study examined the role of alerting in modulating attentional bias to salient events. In a global/local processing task, participants were presented with a large arrow (global level) comprised of smaller arrows (local level) pointing in the same or opposite directions and had to indicate the direction of the large or small arrows in different blocks. Saliency of the global and local levels was manipulated, creating global-salient and local-salient conditions. Alerting signals were presented in half of the trials prior to the target. Results revealed a double dissociation in the effects of alerting on global/local interference effects. In a global salient condition, alerting increased global interference and decreased local interference. In a local salient condition, alerting reduced global interference and increased local interference. We demonstrate that within a single task, alerting can increase and reduce conflict based on perceptual saliency. These findings help to better understand disorders like hemispatial neglect in which both arousal and attention to salient events are impaired. These results also challenge previous theories suggesting that alerting acts to increase conflict interference. We argue that alerting is an adaptive mechanism that diverts attention to salient events, but comes at a cost when selective attention to less salient details is required.

  14. Zooming into creativity: individual differences in attentional global-local biases are linked to creative thinking.

    PubMed

    Zmigrod, Sharon; Zmigrod, Leor; Hommel, Bernhard

    2015-01-01

    While recent studies have investigated how processes underlying human creativity are affected by particular visual-attentional states, we tested the impact of more stable attention-related preferences. These were assessed by means of Navon's global-local task, in which participants respond to the global or local features of large letters constructed from smaller letters. Three standard measures were derived from this task: the sizes of the global precedence effect, the global interference effect (i.e., the impact of incongruent letters at the global level on local processing), and the local interference effect (i.e., the impact of incongruent letters at the local level on global processing). These measures were correlated with performance in a convergent-thinking creativity task (the Remote Associates Task), a divergent-thinking creativity task (the Alternate Uses Task), and a measure of fluid intelligence (Raven's matrices). Flexibility in divergent thinking was predicted by the local interference effect while convergent thinking was predicted by intelligence only. We conclude that a stronger attentional bias to visual information about the "bigger picture" promotes cognitive flexibility in searching for multiple solutions.

  15. Zooming into creativity: individual differences in attentional global-local biases are linked to creative thinking

    PubMed Central

    Zmigrod, Sharon; Zmigrod, Leor; Hommel, Bernhard

    2015-01-01

    While recent studies have investigated how processes underlying human creativity are affected by particular visual-attentional states, we tested the impact of more stable attention-related preferences. These were assessed by means of Navon’s global-local task, in which participants respond to the global or local features of large letters constructed from smaller letters. Three standard measures were derived from this task: the sizes of the global precedence effect, the global interference effect (i.e., the impact of incongruent letters at the global level on local processing), and the local interference effect (i.e., the impact of incongruent letters at the local level on global processing). These measures were correlated with performance in a convergent-thinking creativity task (the Remote Associates Task), a divergent-thinking creativity task (the Alternate Uses Task), and a measure of fluid intelligence (Raven’s matrices). Flexibility in divergent thinking was predicted by the local interference effect while convergent thinking was predicted by intelligence only. We conclude that a stronger attentional bias to visual information about the “bigger picture” promotes cognitive flexibility in searching for multiple solutions. PMID:26579030

  16. On the spin bias of satellite galaxies in the local group-like environment

    SciTech Connect

    Lee, Jounghun; Lemson, Gerard E-mail: lemson@mpa-garching.mpg.de

    2013-05-01

    We utilize the Millennium-II simulation databases to study the spin bias of dark subhalos in the Local Group-like systems which have two prominent satellites with comparable masses. Selecting the group-size halos with total mass similar to that of the Local Group (LG) from the friends-of-friends halo catalog and locating their subhalos from the substructure catalog, we determine the most massive (main) and second to the most massive (submain) ones among the subhalos hosted by each selected halo. When the dimensionless spin parameter (λ) of each subhalo is derived from its specific angular momentum and circular velocity at virial radius, a signal of correlation is detected between the spin parameters of the subhalos and the main-to-submain mass ratios of their host halos at z = 0: the higher main-to-submain mass ratio a host halo has, the higher mean spin parameter its subhalos have. It is also found that the correlations exist even for the subhalo progenitors at z = 0.5 and 1. Our interpretation of this result is that the subhalo spin bias is not a transient effect but an intrinsic property of a LG-like system with higher main-to- submain mass ratio, caused by stronger anisotropic stress in the region. A cosmological implication of our result is also discussed.

  17. Biased diffusion in three-dimensional comb-like structures

    PubMed Central

    Berezhkovskii, Alexander M.; Dagdug, Leonardo; Bezrukov, Sergey M.

    2015-01-01

    In this paper, we study biased diffusion of point Brownian particles in a three-dimensional comb-like structure formed by a main cylindrical tube with identical periodic cylindrical dead ends. It is assumed that the dead ends are thin cylinders whose radius is much smaller than both the radius of the main tube and the distance between neighboring dead ends. It is also assumed that in the main tube, the particle, in addition to its regular diffusion, moves with a uniform constant drift velocity. For such a system, we develop a formalism that allows us to derive analytical expressions for the Laplace transforms of the first two moments of the particle displacement along the main tube axis. Inverting these Laplace transforms numerically, one can find the time dependences of the two moments for arbitrary values of both the drift velocity and the dead-end length, including the limiting case of infinitely long dead ends, where the unbiased diffusion becomes anomalous at sufficiently long times. The expressions for the Laplace transforms are used to find the effective drift velocity and diffusivity of the particle as functions of its drift velocity in the main tube and the tube geometric parameters. As might be expected from common-sense arguments, the effective drift velocity monotonically decreases from the initial drift velocity to zero as the dead-end length increases from zero to infinity. The effective diffusivity is a more complex, non-monotonic function of the dead-end length. As this length increases from zero to infinity, the effective diffusivity first decreases, reaches a minimum, and then increases approaching a plateau value which is proportional to the square of the particle drift velocity in the main tube. PMID:25854222

  18. Removing the ISW-lensing bias from the local-form primordial non-Gaussianity estimation

    SciTech Connect

    Kim, Jaiseung; Komatsu, Eiichiro; Rotti, Aditya E-mail: aditya@iucaa.ernet.in

    2013-04-01

    The Integrated Sachs-Wolfe (ISW) effect produces a secondary temperature aniso\\-tropy of the cosmic microwave background (CMB), as CMB photons travel through time-varying potentials along the line-of-sight. The main contribution comes from redshifts z∼<2, where dark energy leads to a decay of potentials. As the same photons are gravitationally lensed by these decaying potentials, there exists a high degree of correlation between the ISW effect and CMB lensing, leading to a non-zero three-point correlation (bispectrum) of the observed temperature anisotropy. This ISW-lensing bispectrum, whose shape resembles that of the so-called ''local-form'' primordial bispectrum parametrized by f{sub NL}, is known to be the largest contamination of f{sub NL}. In order to avoid a spurious detection of primordial non-Gaussianity, we need to remove the ISW-lensing bias. In this work, we investigate three debiasing methods: (I) subtraction of an expected, ensemble average of the ISW-lensing bispectrum; (II) subtraction of a measured ISW-lensing bispectrum; and (III) direct subtraction of an estimated ISW signal from an observed temperature map. One may use an estimation of the ISW map from external non-CMB data or that from the CMB data themselves. As the methods II and III are based on fewer assumptions about the nature of dark energy, they are preferred over the method I. While the methods I and II yield unbiased estimates of f{sub NL} with comparable error bars, the method III yields a biased result when the underlying primordial f{sub NL} is non-zero and the ISW map is estimated from a lensing potential reconstructed from the observed temperature map. One of the sources of the bias is a lensing reconstruction noise bias which is independent of f{sub NL} and can be calculated precisely, but other f{sub NL}-dependent terms are difficult to compute reliably. We thus conclude that the method II is the best, model-independent way to remove the ISW-lensing bias of f{sub NL

  19. Cosmic Flows and the Structure of the Local Universe

    NASA Astrophysics Data System (ADS)

    Steinmetz, Matthias

    2016-03-01

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

  20. Bias-voltage-controlled ac and dc magnetotransport phenomena in hybrid structures

    NASA Astrophysics Data System (ADS)

    Volkov, N. V.; Tarasov, A. S.; Smolyakov, D. A.; Varnakov, S. N.; Ovchinnikov, S. G.

    2015-06-01

    We report some ac and dc magnetotransport phenomena in silicon-based hybrid structures. The giant impedance change under an applied magnetic field has been experimentally found in the metal/insulator/semiconductor (MIS) diode with the Schottky barrier based on the Fe/SiO2/p-Si and Fe/SiO2/n-Si structures. The maximum effect is found to observe at temperatures of 10-30 K in the frequency range 10 Hz-1 MHz. Below 1 kHz the magnetoresistance can be controlled in a wide range by applying a bias to the device. A photoinduced dc magnetoresistance of over 104% has been found in the Fe/SiO2/p-Si back-to-back Schottky diode. The observed magnetic-field-dependent effects are caused by the interface states localized in the insula-tor/semiconductor interface.

  1. Localized structures in gaseous combustion

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  2. Clustering of Local Group Distances: Publication Bias or Correlated Measurements? II. M31 and Beyond

    NASA Astrophysics Data System (ADS)

    de Grijs, Richard; Bono, Giuseppe

    2014-07-01

    The accuracy of extragalactic distance measurements ultimately depends on robust, high-precision determinations of the distances to the galaxies in the local volume. Following our detailed study addressing possible publication bias in the published distance determinations to the Large Magellanic Cloud (LMC), here we extend our distance range of interest to include published distance moduli to M31 and M33, as well as to a number of their well-known dwarf galaxy companions. We aim at reaching consensus on the best, most homogeneous, and internally most consistent set of Local Group distance moduli to adopt for future, more general use based on the largest set of distance determinations to individual Local Group galaxies available to date. Based on a careful, statistically weighted combination of the main stellar population tracers (Cepheids, RR Lyrae variables, and the magnitude of the tip of the red-giant branch), we derive a recommended distance modulus to M31 of (m-M)_0^M31 = 24.46 +/- 0.10 mag—adopting as our calibration an LMC distance modulus of (m-M)_0^LMC = 18.50 mag—and a fully internally consistent set of benchmark distances to key galaxies in the local volume, enabling us to establish a robust and unbiased, near-field extragalactic distance ladder.

  3. Clustering of local group distances: Publication bias or correlated measurements? II. M31 and beyond

    SciTech Connect

    De Grijs, Richard; Bono, Giuseppe

    2014-07-01

    The accuracy of extragalactic distance measurements ultimately depends on robust, high-precision determinations of the distances to the galaxies in the local volume. Following our detailed study addressing possible publication bias in the published distance determinations to the Large Magellanic Cloud (LMC), here we extend our distance range of interest to include published distance moduli to M31 and M33, as well as to a number of their well-known dwarf galaxy companions. We aim at reaching consensus on the best, most homogeneous, and internally most consistent set of Local Group distance moduli to adopt for future, more general use based on the largest set of distance determinations to individual Local Group galaxies available to date. Based on a careful, statistically weighted combination of the main stellar population tracers (Cepheids, RR Lyrae variables, and the magnitude of the tip of the red-giant branch), we derive a recommended distance modulus to M31 of (m−M){sub 0}{sup M31}=24.46±0.10 mag—adopting as our calibration an LMC distance modulus of (m−M){sub 0}{sup LMC}=18.50 mag—and a fully internally consistent set of benchmark distances to key galaxies in the local volume, enabling us to establish a robust and unbiased, near-field extragalactic distance ladder.

  4. Network Structure and Biased Variance Estimation in Respondent Driven Sampling

    PubMed Central

    Verdery, Ashton M.; Mouw, Ted; Bauldry, Shawn; Mucha, Peter J.

    2015-01-01

    This paper explores bias in the estimation of sampling variance in Respondent Driven Sampling (RDS). Prior methodological work on RDS has focused on its problematic assumptions and the biases and inefficiencies of its estimators of the population mean. Nonetheless, researchers have given only slight attention to the topic of estimating sampling variance in RDS, despite the importance of variance estimation for the construction of confidence intervals and hypothesis tests. In this paper, we show that the estimators of RDS sampling variance rely on a critical assumption that the network is First Order Markov (FOM) with respect to the dependent variable of interest. We demonstrate, through intuitive examples, mathematical generalizations, and computational experiments that current RDS variance estimators will always underestimate the population sampling variance of RDS in empirical networks that do not conform to the FOM assumption. Analysis of 215 observed university and school networks from Facebook and Add Health indicates that the FOM assumption is violated in every empirical network we analyze, and that these violations lead to substantially biased RDS estimators of sampling variance. We propose and test two alternative variance estimators that show some promise for reducing biases, but which also illustrate the limits of estimating sampling variance with only partial information on the underlying population social network. PMID:26679927

  5. Network Structure and Biased Variance Estimation in Respondent Driven Sampling.

    PubMed

    Verdery, Ashton M; Mouw, Ted; Bauldry, Shawn; Mucha, Peter J

    2015-01-01

    This paper explores bias in the estimation of sampling variance in Respondent Driven Sampling (RDS). Prior methodological work on RDS has focused on its problematic assumptions and the biases and inefficiencies of its estimators of the population mean. Nonetheless, researchers have given only slight attention to the topic of estimating sampling variance in RDS, despite the importance of variance estimation for the construction of confidence intervals and hypothesis tests. In this paper, we show that the estimators of RDS sampling variance rely on a critical assumption that the network is First Order Markov (FOM) with respect to the dependent variable of interest. We demonstrate, through intuitive examples, mathematical generalizations, and computational experiments that current RDS variance estimators will always underestimate the population sampling variance of RDS in empirical networks that do not conform to the FOM assumption. Analysis of 215 observed university and school networks from Facebook and Add Health indicates that the FOM assumption is violated in every empirical network we analyze, and that these violations lead to substantially biased RDS estimators of sampling variance. We propose and test two alternative variance estimators that show some promise for reducing biases, but which also illustrate the limits of estimating sampling variance with only partial information on the underlying population social network. PMID:26679927

  6. Network Structure and Biased Variance Estimation in Respondent Driven Sampling.

    PubMed

    Verdery, Ashton M; Mouw, Ted; Bauldry, Shawn; Mucha, Peter J

    2015-01-01

    This paper explores bias in the estimation of sampling variance in Respondent Driven Sampling (RDS). Prior methodological work on RDS has focused on its problematic assumptions and the biases and inefficiencies of its estimators of the population mean. Nonetheless, researchers have given only slight attention to the topic of estimating sampling variance in RDS, despite the importance of variance estimation for the construction of confidence intervals and hypothesis tests. In this paper, we show that the estimators of RDS sampling variance rely on a critical assumption that the network is First Order Markov (FOM) with respect to the dependent variable of interest. We demonstrate, through intuitive examples, mathematical generalizations, and computational experiments that current RDS variance estimators will always underestimate the population sampling variance of RDS in empirical networks that do not conform to the FOM assumption. Analysis of 215 observed university and school networks from Facebook and Add Health indicates that the FOM assumption is violated in every empirical network we analyze, and that these violations lead to substantially biased RDS estimators of sampling variance. We propose and test two alternative variance estimators that show some promise for reducing biases, but which also illustrate the limits of estimating sampling variance with only partial information on the underlying population social network.

  7. Macroscopic locality with equal bias reproduces with high fidelity a quantum distribution achieving the Tsirelson's bound

    NASA Astrophysics Data System (ADS)

    Gazi, Md. Rajjak; Banik, Manik; Das, Subhadipa; Rai, Ashutosh; Kunkri, Samir

    2013-11-01

    Two physical principles, macroscopic locality (ML) and information causality (IC), so far have been most successful in distinguishing quantum correlations from post-quantum correlations. However, there are also some post-quantum probability distributions which cannot be distinguished with the help of these principles. Thus, it is interesting to see whether consideration of these two principles, separately, along with some additional physically plausible constraints, can explain some interesting quantum features which are otherwise hard to reproduce. In this paper we show that in a Bell-Clauser-Horne-Shimony-Holt scenario, ML along with the constraint of equal bias for the concerned observables, almost reproduces the quantum joint probability distribution corresponding to a maximal quantum Bell violation, which is unique up to relabeling. From this example and earlier work of Cavalcanti, Salles, and Scarani, we conclude that IC and ML are inequivalent physical principles; satisfying one does not imply that the other is satisfied.

  8. Probing local bias-induced transitions using photothermal excitation contact resonance atomic force microscopy and voltage spectroscopy

    DOE PAGES

    Li, Qian; Jesse, Stephen; Tselev, Alexander; Collins, Liam; Yu, Pu; Kravchenko, Ivan; Kalinin, Sergei V.; Balke, Nina

    2015-01-05

    In this paper, nanomechanical properties are closely related to the states of matter, including chemical composition, crystal structure, mesoscopic domain configuration, etc. Investigation of these properties at the nanoscale requires not only static imaging methods, e.g., contact resonance atomic force microscopy (CR-AFM), but also spectroscopic methods capable of revealing their dependence on various external stimuli. Here we demonstrate the voltage spectroscopy of CR-AFM, which was realized by combining photothermal excitation (as opposed to the conventional piezoacoustic excitation method) with the band excitation technique. We applied this spectroscopy to explore local bias-induced phenomena ranging from purely physical to surface electromechanical andmore » electrochemical processes. Our measurements show that the changes in the surface properties associated with these bias-induced transitions can be accurately assessed in a fast and dynamic manner, using resonance frequency as a signature. Finally, with many of the advantages offered by photothermal excitation, contact resonance voltage spectroscopy not only is expected to find applications in a broader field of nanoscience but also will provide a basis for future development of other nanoscale elastic spectroscopies.« less

  9. Probing local bias-induced transitions using photothermal excitation contact resonance atomic force microscopy and voltage spectroscopy

    SciTech Connect

    Li, Qian; Jesse, Stephen; Tselev, Alexander; Collins, Liam; Yu, Pu; Kravchenko, Ivan; Kalinin, Sergei V.; Balke, Nina

    2015-01-05

    In this paper, nanomechanical properties are closely related to the states of matter, including chemical composition, crystal structure, mesoscopic domain configuration, etc. Investigation of these properties at the nanoscale requires not only static imaging methods, e.g., contact resonance atomic force microscopy (CR-AFM), but also spectroscopic methods capable of revealing their dependence on various external stimuli. Here we demonstrate the voltage spectroscopy of CR-AFM, which was realized by combining photothermal excitation (as opposed to the conventional piezoacoustic excitation method) with the band excitation technique. We applied this spectroscopy to explore local bias-induced phenomena ranging from purely physical to surface electromechanical and electrochemical processes. Our measurements show that the changes in the surface properties associated with these bias-induced transitions can be accurately assessed in a fast and dynamic manner, using resonance frequency as a signature. Finally, with many of the advantages offered by photothermal excitation, contact resonance voltage spectroscopy not only is expected to find applications in a broader field of nanoscience but also will provide a basis for future development of other nanoscale elastic spectroscopies.

  10. Bias-Corrected Estimation of Noncentrality Parameters of Covariance Structure Models

    ERIC Educational Resources Information Center

    Raykov, Tenko

    2005-01-01

    A bias-corrected estimator of noncentrality parameters of covariance structure models is discussed. The approach represents an application of the bootstrap methodology for purposes of bias correction, and utilizes the relation between average of resample conventional noncentrality parameter estimates and their sample counterpart. The…

  11. Structural content in paintings: artists overregularize oriented content of paintings relative to the typical natural scene bias.

    PubMed

    Schweinhart, April M; Essock, Edward A

    2013-01-01

    Natural scenes tend to be biased in both scale (1/f) and orientation (H > V > O; horizontal > vertical > oblique), and the human visual system has similar biases that serve to partially 'undo' (ie whiten) the resultant representation. The present approach to investigating this relationship considers content in works of art-scenes produced for processing by the human visual system. We analyzed the content of images by a method that minimizes errors inherent in some prior analysis methods. In the first experiment museum paintings were considered by comparing the amplitude spectrum of landscape paintings, natural scene photos, portrait paintings, and photos of faces. In the second experiment we obtained photos of paintings at the time they were produced by local artists and compared structural content in matched photos which contained the same scenes that the artists had painted. Results show that artists produce paintings with both the 1/f bias of scale and the horizontal-effect bias of orientation (H > V > O). More importantly, results from both experiments show that artists overregularize the structure in their works: they impose the natural-scene horizontal effect at all structural scales and in all types of subject matter even though, in the real world, the pattern of anisotropy differs considerably across spatial scale and between faces and natural scenes. It appears that artists unconsciously overregularize the oriented structure in their works to make it conform more uniformly to the 'expected' canonical ideal.

  12. Structural insights into biased G protein-coupled receptor signaling revealed by fluorescence spectroscopy

    PubMed Central

    Rahmeh, Rita; Damian, Marjorie; Cottet, Martin; Orcel, Hélène; Mendre, Christiane; Durroux, Thierry; Sharma, K. Shivaji; Durand, Grégory; Pucci, Bernard; Trinquet, Eric; Zwier, Jurriaan M.; Deupi, Xavier; Bron, Patrick; Banères, Jean-Louis; Mouillac, Bernard; Granier, Sébastien

    2012-01-01

    G protein-coupled receptors (GPCRs) are seven-transmembrane proteins that mediate most cellular responses to hormones and neurotransmitters, representing the largest group of therapeutic targets. Recent studies show that some GPCRs signal through both G protein and arrestin pathways in a ligand-specific manner. Ligands that direct signaling through a specific pathway are known as biased ligands. The arginine-vasopressin type 2 receptor (V2R), a prototypical peptide-activated GPCR, is an ideal model system to investigate the structural basis of biased signaling. Although the native hormone arginine-vasopressin leads to activation of both the stimulatory G protein (Gs) for the adenylyl cyclase and arrestin pathways, synthetic ligands exhibit highly biased signaling through either Gs alone or arrestin alone. We used purified V2R stabilized in neutral amphipols and developed fluorescence-based assays to investigate the structural basis of biased signaling for the V2R. Our studies demonstrate that the Gs-biased agonist stabilizes a conformation that is distinct from that stabilized by the arrestin-biased agonists. This study provides unique insights into the structural mechanisms of GPCR activation by biased ligands that may be relevant to the design of pathway-biased drugs. PMID:22493271

  13. Latent structure in random sequences drives neural learning toward a rational bias

    PubMed Central

    Sun, Yanlong; O’Reilly, Randall C.; Bhattacharyya, Rajan; Smith, Jack W.; Liu, Xun; Wang, Hongbin

    2015-01-01

    People generally fail to produce random sequences by overusing alternating patterns and avoiding repeating ones—the gambler’s fallacy bias. We can explain the neural basis of this bias in terms of a biologically motivated neural model that learns from errors in predicting what will happen next. Through mere exposure to random sequences over time, the model naturally develops a representation that is biased toward alternation, because of its sensitivity to some surprisingly rich statistical structure that emerges in these random sequences. Furthermore, the model directly produces the best-fitting bias-gain parameter for an existing Bayesian model, by which we obtain an accurate fit to the human data in random sequence production. These results show that our seemingly irrational, biased view of randomness can be understood instead as the perfectly reasonable response of an effective learning mechanism to subtle statistical structure embedded in random sequences. PMID:25775565

  14. Follow-the-leader cell migration requires biased cell-cell contact and local microenvironmental signals.

    PubMed

    Wynn, Michelle L; Rupp, Paul; Trainor, Paul A; Schnell, Santiago; Kulesa, Paul M

    2013-06-01

    Directed cell migration often involves at least two types of cell motility that include multicellular streaming and chain migration. However, what is unclear is how cell contact dynamics and the distinct microenvironments through which cells travel influence the selection of one migratory mode or the other. The embryonic and highly invasive neural crest (NC) are an excellent model system to study this question since NC cells have been observed in vivo to display both of these types of cell motility. Here, we present data from tissue transplantation experiments in chick and in silico modeling that test our hypothesis that cell contact dynamics with each other and the microenvironment promote and sustain either multicellular stream or chain migration. We show that when premigratory cranial NC cells (at the pre-otic level) are transplanted into a more caudal region in the head (at the post-otic level), cells alter their characteristic stream behavior and migrate in chains. Similarly, post-otic NC cells migrate in streams after transplantation into the pre-otic hindbrain, suggesting that local microenvironmental signals dictate the mode of NC cell migration. Simulations of an agent-based model (ABM) that integrates the NC cell behavioral data predict that chain migration critically depends on the interplay of biased cell-cell contact and local microenvironment signals. Together, this integrated modeling and experimental approach suggests new experiments and offers a powerful tool to examine mechanisms that underlie complex cell migration patterns.

  15. Bias-dependent molecular-level structure of electrical double layer in ionic liquid on graphite.

    PubMed

    Black, Jennifer M; Walters, Deron; Labuda, Aleksander; Feng, Guang; Hillesheim, Patrick C; Dai, Sheng; Cummings, Peter T; Kalinin, Sergei V; Proksch, Roger; Balke, Nina

    2013-01-01

    Here we report the bias-evolution of the electrical double layer structure of an ionic liquid on highly ordered pyrolytic graphite measured by atomic force microscopy. We observe reconfiguration under applied bias and the orientational transitions in the Stern layer. The synergy between molecular dynamics simulation and experiment provides a comprehensive picture of structural phenomena and long and short-range interactions, which improves our understanding of the mechanism of charge storage on a molecular level.

  16. Investigation on particle swarm optimisation for feature selection on high-dimensional data: local search and selection bias

    NASA Astrophysics Data System (ADS)

    Tran, Binh; Xue, Bing; Zhang, Mengjie; Nguyen, Su

    2016-07-01

    Feature selection is an essential step in classification tasks with a large number of features, such as in gene expression data. Recent research has shown that particle swarm optimisation (PSO) is a promising approach to feature selection. However, it also has potential limitation to get stuck into local optima, especially for gene selection problems with a huge search space. Therefore, we developed a PSO algorithm (PSO-LSRG) with a fast "local search" combined with a gbest resetting mechanism as a way to improve the performance of PSO for feature selection. Furthermore, since many existing PSO-based feature selection approaches on the gene expression data have feature selection bias, i.e. no unseen test data is used, 2 sets of experiments on 10 gene expression datasets were designed: with and without feature selection bias. As compared to standard PSO, PSO with gbest resetting only, and PSO with local search only, PSO-LSRG obtained a substantial dimensionality reduction and a significant improvement on the classification performance in both sets of experiments. PSO-LSRG outperforms the other three algorithms when feature selection bias exists. When there is no feature selection bias, PSO-LSRG selects the smallest number of features in all cases, but the classification performance is slightly worse in a few cases, which may be caused by the overfitting problem. This shows that feature selection bias should be avoided when designing a feature selection algorithm to ensure its generalisation ability on unseen data.

  17. Carrier-density-wave transport and local internal electric field measurements in biased metal-oxide-semiconductor n-Si devices using contactless laser photo-carrier radiometry

    NASA Astrophysics Data System (ADS)

    Mandelis, Andreas; Pawlak, Micha; Shaughnessy, Derrick

    2004-11-01

    Laser infrared photo-carrier radiometry was used with an n-type Si metal-oxide-semiconductor (MOS) diode and with a Si-SiO2 structure with a transparent electrode and under external bias. Application of three-dimensional PCR theory yielded values of the minority carrier (hole) transport properties in the presence of the thus created local internal electric field at fixed frequencies. Furthermore, the internal electric field at fixed applied voltage was calculated. Under the combination of increased temperature and voltage, the sub-interface position of the carrier-density-wave centroid was found to depend on a trade-off between increased recombination lifetime and decreased ambipolar (conductivity) mobility. The ability of PCR to measure local internal electric fields by combining applied bias sweeps and frequency scans appears to pave the way towards the contactless reconstruction of depth profiles of these fields in active devices.

  18. Combinatorics of locally optimal RNA secondary structures.

    PubMed

    Fusy, Eric; Clote, Peter

    2014-01-01

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

  19. Combinatorics of locally optimal RNA secondary structures.

    PubMed

    Fusy, Eric; Clote, Peter

    2014-01-01

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

  20. Bias to CMB lensing measurements from the bispectrum of large-scale structure

    NASA Astrophysics Data System (ADS)

    Böhm, Vanessa; Schmittfull, Marcel; Sherwin, Blake D.

    2016-08-01

    The rapidly improving precision of measurements of gravitational lensing of the cosmic microwave background (CMB) also requires a corresponding increase in the precision of theoretical modeling. A commonly made approximation is to model the CMB deflection angle or lensing potential as a Gaussian random field. In this paper, however, we analytically quantify the influence of the non-Gaussianity of large-scale structure (LSS) lenses, arising from nonlinear structure formation, on CMB lensing measurements. In particular, evaluating the impact of the nonzero bispectrum of large-scale structure on the relevant CMB four-point correlation functions, we find that there is a bias to estimates of the CMB lensing power spectrum. For temperature-based lensing reconstruction with CMB stage III and stage IV experiments, we find that this lensing power spectrum bias is negative and is of order 1% of the signal. This corresponds to a shift of multiple standard deviations for these upcoming experiments. We caution, however, that our numerical calculation only evaluates two of the largest bias terms and, thus, only provides an approximate estimate of the full bias. We conclude that further investigation into lensing biases from nonlinear structure formation is required and that these biases should be accounted for in future lensing analyses.

  1. Lost in the forest, stuck in the trees: dispositional global/local bias is resistant to exposure to high and low spatial frequencies.

    PubMed

    Dale, Gillian; Arnell, Karen M

    2014-01-01

    Visual stimuli can be perceived at a broad, "global" level, or at a more focused, "local" level. While research has shown that many individuals demonstrate a preference for global information, there are large individual differences in the degree of global/local bias, such that some individuals show a large global bias, some show a large local bias, and others show no bias. The main purpose of the current study was to examine whether these dispositional differences in global/local bias could be altered through various manipulations of high/low spatial frequency. Through 5 experiments, we examined various measures of dispositional global/local bias and whether performance on these measures could be altered by manipulating previous exposure to high or low spatial frequency information (with high/low spatial frequency faces, gratings, and Navon letters). Ultimately, there was little evidence of change from pre-to-post manipulation on the dispositional measures, and dispositional global/local bias was highly reliable pre- to post-manipulation. The results provide evidence that individual differences in global/local bias or preference are relatively resistant to exposure to spatial frequency information, and suggest that the processing mechanisms underlying high/low spatial frequency use and global/local bias may be more independent than previously thought.

  2. Fine-scale population genetic structure and sex-biased dispersal in the smooth snake (Coronella austriaca) in southern England

    PubMed Central

    Pernetta, A P; Allen, J A; Beebee, T J C; Reading, C J

    2011-01-01

    Human-induced alteration of natural habitats has the potential to impact on the genetic structuring of remnant populations at multiple spatial scales. Species from higher trophic levels, such as snakes, are expected to be particularly susceptible to land-use changes. We examined fine-scale population structure and looked for evidence of sex-biased dispersal in smooth snakes (Coronella austriaca), sampled from 10 heathland localities situated within a managed coniferous forest in Dorset, United Kingdom. Despite the limited distances between heathland areas (maximum <6 km), there was a small but significant structuring of populations based on eight microsatellite loci. This followed an isolation-by-distance model using both straight line and ‘biological' distances between sampling sites, suggesting C. austriaca's low vagility as the causal factor, rather than closed canopy conifer forest exerting an effect as a barrier to dispersal. Within population comparisons of male and female snakes showed evidence for sex-biased dispersal, with three of four analyses finding significantly higher dispersal in males than in females. We suggest that the fine-scale spatial genetic structuring and sex-biased dispersal have important implications for the conservation of C. austriaca, and highlight the value of heathland areas within commercial conifer plantations with regards to their future management. PMID:21343947

  3. Visual capture of a stereo sound: Interactions between cue reliability, sound localization variability, and cross-modal bias.

    PubMed

    Montagne, Christopher; Zhou, Yi

    2016-07-01

    Multisensory interactions involve coordination and sometimes competition between multiple senses. Vision usually dominates audition in spatial judgments when light and sound stimuli are presented from two different physical locations. This study investigated the influence of vision on the perceived location of a phantom sound source placed in a stereo sound field using a pair of loudspeakers emitting identical signals that were delayed or attenuated relative to each other. Results show that although a similar horizontal range (+/-45°) was reported for timing-modulated and level-modulated signals, listeners' localization performance showed greater variability for the timing signals. When visual stimuli were presented simultaneously with the auditory stimuli, listeners showed stronger visual bias for timing-modulated signals than level-modulated and single-speaker control signals. Trial-to-trial errors remained relatively stable over time, suggesting that sound localization uncertainty has an immediate and long-lasting effect on the across-modal bias. Binaural signal analyses further reveal that interaural differences of time and intensity-the two primary cues for sound localization in the azimuthal plane-are inherently more ambiguous for signals placed using timing. These results suggest that binaural ambiguity is intrinsically linked with localization variability and the strength of cross-modal bias in sound localization. PMID:27475171

  4. Deterministic weak localization in periodic structures.

    PubMed

    Tian, C; Larkin, A

    2005-12-01

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

  5. Bias-dependent molecular-level structure of electrical double layer in ionic liquid on graphite

    SciTech Connect

    Black, Jennifer M; Walters, Deron; Labuda, Aleksander; Feng, Guang; Hillesheim, Patrick C; Dai, Sheng; Cummings, Peter T; Kalinin, Sergei V; Proksch, Roger; Balke, Nina

    2013-01-01

    Bias-dependent structure of electrochemical double layers at liquid-solid interfaces underpin a multitude of phenomena in virtually all areas of scientific enquiry ranging from energy storage and conversion systems, biology, to geophysics and geochemistry. Here we report the bias-evolution of the electric double layer structure of an ionic liquid on highly ordered pyrolytic graphite as a model system for carbon-based electrodes for electrochemical supercapacitors measured by atomic force microscopy. Matching the observed structures to molecular dynamics simulations allows us to resolve steric effects due to cation and anion layers. We observe reconfiguration under applied bias and the orientational transitions in the Stern layer. The synergy between molecular dynamics simulation and experiment provides a comprehensive picture of structural phenomena and long- and short range interactions. This insight will improve understanding of the mechanism of charge storage in electrochemical capacitors on a molecular level which can be used to enhance their electrochemical performance.

  6. Clustering of Local Group Distances: Publication Bias or Correlated Measurements? I. The Large Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    de Grijs, Richard; Wicker, James E.; Bono, Giuseppe

    2014-05-01

    The distance to the Large Magellanic Cloud (LMC) represents a key local rung of the extragalactic distance ladder yet the galaxy's distance modulus has long been an issue of contention, in particular in view of claims that most newly determined distance moduli cluster tightly—and with a small spread—around the "canonical" distance modulus, (m - M)0 = 18.50 mag. We compiled 233 separate LMC distance determinations published between 1990 and 2013. Our analysis of the individual distance moduli, as well as of their two-year means and standard deviations resulting from this largest data set of LMC distance moduli available to date, focuses specifically on Cepheid and RR Lyrae variable-star tracer populations, as well as on distance estimates based on features in the observational Hertzsprung-Russell diagram. We conclude that strong publication bias is unlikely to have been the main driver of the majority of published LMC distance moduli. However, for a given distance tracer, the body of publications leading to the tightly clustered distances is based on highly non-independent tracer samples and analysis methods, hence leading to significant correlations among the LMC distances reported in subsequent articles. Based on a careful, weighted combination, in a statistical sense, of the main stellar population tracers, we recommend that a slightly adjusted canonical distance modulus of (m - M)0 = 18.49 ± 0.09 mag be used for all practical purposes that require a general distance scale without the need for accuracies of better than a few percent.

  7. Clustering of local group distances: publication bias or correlated measurements? I. The large Magellanic cloud

    SciTech Connect

    De Grijs, Richard; Wicker, James E.; Bono, Giuseppe

    2014-05-01

    The distance to the Large Magellanic Cloud (LMC) represents a key local rung of the extragalactic distance ladder yet the galaxy's distance modulus has long been an issue of contention, in particular in view of claims that most newly determined distance moduli cluster tightly—and with a small spread—around the 'canonical' distance modulus, (m – M){sub 0} = 18.50 mag. We compiled 233 separate LMC distance determinations published between 1990 and 2013. Our analysis of the individual distance moduli, as well as of their two-year means and standard deviations resulting from this largest data set of LMC distance moduli available to date, focuses specifically on Cepheid and RR Lyrae variable-star tracer populations, as well as on distance estimates based on features in the observational Hertzsprung-Russell diagram. We conclude that strong publication bias is unlikely to have been the main driver of the majority of published LMC distance moduli. However, for a given distance tracer, the body of publications leading to the tightly clustered distances is based on highly non-independent tracer samples and analysis methods, hence leading to significant correlations among the LMC distances reported in subsequent articles. Based on a careful, weighted combination, in a statistical sense, of the main stellar population tracers, we recommend that a slightly adjusted canonical distance modulus of (m – M){sub 0} = 18.49 ± 0.09 mag be used for all practical purposes that require a general distance scale without the need for accuracies of better than a few percent.

  8. Realistic Drawing Talent in Typical Adults Is Associated with the Same Kind of Local Processing Bias Found in Individuals with ASD

    ERIC Educational Resources Information Center

    Drake, Jennifer E.; Winner, Ellen

    2011-01-01

    A local processing bias has been found in individuals with autism as well as in typical children with a gift for drawing realistically. This study investigated whether a local processing bias in typical adults is more strongly associated with drawing realism or autistic-like traits. Forty-two adults made an observational drawing (scored for…

  9. Nanoscale Internal Fields in a Biased Graphene-Insulator-Semiconductor Structure.

    PubMed

    Rangan, Sylvie; Kalyanikar, Malathi; Duan, Junxi; Liu, Gang; Bartynski, Robert Allen; Andrei, Eva Y; Feldman, Leonard; Garfunkel, Eric

    2016-09-01

    Measuring and understanding electric fields in multilayered materials at the nanoscale remains a challenging problem impeding the development of novel devices. At this scale, it is far from obvious that materials can be accurately described by their intrinsic bulk properties, and considerations of the interfaces between layered materials become unavoidable for a complete description of the system's electronic properties. Here, a general approach to the direct measurement of nanoscale internal fields is proposed. Small spot X-ray photoemission was performed on a biased graphene/SiO2/Si structure in order to experimentally determine the potential profile across the system, including discontinuities at the interfaces. Core levels provide a measure of the local potential and are used to reconstruct the potential profile as a function of the depth through the stack. It is found that each interface plays a critical role in establishing the potential across the dielectric, and the origin of the potential discontinuities at each interface is discussed. PMID:27530545

  10. 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.

  11. Local fields in conductor surface electromigration: A first-principles study in the low-bias ballistic limit

    SciTech Connect

    Bevan, Kirk H; Zhu, Wenguang; Stocks, George Malcolm; Guo, Hong; Zhang, Zhenyu

    2012-01-01

    Utilizing first-principles quantum transport calculations, we investigate the role of local fields in conductor surface electromigration. A nanometer-thick Ag(100) thin film is adopted as our prototypical conductor, where we demonstrate the existence of intense local electric fields at atomic surface defects under an external bias. It is shown that such local fields can play an important role in driving surface electromigration and electrical breakdown. The intense fields originate from the relatively short (atomic-scale) screening lengths common to most elemental metals. This general short-range screening trend is established self-consistently within an intuitive picture of linear response electrostatics. The findings shed new light on the underlying physical origins of surface electromigration and point to the possibility of harnessing local fields to engineer electromigration at the nanoscale.

  12. Detecting structure of haplotypes and local ancestry

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  13. Sister cohesion and structural axis components mediate homolog bias of meiotic recombination

    PubMed Central

    Kim, Keun P.; Weiner, Beth M.; Zhang, Liangran; Jordan, Amy; Dekker, Job; Kleckner, Nancy

    2010-01-01

    SUMMARY Meiotic recombination occurs between one chromatid of each maternal and paternal homolog (homolog bias) versus between sister chromatids (sister bias). Physical DNA analysis reveals that meiotic cohesin/axis component Rec8 promotes sister bias, likely via its cohesion activity. Two meiosis-specific axis components, Red1/Mek1kinase, counteract this effect. With this precondition satisfied, other molecules directly specify homolog bias per se. Rec8 also acts positively to maintain homolog bias during crossover recombination. These observations point to sequential release of double-strand break ends from association with their sister. Red1 and Rec8 are found to play distinct roles for sister cohesion, DSB formation and recombination progression kinetics. Also, the two components are enriched in spatially distinct domains of axial structure that develop prior to DSB formation. We propose that Red1 and Rec8 domains provide functionally complementary environments whereby inputs evolved from DSB repair and late-stage chromosome morphogenesis are integrated to give the complete meiotic chromosomal program. PMID:21145459

  14. Crystal Structure Manipulation of the Exchange Bias in an Antiferromagnetic Film

    PubMed Central

    Yuan, Wei; Su, Tang; Song, Qi; Xing, Wenyu; Chen, Yangyang; Wang, Tianyu; Zhang, Zhangyuan; Ma, Xiumei; Gao, Peng; Shi, Jing; Han, Wei

    2016-01-01

    Exchange bias is one of the most extensively studied phenomena in magnetism, since it exerts a unidirectional anisotropy to a ferromagnet (FM) when coupled to an antiferromagnet (AFM) and the control of the exchange bias is therefore very important for technological applications, such as magnetic random access memory and giant magnetoresistance sensors. In this letter, we report the crystal structure manipulation of the exchange bias in epitaxial hcp Cr2O3 films. By epitaxially growing twined oriented Cr2O3 thin films, of which the c axis and spins of the Cr atoms lie in the film plane, we demonstrate that the exchange bias between Cr2O3 and an adjacent permalloy layer is tuned to in-plane from out-of-plane that has been observed in oriented Cr2O3 films. This is owing to the collinear exchange coupling between the spins of the Cr atoms and the adjacent FM layer. Such a highly anisotropic exchange bias phenomenon is not possible in polycrystalline films. PMID:27329336

  15. Crystal Structure Manipulation of the Exchange Bias in an Antiferromagnetic Film

    NASA Astrophysics Data System (ADS)

    Yuan, Wei; Su, Tang; Song, Qi; Xing, Wenyu; Chen, Yangyang; Wang, Tianyu; Zhang, Zhangyuan; Ma, Xiumei; Gao, Peng; Shi, Jing; Han, Wei

    2016-06-01

    Exchange bias is one of the most extensively studied phenomena in magnetism, since it exerts a unidirectional anisotropy to a ferromagnet (FM) when coupled to an antiferromagnet (AFM) and the control of the exchange bias is therefore very important for technological applications, such as magnetic random access memory and giant magnetoresistance sensors. In this letter, we report the crystal structure manipulation of the exchange bias in epitaxial hcp Cr2O3 films. By epitaxially growing twined oriented Cr2O3 thin films, of which the c axis and spins of the Cr atoms lie in the film plane, we demonstrate that the exchange bias between Cr2O3 and an adjacent permalloy layer is tuned to in-plane from out-of-plane that has been observed in oriented Cr2O3 films. This is owing to the collinear exchange coupling between the spins of the Cr atoms and the adjacent FM layer. Such a highly anisotropic exchange bias phenomenon is not possible in polycrystalline films.

  16. Structural tuning of nanogaps using electromigration induced by field emission current with bipolar biasing

    SciTech Connect

    Yagi, Mamiko; Ito, Mitsuki; Shirakashi, Jun-ichi

    2015-07-07

    We report a new method for fabrication of Ni nanogaps based on electromigration induced by a field emission current. This method is called “activation” and is demonstrated here using a current source with alternately reversing polarities. The activation procedure with alternating current bias, in which the current source polarity alternates between positive and negative bias conditions, is performed with planar Ni nanogaps defined on SiO{sub 2}/Si substrates at room temperature. During negative biasing, a Fowler-Nordheim field emission current flows from the source (cathode) to the drain (anode) electrode. The Ni atoms at the tip of the drain electrode are thus activated and then migrate across the gap from the drain to the source electrode. In contrast, in the positive bias case, the field emission current moves the activated atoms from the source to the drain electrode. These two procedures are repeated until the tunnel resistance of the nanogaps is successively reduced from 100 TΩ to 48 kΩ. Scanning electron microscopy and atomic force microscopy studies showed that the gap separation narrowed from approximately 95 nm to less than 10 nm because of the Ni atoms that accumulated at the tips of both the source and drain electrodes. These results show that the alternately biased activation process, which is a newly proposed atom transfer technique, can successfully control the tunnel resistance of the Ni nanogaps and is a suitable method for formation of ultrasmall nanogap structures.

  17. Spin Propagation Through Antiferromagnetic Bulk Structure in Exchange Biased Magnetic Trilayers

    NASA Astrophysics Data System (ADS)

    Crumrine, Michael; Kirby, Hillary; Miller, Casey

    2013-03-01

    When an exchange bias is induced in materials with a ferromagnetic (FM) - antiferromagnetic (AF) interface, the interfacial coupling between the antiferromagnet and FM manifests itself as a shift in the magnetic hysteresis loop. It has been an unresolved issue as to the role the bulk spin of the antiferromagnet plays in exchange bias and whether or not exchange bias is entirely an interfacial effect. We fabricated several FM/AF/FM trilayer structures of Py(100Å)/FeMn(x)/Ni69Cu31(200Å) with varying antiferromagnet thicknesses and used a field cool procedure to induce an exchange bias. A Magneto-Optical Kerr Effect magnetometer was used to investigate the propagation of spin information through the antiferromagnet by examining the hysteresis loops at different angles of applied field with respect to the magnetization. It was observed that there was no induced exchange bias in the NiCu probe layer for any of the antiferromagnet thicknesses, and we conclude that the patterning of the antiferromagnetic layer transmits no spin information for thicknesses greater than 100Å.

  18. 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.

  19. Finding local community structure in networks

    NASA Astrophysics Data System (ADS)

    Clauset, Aaron

    2005-08-01

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

  20. Performance enhancement of ITO/oxide/semiconductor MOS-structure silicon solar cells with voltage biasing

    NASA Astrophysics Data System (ADS)

    Ho, Wen-Jeng; Huang, Min-Chun; Lee, Yi-Yu; Hou, Zhong-Fu; Liao, Changn-Jyun

    2014-12-01

    In this study, we demonstrate the photovoltaic performance enhancement of a p-n junction silicon solar cell using a transparent-antireflective ITO/oxide film deposited on the spacing of the front-side finger electrodes and with a DC voltage applied on the ITO-electrode. The depletion width of the p-n junction under the ITO-electrode was induced and extended while the absorbed volume and built-in electric field were also increased when the biasing voltage was increased. The photocurrent and conversion efficiency were increased because more photo-carriers are generated in a larger absorbed volume and because the carriers transported and collected more effectively due to higher biasing voltage effects. Compared to a reference solar cell (which was biased at 0 V), a conversion efficiency enhancement of 26.57% (from 12.42% to 15.72%) and short-circuit current density enhancement of 42.43% (from 29.51 to 42.03 mA/cm2) were obtained as the proposed MOS-structure solar cell biased at 2.5 V. In addition, the capacitance-volt (C-V) measurement was also used to examine the mechanism of photovoltaic performance enhancement due to the depletion width being enlarged by applying a DC voltage on an ITO-electrode.

  1. Guanine quadruplex structures localize to heterochromatin

    PubMed Central

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

    2016-01-01

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

  2. Localizing Target Structures in Ultrasound Video

    PubMed Central

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

    2013-01-01

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

  3. On the effect of bias on the behavior of MOS structures subjected to ionizing radiation

    SciTech Connect

    Aleksandrov, O. V.

    2015-06-15

    Using a quantitative model [6], the analysis of published data on the effect of the gate bias on the behavior of MOS structure subjected to ionizing radiation is performed. It is shown that, along with hydrogen-containing traps, there are hydrogen-free hole traps in samples with a low content of hydrogen; traps of both types are distributed inhomogeneously over the thickness of the gate insulator. In addition to ionized hydrogen, neutral hydrogen is involved in the formation of surface states and provides the main contribution to this process at negative gate bias. A decrease in the shift of the threshold voltage in the case of high fields is caused by an increase in the drift component of the hole drain to the electrodes.

  4. Does amplitude scaling of ground motion records result in biased nonlinear structural drift responses?

    USGS Publications Warehouse

    Luco, N.; Bazzurro, P.

    2007-01-01

    Limitations of the existing earthquake ground motion database lead to scaling of records to obtain seismograms consistent with a ground motion target for structural design and evaluation. In the engineering seismology community, acceptable limits for 'legitimate' scaling vary from one (no scaling allowed) to 10 or more. The concerns expressed by detractors of scaling are mostly based on the knowledge of, for example, differences in ground motion characteristics for different earthquake magnitude-distance (Mw-Rclose) scenarios, and much less on their effects on structures. At the other end of the spectrum, proponents have demonstrated that scaling is not only legitimate but also useful for assessing structural response statistics for Mw-Rclose scenarios. Their studies, however, have not investigated more recent purposes of scaling and have not always drawn conclusions for a wide spectrum of structural vibration periods and strengths. This article investigates whether scaling of records randomly selected from an Mw-Rclose bin (or range) to a target fundamental-mode spectral acceleration (Sa) level introduces bias in the expected nonlinear structural drift response of both single-degree-of-freedom oscillators and one multi-degree-of-freedom building. The bias is quantified relative to unscaled records from the target Mw-Rclose bin that are 'naturally' at the target Sa level. We consider scaling of records from the target Mw-Rclose bin and from other Mw-Rclose bins. The results demonstrate that scaling can indeed introduce a bias that, for the most part, ca be explained by differences between the elastic response spectra of the scaled versus unscaled records. Copyright ?? 2007 John Wiley & Sons, Ltd.

  5. 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.

  6. Exchange-bias in amorphous ferromagnetic and polycrystalline antiferromagnetic bilayers: Structural study and micromagnetic modeling

    NASA Astrophysics Data System (ADS)

    Kohn, A.; Dean, J.; Kovacs, A.; Zeltser, A.; Carey, M. J.; Geiger, D.; Hrkac, G.; Schrefl, T.; Allwood, D.

    2011-04-01

    We study the role of the structure of antiferromagnetic polycrystalline metallic films in determining the magnetic properties of an exchange-coupled amorphous ferromagnetic layer. The bilayers are sputter-deposited, highly textured {111} Ir22Mn78 and Co65.5Fe14.5B20 thin films. We focus on structural characterization of Ir22Mn78 as a function of layer thickness in the range having the strongest influence over the exchange-bias field and training effect. We have used transmission electron microscopy to characterize defects in the form of interface steps and roughness, interdiffusion, twin- and grain-boundaries. Such defects can result in uncompensated magnetic spins in the antiferromagnet, which then contribute to exchange-bias. These experimental results form the basis of a general model, which uses finite element micromagnetic simulations. The model incorporates the experimental structural parameters of the bilayer by implementing a surface integral technique that allows numerical calculations to solve the transition from an amorphous to a granular structure. As a result, a detailed calculation of the underlying magnetic structure within the antiferromagnetic material is achieved. These calculations are in good agreement with micromagnetic imaging using Lorentz transmission electron microscopy and the macro-magnetic properties of these bilayers.

  7. Amazonian landscapes and the bias in field studies of forest structure and biomass.

    PubMed

    Marvin, David C; Asner, Gregory P; Knapp, David E; Anderson, Christopher B; Martin, Roberta E; Sinca, Felipe; Tupayachi, Raul

    2014-12-01

    Tropical forests convert more atmospheric carbon into biomass each year than any terrestrial ecosystem on Earth, underscoring the importance of accurate tropical forest structure and biomass maps for the understanding and management of the global carbon cycle. Ecologists have long used field inventory plots as the main tool for understanding forest structure and biomass at landscape-to-regional scales, under the implicit assumption that these plots accurately represent their surrounding landscape. However, no study has used continuous, high-spatial-resolution data to test whether field plots meet this assumption in tropical forests. Using airborne LiDAR (light detection and ranging) acquired over three regions in Peru, we assessed how representative a typical set of field plots are relative to their surrounding host landscapes. We uncovered substantial mean biases (9-98%) in forest canopy structure (height, gaps, and layers) and aboveground biomass in both lowland Amazonian and montane Andean landscapes. Moreover, simulations reveal that an impractical number of 1-ha field plots (from 10 to more than 100 per landscape) are needed to develop accurate estimates of aboveground biomass at landscape scales. These biases should temper the use of plots for extrapolations of forest dynamics to larger scales, and they demonstrate the need for a fundamental shift to high-resolution active remote sensing techniques as a primary sampling tool in tropical forest biomass studies. The potential decrease in the bias and uncertainty of remotely sensed estimates of forest structure and biomass is a vital step toward successful tropical forest conservation and climate-change mitigation policy.

  8. Amazonian landscapes and the bias in field studies of forest structure and biomass.

    PubMed

    Marvin, David C; Asner, Gregory P; Knapp, David E; Anderson, Christopher B; Martin, Roberta E; Sinca, Felipe; Tupayachi, Raul

    2014-12-01

    Tropical forests convert more atmospheric carbon into biomass each year than any terrestrial ecosystem on Earth, underscoring the importance of accurate tropical forest structure and biomass maps for the understanding and management of the global carbon cycle. Ecologists have long used field inventory plots as the main tool for understanding forest structure and biomass at landscape-to-regional scales, under the implicit assumption that these plots accurately represent their surrounding landscape. However, no study has used continuous, high-spatial-resolution data to test whether field plots meet this assumption in tropical forests. Using airborne LiDAR (light detection and ranging) acquired over three regions in Peru, we assessed how representative a typical set of field plots are relative to their surrounding host landscapes. We uncovered substantial mean biases (9-98%) in forest canopy structure (height, gaps, and layers) and aboveground biomass in both lowland Amazonian and montane Andean landscapes. Moreover, simulations reveal that an impractical number of 1-ha field plots (from 10 to more than 100 per landscape) are needed to develop accurate estimates of aboveground biomass at landscape scales. These biases should temper the use of plots for extrapolations of forest dynamics to larger scales, and they demonstrate the need for a fundamental shift to high-resolution active remote sensing techniques as a primary sampling tool in tropical forest biomass studies. The potential decrease in the bias and uncertainty of remotely sensed estimates of forest structure and biomass is a vital step toward successful tropical forest conservation and climate-change mitigation policy. PMID:25422434

  9. Amazonian landscapes and the bias in field studies of forest structure and biomass

    PubMed Central

    Marvin, David C.; Asner, Gregory P.; Knapp, David E.; Anderson, Christopher B.; Martin, Roberta E.; Sinca, Felipe; Tupayachi, Raul

    2014-01-01

    Tropical forests convert more atmospheric carbon into biomass each year than any terrestrial ecosystem on Earth, underscoring the importance of accurate tropical forest structure and biomass maps for the understanding and management of the global carbon cycle. Ecologists have long used field inventory plots as the main tool for understanding forest structure and biomass at landscape-to-regional scales, under the implicit assumption that these plots accurately represent their surrounding landscape. However, no study has used continuous, high-spatial-resolution data to test whether field plots meet this assumption in tropical forests. Using airborne LiDAR (light detection and ranging) acquired over three regions in Peru, we assessed how representative a typical set of field plots are relative to their surrounding host landscapes. We uncovered substantial mean biases (9–98%) in forest canopy structure (height, gaps, and layers) and aboveground biomass in both lowland Amazonian and montane Andean landscapes. Moreover, simulations reveal that an impractical number of 1-ha field plots (from 10 to more than 100 per landscape) are needed to develop accurate estimates of aboveground biomass at landscape scales. These biases should temper the use of plots for extrapolations of forest dynamics to larger scales, and they demonstrate the need for a fundamental shift to high-resolution active remote sensing techniques as a primary sampling tool in tropical forest biomass studies. The potential decrease in the bias and uncertainty of remotely sensed estimates of forest structure and biomass is a vital step toward successful tropical forest conservation and climate-change mitigation policy. PMID:25422434

  10. A single bout of meditation biases cognitive control but not attentional focusing: Evidence from the global-local task.

    PubMed

    Colzato, Lorenza S; van der Wel, Pauline; Sellaro, Roberta; Hommel, Bernhard

    2016-01-01

    Recent studies show that a single bout of meditation can impact information processing. We were interested to see whether this impact extends to attentional focusing and the top-down control over irrelevant information. Healthy adults underwent brief single bouts of either focused attention meditation (FAM), which is assumed to increase top-down control, or open monitoring meditation (OMM), which is assumed to weaken top-down control, before performing a global-local task. While the size of the global-precedence effect (reflecting attentional focusing) was unaffected by type of meditation, the congruency effect (indicating the failure to suppress task-irrelevant information) was considerably larger after OMM than after FAM. Our findings suggest that engaging in particular kinds of meditation creates particular cognitive-control states that bias the individual processing style toward either goal-persistence or cognitive flexibility.

  11. Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness

    PubMed Central

    Mangin, B; Siberchicot, A; Nicolas, S; Doligez, A; This, P; Cierco-Ayrolles, C

    2012-01-01

    Among the several linkage disequilibrium measures known to capture different features of the non-independence between alleles at different loci, the most commonly used for diallelic loci is the r2 measure. In the present study, we tackled the problem of the bias of r2 estimate, which results from the sample structure and/or the relatedness between genotyped individuals. We derived two novel linkage disequilibrium measures for diallelic loci that are both extensions of the usual r2 measure. The first one, rS2, uses the population structure matrix, which consists of information about the origins of each individual and the admixture proportions of each individual genome. The second one, rV2, includes the kinship matrix into the calculation. These two corrections can be applied together in order to correct for both biases and are defined either on phased or unphased genotypes. We proved that these novel measures are linked to the power of association tests under the mixed linear model including structure and kinship corrections. We validated them on simulated data and applied them to real data sets collected on Vitis vinifera plants. Our results clearly showed the usefulness of the two corrected r2 measures, which actually captured ‘true' linkage disequilibrium unlike the usual r2 measure. PMID:21878986

  12. Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness.

    PubMed

    Mangin, B; Siberchicot, A; Nicolas, S; Doligez, A; This, P; Cierco-Ayrolles, C

    2012-03-01

    Among the several linkage disequilibrium measures known to capture different features of the non-independence between alleles at different loci, the most commonly used for diallelic loci is the r(2) measure. In the present study, we tackled the problem of the bias of r(2) estimate, which results from the sample structure and/or the relatedness between genotyped individuals. We derived two novel linkage disequilibrium measures for diallelic loci that are both extensions of the usual r(2) measure. The first one, r(S)(2), uses the population structure matrix, which consists of information about the origins of each individual and the admixture proportions of each individual genome. The second one, r(V)(2), includes the kinship matrix into the calculation. These two corrections can be applied together in order to correct for both biases and are defined either on phased or unphased genotypes.We proved that these novel measures are linked to the power of association tests under the mixed linear model including structure and kinship corrections. We validated them on simulated data and applied them to real data sets collected on Vitis vinifera plants. Our results clearly showed the usefulness of the two corrected r(2) measures, which actually captured 'true' linkage disequilibrium unlike the usual r(2) measure. PMID:21878986

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

    NASA Astrophysics Data System (ADS)

    Velásquez, Rober

    2003-04-01

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

  14. Clustering of Local Group Distances: Publication Bias or Correlated Measurements? III. The Small Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    de Grijs, Richard; Bono, Giuseppe

    2015-06-01

    Aiming at providing a firm mean distance estimate to the SMC, and thus to place it within the internally consistent Local Group distance framework we recently established, we compiled the current largest database of published distance estimates to the galaxy. Based on careful statistical analysis, we derive mean distance estimates to the SMC using eclipsing binary systems, variable stars, stellar population tracers, and star cluster properties. Their weighted mean leads to a final recommendation for the mean SMC distance of (m-M)0SMC=18.96+/- 0.02 mag, where the uncertainty represents the formal error. Systematic effects related to lingering uncertainties in extinction corrections, our physical understanding of the stellar tracers used, and the SMC's complex geometry—including its significant line of sight depth, its irregular appearance which renders definition of the galaxy's center uncertain, as well as its high inclination and possibly warped disk—may contribute additional uncertainties possibly exceeding 0.15-0.20 mag.

  15. On the statistics of biased tracers in the Effective Field Theory of Large Scale Structures

    SciTech Connect

    Angulo, Raul; Fasiello, Matteo; Senatore, Leonardo; Vlah, Zvonimir

    2015-09-09

    With the completion of the Planck mission, in order to continue to gather cosmological information it has become crucial to understand the Large Scale Structures (LSS) of the universe to percent accuracy. The Effective Field Theory of LSS (EFTofLSS) is a novel theoretical framework that aims to develop an analytic understanding of LSS at long distances, where inhomogeneities are small. We further develop the description of biased tracers in the EFTofLSS to account for the effect of baryonic physics and primordial non-Gaussianities, finding that new bias coefficients are required. Then, restricting to dark matter with Gaussian initial conditions, we describe the prediction of the EFTofLSS for the one-loop halo-halo and halo-matter two-point functions, and for the tree-level halo-halo-halo, matter-halo-halo and matter-matter-halo three-point functions. Several new bias coefficients are needed in the EFTofLSS, even though their contribution at a given order can be degenerate and the same parameters contribute to multiple observables. We develop a method to reduce the number of biases to an irreducible basis, and find that, at the order at which we work, seven bias parameters are enough to describe this extremely rich set of statistics. We then compare with the output of an N-body simulation where the normalization parameter of the linear power spectrum is set to σ8 = 0.9. For the lowest mass bin, we find percent level agreement up to k ≃ 0.3 h Mpc–1 for the one-loop two-point functions, and up to k ≃ 0.15 h Mpc–1 for the tree-level three-point functions, with the k-reach decreasing with higher mass bins. In conclusion, this is consistent with the theoretical estimates, and suggests that the cosmological information in LSS amenable to analytical control is much more than previously believed.

  16. On the statistics of biased tracers in the Effective Field Theory of Large Scale Structures

    DOE PAGES

    Angulo, Raul; Fasiello, Matteo; Senatore, Leonardo; Vlah, Zvonimir

    2015-09-09

    With the completion of the Planck mission, in order to continue to gather cosmological information it has become crucial to understand the Large Scale Structures (LSS) of the universe to percent accuracy. The Effective Field Theory of LSS (EFTofLSS) is a novel theoretical framework that aims to develop an analytic understanding of LSS at long distances, where inhomogeneities are small. We further develop the description of biased tracers in the EFTofLSS to account for the effect of baryonic physics and primordial non-Gaussianities, finding that new bias coefficients are required. Then, restricting to dark matter with Gaussian initial conditions, we describemore » the prediction of the EFTofLSS for the one-loop halo-halo and halo-matter two-point functions, and for the tree-level halo-halo-halo, matter-halo-halo and matter-matter-halo three-point functions. Several new bias coefficients are needed in the EFTofLSS, even though their contribution at a given order can be degenerate and the same parameters contribute to multiple observables. We develop a method to reduce the number of biases to an irreducible basis, and find that, at the order at which we work, seven bias parameters are enough to describe this extremely rich set of statistics. We then compare with the output of an N-body simulation where the normalization parameter of the linear power spectrum is set to σ8 = 0.9. For the lowest mass bin, we find percent level agreement up to k ≃ 0.3 h Mpc–1 for the one-loop two-point functions, and up to k ≃ 0.15 h Mpc–1 for the tree-level three-point functions, with the k-reach decreasing with higher mass bins. In conclusion, this is consistent with the theoretical estimates, and suggests that the cosmological information in LSS amenable to analytical control is much more than previously believed.« less

  17. Striatal structure and function predict individual biases in learning to avoid pain

    PubMed Central

    Eldar, Eran; Hauser, Tobias U.; Dayan, Peter; Dolan, Raymond J.

    2016-01-01

    Pain is an elemental inducer of avoidance. Here, we demonstrate that people differ in how they learn to avoid pain, with some individuals refraining from actions that resulted in painful outcomes, whereas others favor actions that helped prevent pain. These individual biases were best explained by differences in learning from outcome prediction errors and were associated with distinct forms of striatal responses to painful outcomes. Specifically, striatal responses to pain were modulated in a manner consistent with an aversive prediction error in individuals who learned predominantly from pain, whereas in individuals who learned predominantly from success in preventing pain, modulation was consistent with an appetitive prediction error. In contrast, striatal responses to success in preventing pain were consistent with an appetitive prediction error in both groups. Furthermore, variation in striatal structure, encompassing the region where pain prediction errors were expressed, predicted participants’ predominant mode of learning, suggesting the observed learning biases may reflect stable individual traits. These results reveal functional and structural neural components underlying individual differences in avoidance learning, which may be important contributors to psychiatric disorders involving pathological harm avoidance behavior. PMID:27071092

  18. Does survey method bias the description of northern goshawk nest-site structure?

    USGS Publications Warehouse

    Daw, S.K.; DeStefano, S.; Steidl, R.J.

    1998-01-01

    Past studies on the nesting habitat of northern goshawks (Accipiter gentilis) often relied on nests found opportunistically, either during timber-sale operations, by searching apparently 'good' goshawk habitat, or by other search methods where areas were preselected based on known forest conditions. Therefore, a bias in the characterization of habitat surrounding northern goshawk nest sites may exist toward late-forest structure (large trees, high canopy closure). This potential problem has confounded interpretation of data on nesting habitat of northern goshawks and added to uncertainty in the review process to consider the species for federal listing as threatened or endangered. Systematic survey methods, which strive for complete coverage of an area and often use broadcasts of conspecific calls, have been developed to overcome these potential biases, but no study has compared habitat characteristics around nests found opportunistically with those found systematically. We compared habitat characteristics in a 0.4-ha area around nests found systematically (n = 27) versus those found opportunistically (n = 22) on 3 national forests in eastern Oregon. We found that both density of large trees (systematic: x?? = 16.4 ?? 3.1 trees/ha; x?? ?? SE; opportunistic: x?? = 21.3 ?? 3.2; P = 0.56) and canopy closure (systematic: x?? = 72 ?? 2%; opportunistic: x?? = 70 ?? 2%; P = 0.61) were similar around nests found with either search method. Our results diminish concern that past survey methods mischaracterized northern goshawk nest-site structure. However, because northern goshawks nest in a variety of forest cover types with a wide range of structural characteristics, these results do not decrease the value of systematic survey methods in determining the most representative habitat descriptions for northern goshawks. Rigorous survey protocols allow repeatability and comparability of monitoring efforts and results over time.

  19. Selection bias in species distribution models: An econometric approach on forest trees based on structural modeling

    NASA Astrophysics Data System (ADS)

    Martin-StPaul, N. K.; Ay, J. S.; Guillemot, J.; Doyen, L.; Leadley, P.

    2014-12-01

    Species distribution models (SDMs) are widely used to study and predict the outcome of global changes on species. In human dominated ecosystems the presence of a given species is the result of both its ecological suitability and human footprint on nature such as land use choices. Land use choices may thus be responsible for a selection bias in the presence/absence data used in SDM calibration. We present a structural modelling approach (i.e. based on structural equation modelling) that accounts for this selection bias. The new structural species distribution model (SSDM) estimates simultaneously land use choices and species responses to bioclimatic variables. A land use equation based on an econometric model of landowner choices was joined to an equation of species response to bioclimatic variables. SSDM allows the residuals of both equations to be dependent, taking into account the possibility of shared omitted variables and measurement errors. We provide a general description of the statistical theory and a set of applications on forest trees over France using databases of climate and forest inventory at different spatial resolution (from 2km to 8km). We also compared the outputs of the SSDM with outputs of a classical SDM (i.e. Biomod ensemble modelling) in terms of bioclimatic response curves and potential distributions under current climate and climate change scenarios. The shapes of the bioclimatic response curves and the modelled species distribution maps differed markedly between SSDM and classical SDMs, with contrasted patterns according to species and spatial resolutions. The magnitude and directions of these differences were dependent on the correlations between the errors from both equations and were highest for higher spatial resolutions. A first conclusion is that the use of classical SDMs can potentially lead to strong miss-estimation of the actual and future probability of presence modelled. Beyond this selection bias, the SSDM we propose represents

  20. How semantic biases in simple adjacencies affect learning a complex structure with non-adjacencies in AGL: a statistical account

    PubMed Central

    Poletiek, Fenna H.; Lai, Jun

    2012-01-01

    A major theoretical debate in language acquisition research regards the learnability of hierarchical structures. The artificial grammar learning methodology is increasingly influential in approaching this question. Studies using an artificial centre-embedded AnBn grammar without semantics draw conflicting conclusions. This study investigates the facilitating effect of distributional biases in simple AB adjacencies in the input sample—caused in natural languages, among others, by semantic biases—on learning a centre-embedded structure. A mathematical simulation of the linguistic input and the learning, comparing various distributional biases in AB pairs, suggests that strong distributional biases might help us to grasp the complex AnBn hierarchical structure in a later stage. This theoretical investigation might contribute to our understanding of how distributional features of the input—including those caused by semantic variation—help learning complex structures in natural languages. PMID:22688639

  1. The relationship between level of autistic traits and local bias in the context of the McGurk effect

    PubMed Central

    Ujiie, Yuta; Asai, Tomohisa; Wakabayashi, Akio

    2015-01-01

    The McGurk effect is a well-known illustration that demonstrates the influence of visual information on hearing in the context of speech perception. Some studies have reported that individuals with autism spectrum disorder (ASD) display abnormal processing of audio-visual speech integration, while other studies showed contradictory results. Based on the dimensional model of ASD, we administered two analog studies to examine the link between level of autistic traits, as assessed by the Autism Spectrum Quotient (AQ), and the McGurk effect among a sample of university students. In the first experiment, we found that autistic traits correlated negatively with fused (McGurk) responses. Then, we manipulated presentation types of visual stimuli to examine whether the local bias toward visual speech cues modulated individual differences in the McGurk effect. The presentation included four types of visual images, comprising no image, mouth only, mouth and eyes, and full face. The results revealed that global facial information facilitates the influence of visual speech cues on McGurk stimuli. Moreover, individual differences between groups with low and high levels of autistic traits appeared when the full-face visual speech cue with an incongruent voice condition was presented. These results suggest that individual differences in the McGurk effect might be due to a weak ability to process global facial information in individuals with high levels of autistic traits. PMID:26175705

  2. The relationship between level of autistic traits and local bias in the context of the McGurk effect.

    PubMed

    Ujiie, Yuta; Asai, Tomohisa; Wakabayashi, Akio

    2015-01-01

    The McGurk effect is a well-known illustration that demonstrates the influence of visual information on hearing in the context of speech perception. Some studies have reported that individuals with autism spectrum disorder (ASD) display abnormal processing of audio-visual speech integration, while other studies showed contradictory results. Based on the dimensional model of ASD, we administered two analog studies to examine the link between level of autistic traits, as assessed by the Autism Spectrum Quotient (AQ), and the McGurk effect among a sample of university students. In the first experiment, we found that autistic traits correlated negatively with fused (McGurk) responses. Then, we manipulated presentation types of visual stimuli to examine whether the local bias toward visual speech cues modulated individual differences in the McGurk effect. The presentation included four types of visual images, comprising no image, mouth only, mouth and eyes, and full face. The results revealed that global facial information facilitates the influence of visual speech cues on McGurk stimuli. Moreover, individual differences between groups with low and high levels of autistic traits appeared when the full-face visual speech cue with an incongruent voice condition was presented. These results suggest that individual differences in the McGurk effect might be due to a weak ability to process global facial information in individuals with high levels of autistic traits.

  3. AFM-induced amine deprotection: triggering localized bond cleavage by application of tip/substrate voltage bias for the surface self-assembly of nanosized dendritic objects.

    PubMed

    Fresco, Zachary M; Suez, Itai; Backer, Scott A; Fréchet, Jean M J

    2004-07-14

    An alpha,alpha-dimethyl-3,5-dimethoxybenzyloxycarbonyl (DDZ)-protected amine monolayer can be selectively deprotected by the application of a voltage bias from a conducting AFM tip to afford localized nanoscale patterns that can be visualized by self-assembly of dendritic molecular objects with terminal carboxylic acid groups and different aspect ratios.

  4. Multipeak self-biased magnetoelectric coupling characteristics in four-phase Metglas/Terfenol-D/Be-bronze/PMN-PT structure

    NASA Astrophysics Data System (ADS)

    Huang, Dongyan; Lu, Caijiang; Bing, Han

    2015-04-01

    This letter develops a self-biased magnetoelectric (ME) structure Metglas/Terfenol-D/Be-bronze/PMN-PT (MTBP) consisting of a magnetization-graded Metglas/Terfenol-D layer, a elastic Be-bronze plate, and a piezoelectric 0.67Pb(Mg1/3Nb2/3)O3-0.33PbTiO3 (PMN-PT) plate. By using the magnetization-graded Metglas/Terfenol-D layer and the elastic Be-bronze plate, multi-peak self-biased ME responses are obtained in MTBP structure. The experimental results show that the MTBP structure with two layers of Metglas foil has maximum zero-biased ME voltage coefficient (MEVC). As frequency increases from 0.5 to 90 kHz, eleven large peaks of MEVC with magnitudes of 0.75-33 V/(cm Oe) are observed at zero-biased magnetic field. The results demonstrate that the proposed multi-peak self-biased ME structure may be useful for multifunctional devices such as multi-frequency energy harvesters or low-frequency ac magnetic field sensors.

  5. Spatial structure arising from neighbour-dependent bias in collective cell movement.

    PubMed

    Binny, Rachelle N; Haridas, Parvathi; James, Alex; Law, Richard; Simpson, Matthew J; Plank, Michael J

    2016-01-01

    Mathematical models of collective cell movement often neglect the effects of spatial structure, such as clustering, on the population dynamics. Typically, they assume that individuals interact with one another in proportion to their average density (the mean-field assumption) which means that cell-cell interactions occurring over short spatial ranges are not accounted for. However, in vitro cell culture studies have shown that spatial correlations can play an important role in determining collective behaviour. Here, we take a combined experimental and modelling approach to explore how individual-level interactions give rise to spatial structure in a moving cell population. Using imaging data from in vitro experiments, we quantify the extent of spatial structure in a population of 3T3 fibroblast cells. To understand how this spatial structure arises, we develop a lattice-free individual-based model (IBM) and simulate cell movement in two spatial dimensions. Our model allows an individual's direction of movement to be affected by interactions with other cells in its neighbourhood, providing insights into how directional bias generates spatial structure. We consider how this behaviour scales up to the population level by using the IBM to derive a continuum description in terms of the dynamics of spatial moments. In particular, we account for spatial correlations between cells by considering dynamics of the second spatial moment (the average density of pairs of cells). Our numerical results suggest that the moment dynamics description can provide a good approximation to averaged simulation results from the underlying IBM. Using our in vitro data, we estimate parameters for the model and show that it can generate similar spatial structure to that observed in a 3T3 fibroblast cell population.

  6. Spatial structure arising from neighbour-dependent bias in collective cell movement.

    PubMed

    Binny, Rachelle N; Haridas, Parvathi; James, Alex; Law, Richard; Simpson, Matthew J; Plank, Michael J

    2016-01-01

    Mathematical models of collective cell movement often neglect the effects of spatial structure, such as clustering, on the population dynamics. Typically, they assume that individuals interact with one another in proportion to their average density (the mean-field assumption) which means that cell-cell interactions occurring over short spatial ranges are not accounted for. However, in vitro cell culture studies have shown that spatial correlations can play an important role in determining collective behaviour. Here, we take a combined experimental and modelling approach to explore how individual-level interactions give rise to spatial structure in a moving cell population. Using imaging data from in vitro experiments, we quantify the extent of spatial structure in a population of 3T3 fibroblast cells. To understand how this spatial structure arises, we develop a lattice-free individual-based model (IBM) and simulate cell movement in two spatial dimensions. Our model allows an individual's direction of movement to be affected by interactions with other cells in its neighbourhood, providing insights into how directional bias generates spatial structure. We consider how this behaviour scales up to the population level by using the IBM to derive a continuum description in terms of the dynamics of spatial moments. In particular, we account for spatial correlations between cells by considering dynamics of the second spatial moment (the average density of pairs of cells). Our numerical results suggest that the moment dynamics description can provide a good approximation to averaged simulation results from the underlying IBM. Using our in vitro data, we estimate parameters for the model and show that it can generate similar spatial structure to that observed in a 3T3 fibroblast cell population. PMID:26893970

  7. Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata

    PubMed Central

    Sarno, Stefania; Harmant, Christine; Useli, Antonella; Sanz, Paula; Yang-Yao, Daniele; Manry, Jeremy; Ciani, Graziella; Luiselli, Donata; Quintana-Murci, Lluis; Comas, David; Pettener, Davide

    2013-01-01

    Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern and understanding which processes more importantly shaped the distribution of diversity, we have analyzed the uniparentally-inherited markers in ∼900 individuals from an extensive sampling across the Italian peninsula, Sardinia and Sicily. Spatial PCAs and DAPCs revealed a sex-biased pattern indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West–South East Y-chromosome structure is found in continental Italy. Such structure is in agreement with recent archeological syntheses indicating two independent and parallel processes of Neolithisation. In addition, date estimates pinpoint the importance of the cultural and demographic events during the late Neolithic and Metal Ages. On the other hand, mitochondrial diversity is distributed more homogeneously in agreement with older population events that might be related to the presence of an Italian Refugium during the last glacial period in Europe. PMID:23734255

  8. Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata.

    PubMed

    Boattini, Alessio; Martinez-Cruz, Begoña; Sarno, Stefania; Harmant, Christine; Useli, Antonella; Sanz, Paula; Yang-Yao, Daniele; Manry, Jeremy; Ciani, Graziella; Luiselli, Donata; Quintana-Murci, Lluis; Comas, David; Pettener, Davide

    2013-01-01

    Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern and understanding which processes more importantly shaped the distribution of diversity, we have analyzed the uniparentally-inherited markers in ∼900 individuals from an extensive sampling across the Italian peninsula, Sardinia and Sicily. Spatial PCAs and DAPCs revealed a sex-biased pattern indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West-South East Y-chromosome structure is found in continental Italy. Such structure is in agreement with recent archeological syntheses indicating two independent and parallel processes of Neolithisation. In addition, date estimates pinpoint the importance of the cultural and demographic events during the late Neolithic and Metal Ages. On the other hand, mitochondrial diversity is distributed more homogeneously in agreement with older population events that might be related to the presence of an Italian Refugium during the last glacial period in Europe.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  11. Sex-biased dispersal in sperm whales: contrasting mitochondrial and nuclear genetic structure of global populations.

    PubMed

    Lyrholm, T; Leimar, O; Johanneson, B; Gyllensten, U

    1999-02-22

    The social organization of most mammals is characterized by female philopatry and male dispersal. Such sex-biased dispersal can cause the genetic structure of populations to differ between the maternally inherited mitochondrial DNA (mtDNA) and the bi-parental nuclear genome. Here we report on the global genetic structure of oceanic populations of the sperm whale, one of the most widely distributed mammalian species. Groups of females and juveniles are mainly found at low latitudes, while males reach polar waters, returning to tropical and subtropical waters to breed. In comparisons between oceans, we did not find significant heterogeneity in allele frequencies of microsatellite loci (exact test; p = 0.23). Estimates of GST = 0.001 and RST = 0.005 also indicated negligible if any nuclear DNA differentiation. We have previously reported significant differentiation between oceans in mtDNA sequences. These contrasting patterns suggest that interoceanic movements have been more prevalent among males than among females, consistent with observations of females being the philopatric sex and having a more limited latitudinal distribution than males. Consequently, the typical mammalian dispersal pattern may have operated on a global scale in sperm whales.

  12. 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.

  13. Structures of Local Rearrangements in Soft Colloidal Glasses.

    PubMed

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

    2016-06-10

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

  14. Effect of negative bias on the composition and structure of the tungsten oxide thin films deposited by magnetron sputtering

    NASA Astrophysics Data System (ADS)

    Wang, Meihan; Lei, Hao; Wen, Jiaxing; Long, Haibo; Sawada, Yutaka; Hoshi, Yoichi; Uchida, Takayuki; Hou, Zhaoxia

    2015-12-01

    Tungsten oxide thin films were deposited at room temperature under different negative bias voltages (Vb, 0 to -500 V) by DC reactive magnetron sputtering, and then the as-deposited films were annealed at 500 °C in air atmosphere. The crystal structure, surface morphology, chemical composition and transmittance of the tungsten oxide thin films were characterized by X-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM), X-ray photoelectron spectroscopy (XPS) and UV-vis spectrophotometer. The XRD analysis reveals that the tungsten oxide films deposited at different negative bias voltages present a partly crystallized amorphous structure. All the films transfer from amorphous to crystalline (monoclinic + hexagonal) after annealing 3 h at 500 °C. Furthermore, the crystallized tungsten oxide films show different preferred orientation. The morphology of the tungsten oxide films deposited at different negative bias voltages is consisted of fine nanoscale grains. The grains grow up and conjunct with each other after annealing. The tungsten oxide films deposited at higher negative bias voltages after annealing show non-uniform special morphology. Substoichiometric tungsten oxide films were formed as evidenced by XPS spectra of W4f and O1s. As a result, semi-transparent films were obtained in the visible range for all films deposited at different negative bias voltages.

  15. Undesirable Choice Biases with Small Differences in the Spatial Structure of Chance Stimulus Sequences

    PubMed Central

    Herrera, David; Treviño, Mario

    2015-01-01

    In two-alternative discrimination tasks, experimenters usually randomize the location of the rewarded stimulus so that systematic behavior with respect to irrelevant stimuli can only produce chance performance on the learning curves. One way to achieve this is to use random numbers derived from a discrete binomial distribution to create a 'full random training schedule' (FRS). When using FRS, however, sporadic but long laterally-biased training sequences occur by chance and such 'input biases' are thought to promote the generation of laterally-biased choices (i.e., 'output biases'). As an alternative, a 'Gellerman-like training schedule' (GLS) can be used. It removes most input biases by prohibiting the reward from appearing on the same location for more than three consecutive trials. The sequence of past rewards obtained from choosing a particular discriminative stimulus influences the probability of choosing that same stimulus on subsequent trials. Assuming that the long-term average ratio of choices matches the long-term average ratio of reinforcers, we hypothesized that a reduced amount of input biases in GLS compared to FRS should lead to a reduced production of output biases. We compared the choice patterns produced by a 'Rational Decision Maker' (RDM) in response to computer-generated FRS and GLS training sequences. To create a virtual RDM, we implemented an algorithm that generated choices based on past rewards. Our simulations revealed that, although the GLS presented fewer input biases than the FRS, the virtual RDM produced more output biases with GLS than with FRS under a variety of test conditions. Our results reveal that the statistical and temporal properties of training sequences interacted with the RDM to influence the production of output biases. Thus, discrete changes in the training paradigms did not translate linearly into modifications in the pattern of choices generated by a RDM. Virtual RDMs could be further employed to guide the selection of

  16. Bias activated dielectric response of excitons and excitonic Mott transition in quantum confined lasers structures.

    NASA Astrophysics Data System (ADS)

    Bhunia, Amit; Bansal, Kanika; Datta, Shouvik; Alshammari, Marzook S.; Henini, Mohamed

    In contrast to the widely reported optical techniques, there are hardly any investigations on corresponding electrical signatures of condensed matter physics of excitonic phenomena. We studied small signal steady state capacitance response in III-V materials based multi quantum well (AlGaInP) and MBE grown quantum dot (InGaAs) laser diodes to identify signatures of excitonic presence. Conductance activation by forward bias was probed using frequency dependent differential capacitance response (fdC/df), which changes characteristically with the onset of light emission indicating the occurrence of negative activation energy. Our analysis shows that it is connected with a steady state population of exciton like bound states. Calculated average energy of this bound state matches well with the binding energy of weakly confined excitons in this type of structures. Further increase in charge injection decreases the differential capacitive response in AlGaInP based diodes, indicating a gradual Mott transition of excitonic states into electron hole plasma. This electrical description of excitonic Mott transition is fully supplemented by standard optical spectroscopic signatures of band gap renormalization and phase space filling effects.

  17. Climate, physiological tolerance and sex-biased dispersal shape genetic structure of Neotropical orchid bees.

    PubMed

    López-Uribe, Margarita M; Zamudio, Kelly R; Cardoso, Carolina F; Danforth, Bryan N

    2014-04-01

    Understanding the impact of past climatic events on the demographic history of extant species is critical for predicting species' responses to future climate change. Palaeoclimatic instability is a major mechanism of lineage diversification in taxa with low dispersal and small geographical ranges in tropical ecosystems. However, the impact of these climatic events remains questionable for the diversification of species with high levels of gene flow and large geographical distributions. In this study, we investigate the impact of Pleistocene climate change on three Neotropical orchid bee species (Eulaema bombiformis, E. meriana and E. cingulata) with transcontinental distributions and different physiological tolerances. We first generated ecological niche models to identify species-specific climatically stable areas during Pleistocene climatic oscillations. Using a combination of mitochondrial and nuclear markers, we inferred calibrated phylogenies and estimated historical demographic parameters to reconstruct the phylogeographical history of each species. Our results indicate species with narrower physiological tolerance experienced less suitable habitat during glaciations and currently exhibit strong population structure in the mitochondrial genome. However, nuclear markers with low and high mutation rates show lack of association with geography. These results combined with lower migration rate estimates from the mitochondrial than the nuclear genome suggest male-biased dispersal. We conclude that despite large effective population sizes and capacity for long-distance dispersal, climatic instability is an important mechanism of maternal lineage diversification in orchid bees. Thus, these Neotropical pollinators are susceptible to disruption of genetic connectivity in the event of large-scale climatic changes.

  18. Using previous models to bias structural learning in the hierarchical BOA.

    PubMed

    Hauschild, M W; Pelikan, M; Sastry, K; Goldberg, D E

    2012-01-01

    Estimation of distribution algorithms (EDAs) are stochastic optimization techniques that explore the space of potential solutions by building and sampling explicit probabilistic models of promising candidate solutions. While the primary goal of applying EDAs is to discover the global optimum or at least its accurate approximation, besides this, any EDA provides us with a sequence of probabilistic models, which in most cases hold a great deal of information about the problem. Although using problem-specific knowledge has been shown to significantly improve performance of EDAs and other evolutionary algorithms, this readily available source of problem-specific information has been practically ignored by the EDA community. This paper takes the first step toward the use of probabilistic models obtained by EDAs to speed up the solution of similar problems in the future. More specifically, we propose two approaches to biasing model building in the hierarchical Bayesian optimization algorithm (hBOA) based on knowledge automatically learned from previous hBOA runs on similar problems. We show that the proposed methods lead to substantial speedups and argue that the methods should work well in other applications that require solving a large number of problems with similar structure.

  19. Structure-Activity Analysis of Biased Agonism at the Human Adenosine A3 Receptor

    PubMed Central

    Baltos, Jo-Anne; Paoletta, Silvia; Nguyen, Anh T. N.; Gregory, Karen J.; Tosh, Dilip K.; Christopoulos, Arthur; Jacobson, Kenneth A.

    2016-01-01

    Biased agonism at G protein–coupled receptors (GPCRs) has significant implications for current drug discovery, but molecular determinants that govern ligand bias remain largely unknown. The adenosine A3 GPCR (A3AR) is a potential therapeutic target for various conditions, including cancer, inflammation, and ischemia, but for which biased agonism remains largely unexplored. We now report the generation of bias “fingerprints” for prototypical ribose containing A3AR agonists and rigidified (N)-methanocarba 5′-N-methyluronamide nucleoside derivatives with regard to their ability to mediate different signaling pathways. Relative to the reference prototypical agonist IB-MECA, (N)-methanocarba 5′-N-methyluronamide nucleoside derivatives with significant N6 or C2 modifications, including elongated aryl-ethynyl groups, exhibited biased agonism. Significant positive correlation was observed between the C2 substituent length (in Å) and bias toward cell survival. Molecular modeling suggests that extended C2 substituents on (N)-methanocarba 5′-N-methyluronamide nucleosides promote a progressive outward shift of the A3AR transmembrane domain 2, which may contribute to the subset of A3AR conformations stabilized on biased agonist binding. PMID:27136943

  20. Diversity in in-group bias: structural factors, situational features, and social functions.

    PubMed

    Scheepers, Daan; Spears, Russell; Doosje, Bertjan; Manstead, Antony S R

    2006-06-01

    Four experiments addressed the different forms and functions of in-group bias in different contexts. The authors proposed 2 functions: an identity-expressive function and an instrumental function (or promotion of positive social change). The authors manipulated status differentials, the stability of these differences, and the communication context (intra- vs. intergroup) and measured in-group bias and both functions. As predicted, identity expression via in-group bias on symbolic measures was most important for stable, high-status groups. By contrast, material in-group bias for instrumental motives was most prevalent in unstable, low-status groups but only when communicating with in-group members. This latter effect illustrates the strategic adaptation of group behavior to audience (i.e., displaying in-group bias may provoke the out-group and be counterproductive in instrumental terms). Stable, low-status groups displayed more extreme forms of in-group bias for instrumental reasons regardless of communication context (i.e., they had nothing to lose). Results are discussed in terms of a contextual-functional approach to in-group bias.

  1. Local structure of equality constrained NLP problems

    SciTech Connect

    Mari, J.

    1994-12-31

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

  2. Structural and magnetic properties of (Fe/Mn) exchange-biased multilayers

    NASA Astrophysics Data System (ADS)

    El Bahoui, A.; Genevois, C.; Juraszek, J.; Bordel, C.; Ledue, D.

    2013-05-01

    Exchange-biasing of ferromagnetic (F) Fe layers by adjacent antiferromagnetic (AF) Mn layers has been investigated in (Fe/Mn)10 multilayered films. This study has been focused on the relationship between the evolution of the exchange-bias field and the evolution of the film microstructure as a function of the deposition temperature. The increase of the deposition temperature results in the formation of an Fe-Mn alloy at the interfaces and columnar features whose size increases with the deposition temperature. In parallel, the exchange-bias field decreases significantly, due to interface roughness.

  3. 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.

  4. Implications of room temperature oxidation on crystal structure and exchange bias effect in Co/CoO nanoparticles

    DOE PAGES

    Feygenson, Mikhail; Formo, Eric V.; Freeman, Katherine; Schieber, Natalie P.; Gai, Zheng; Rondinone, Adam J.

    2015-11-02

    In this study, we describe how the exchange bias effect in Co/CoO nanoparticles depends on the size focusing and temperature treatment of precursor Co nanoparticles before oxidation at ambient conditions. By appealing to magnetization, microscopy, neutron and synchrotron x-ray measurements we found that as-synthesized Co nanoparticles readily oxidize in air only after 20 days. The highest exchange bias field of 814 Oe is observed at T = 2K. When the same nanoparticles are centrifuged and annealed at 70 °C in vacuum prior to oxidation, the exchange bias field is increased to 2570 Oe. Annealing of Co nanoparticles in vacuum improvesmore » their crystallinity and prevents complete oxidation, so that Co-core/CoO-shell structure is preserved even after 120 days. The crystal structure of CoO shell in both samples is different from its bulk counterpart. Implications of such distorted CoO shells on exchange bias are discussed. Coating of Co nanoparticles with amorphous silica shell makes them resistant to oxidation, but ultimately modifies the crystal structure of both Co core and SiO2 shell.« less

  5. Implications of room temperature oxidation on crystal structure and exchange bias effect in Co/CoO nanoparticles

    SciTech Connect

    Feygenson, Mikhail; Formo, Eric V.; Freeman, Katherine; Schieber, Natalie P.; Gai, Zheng; Rondinone, Adam J.

    2015-11-02

    In this study, we describe how the exchange bias effect in Co/CoO nanoparticles depends on the size focusing and temperature treatment of precursor Co nanoparticles before oxidation at ambient conditions. By appealing to magnetization, microscopy, neutron and synchrotron x-ray measurements we found that as-synthesized Co nanoparticles readily oxidize in air only after 20 days. The highest exchange bias field of 814 Oe is observed at T = 2K. When the same nanoparticles are centrifuged and annealed at 70 °C in vacuum prior to oxidation, the exchange bias field is increased to 2570 Oe. Annealing of Co nanoparticles in vacuum improves their crystallinity and prevents complete oxidation, so that Co-core/CoO-shell structure is preserved even after 120 days. The crystal structure of CoO shell in both samples is different from its bulk counterpart. Implications of such distorted CoO shells on exchange bias are discussed. Coating of Co nanoparticles with amorphous silica shell makes them resistant to oxidation, but ultimately modifies the crystal structure of both Co core and SiO2 shell.

  6. Influence of substrate bias voltage on structural and optical properties of RF reactive magnetron sputtered WO3 thin films

    NASA Astrophysics Data System (ADS)

    Madhavi, V.; Kondaiah, P.; Uthanna, S.

    2012-11-01

    In this investigation, tungsten oxide (WO3) thin films have been deposited on unheated glass substrates by RF magnetron sputtering of tungsten target at constant oxygen partial pressure of 6×10-2 Pa, sputtering power of 150 W and at different substrate bias voltages in the range from 0 to -150 V. The structural and optical properties of the films were investigated by using X-ray diffraction, Fourier transform infrared spectroscopy and UV-Vis-NIR spectrophotometers. The films formed up to substrate bias voltage of -50 V were found to be amorphous in nature, while those films formed at -100 V showed a weak (200) reflection indicates the presence of monoclinic phase of WO3 in amorphous matrix. The optical transmittance of the films was in the range 78 - 95 % in the wavelength range of 500 - 1200 nm. The absorption band edge was shifted towards higher wavelength side with increasing substrate bias voltage. The optical band gap of the films decrease from 2.81 to 2.69 eV with increase of substrate bias voltage from 0 to -150 V respectively. The refractive index of the films increased from 2.19 to 2.27 with increase of substrate bias voltage from 0 to -150 V respectively.

  7. Phonon localization in ultrathin layered structures

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  8. Local Structural Alignment of RNA with Affine Gap Model

    NASA Astrophysics Data System (ADS)

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

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

  9. Genetic Population Structure of the Ground Beetle, Pterostichus oblongopunctatus, Inhabiting a Fragmented and Polluted Landscape: Evidence for Sex-Biased Dispersal

    PubMed Central

    Lagisz, Malgorzata; Wolff, Kirsten; Sanderson, Roy A; Laskowski, Ryszard

    2010-01-01

    Ground beetles are an integral and functionally important part of many terrestrial ecosystems. Habitat change often influences population genetic structure of carabid beetles. In this study, genetic variation, population differentiation, and sex-specific dispersal patterns were studied in the forest ground beetle, Pterostichus oblongopunctatus F. (Coleoptera: Carabidae), in a fragmented and metal-polluted landscape to assess the consequences of human-induced changes on the population genetic structure. Genotypic variation at five microsatellite loci was screened in 309 beetles from 21 sample locations around zinc-and-lead smelter in southern Poland. Low levels of genetic differentiation among sampling sites were observed, suggesting high gene flow among populations. A negative correlation was found between levels of genetic differentiation and habitat patch size. No significant effects of metal pollution, in terms of genetic bottlenecks and genetic differentiation, were observed. Analyses revealed weak genetic clustering that is loosely tied to the geographic position of the sampled populations. Several tests of sex-biased dispersal were conducted. Most of them indicated male-biased dispersal. Differing levels of dispersal between females and males resulted in sex-specific spatial genetic patterns. Genetic differentiation was significantly correlated with geographical distance for males, but not for females, who were more diverged locally. Also, the effect of habitat patch size was sex-dependent, supporting the finding of different dispersal patterns between the sexes. This study demonstrated the application of microsatellite markers to answer questions regarding complex interactions between population structure and physical properties of the landscape. In the study system, migration appears to be sufficient to override potential effects of environmental pollution as well as habitat fragmentation. This investigation of population genetic structure indicated, for

  10. Geometrical Structure and Interface Dependence of Bias Stress Induced Threshold Voltage Shift in C60-Based OFETs

    PubMed Central

    2014-01-01

    The influence of the nature of interface between organic semiconductor and gate dielectric on bias stress electrical stability of n-type C60-based organic field effect transistors (OFETs) was studied. The bias stress induced threshold voltage (Vth) shift was found to depend critically on the OFET device structure: the direction of Vth shift in top-gate OFETs was opposite to that in bottom-gate OFETs, while the use of the dual-gate OFET structure resulted in just very small variations in Vth. The opposite direction of Vth shift is attributed to the different nature of interfaces between C60 semiconductor and Parylene dielectric in these devices. The Vth shift to more positive voltages upon bias stress in bottom-gate C60-OFET was similar to that observed for other n-type semiconductors and rationalized by electron trapping in the dielectric or at the gate dielectric/C60 interface. The opposite direction of Vth shift in top-gate C60-OFETs is attributed to free radical species created in the course of Parylene deposition on the surface of C60 during device fabrication, which produce plenty of hole traps. It was also realized that the dual-gate OFETs gives stable characteristics, which are immune to bias stress effects. PMID:25142130

  11. Non Linear Optimization Applied to Angle-Of Satellite Based Geo-Localization for Biased and Time-Drifting Sensors

    NASA Astrophysics Data System (ADS)

    Levy, Daniel; Roos, Jason; Robinson, Jace; Carpenter, William; Martin, Richard; Taylor, Clark; Sugrue, Joseph; Terzuoli, Andrew

    2016-06-01

    Multiple sensors are used in a variety of geolocation systems. Many use Time Difference of Arrival (TDOA) or Received Signal Strength (RSS) measurements to estimate the most likely location of a signal. When an object does not emit an RF signal, Angle of Arrival (AOA) measurements using optical or infrared frequencies become more feasible than TDOA or RSS measurements. AOA measurements can be created from any sensor platform with any sort of optical sensor, location and attitude knowledge to track passive objects. Previous work has created a non-linear optimization (NLO) method for calculating the most likely estimate from AOA measurements. Two new modifications to the NLO algorithm are created and shown to correct AOA measurement errors by estimating the inherent bias and time-drift in the Inertial Measurement Unit (IMU) of the AOA sensing platform. One method corrects the sensor bias in post processing while treating the NLO method as a module. The other method directly corrects the sensor bias within the NLO algorithm by incorporating the bias parameters as a state vector in the estimation process. These two methods are analyzed using various Monte-Carlo simulations to check the general performance of the two modifications in comparison to the original NLO algorithm.

  12. Correlation of exchange bias with magneto-structural effects across the compensation temperature of Co(Cr1-xFex)2O4 (x = 0.05 and 0.075)

    NASA Astrophysics Data System (ADS)

    Kumar, Ram; Padam, R.; Rayaprol, S.; Siruguri, Vasudeva; Pal, D.

    2016-03-01

    A small amount of Fe (5% and 7.5%) substitution in the Cr-site of the multiferroic compound CoCr2O4 leads to a magnetization reversal. In these compounds, we report a sign change in the exchange bias across the compensation temperature, accompanied by a non-monotonic change in the local moments across the compensation temperature. Such non-monotonic change in the magnetic moments is triggered by a similar change in the lattice structure. We relate here the sign change of exchange bias with that of the crystalline energy of the lattice and the Zeeman energy term arising from the anti-site disorder.

  13. Structure and properties of TiAlLaN films deposited at various bias voltages

    NASA Astrophysics Data System (ADS)

    Du, Hao; Xiong, Ji; Zhao, Haibo; Wu, Yuemei; Wan, Weicai; Wang, Linlin

    2014-02-01

    The TiAlLaN films were deposited on YG8 and silicon (1 1 1) substrates by a hybrid PVD coater which is combined with medium frequency reactive magnetron sputtering and ion-plating evaporation. The effects of lanthanum addition and bias voltages on the composition, crystal morphology, microstructure, mechanical properties, and oxidation resistance of the TiAlLaN films were investigated systematically. With lanthanum addition in the TiAlN film, the crystal morphology changed from columnar to equiaxial, and the grain refinement accompanied by the increase of hardness and elastic modulus was found. The indentation adhesion test showed that the adhesion strength was deteriorated by adding lanthanum in the deposited film; however, the scratch adhesion test expressed a better morphology of the scratch track line for the TiAlLaN film. With the substrate bias increasing, the elements concentration of films were alternated, and the equiaxial crystals were turned to columnar crystals. The oxidation resistance of the deposited films increased with the increase of bias voltage. The adhesion qualities, which are affected by the increasing hardness and elastic modulus, were worse for the TiAlLaN films under higher bias voltages. The TiAlLaN film under the bias of -10 V showed the highest H/E ratio.

  14. Local Influence Analysis of Nonlinear Structural Equation Models

    ERIC Educational Resources Information Center

    Lee, Sik-Yum; Tang, Nian-Sheng

    2004-01-01

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

  15. 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.

  16. Dynamic quasi-energy-band modulation and exciton effects in biased superlattices driven by a two-color far-infrared field: Disappearance of dynamic localization

    NASA Astrophysics Data System (ADS)

    Yashima, Kenta; Hino, Ken-Ichi; Toshima, Nobuyuki

    2003-12-01

    A theoretical study of the optical and electronic properties of semiconductor superlattices in ac-dc fields, termed the dynamic Wannier-Stark ladder (DWSL), is done. The biased superlattices are driven by two far-infrared fields with different frequencies and relative phase of δ. Here, the frequency of the first laser is equal to the Bloch frequency ωB of the system under study, while that of the second laser is equal to 2ωB. Quasienergies of the DWSL are calculated based on the Floquet theorem, and the associated linear photoabsorption spectra are evaluated. For δ=0, a gourd-shaped quasi-energy structure characteristic of both dynamic localization (DL) and delocalization (DDL), similar to the usual DWSL driven by a single laser, appears. By changing the ratio of the two laser strengths, however, the width of the quasi-energy band and the locations of both DL and DDL vary noticeably. As for δ≠0, on the other hand, band collapse and the associated DL do not necessarily follow. In fact, DL vanishes and the quasi-energy degeneracy is lifted in a certain range of δ. Just DDL remains over the entire range of the laser strength, eventually resulting in a plateaulike band structure in the linear absorption spectra. The basic physics underlying this phenomenon, which can be readily interpreted in terms of a closed analytical expression, is that all quasi-energies for given crystal momenta are out of phase with each other as a function of laser strength without converging to a single point of energy. This is a feature of this DWSL which sharply distinguishes it from a conventional DWSL generated using a single laser to drive it. Furthermore, an exciton effect is incorporated with the above noninteracting problem, so that exciton dressed states are formed. It is found that this effect gives rise to more involved quasi-energy structures and a more pronounced release of the energy degeneracy of DL, leading again to the formation of a band structure in the absorption

  17. A local difference in Hedgehog signal transduction increases mechanical cell bond tension and biases cell intercalations along the Drosophila anteroposterior compartment boundary.

    PubMed

    Rudolf, Katrin; Umetsu, Daiki; Aliee, Maryam; Sui, Liyuan; Jülicher, Frank; Dahmann, Christian

    2015-11-15

    Tissue organization requires the interplay between biochemical signaling and cellular force generation. The formation of straight boundaries separating cells with different fates into compartments is important for growth and patterning during tissue development. In the developing Drosophila wing disc, maintenance of the straight anteroposterior (AP) compartment boundary involves a local increase in mechanical tension at cell bonds along the boundary. The biochemical signals that regulate mechanical tension along the AP boundary, however, remain unknown. Here, we show that a local difference in Hedgehog signal transduction activity between anterior and posterior cells is necessary and sufficient to increase mechanical tension along the AP boundary. This difference in Hedgehog signal transduction is also required to bias cell rearrangements during cell intercalations to keep the characteristic straight shape of the AP boundary. Moreover, severing cell bonds along the AP boundary does not reduce tension at neighboring bonds, implying that active mechanical tension is upregulated, cell bond by cell bond. Finally, differences in the expression of the homeodomain-containing protein Engrailed also contribute to the straight shape of the AP boundary, independently of Hedgehog signal transduction and without modulating cell bond tension. Our data reveal a novel link between local differences in Hedgehog signal transduction and a local increase in active mechanical tension of cell bonds that biases junctional rearrangements. The large-scale shape of the AP boundary thus emerges from biochemical signals inducing patterns of active tension on cell bonds.

  18. Influence of bias voltage on structural and optical properties of TiN{sub x} thin films

    SciTech Connect

    Singh, Omveer; Dahiya, Raj P.; Malik, Hitendra K.; Kumar, Parmod

    2015-08-28

    In the present work, Ti thin films were deposited on Si substrate using DC sputtering technique. Indigenous hot cathode arc discharge plasma system was used for nitriding over these samples, where the plasma parameters and work piece can be controlled independently. A mixture of H{sub 2} and N{sub 2} gases (in the ratio of 80:20) was supplied into the plasma chamber. The effect of bias voltage on the crystal structure, morphology and optical properties was investigated by employing various physical techniques such as X-ray Diffraction, Atomic Force Microscopy and UV-Vis spectrometry. It was found that bias voltage affects largely the crystal structure and band gap which in turn is responsible for the modifications in optical properties of the deposited films.

  19. Comparison of large-scale structures and velocities in the local universe

    NASA Technical Reports Server (NTRS)

    Yahil, Amos

    1994-01-01

    Comparison of the large-scale density and velocity fields in the local universe shows detailed agreement, strengthening the standard paradigm of the gravitational origin of these structures. Quantitative analysis can determine the cosmological density parameter, Omega, and biasing factor, b; there is virtually no sensitivity in any local analyses to the cosmologial constant, lambda. Comparison of the dipole anisotropy of the cosmic microwave background with the acceleration due to the Infrared Astronomy Satellite (IRAS) galaxies puts the linear growth factor in the range beta approximately equals Omega (exp 0.6)/b = 0.6(+0.7/-0.3) (95% confidence). A direct comparison of the density and velocity fields of nearby galaxies gives beta = 1.3 (+0.7/-0.6), and from nonlinear analysis the weaker limit (Omega greater than 0.45 for b greater than 0.5 (again 95% confidence). A tighter limit (Omega greater than 0.3 (4-6 sigma)), is obtained by a reconstruction of the probability distribution function of the initial fluctuations from which the structures observed today arose. The last two methods depend critically on the smooth velocity field determined from the observed velocities of nearby galaxies by the POTENT method. A new analysis of these velocities, with more than three times the data used to obtain the above quoted results, is now underway and promises to tighten the uncertainties considerably, as well as reduce systematic bias.

  20. Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing

    PubMed Central

    Polson, Shawn W.; Wommack, K. Eric; Williamson, Shannon J.; McDonald, Ian R.; Cary, S. Craig

    2012-01-01

    Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa–a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3–V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure. PMID:22970184

  1. Local and sex-specific biases in crossover vs. noncrossover outcomes at meiotic recombination hot spots in mice.

    PubMed

    de Boer, Esther; Jasin, Maria; Keeney, Scott

    2015-08-15

    Meiotic recombination initiated by programmed double-strand breaks (DSBs) yields two types of interhomolog recombination products, crossovers and noncrossovers, but what determines whether a DSB will yield a crossover or noncrossover is not understood. In this study, we analyzed the influence of sex and chromosomal location on mammalian recombination outcomes by constructing fine-scale recombination maps in both males and females at two mouse hot spots located in different regions of the same chromosome. These include the most comprehensive maps of recombination hot spots in oocytes to date. One hot spot, located centrally on chromosome 1, behaved similarly in male and female meiosis: Crossovers and noncrossovers formed at comparable levels and ratios in both sexes. In contrast, at a distal hot spot, crossovers were recovered only in males even though noncrossovers were obtained at similar frequencies in both sexes. These findings reveal an example of extreme sex-specific bias in recombination outcome. We further found that estimates of relative DSB levels are surprisingly poor predictors of relative crossover frequencies between hot spots in males. Our results demonstrate that the outcome of mammalian meiotic recombination can be biased, that this bias can vary depending on location and cellular context, and that DSB frequency is not the only determinant of crossover frequency.

  2. Local and sex-specific biases in crossover vs. noncrossover outcomes at meiotic recombination hot spots in mice

    PubMed Central

    de Boer, Esther; Jasin, Maria; Keeney, Scott

    2015-01-01

    Meiotic recombination initiated by programmed double-strand breaks (DSBs) yields two types of interhomolog recombination products, crossovers and noncrossovers, but what determines whether a DSB will yield a crossover or noncrossover is not understood. In this study, we analyzed the influence of sex and chromosomal location on mammalian recombination outcomes by constructing fine-scale recombination maps in both males and females at two mouse hot spots located in different regions of the same chromosome. These include the most comprehensive maps of recombination hot spots in oocytes to date. One hot spot, located centrally on chromosome 1, behaved similarly in male and female meiosis: Crossovers and noncrossovers formed at comparable levels and ratios in both sexes. In contrast, at a distal hot spot, crossovers were recovered only in males even though noncrossovers were obtained at similar frequencies in both sexes. These findings reveal an example of extreme sex-specific bias in recombination outcome. We further found that estimates of relative DSB levels are surprisingly poor predictors of relative crossover frequencies between hot spots in males. Our results demonstrate that the outcome of mammalian meiotic recombination can be biased, that this bias can vary depending on location and cellular context, and that DSB frequency is not the only determinant of crossover frequency. PMID:26251527

  3. How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire.

    PubMed

    Blevins, Sydney J; Pierce, Brian G; Singh, Nishant K; Riley, Timothy P; Wang, Yuan; Spear, Timothy T; Nishimura, Michael I; Weng, Zhiping; Baker, Brian M

    2016-03-01

    How T-cell receptors (TCRs) can be intrinsically biased toward MHC proteins while simultaneously display the structural adaptability required to engage diverse ligands remains a controversial puzzle. We addressed this by examining αβ TCR sequences and structures for evidence of physicochemical compatibility with MHC proteins. We found that human TCRs are enriched in the capacity to engage a polymorphic, positively charged "hot-spot" region that is almost exclusive to the α1-helix of the common human class I MHC protein, HLA-A*0201 (HLA-A2). TCR binding necessitates hot-spot burial, yielding high energetic penalties that must be offset via complementary electrostatic interactions. Enrichment of negative charges in TCR binding loops, particularly the germ-line loops encoded by the TCR Vα and Vβ genes, provides this capacity and is correlated with restricted positioning of TCRs over HLA-A2. Notably, this enrichment is absent from antibody genes. The data suggest a built-in TCR compatibility with HLA-A2 that biases receptors toward, but does not compel, particular binding modes. Our findings provide an instructional example for how structurally pliant MHC biases can be encoded within TCRs. PMID:26884163

  4. How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire

    PubMed Central

    Blevins, Sydney J.; Pierce, Brian G.; Singh, Nishant K.; Riley, Timothy P.; Wang, Yuan; Spear, Timothy T.; Nishimura, Michael I.; Weng, Zhiping; Baker, Brian M.

    2016-01-01

    How T-cell receptors (TCRs) can be intrinsically biased toward MHC proteins while simultaneously display the structural adaptability required to engage diverse ligands remains a controversial puzzle. We addressed this by examining αβ TCR sequences and structures for evidence of physicochemical compatibility with MHC proteins. We found that human TCRs are enriched in the capacity to engage a polymorphic, positively charged “hot-spot” region that is almost exclusive to the α1-helix of the common human class I MHC protein, HLA-A*0201 (HLA-A2). TCR binding necessitates hot-spot burial, yielding high energetic penalties that must be offset via complementary electrostatic interactions. Enrichment of negative charges in TCR binding loops, particularly the germ-line loops encoded by the TCR Vα and Vβ genes, provides this capacity and is correlated with restricted positioning of TCRs over HLA-A2. Notably, this enrichment is absent from antibody genes. The data suggest a built-in TCR compatibility with HLA-A2 that biases receptors toward, but does not compel, particular binding modes. Our findings provide an instructional example for how structurally pliant MHC biases can be encoded within TCRs. PMID:26884163

  5. Community Structure Analysis of Methanogens Associated with Rumen Protozoa Reveals Bias in Universal Archaeal Primers

    PubMed Central

    McAllister, Tim A.

    2012-01-01

    The diversity of protozoan-associated methanogens in cattle was investigated using five universal archaeal small-subunit (SSU) rRNA gene primer sets. Methanobrevibacter spp. and rumen cluster C (distantly related to Thermoplasma spp.) were predominant. Significant differences in species composition among libraries indicate that some primers used previously to characterize rumen methanogens exhibit biased amplification. PMID:22447586

  6. Convergence among Data Sources, Response Bias, and Reliability and Validity of a Structured Job Analysis Questionnaire.

    ERIC Educational Resources Information Center

    Smith, Jack E.; Hakel, Milton D.

    1979-01-01

    Examined are questions pertinent to the use of the Position Analysis Questionnaire: Who can use the PAQ reliably and validly? Must one rely on trained job analysts? Can people having no direct contact with the job use the PAQ reliably and validly? Do response biases influence PAQ responses? (Author/KC)

  7. 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.

  8. Structure of local interactions in complex financial dynamics

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Hou, Jilin; Jankowski, Łukasz; Ou, Jinping

    2013-09-01

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

  10. Charge movement in a GaN-based hetero-structure field effect transistor structure with carbon doped buffer under applied substrate bias

    SciTech Connect

    Pooth, Alexander; Uren, Michael J.; Cäsar, Markus; Kuball, Martin; Martin, Trevor

    2015-12-07

    Charge trapping and transport in the carbon doped GaN buffer of a GaN-based hetero-structure field effect transistor (HFET) has been investigated under both positive and negative substrate bias. Clear evidence of redistribution of charges in the carbon doped region by thermally generated holes is seen, with electron injection and capture observed during positive bias. Excellent agreement is found with simulations. It is shown that these effects are intrinsic to the carbon doped GaN and need to be controlled to provide reliable and efficient GaN-based power HFETs.

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

    SciTech Connect

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

    2014-11-07

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

  12. A Novel Integrated Structure with a Radial Displacement Sensor and a Permanent Magnet Biased Radial Magnetic Bearing

    PubMed Central

    Sun, Jinji; Zhang, Yin

    2014-01-01

    In this paper, a novel integrated structure is proposed in order to reduce the axial length of the high speed of a magnetically suspended motor (HSMSM) to ensure the maximum speed, which combines radial displacement sensor probes and the permanent magnet biased radial magnetic bearing in HSMSM. The sensor probes are integrated in the magnetic bearing, and the sensor preamplifiers are placed in the control system of the HSMSM, separate from the sensor probes. The proposed integrated structure can save space in HSMSMs, improve the working frequency, reduce the influence of temperature on the sensor circuit, and improve the stability of HSMSMs. PMID:24469351

  13. A novel integrated structure with a radial displacement sensor and a permanent magnet biased radial magnetic bearing.

    PubMed

    Sun, Jinji; Zhang, Yin

    2014-01-01

    In this paper, a novel integrated structure is proposed in order to reduce the axial length of the high speed of a magnetically suspended motor (HSMSM) to ensure the maximum speed, which combines radial displacement sensor probes and the permanent magnet biased radial magnetic bearing in HSMSM. The sensor probes are integrated in the magnetic bearing, and the sensor preamplifiers are placed in the control system of the HSMSM, separate from the sensor probes. The proposed integrated structure can save space in HSMSMs, improve the working frequency, reduce the influence of temperature on the sensor circuit, and improve the stability of HSMSMs. PMID:24469351

  14. Structure and interfacial analysis of nanoscale TiNi thin film prepared by biased target ion beam deposition

    SciTech Connect

    Hou, Huilong; Hamilton, Reginald F. Horn, Mark W.

    2015-07-15

    Ultrathin, 65 nm thick, TiNi alloy films were fabricated by cosputtering Ti and Ni targets using the recently developed biased target ion beam deposition technique. Preheating the substrate by exposure to a low energy ion source resulted in as-deposited films with a pure B2 atomic crystal structure containing no secondary crystal structures or precipitates. Continuous films were produced with a smooth surface and minimal substrate/film interfacial diffusion. The diffusion layer was a small ratio of film thickness, which is a prerequisite for the B2 phase to undergo the martensitic transformation in ultrathin films.

  15. A novel integrated structure with a radial displacement sensor and a permanent magnet biased radial magnetic bearing.

    PubMed

    Sun, Jinji; Zhang, Yin

    2014-01-24

    In this paper, a novel integrated structure is proposed in order to reduce the axial length of the high speed of a magnetically suspended motor (HSMSM) to ensure the maximum speed, which combines radial displacement sensor probes and the permanent magnet biased radial magnetic bearing in HSMSM. The sensor probes are integrated in the magnetic bearing, and the sensor preamplifiers are placed in the control system of the HSMSM, separate from the sensor probes. The proposed integrated structure can save space in HSMSMs, improve the working frequency, reduce the influence of temperature on the sensor circuit, and improve the stability of HSMSMs.

  16. Suppression of photo-bias induced instability for amorphous indium tungsten oxide thin film transistors with bi-layer structure

    NASA Astrophysics Data System (ADS)

    Liu, Po-Tsun; Chang, Chih-Hsiang; Chang, Chih-Jui

    2016-06-01

    This study investigates the instability induced by bias temperature illumination stress (NBTIS) for an amorphous indium-tungsten-oxide thin film transistor (a-IWO TFT) with SiO2 backchannel passivation layer (BPL). It is found that this electrical degradation phenomenon can be attributed to the generation of defect states during the BPL process, which deteriorates the photo-bias stability of a-IWO TFTs. A method proposed by adding an oxygen-rich a-IWO thin film upon the a-IWO active channel layer could effectively suppress the plasma damage to channel layer during BPL deposition process. The bi-layer a-IWO TFT structure with an oxygen-rich back channel exhibits superior electrical reliability of device under NBTIS.

  17. Communication: Estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth

    NASA Astrophysics Data System (ADS)

    Bieler, Noah S.; Hünenberger, Philippe H.

    2014-11-01

    In a recent article [Bieler et al., J. Chem. Theory Comput. 10, 3006-3022 (2014)], we introduced a combination of the λ-dynamics (λD) approach for calculating alchemical free-energy differences and of the local-elevation umbrella-sampling (LEUS) memory-based biasing method to enhance the sampling along the alchemical coordinate. The combined scheme, referred to as λ-LEUS, was applied to the perturbation of hydroquinone to benzene in water as a test system, and found to represent an improvement over thermodynamic integration (TI) in terms of sampling efficiency at equivalent accuracy. However, the preoptimization of the biasing potential required in the λ-LEUS method requires "filling up" all the basins in the potential of mean force. This introduces a non-productive pre-sampling time that is system-dependent, and generally exceeds the corresponding equilibration time in a TI calculation. In this letter, a remedy is proposed to this problem, termed the slow growth memory guessing (SGMG) approach. Instead of initializing the biasing potential to zero at the start of the preoptimization, an approximate potential of mean force is estimated from a short slow growth calculation, and its negative used to construct the initial memory. Considering the same test system as in the preceding article, it is shown that of the application of SGMG in λ-LEUS permits to reduce the preoptimization time by about a factor of four.

  18. Communication: Estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth

    SciTech Connect

    Bieler, Noah S.; Hünenberger, Philippe H.

    2014-11-28

    In a recent article [Bieler et al., J. Chem. Theory Comput. 10, 3006–3022 (2014)], we introduced a combination of the λ-dynamics (λD) approach for calculating alchemical free-energy differences and of the local-elevation umbrella-sampling (LEUS) memory-based biasing method to enhance the sampling along the alchemical coordinate. The combined scheme, referred to as λ-LEUS, was applied to the perturbation of hydroquinone to benzene in water as a test system, and found to represent an improvement over thermodynamic integration (TI) in terms of sampling efficiency at equivalent accuracy. However, the preoptimization of the biasing potential required in the λ-LEUS method requires “filling up” all the basins in the potential of mean force. This introduces a non-productive pre-sampling time that is system-dependent, and generally exceeds the corresponding equilibration time in a TI calculation. In this letter, a remedy is proposed to this problem, termed the slow growth memory guessing (SGMG) approach. Instead of initializing the biasing potential to zero at the start of the preoptimization, an approximate potential of mean force is estimated from a short slow growth calculation, and its negative used to construct the initial memory. Considering the same test system as in the preceding article, it is shown that of the application of SGMG in λ-LEUS permits to reduce the preoptimization time by about a factor of four.

  19. Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.

    PubMed

    Reddy, Vinod; Swanson, Stanley M; Segelke, Brent; Kantardjieff, Katherine A; Sacchettini, James C; Rupp, Bernhard

    2003-12-01

    Anticipating a continuing increase in the number of structures solved by molecular replacement in high-throughput crystallography and drug-discovery programs, a user-friendly web service for automated molecular replacement, map improvement, bias removal and real-space correlation structure validation has been implemented. The service is based on an efficient bias-removal protocol, Shake&wARP, and implemented using EPMR and the CCP4 suite of programs, combined with various shell scripts and Fortran90 routines. The service returns improved maps, converted data files and real-space correlation and B-factor plots. User data are uploaded through a web interface and the CPU-intensive iteration cycles are executed on a low-cost Linux multi-CPU cluster using the Condor job-queuing package. Examples of map improvement at various resolutions are provided and include model completion and reconstruction of absent parts, sequence correction, and ligand validation in drug-target structures.

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

    NASA Technical Reports Server (NTRS)

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

    1988-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Shen, Juntai

    2015-08-01

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

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

    PubMed Central

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

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

    PubMed

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

    2016-08-12

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

  5. The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr.

    PubMed Central

    Carlini, D B; Chen, Y; Stephan, W

    2001-01-01

    To gain insights into the relationship between codon bias, mRNA secondary structure, third-codon position nucleotide distribution, and gene expression, we predicted secondary structures in two related drosophilid genes, Adh and Adhr, which differ in degree of codon bias and level of gene expression. Individual structural elements (helices) were inferred using the comparative method. For each gene, four types of randomization simulations were performed to maintain/remove codon bias and/or to maintain or alter third-codon position nucleotide composition (N3). In the weakly expressed, weakly biased gene Adhr, the potential for secondary structure formation was found to be much stronger than in the highly expressed, highly biased gene Adh. This is consistent with the observation of approximately equal G and C percentages in Adhr ( approximately 31% across species), whereas in Adh the N3 distribution is shifted toward C (42% across species). Perturbing the N3 distribution to approximately equal amounts of A, G, C, and T increases the potential for secondary structure formation in Adh, but decreases it in Adhr. On the other hand, simulations that reduce codon bias without changing N3 content indicate that codon bias per se has only a weak effect on the formation of secondary structures. These results suggest that, for these two drosophilid genes, secondary structure is a relatively independent, negative regulator of gene expression. Whereas the degree of codon bias is positively correlated with level of gene expression, strong individual secondary structural elements may be selected for to retard mRNA translation and to decrease gene expression. PMID:11606539

  6. The Changing Market Structure of Local Television News.

    ERIC Educational Resources Information Center

    Powers, Angela

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

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

    ERIC Educational Resources Information Center

    Evans, Penny; Irish, Sharon

    2013-01-01

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

  8. Local structure of numerically generated worm hole spacetime.

    NASA Astrophysics Data System (ADS)

    Siino, M.

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

  9. 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.

  10. 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

  11. Viscoplastic response of structures for intense local heating

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

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

    PubMed

    Geiger, Philipp; Dellago, Christoph

    2013-10-28

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

  13. 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.

  14. Impact of scale dependent bias and nonlinear structure growth on the integrated Sachs-Wolfe effect: Angular power spectra

    SciTech Connect

    Smith, Robert E.; Hernandez-Monteagudo, Carlos; Seljak, Uros

    2009-09-15

    We investigate the impact of nonlinear evolution of the gravitational potentials in the {lambda}CDM model on the integrated Sachs-Wolfe (ISW) contribution to the cosmic microwave background (CMB) temperature power spectrum, and on the cross-power spectrum of the CMB and a set of biased tracers of the mass. We use an ensemble of N-body simulations to directly follow the potentials and compare the results to analytic PT methods. The predictions from the PT match the results to high precision for k<0.2h Mpc{sup -1}. We compute the nonlinear corrections to the angular power spectrum and find them to be <10% of linear theory for l<100. These corrections are swamped by the cosmic variance. On scales l>100 the departures are more significant; however, the CMB signal is more than a factor 10{sup 3} larger at this scale. Nonlinear ISW effects therefore play no role in shaping the CMB power spectrum for l<1500. We analyze the CMB-density tracer cross spectrum using simulations and renormalized bias PT, and find good agreement. The usual assumption is that nonlinear evolution enhances the growth of structure and counteracts the linear ISW on small scales, leading to a change in sign of the CMB large-scale structure cross spectrum at small scales. However, PT analysis suggests that this trend reverses at late times when the logarithmic growth rate f=dlnD/dlna<0.5 or {omega}{sub m}(z)<0.3. Numerical results confirm these expectations and we find no sign change in ISW large-scale structure cross power for low redshifts. Corrections due to nonlinearity and scale dependence of the bias are found to be <10% for l<100, and are therefore below the signal to noise of the current and future measurements. Finally, we estimate the cross-correlation coefficient between the CMB and halos and show that it can be made to match that for the dark matter and CMB to within 5% for thin redshift shells, thus mitigating the need to model bias evolution.

  15. 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

  16. Clipping the cosmos: the bias and bispectrum of large scale structure.

    PubMed

    Simpson, Fergus; James, J Berian; Heavens, Alan F; Heymans, Catherine

    2011-12-30

    A large fraction of the information collected by cosmological surveys is simply discarded to avoid length scales which are difficult to model theoretically. We introduce a new technique which enables the extraction of useful information from the bispectrum of galaxies well beyond the conventional limits of perturbation theory. Our results strongly suggest that this method increases the range of scales where the relation between the bispectrum and power spectrum in tree-level perturbation theory may be applied, from k(max) ∼ 0.1 to ∼0.7 hMpc(-1). This leads to correspondingly large improvements in the determination of galaxy bias. Since the clipped matter power spectrum closely follows the linear power spectrum, there is the potential to use this technique to probe the growth rate of linear perturbations and confront theories of modified gravity with observation.

  17. 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.

  18. Off-easy-plane antiferromagnetic spin canting in coupled FePt/NiO bilayer structure with perpendicular exchange bias

    NASA Astrophysics Data System (ADS)

    Gao, Tenghua; Itokawa, Nobuhide; Wang, Jian; Yu, Youxing; Harumoto, Takashi; Nakamura, Yoshio; Shi, Ji

    2016-08-01

    We report on the investigation of perpendicular exchange bias in FePt (001 ) /NiO (1 ¯1 ¯1 ) orthogonal exchange couple with FePt partially L 10 ordered. From initial magnetization curve measurement and magnetic domain imaging, we find that, for the as-grown bilayer structure, the FePt layer experiences a small-angle magnetization rotation when it is magnetized near to saturation in film normal direction. After field cooling, the bilayer structure shows a significant enhancement of perpendicular magnetic anisotropy, indicating the field mediated coupling between the spins across the FePt/NiO interface. According to Koon's theoretical calculation on the basis of lowest energy ferromagnetic/antiferromagnetic coupling configuration for compensated spins at antiferromagnetic side, we consider slightly slanted Ni spins at the interface off the (1 ¯1 ¯1 ) easy plane can stabilize the spin coupling between FePt and NiO and result in the observed exchange bias in this paper. This consideration was further confirmed by stripe domain width calculation.

  19. Electron-beam-induced current measurements with applied bias provide insight to locally resolved acceptor concentrations at p-n junctions

    NASA Astrophysics Data System (ADS)

    Abou-Ras, D.; Schäfer, N.; Baldaz, N.; Brunken, S.; Boit, C.

    2015-07-01

    Electron-beam-induced current (EBIC) measurements have been employed for the investigation of the local electrical properties existing at various types of electrical junctions during the past decades. In the standard configuration, the device under investigation is analyzed under short-circuit conditions. Further insight into the function of the electrical junction can be obtained when applying a bias voltage. The present work gives insight into how EBIC measurements at applied bias can be conducted at the submicrometer level, at the example of CuInSe2 solar cells. From the EBIC profiles acquired across ZnO/CdS/CuInSe2/Mo stacks exhibiting p-n junctions with different net doping densities in the CuInSe2 layers, values for the width of the space-charge region, w, were extracted. For all net doping densities, these values decreased with increasing applied voltage. Assuming a linear relationship between w2 and the applied voltage, the resulting net doping densities agreed well with the ones obtained by means of capacitance-voltage measurements.

  20. Electron-beam-induced current measurements with applied bias provide insight to locally resolved acceptor concentrations at p-n junctions

    SciTech Connect

    Abou-Ras, D. Schäfer, N.; Baldaz, N.; Brunken, S.; Boit, C.

    2015-07-15

    Electron-beam-induced current (EBIC) measurements have been employed for the investigation of the local electrical properties existing at various types of electrical junctions during the past decades. In the standard configuration, the device under investigation is analyzed under short-circuit conditions. Further insight into the function of the electrical junction can be obtained when applying a bias voltage. The present work gives insight into how EBIC measurements at applied bias can be conducted at the submicrometer level, at the example of CuInSe{sub 2} solar cells. From the EBIC profiles acquired across ZnO/CdS/CuInSe{sub 2}/Mo stacks exhibiting p-n junctions with different net doping densities in the CuInSe{sub 2} layers, values for the width of the space-charge region, w, were extracted. For all net doping densities, these values decreased with increasing applied voltage. Assuming a linear relationship between w{sup 2} and the applied voltage, the resulting net doping densities agreed well with the ones obtained by means of capacitance-voltage measurements.

  1. 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

  2. Support for a link between the local processing bias and social deficits in autism: an investigation of embedded figures test performance in non-clinical individuals.

    PubMed

    Russell-Smith, Suzanna N; Maybery, Murray T; Bayliss, Donna M; Sng, Adelln A H

    2012-11-01

    The aim of this investigation was to explore the degree to which specific subsets of autistic-like traits relate to performance on the Embedded Figures Test (Witkin et al. in A manual for the embedded figures test. Consulting Psychologists Press, Palo Alto, CA, 1971). In the first group-based investigation with this focus, students were selected for their extreme scores (either high or low) on each of the 'Social Skills' and 'Details/Patterns' factors of the Autism Spectrum Quotient (Baron-Cohen et al. in J Austim Dev Disord 31:5-17, 2001). The resulting 2 × 2 factorial design permitted examination of the degree to which the social and non-social autistic-like traits separately relate to EFT performance. Surprisingly, in two studies, superior EFT performance was found to relate only to greater social difficulty, suggesting that the local processing bias in autism may be linked specifically to the social deficits.

  3. 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

  4. 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.

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

    NASA Technical Reports Server (NTRS)

    Hoffman, Y.; Shaham, J.

    1985-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  7. Highly efficient tunable and localized on-chip electrical plasmon source using protruded metal-insulator-metal structure.

    PubMed

    Phua, Wee Kee; Akimov, Yuriy; Wu, Lin; Chu, Hong Son; Bai, Ping; Danner, Aaron

    2016-05-16

    A compact and highly efficient tunable and localized source of propagating surface plasmon-polaritons is proposed based on a protruded metal-insulator-metal (pMIM) structure. The protrusion along a segment of the pMIM forms a nanometer gap and allows a low voltage bias to generate a localized tunneling current. The tunneling current excited plasmons can be fully coupled to the metal-insulator-metal (MIM) waveguiding segment of the pMIM without leakage and propagate a long distance as the gap in the MIM waveguiding segment is much larger than the gap in the protruded segment of the pMIM. Eigenmode and numerical analyses show that by using MIM structures as a benchmark, the pMIM structure enhances the total amount of average power that is transferred from the tunneling current into the excitation of intrinsic eigenmodes of the MIM waveguiding segment. Depending on the magnitude of the applied voltage bias, the pMIM structure supports single, dual and multi modes for a typical Au-SiO2-Au design with a 500 nm-thick SiO2. Among all excited modes, the single mode operation allows highly efficient excitation of long travelling surface plasmon-polaritons (SPPs) of up to 30 µm. The electrical excitation of SPPs using pMIM structures opens up the possibility of integrating plasmon sources into nanoscale optoelectronic circuits to facilitate on-chip data communications.

  8. Highly efficient tunable and localized on-chip electrical plasmon source using protruded metal-insulator-metal structure.

    PubMed

    Phua, Wee Kee; Akimov, Yuriy; Wu, Lin; Chu, Hong Son; Bai, Ping; Danner, Aaron

    2016-05-16

    A compact and highly efficient tunable and localized source of propagating surface plasmon-polaritons is proposed based on a protruded metal-insulator-metal (pMIM) structure. The protrusion along a segment of the pMIM forms a nanometer gap and allows a low voltage bias to generate a localized tunneling current. The tunneling current excited plasmons can be fully coupled to the metal-insulator-metal (MIM) waveguiding segment of the pMIM without leakage and propagate a long distance as the gap in the MIM waveguiding segment is much larger than the gap in the protruded segment of the pMIM. Eigenmode and numerical analyses show that by using MIM structures as a benchmark, the pMIM structure enhances the total amount of average power that is transferred from the tunneling current into the excitation of intrinsic eigenmodes of the MIM waveguiding segment. Depending on the magnitude of the applied voltage bias, the pMIM structure supports single, dual and multi modes for a typical Au-SiO2-Au design with a 500 nm-thick SiO2. Among all excited modes, the single mode operation allows highly efficient excitation of long travelling surface plasmon-polaritons (SPPs) of up to 30 µm. The electrical excitation of SPPs using pMIM structures opens up the possibility of integrating plasmon sources into nanoscale optoelectronic circuits to facilitate on-chip data communications. PMID:27409887

  9. 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

  10. The perceived effectiveness of persuasive messages: questions of structure, referent, and bias.

    PubMed

    Dillard, James Price; Ye, Sun

    2008-03-01

    To gain a sense of the persuasive efficacy of a message prior to implementation of a campaign, researchers often gather judgments of perceived effectiveness (PE). At present, they do so without much knowledge of the conceptual meaning or empirical properties of PE. In the spirit of construct explication, we report a study intended to address a series of questions about PE. Using student (N = 155) and community samples (N = 100), we found the following: (a) PE is a two-dimensional judgment involving global evaluations of message impact and specific judgments of message attributes, but it may be reducible to a single second-order factor, (b) most individuals reported using more than one referent (i.e., person or group) when making PE judgments, but the choice of referents varies by message and judge, and (c) judgments of PE are biased upward as a function of the number of referents chosen. Suggestions are offered for enhancing the validity of PE judgments in formative campaign research.

  11. Structural complexity, movement bias, and metapopulation extinction risk in dendritic ecological networks

    USGS Publications Warehouse

    Campbell Grant, Evan H.

    2011-01-01

    Spatial complexity in metacommunities can be separated into 3 main components: size (i.e., number of habitat patches), spatial arrangement of habitat patches (network topology), and diversity of habitat patch types. Much attention has been paid to lattice-type networks, such as patch-based metapopulations, but interest in understanding ecological networks of alternative geometries is building. Dendritic ecological networks (DENs) include some increasingly threatened ecological systems, such as caves and streams. The restrictive architecture of dendritic ecological networks might have overriding implications for species persistence. I used a modeling approach to investigate how number and spatial arrangement of habitat patches influence metapopulation extinction risk in 2 DENs of different size and topology. Metapopulation persistence was higher in larger networks, but this relationship was mediated by network topology and the dispersal pathways used to navigate the network. Larger networks, especially those with greater topological complexity, generally had lower extinction risk than smaller and less-complex networks, but dispersal bias and magnitude affected the shape of this relationship. Applying these general results to real systems will require empirical data on the movement behavior of organisms and will improve our understanding of the implications of network complexity on population and community patterns and processes.

  12. Origin of spontaneous exchange bias in Co/NiMn bilayer structure

    NASA Astrophysics Data System (ADS)

    Akbulut, A.; Akbulut, S.; Yildiz, F.

    2016-11-01

    Spontaneous exchange bias (EB) is reported for as deposited Si/Pt(tPt)/Ni45Mn55(tAFM/Co(tFM)/Pt(30 Å) thin film system without requiring any post annealing, deposition with field or field cooling procedures. Magnetic properties of this system were investigated with respect to thicknesses of buffer Pt layer (tPt), antiferromagnetic NiMn layer (tAFM) and ferromagnetic Co layer (tFM). Exchange coupling between NiMn and Co layers enhanced considerably by increasing tPt. In order to observe a spontaneous EB in the system, Pt buffer layer must be thicker than a certain thickness, and NiMn layer must be grown directly on the buffer layer. On the other hand, significant increments in the coercive fields (HC) were reported for thinner Pt buffer layers. The thickness ranges for Co and NiMn layers were also determined to obtain spontaneous EB. This spontaneous EB is discussed to be a result of NiMn (111) texture which is induced by Pt buffer layer. Greater EB fields (HEB) are measured for the samples in the negative field direction by the effect of annealing and field cooling (from 400 K to 300 K at 2 kOe).

  13. Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow.

    PubMed

    Nyakaana, S; Arctander, P

    1999-07-01

    A drastic decline has occurred in the size of the Uganda elephant population in the last 40 years, exacerbated by two main factors; an increase in the size of the human population and poaching for ivory. One of the attendant consequences of such a decline is a reduction in the amount of genetic diversity in the surviving populations due to increased effects of random genetic drift. Information about the amount of genetic variation within and between the remaining populations is vital for their future conservation and management. The genetic structure of the African elephant in Uganda was examined using nucleotide variation of mitochondrial control region sequences and four nuclear microsatellite loci in 72 individuals from three localities. Eleven mitochondrial DNA (mtDNA) haplotypes were observed, nine of which were geographically localized. We found significant genetic differentiation between the three populations at the mitochondrial locus while three out of the four microsatellite loci differentiated KV and QE, one locus differentiated KV and MF and no loci differentiated MF and QE. Expected heterozygosity at the four loci varied between 0.51 and 0.84 while nucleotide diversity at the mitochondrial locus was 1.4%. Incongruent patterns of genetic variation within and between populations were revealed by the two genetic systems, and we have explained these in terms of the differences in the effective population sizes of the two genomes and male-biased gene flow between populations.

  14. Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow.

    PubMed

    Nyakaana, S; Arctander, P

    1999-07-01

    A drastic decline has occurred in the size of the Uganda elephant population in the last 40 years, exacerbated by two main factors; an increase in the size of the human population and poaching for ivory. One of the attendant consequences of such a decline is a reduction in the amount of genetic diversity in the surviving populations due to increased effects of random genetic drift. Information about the amount of genetic variation within and between the remaining populations is vital for their future conservation and management. The genetic structure of the African elephant in Uganda was examined using nucleotide variation of mitochondrial control region sequences and four nuclear microsatellite loci in 72 individuals from three localities. Eleven mitochondrial DNA (mtDNA) haplotypes were observed, nine of which were geographically localized. We found significant genetic differentiation between the three populations at the mitochondrial locus while three out of the four microsatellite loci differentiated KV and QE, one locus differentiated KV and MF and no loci differentiated MF and QE. Expected heterozygosity at the four loci varied between 0.51 and 0.84 while nucleotide diversity at the mitochondrial locus was 1.4%. Incongruent patterns of genetic variation within and between populations were revealed by the two genetic systems, and we have explained these in terms of the differences in the effective population sizes of the two genomes and male-biased gene flow between populations. PMID:10447852

  15. Pulse-biased etching of Si3N4-layer in capacitively-coupled plasmas for nano-scale patterning of multi-level resist structures.

    PubMed

    Lee, Hyelim; Kim, Sechan; Choi, Gyuhyun; Lee, Nae-Eung

    2014-12-01

    Pulse-biased plasma etching of various dielectric layers is investigated for patterning nano-scale, multi-level resist (MLR) structures composed of multiple layers via dual-frequency, capacitively-coupled plasmas (CCPs). We compare the effects of pulse and continuous-wave (CW) biasing on the etch characteristics of a Si3N4 layer in CF4/CH2F2/O2/Aretch chemistries using a dual-frequency, superimposed CCP system. Pulse-biasing conditions using a low-frequency power source of 2 MHz were varied by controlling duty ratio, period time, power, and the gas flow ratio in the plasmas generated by the 27.12 MHz high-frequency power source. Application of pulse-biased plasma etching significantly affected the surface chemistry of the etched Si3N4 surfaces, and thus modified the etching characteristics of the Si3N4 layer. Pulse-biased etching was successfully applied to patterning of the nano-scale line and space pattern of Si3N4 in the MLR structure of KrF photoresist/bottom anti-reflected coating/SiO2/amorphous carbon layer/Si3N4. Pulse-biased etching is useful for tuning the patterning of nano-scale dielectric hard-mask layers in MLR structures. PMID:25971085

  16. Accounting for selection bias in species distribution models: An econometric approach on forested trees based on structural modeling

    NASA Astrophysics Data System (ADS)

    Ay, Jean-Sauveur; Guillemot, Joannès; Martin-StPaul, Nicolas K.; Doyen, Luc; Leadley, Paul

    2015-04-01

    Species distribution models (SDMs) are widely used to study and predict the outcome of global change on species. In human dominated ecosystems the presence of a given species is the result of both its ecological suitability and human footprint on nature such as land use choices. Land use choices may thus be responsible for a selection bias in the presence/absence data used in SDM calibration. We present a structural modelling approach (i.e. based on structural equation modelling) that accounts for this selection bias. The new structural species distribution model (SSDM) estimates simultaneously land use choices and species responses to bioclimatic variables. A land use equation based on an econometric model of landowner choices was joined to an equation of species response to bioclimatic variables. SSDM allows the residuals of both equations to be dependent, taking into account the possibility of shared omitted variables and measurement errors. We provide a general description of the statistical theory and a set of application on forested trees over France using databases of climate and forest inventory at different spatial resolution (from 2km to 8 km). We also compared the output of the SSDM with outputs of a classical SDM in term of bioclimatic response curves and potential distribution under current climate. According to the species and the spatial resolution of the calibration dataset, shapes of bioclimatic response curves the modelled species distribution maps differed markedly between the SSDM and classical SDMs. The magnitude and directions of these differences were dependent on the correlations between the errors from both equations and were highest for higher spatial resolutions. A first conclusion is that the use of classical SDMs can potentially lead to strong miss-estimation of the actual and future probability of presence modelled. Beyond this selection bias, the SSDM we propose represents a crucial step to account for economic constraints on tree

  17. Local thermal properties of the crust and thermochronometric data - how much can we bias the calculated denudation amount?

    NASA Astrophysics Data System (ADS)

    Łuszczak, Katarzyna; Persano, Cristina; Braun, Jean; Stuart, Finlay

    2016-04-01

    Low temperature thermochronometers are mainly used to decipher crustal denudation histories. However, these methods provide cooling paths that can be confidently translated into denudation rates only if the geothermal gradient at the time of cooling is known. As past geothermal gradients cannot be directly measured, they can be sometimes estimated from the thermochronometric data, when borehole data or vertical profiles are available. In all the other cases, our knowledge of the spatial and temporal variation of the geothermal gradient is limited. It is common practice in many thermochronometric studies to calculate the amounts and rates of denudation through time assuming a constant, average present-day value for the geothermal gradient. In this study, using 1D and 3D (Pecube) models, we have investigated the impact of crustal heat production and thermal conductivity (κ) on the estimated values of denudation, taking central west Britain as our case study. In this region, the apatite fission track (AFT) ages describe a characteristic U-shape pattern with early Cenozoic ages in the English Lake District and older, up to 200 Ma ages northwards in S Scotland, and southwards in N Wales. This pattern, which could be referred to a difficult to justify localized, differential denudation, can actually be best explained as an effect of the spatially variable heat production. The insulating effect of low thermal conductivity Upper Mesozoic sedimentary rocks, composed largely by chalk, increases the palaeogeothermal gradient and reduces the amounts of denudation, especially in the Lake District, where a heat productive granite batholith increases the local heat flow. The observed AFT age pattern may be, therefore, explained without any significant variation of early Cenozoic denudation across central west Britain. If the thermal proprieties of the crust are not taken into account, denudation in the Lake District will be overestimated by a factor of 1.5-2.0 and the mechanisms

  18. Assessing the local identifiability of probabilistic knowledge structures.

    PubMed

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

    2012-12-01

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

  19. 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.

  20. 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.

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

    PubMed

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

    2004-08-01

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

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

    PubMed

    Amirikian, Bagrat

    2005-06-01

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

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

    SciTech Connect

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

    2012-05-03

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

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

    PubMed

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

    2004-08-01

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

  5. 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.

  6. Electron transport in electrically biased inverse parabolic double-barrier structure

    NASA Astrophysics Data System (ADS)

    M, Bati; S, Sakiroglu; I, Sokmen

    2016-05-01

    A theoretical study of resonant tunneling is carried out for an inverse parabolic double-barrier structure subjected to an external electric field. Tunneling transmission coefficient and density of states are analyzed by using the non-equilibrium Green’s function approach based on the finite difference method. It is found that the resonant peak of the transmission coefficient, being unity for a symmetrical case, reduces under the applied electric field and depends strongly on the variation of the structure parameters.

  7. Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates

    USGS Publications Warehouse

    Roffler, Gretchen H.; Talbot, Sandra L.; Luikart, Gordon; Sage, George K.; Pilgrim, Kristy L.; Adams, Layne G.; Schwartz, Michael K.

    2014-01-01

    Identifying patterns of fine-scale genetic structure in natural populations can advance understanding of critical ecological processes such as dispersal and gene flow across heterogeneous landscapes. Alpine ungulates generally exhibit high levels of genetic structure due to female philopatry and patchy configuration of mountain habitats. We assessed the spatial scale of genetic structure and the amount of gene flow in 301 Dall’s sheep (Ovis dalli dalli) at the landscape level using 15 nuclear microsatellites and 473 base pairs of the mitochondrial (mtDNA) control region. Dall’s sheep exhibited significant genetic structure within contiguous mountain ranges, but mtDNA structure occurred at a broader geographic scale than nuclear DNA within the study area, and mtDNA structure for other North American mountain sheep populations. No evidence of male-mediated gene flow or greater philopatry of females was observed; there was little difference between markers with different modes of inheritance (pairwise nuclear DNA F ST = 0.004–0.325; mtDNA F ST = 0.009–0.544), and males were no more likely than females to be recent immigrants. Historical patterns based on mtDNA indicate separate northern and southern lineages and a pattern of expansion following regional glacial retreat. Boundaries of genetic clusters aligned geographically with prominent mountain ranges, icefields, and major river valleys based on Bayesian and hierarchical modeling of microsatellite and mtDNA data. Our results suggest that fine-scale genetic structure in Dall’s sheep is influenced by limited dispersal, and structure may be weaker in populations occurring near ancestral levels of density and distribution in continuous habitats compared to other alpine ungulates that have experienced declines and marked habitat fragmentation.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    SciTech Connect

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

    2002-07-01

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

  10. Protein structure prediction with local adjust tabu search algorithm

    PubMed Central

    2014-01-01

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

  11. Influence of 8-Oxoguanosine on the Fine Structure of DNA Studied with Biasing-Potential Replica Exchange Simulations

    SciTech Connect

    Kara, Mahmut; Zacharias, Martin W.

    2013-03-05

    Chemical modification or radiation can cause DNA damage, which plays a crucial role for mutagenesis of DNA, carcinogenesis, and aging. DNA damage can also alter the fine structure of DNA that may serve as a recognition signal for DNA repair enzymes. A new, advanced sampling replica-exchange method has been developed to specifically enhance the sampling of conformational substates in duplex DNA during molecular dynamics (MD) simulations. The approach employs specific biasing potentials acting on pairs of pseudodihedral angles of the nucleic acid backbone that are added in the replica simulations to promote transitions of the most common substates of the DNA backbone. The sampled states can exchange with a reference simulation under the control of the original force field. The application to 7,8-dihydro-8oxo-guanosine, one of the most common oxidative damage in DNA indicated better convergence of sampled states during 10 ns simulations compared to 20 times longer standard MD simulations. It is well suited to study systematically the fine structure and dynamics of large nucleic acids under realistic conditions, including explicit solvent and ions. The biasing potential-replica exchange MD simulations indicated significant differences in the population of nucleic acid backbone substates in the case of 7,8-dihydro-8oxo-guanosine compared to a regular guanosine in the same sequence context. This concerns both the ratio of the B-DNA substates BI and BII associated with the backbone dihedral angles ε and z but also coupled changes in the backbone dihedral angles a and g. Such differences may play a crucial role in the initial recognition of damaged DNA by repair enzymes.

  12. Influence of 8-Oxoguanosine on the Fine Structure of DNA Studied with Biasing-Potential Replica Exchange Simulations

    PubMed Central

    Kara, Mahmut; Zacharias, Martin

    2013-01-01

    Chemical modification or radiation can cause DNA damage, which plays a crucial role for mutagenesis of DNA, carcinogenesis, and aging. DNA damage can also alter the fine structure of DNA that may serve as a recognition signal for DNA repair enzymes. A new, advanced sampling replica-exchange method has been developed to specifically enhance the sampling of conformational substates in duplex DNA during molecular dynamics (MD) simulations. The approach employs specific biasing potentials acting on pairs of pseudodihedral angles of the nucleic acid backbone that are added in the replica simulations to promote transitions of the most common substates of the DNA backbone. The sampled states can exchange with a reference simulation under the control of the original force field. The application to 7,8-dihydro-8oxo-guanosine, one of the most common oxidative damage in DNA indicated better convergence of sampled states during 10 ns simulations compared to 20 times longer standard MD simulations. It is well suited to study systematically the fine structure and dynamics of large nucleic acids under realistic conditions, including explicit solvent and ions. The biasing potential-replica exchange MD simulations indicated significant differences in the population of nucleic acid backbone substates in the case of 7,8-dihydro-8oxo-guanosine compared to a regular guanosine in the same sequence context. This concerns both the ratio of the B-DNA substates BI and BII associated with the backbone dihedral angles ε and ζ but also coupled changes in the backbone dihedral angles α and γ. Such differences may play a crucial role in the initial recognition of damaged DNA by repair enzymes. PMID:23473492

  13. Origin of the vertebrate body plan via mechanically biased conservation of regular geometrical patterns in the structure of the blastula.

    PubMed

    Edelman, David B; McMenamin, Mark; Sheesley, Peter; Pivar, Stuart

    2016-09-01

    We present a plausible account of the origin of the archetypal vertebrate bauplan. We offer a theoretical reconstruction of the geometrically regular structure of the blastula resulting from the sequential subdivision of the egg, followed by mechanical deformations of the blastula in subsequent stages of gastrulation. We suggest that the formation of the vertebrate bauplan during development, as well as fixation of its variants over the course of evolution, have been constrained and guided by global mechanical biases. Arguably, the role of such biases in directing morphology-though all but neglected in previous accounts of both development and macroevolution-is critical to any substantive explanation for the origin of the archetypal vertebrate bauplan. We surmise that the blastula inherently preserves the underlying geometry of the cuboidal array of eight cells produced by the first three cleavages that ultimately define the medial-lateral, dorsal-ventral, and anterior-posterior axes of the future body plan. Through graphical depictions, we demonstrate the formation of principal structures of the vertebrate body via mechanical deformation of predictable geometrical patterns during gastrulation. The descriptive rigor of our model is supported through comparisons with previous characterizations of the embryonic and adult vertebrate bauplane. Though speculative, the model addresses the poignant absence in the literature of any plausible account of the origin of vertebrate morphology. A robust solution to the problem of morphogenesis-currently an elusive goal-will only emerge from consideration of both top-down (e.g., the mechanical constraints and geometric properties considered here) and bottom-up (e.g., molecular and mechano-chemical) influences. PMID:27392530

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  17. Bias and Efficiency in Structural Equation Modeling: Maximum Likelihood versus Robust Methods

    ERIC Educational Resources Information Center

    Zhong, Xiaoling; Yuan, Ke-Hai

    2011-01-01

    In the structural equation modeling literature, the normal-distribution-based maximum likelihood (ML) method is most widely used, partly because the resulting estimator is claimed to be asymptotically unbiased and most efficient. However, this may not hold when data deviate from normal distribution. Outlying cases or nonnormally distributed data,…

  18. Sample Size Requirements for Structural Equation Models: An Evaluation of Power, Bias, and Solution Propriety

    ERIC Educational Resources Information Center

    Wolf, Erika J.; Harrington, Kelly M.; Clark, Shaunna L.; Miller, Mark W.

    2013-01-01

    Determining sample size requirements for structural equation modeling (SEM) is a challenge often faced by investigators, peer reviewers, and grant writers. Recent years have seen a large increase in SEMs in the behavioral science literature, but consideration of sample size requirements for applied SEMs often relies on outdated rules-of-thumb.…

  19. Localized structural health monitoring via transmission zero invariance

    NASA Astrophysics Data System (ADS)

    Reich, Gregory William

    2000-11-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

    Kanchanawong, Pakorn; Waterman, Clare M.

    2013-01-01

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

  3. Tailoring exchange bias through chemical order in epitaxial FePt3 films

    NASA Astrophysics Data System (ADS)

    Saerbeck, T.; Zhu, H.; Lott, D.; Lee, H.; LeClair, P. R.; Mankey, G. J.; Stampfl, A. P. J.; Klose, F.

    2013-07-01

    Intentional introduction of chemical disorder into mono-stoichiometric epitaxial FePt3 films allows to create a ferro-/antiferromagnetic two-phase system, which shows a pronounced and controllable exchange bias effect. In contrast to conventional exchange bias systems, granular magnetic interfaces are created within the same crystallographic structure by local variation of chemical order. The amount of the exchange bias can be controlled by the relative amount and size of ferromagnetic and antiferromagnetic volume fractions and the interface between them. The tailoring of the magnetic composition alone, without affecting the chemical and structural compositions, opens the way to study granular magnetic exchange bias concepts separated from structural artifacts.

  4. 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.

  5. Optical spectrum and local lattice structure for ruby

    NASA Astrophysics Data System (ADS)

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

    2007-01-01

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

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

    PubMed

    Preishuber-Pflügl, Florian; Wilkening, Martin

    2016-06-01

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

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

    PubMed

    Preishuber-Pflügl, Florian; Wilkening, Martin

    2016-06-01

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

  8. 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.

  9. Thresholds of surface codes on the general lattice structures suffering biased error and loss

    SciTech Connect

    Tokunaga, Yuuki; Fujii, Keisuke

    2014-12-04

    A family of surface codes with general lattice structures is proposed. We can control the error tolerances against bit and phase errors asymmetrically by changing the underlying lattice geometries. The surface codes on various lattices are found to be efficient in the sense that their threshold values universally approach the quantum Gilbert-Varshamov bound. We find that the error tolerance of the surface codes depends on the connectivity of the underlying lattices; the error chains on a lattice of lower connectivity are easier to correct. On the other hand, the loss tolerance of the surface codes exhibits an opposite behavior; the logical information on a lattice of higher connectivity has more robustness against qubit loss. As a result, we come upon a fundamental trade-off between error and loss tolerances in the family of surface codes with different lattice geometries.

  10. Biased predecision processing.

    PubMed

    Brownstein, Aaron L

    2003-07-01

    Decision makers conduct biased predecision processing when they restructure their mental representation of the decision environment to favor one alternative before making their choice. The question of whether biased predecision processing occurs has been controversial since L. Festinger (1957) maintained that it does not occur. The author reviews relevant research in sections on theories of cognitive dissonance, decision conflict, choice certainty, action control, action phases, dominance structuring, differentiation and consolidation, constructive processing, motivated reasoning, and groupthink. Some studies did not find evidence of biased predecision processing, but many did. In the Discussion section, the moderators are summarized and used to assess the theories. PMID:12848220

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  13. 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.

  14. 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.

  15. 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.

  16. Exchange scattering as the driving force for ultrafast all-optical and bias-controlled reversal in ferrimagnetic metallic structures

    NASA Astrophysics Data System (ADS)

    Kalashnikova, A. M.; Kozub, V. I.

    2016-02-01

    Experimentally observed ultrafast all-optical magnetization reversal in ferrimagnetic metals and heterostructures based on antiferromagnetically coupled ferromagnetic d - and f -metallic layers relies on intricate energy and angular momentum flow between electrons, phonons, and spins. Here we treat the problem of angular momentum transfer in the course of ultrafast laser-induced dynamics in a ferrimagnetic metallic system using microscopical approach based on the system of rate equations. We show that the magnetization reversal is supported by a coupling of d and f subsystems to delocalized s or p electrons. The latter can transfer spin between the two subsystems in an incoherent way owing to the (s ;p )-(d ;f ) exchange scattering. Since the effect of the external excitation in this process is reduced to the transient heating of the mobile electron subsystem, we also discuss the possibility to trigger the magnetization reversal by applying a voltage bias pulse to antiferromagnetically coupled metallic ferromagnetic layers embedded in point contact or tunneling structures. We argue that such devices allow controlling reversal with high accuracy. We also suggest using the anomalous Hall effect to register the reversal, thus playing a role of reading probes.

  17. Population genetic structure of Cichla pleiozona (Perciformes: Cichlidae) in the Upper Madera basin (Bolivian Amazon): sex-biased dispersal?

    PubMed

    Carvajal-Vallejos, F M; Duponchelle, F; Ballivian, J P Torrico; Hubert, Nicolas; Rodríguez, J Nuñez; Berrebi, P; Cornejo, S Sirvas; Renno, J-F

    2010-12-01

    This study investigates the population structure of the Tucunaré (Cichla pleiozona) in the Bolivian Amazon (Upper Madera) by using nuclear (EPIC-PCR, 67 individuals) and mitochondrial (Control Region, 41 published and 76 new sequences) DNA analyses, in relation with ecological (water quality: muddy, clear and mix) and geographic factors. Our analyses of both markers showed the highest diversity in clear waters (Yata, Middle and Upper Iténez), and the existence of two populations in muddy waters (Sécure and Ichilo) and one in mix waters (Manuripi). On the other hand, mitochondrial analyses identified three populations in clear waters where nuclear analyses identified a panmictic population. The highest diversity observed in the Yata-Iténez system suggests that an aquatic refuge occurred during the past in this area. The possible explanations for the observed discrepancy between nuclear and mitochondrial markers are discussed, and a sex-biased dispersal seems to be the most plausible hypothesis in the light of the available information and field observations. PMID:20817108

  18. Exchange bias and crystal structure of epitaxial (111) FePt/BiFeO{sub 3} sputtered thin films

    SciTech Connect

    Chiu, Shang-Jui; Hsiao, Shih-Nan Lee, Hsin-Yi; Huang, Li-Chun; Yu, Ge-Ping; Chang, Huang-Wei

    2014-05-07

    Crystallographic structure and magnetic properties of the epitaxial FePt (10 nm)/BiFeO{sub 3} (BFO) (10 nm) bilayer films grown on (111) SrTiO{sub 3} (STO) substrates with different deposition temperatures of FePt layers (T{sub d}) have been investigated using magnetron sputtering. Out-of-plane radial scan along (111) direction and off-normal (002) azimuthal scan, determined by synchrotron radiation x-ray diffractometry, evidence that the FePt layers were well epitaxially grown on the (111) epitaxial BFO layers for the samples with T{sub d} = 300 and 700 °C. On the contrary, for the bilayer films with T{sub d} = 500 °C, the FePt and BFO layers exhibit low epitaxial quality. Large in-plane exchange bias field (H{sub eb}) values of 45–412 Oe are obtained for the L1{sub 0}-FePt/BFO bilayer films measured with applied field of 12 kOe at room temperature. The change of effective interfacial area, observed by scanning electron microscopy, between FePt island-like particles and BFO continuous layers, and epitaxiality of the bilayer were correlated with the evolution of H{sub eb}.

  19. Long-distance correlation and zonal flow structures induced by mean ExB shear flows in the biasing H-mode at TEXTOR

    SciTech Connect

    Xu, Y.; Jachmich, S.; Weynants, R. R.; Schoor, M. van; Vergote, M.; Kraemer-Flecken, A.; Schmitz, O.; Unterberg, B.

    2009-11-15

    Long-distance toroidal correlations of potential and density fluctuations have been investigated at the TEXTOR tokamak [H. Soltwisch et al., Plasma Phys. Controlled Fusion 26, 23 (1984)] in edge electrode-biasing experiments. During the biasing-induced H-mode, the dc ExB shear flow triggers a zonal flow structure and hence long-distance correlation in potential fluctuations, whereas for density fluctuations there is nearly no correlation. These results indicate an intimate interaction between the mean and zonal flows, and the significance of long range correlations in improved-confinement regimes.

  20. Local structures of copper-doped ZnO films

    SciTech Connect

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

    2009-01-05

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

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

    PubMed

    Lee, Hui Sun; Im, Wonpil

    2012-10-22

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

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

    PubMed Central

    Qi, Dong; Innes, Roger W.

    2013-01-01

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

  3. Bias-induced offset effect overlapped on bipolar-resistance effect based on Co/SiO{sub 2}/Si structure

    SciTech Connect

    Yu Chongqi; Wang Hui

    2010-07-26

    Recent study shows the resistance of a metal-oxide-semiconductor (MOS) structure can be controlled by a laser via a bipolar-resistance effect (BRE). Based on this BRE phenomenon, we find an overlapped offset effect which is induced by an external bias applying to the structure. This offset effect features with a moveable equilibrium point of BRE, suggesting a combined control to the resistance and adding functionality to the MOS-based photoelectric devices.

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

    NASA Astrophysics Data System (ADS)

    Ngai, King-Wah

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

  5. Seismic Structure of Villarrica Volcano obtained through Local Tomography

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed Central

    Rose, Dominic; Backofen, Rolf

    2012-01-01

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

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

    PubMed

    Höglund, Jacob; Shorey, Lisa

    2003-09-01

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

  8. 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

  9. Bias-polarity-dependent resistance switching in W/SiO2/Pt and W/SiO2/Si/Pt structures

    PubMed Central

    Jiang, Hao; Li, Xiang Yuan; Chen, Ran; Shao, Xing Long; Yoon, Jung Ho; Hu, Xiwen; Hwang, Cheol Seong; Zhao, Jinshi

    2016-01-01

    SiO2 is the most significantly used insulator layer in semiconductor devices. Its functionality was recently extended to resistance switching random access memory, where the defective SiO2 played an active role as the resistance switching (RS) layer. In this report, the bias-polarity-dependent RS behaviours in the top electrode W-sputtered SiO2-bottom electrode Pt (W/SiO2/Pt) structure were examined based on the current-voltage (I-V) sweep. When the memory cell was electroformed with a negative bias applied to the W electrode, the memory cell showed a typical electronic switching mechanism with a resistance ratio of ~100 and high reliability. For electroforming with opposite bias polarity, typical ionic-defect-mediated (conducting filament) RS was observed with lower reliability. Such distinctive RS mechanisms depending on the electroforming-bias polarity could be further confirmed using the light illumination study. Devices with similar electrode structures with a thin intervening Si layer between the SiO2 and Pt electrode, to improve the RS film morphology (root-mean-squared roughness of ~1.7 nm), were also fabricated. Their RS performances were almost identical to that of the single-layer SiO2 sample with very high roughness (root-mean-squared roughness of ~10 nm), suggesting that the reported RS behaviours were inherent to the material property. PMID:26916050

  10. Bias-polarity-dependent resistance switching in W/SiO2/Pt and W/SiO2/Si/Pt structures

    NASA Astrophysics Data System (ADS)

    Jiang, Hao; Li, Xiang Yuan; Chen, Ran; Shao, Xing Long; Yoon, Jung Ho; Hu, Xiwen; Hwang, Cheol Seong; Zhao, Jinshi

    2016-02-01

    SiO2 is the most significantly used insulator layer in semiconductor devices. Its functionality was recently extended to resistance switching random access memory, where the defective SiO2 played an active role as the resistance switching (RS) layer. In this report, the bias-polarity-dependent RS behaviours in the top electrode W-sputtered SiO2-bottom electrode Pt (W/SiO2/Pt) structure were examined based on the current-voltage (I-V) sweep. When the memory cell was electroformed with a negative bias applied to the W electrode, the memory cell showed a typical electronic switching mechanism with a resistance ratio of ~100 and high reliability. For electroforming with opposite bias polarity, typical ionic-defect-mediated (conducting filament) RS was observed with lower reliability. Such distinctive RS mechanisms depending on the electroforming-bias polarity could be further confirmed using the light illumination study. Devices with similar electrode structures with a thin intervening Si layer between the SiO2 and Pt electrode, to improve the RS film morphology (root-mean-squared roughness of ~1.7 nm), were also fabricated. Their RS performances were almost identical to that of the single-layer SiO2 sample with very high roughness (root-mean-squared roughness of ~10 nm), suggesting that the reported RS behaviours were inherent to the material property.

  11. Structural modification of nanocrystalline diamond films via positive/negative bias enhanced nucleation and growth processes for improving their electron field emission properties

    SciTech Connect

    Saravanan, A.; Huang, B. R.; Sankaran, K. J.; Tai, N. H.; Keiser, G.; Kurian, J.; Lin, I. N.

    2015-06-07

    Electron field emission (EFE) properties of nanocrystalline diamond (NCD) films synthesized by the bias-enhanced growth (beg) process under different bias voltages were investigated. The induction of the nanographitic phases is presumed to be the prime factor in enhancing the EFE properties of negative biased NCD films. Transmission electron microscopic investigations reveal that a negative bias voltage of −300 V increases the rate of growth for NCD films with the size of the grains changing from nano to ultranano size. This effect also is accompanied by the induction of nanographitic filaments in the grain boundaries of the films. The turn-on field (E{sub 0}) for the EFE process then effectively gets reduced. The EFE process of the beg-NCD{sub −300V} films can be turned on at E{sub 0} = 3.86 V/μm, and the EFE current density achieved is 1.49 mA/cm{sup 2} at an applied field of 7.85 V/μm. On the other hand, though a positive-bias beg process (+200 V) results in the reduction of grain size, it does not induce sufficient nanographitic phases to lower the E{sub 0} value of the EFE process. Moreover, the optical emission spectroscopic investigation indicates that one of the primary causes that changes the granular structure of the NCD films is the increase in the proportion of C{sub 2} and CH species induced in the growing plasma. The polarity of the bias voltage is of less importance in the microstructural evolution of the films.

  12. First principle simulations of a bias-dependent electrochemical cell

    NASA Astrophysics Data System (ADS)

    Pedroza, Luana; Brandimarte, Pedro; Fernandez-Serra, Marivi; Rocha, Alexandre R.

    Understanding the local structure of water molecules at the interfaces of metallic electrodes is a key problem in many electrochemical problems. Notably the system is under an external potential bias, which makes the task of simulating this setup difficult. To correctly compute the effect of an external bias potential applied to electrodes, we combine density functional theory and non-equilibrium Green's functions methods, with and without van der Waals interactions. In this work, we apply this methodology to study the electronic properties and forces of water molecules at the interface of different metallic electrodes. We find that the water molecule is sensitive to the sign and magnitude of the applied bias. We also show that it changes the position and orientation of the most stable configuration indicating that the external bias plays an important role in the structural properties of the interface. The authors thank FAPESP and CNPq for financial support.

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

    PubMed

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

    2012-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Wang, Yina; Huang, Zhen-li

    2016-07-01

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

  15. Giant low-frequency multipeak self-biased magnetoelectric properties in four-phase structure with stepped ultrasonic horn

    NASA Astrophysics Data System (ADS)

    Li, Jie; Lu, Caijiang

    2016-11-01

    This paper develops a self-biased magnetoelectric (ME) heterostructure FeCuNbSiB/terfenol-d/ultrasonic-horn/PZT by sandwiching a piezoelectric Pb(Zr,Ti)O3 (PZT) plate and a magnetization-graded FeCuNbSiB/terfenol-d layer on a rectangular-stepped ultrasonic horn substrate. The rectangular-stepped ultrasonic horn substrate severs as the resonance frequency determining element of the ME heterostructure, converges and amplifies the vibration excited by the magnetization-graded FeCuNbSiB/terfenol-d layer. The experiments show that fifteen large peaks of ME response with magnitudes of 0.2–7.5 V/(cm·Oe) in 0.5–50 kHz range are observed at zero-biased magnetic field. This demonstrates that the proposed multi-peak self-biased heterostructure may be useful for multifunctional devices for multi-frequency operation.

  16. 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)

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

    PubMed

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

    2011-11-01

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

  18. 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.

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

    PubMed

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

    2011-11-01

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

  20. Direct imaging of thermally-activated grain-boundary diffusion in Cu/Co/IrMn/Pt exchange-bias structures using atom-probe tomography

    SciTech Connect

    Letellier, F.; Lardé, R.; Le Breton, J.-M.; Akmaldinov, K.; Auffret, S.; Dieny, B.; Baltz, V.

    2014-11-28

    Magnetic devices are often subject to thermal processing steps, such as field cooling to set exchange bias and annealing to crystallize amorphous magnetic electrodes. These processing steps may result in interdiffusion and the subsequent deterioration of magnetic properties. In this study, we investigated thermally-activated diffusion in Cu/Co/IrMn/Pt exchange biased polycrystalline thin-film structures using atom probe tomography. Images taken after annealing at 400 °C for 60 min revealed Mn diffusion into Co grains at the Co/IrMn interface and along Pt grain boundaries for the IrMn/Pt stack, i.e., a Harrison type C regime. Annealing at 500 °C showed further Mn diffusion into Co grains. At the IrMn/Pt interface, annealing at 500 °C led to a type B behavior since Mn diffusion was detected both along Pt grain boundaries and also into Pt grains. The deterioration of the films' exchange bias properties upon annealing was correlated to the observed diffusion. In particular, the topmost Pt capping layer thickness turned out to be crucial since a faster deterioration of the exchange bias properties for thicker caps was observed. This is consistent with the idea that Pt acts as a getter for Mn, drawing Mn out of the IrMn layer.

  1. Direct imaging of thermally-activated grain-boundary diffusion in Cu/Co/IrMn/Pt exchange-bias structures using atom-probe tomography

    NASA Astrophysics Data System (ADS)

    Letellier, F.; Lechevallier, L.; Lardé, R.; Le Breton, J.-M.; Akmaldinov, K.; Auffret, S.; Dieny, B.; Baltz, V.

    2014-11-01

    Magnetic devices are often subject to thermal processing steps, such as field cooling to set exchange bias and annealing to crystallize amorphous magnetic electrodes. These processing steps may result in interdiffusion and the subsequent deterioration of magnetic properties. In this study, we investigated thermally-activated diffusion in Cu/Co/IrMn/Pt exchange biased polycrystalline thin-film structures using atom probe tomography. Images taken after annealing at 400 °C for 60 min revealed Mn diffusion into Co grains at the Co/IrMn interface and along Pt grain boundaries for the IrMn/Pt stack, i.e., a Harrison type C regime. Annealing at 500 °C showed further Mn diffusion into Co grains. At the IrMn/Pt interface, annealing at 500 °C led to a type B behavior since Mn diffusion was detected both along Pt grain boundaries and also into Pt grains. The deterioration of the films' exchange bias properties upon annealing was correlated to the observed diffusion. In particular, the topmost Pt capping layer thickness turned out to be crucial since a faster deterioration of the exchange bias properties for thicker caps was observed. This is consistent with the idea that Pt acts as a getter for Mn, drawing Mn out of the IrMn layer.

  2. STRUCTURAL AND HIDDEN BARRIERS TO A LOCAL PRIMARY HEALTH CARE INFRASTRUCTURE: AUTONOMY, DECISIONS ABOUT PRIMARY HEALTH CARE, AND THE CENTRALITY AND SIGNIFICANCE OF POWER

    PubMed Central

    Freed, Christopher R.; Hansberry, Shantisha T.; Arrieta, Martha I.

    2014-01-01

    Purpose: To examine a local primary health care infrastructure and the reality of primary health care from the perspective of residents of a small, urban community in the southern United States. Methodology/approach: Data derive from 13 semi-structured focus groups, plus three semi-structured interviews, and were analyzed inductively consistent with a grounded theory approach. Findings: Structural barriers to the local primary health care infrastructure include transportation, clinic and appointment wait time, and co-payments and health insurance. Hidden barriers consist of knowledge about local health care services, non-physician gatekeepers, and fear of medical care. Community residents have used home remedies and the emergency department at the local academic medical center to manage these structural and hidden barriers. Research limitations/implications: Findings might not generalize to primary health care infrastructures in other communities, respondent perspectives can be biased, and the data are subject to various interpretations and conceptual and thematic frameworks. Nevertheless, the structural and hidden barriers to the local primary health care infrastructure have considerably diminished the autonomy community residents have been able to exercise over their decisions about primary health care, ultimately suggesting that efforts concerned with increasing the access of medically underserved groups to primary health care in local communities should recognize the centrality and significance of power. Originality/value: This study addresses a gap in the sociological literature regarding the impact of specific barriers to primary health care among medically underserved groups. PMID:24532864

  3. Direct observation of bias-dependence potential distribution in metal/HfO{sub 2} gate stack structures by hard x-ray photoelectron spectroscopy under device operation

    SciTech Connect

    Yamashita, Y.; Yoshikawa, H.; Kobayashi, K.; Chikyo, T.

    2014-01-28

    Although gate stack structures with high-k materials have been extensively investigated, there are some issues to be solved for the formation of high quality gate stack structures. In the present study, we employed hard x-ray photoelectron spectroscopy in operating devices. This method allows us to investigate bias dependent electronic states, while keeping device structures intact. Using this method, we have investigated electronic states and potential distribution in gate metal/HfO{sub 2} gate stack structures under device operation. Analysis of the core levels shifts as a function of the bias voltage indicated that a potential drop occurred at the Pt/HfO{sub 2} interface for a Pt/HfO{sub 2} gate structure, while a potential gradient was not observed at the Ru/HfO{sub 2} interface for a Ru/HfO{sub 2} gate structure. Angle resolved photoelectron spectroscopy revealed that a thicker SiO{sub 2} layer was formed at the Pt/HfO{sub 2} interface, indicating that the origin of potential drop at Pt/HfO{sub 2} interface is formation of the thick SiO{sub 2} layer at the interface. The formation of the thick SiO{sub 2} layer at the metal/high-k interface might concern the Fermi level pinning, which is observed in metal/high-k gate stack structures.

  4. Exchange bias in Fe/Cr double superlattices.

    SciTech Connect

    Jiang, J. S.; Felcher, G. P.; Inomata, A.; Goyette, R.; Nelson, C.; Bader, S. D.

    1999-11-30

    Utilizing the oscillatory interlayer exchange coupling in Fe/Cr superlattices, we have constructed ''double superlattice'' structures where a ferromagnetic (F) and an antiferromagnetic (AF) Fe/Cr superlattice are coupled through a Cr spacer. The minor hysteresis loops in the magnetization are shifted from zero field, i.e., the F superlattice is exchange biased by the AF one. The double superlattices are sputter-deposited with (211) epitaxy and possess uniaxial in-plane magnetic anisotropy. The magnitude of the bias field is satisfactorily described by the classic formula for collinear spin structures. The coherent structure and insensitivity to atomic-scale roughness makes it possible to determine the spin distribution by polarized neutron reflectivity, which confirms that the spin structure is collinear. The magnetic reversal behavior of the double superlattices suggests that a realistic model of exchange bias needs to address the process of nucleating local reverse domains.

  5. Structure-based molecular simulations reveal the enhancement of biased Brownian motions in single-headed kinesin.

    PubMed

    Kanada, Ryo; Kuwata, Takeshi; Kenzaki, Hiroo; Takada, Shoji

    2013-01-01

    Kinesin is a family of molecular motors that move unidirectionally along microtubules (MT) using ATP hydrolysis free energy. In the family, the conventional two-headed kinesin was experimentally characterized to move unidirectionally through "walking" in a hand-over-hand fashion by coordinated motions of the two heads. Interestingly a single-headed kinesin, a truncated KIF1A, still can generate a biased Brownian movement along MT, as observed by in vitro single molecule experiments. Thus, KIF1A must use a different mechanism from the conventional kinesin to achieve the unidirectional motions. Based on the energy landscape view of proteins, for the first time, we conducted a set of molecular simulations of the truncated KIF1A movements over an ATP hydrolysis cycle and found a mechanism exhibiting and enhancing stochastic forward-biased movements in a similar way to those in experiments. First, simulating stand-alone KIF1A, we did not find any biased movements, while we found that KIF1A with a large friction cargo-analog attached to the C-terminus can generate clearly biased Brownian movements upon an ATP hydrolysis cycle. The linked cargo-analog enhanced the detachment of the KIF1A from MT. Once detached, diffusion of the KIF1A head was restricted around the large cargo which was located in front of the head at the time of detachment, thus generating a forward bias of the diffusion. The cargo plays the role of a diffusional anchor, or cane, in KIF1A "walking."

  6. The impact of substrate bias on a remote plasma sputter coating process for conformal coverage of trenches and 3D structures

    NASA Astrophysics Data System (ADS)

    Brown, H. L.; Thornley, S. A.; Wakeham, S. J.; Thwaites, M. J.; Curry, R. J.; Baker, M. A.

    2015-08-01

    With the progression towards higher aspect ratios and finer topographical dimensions in many micro- and nano-systems, it is of technological importance to be able to conformally deposit thin films onto such structures. Sputtering techniques have been developed to provide such conformal coverage through a combination of coating re-sputtering and ionised physical vapour deposition (IPVD), the latter by use of a secondary plasma source or a pulsed high target power (HiPIMS). This paper reports on the use of an alternate remote plasma sputtering technique in which a high density (>1013 cm-3) magnetised plasma is used for sputter deposition, and additionally is shown to provide IPVD and a re-sputtering capability. From the substrate I-V characteristics and optical emission spectroscopy (OES) data, it is shown that remote plasma sputtering is an inherently continuous IPVD process (without the need of a secondary discharge). Through the reactive deposition of Al2O3 onto complex structures, scanning electron microscopy (SEM) and energy dispersive x-ray spectroscopy (EDX) results demonstrate that applying a negative substrate bias during film growth can result in re-sputtering of deposited material and film growth on surfaces obscured from the initial sputter flux. Using 5 : 1 (height : width) aspect ratio trenches, the substrate bias was set to 0,-245 and  -334 V. At 0 V substrate bias, the alumina coating is predominantly deposited on the horizontal surfaces; at  -344 V, it is predominantly deposited onto the side walls and at  -245 V a more uniform layer thickness is obtained over the trench. The process was optimised further by alternating the substrate bias between  -222 and  -267 V, with a 50% residence time at each voltage, yielding a more uniform conformal coverage of the 5 : 1 aspect ratio structures over large areas.

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Zhou, Jiawei; Qin, Binjie

    2011-06-01

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

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

    ERIC Educational Resources Information Center

    Irish National Association of Adult Education, Dublin.

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

  10. Effect of the bias electric field on the spectral distribution of the photodielectric effect in the Schottky-barrier structures based on the cadmium-zinc telluride crystals

    SciTech Connect

    Komar', V. K.; Puzikov, V. M.; Chugai, O. N. Nalivaiko, D. P.; Sulima, S. V.; Abashin, S. L.

    2007-06-15

    Spectral dependences of effective values of the real and imaginary parts of the low-frequency permittivity of the Cd{sub 1-x}Zn{sub x}Te crystals (x=0.12-0.16) with the Schottky barrier fabricated on the surface are measured. It is found that the boundary wavelengths of the characteristic portions of the measured dependences represented in the complex plane correspond to energies of photons, which cause the radical variations in the state of negatively charged and electrically neutral localized acceptor states. The variations in the energy spectrum of the localized states, which are determined by the magnitude and polarity of the electric bias applied to the Shottky barrier, are found.

  11. Biased Allostery.

    PubMed

    Edelstein, Stuart J; Changeux, Jean-Pierre

    2016-09-01

    G-protein-coupled receptors (GPCRs) constitute a large group of integral membrane proteins that transduce extracellular signals from a wide range of agonists into targeted intracellular responses. Although the responses can vary depending on the category of G-proteins activated by a particular receptor, responses were also found to be triggered by interactions of the receptor with β-arrestins. It was subsequently discovered that for the same receptor molecule (e.g., the β-adrenergic receptor), some agonists have a propensity to specifically favor responses by G-proteins, others by β-arrestins, as has now been extensively studied. This feature of the GPCR system is known as biased agonism and is subject to various interpretations, including agonist-induced conformational change versus selective stabilization of preexisting active conformations. Here, we explore a complete allosteric framework for biased agonism based on alternative preexisting conformations that bind more strongly, but nonexclusively, either G-proteins or β-arrestins. The framework incorporates reciprocal effects among all interacting molecules. As a result, G-proteins and β-arrestins are in steric competition for binding to the cytoplasmic surface of either the G-protein-favoring or β-arrestin-favoring GPCR conformation. Moreover, through linkage relations, the strength of the interactions of G-proteins or β-arrestins with the corresponding active conformation potentiates the apparent affinity for the agonist, effectively equating these two proteins to allosteric modulators. The balance between response alternatives can also be influenced by the physiological concentrations of either G-proteins or β-arrestins, as well as by phosphorylation or interactions with positive or negative allosteric modulators. The nature of the interactions in the simulations presented suggests novel experimental tests to distinguish more fully among alternative mechanisms. PMID:27602718

  12. Classifying sex biased congenital anomalies

    SciTech Connect

    Lubinsky, M.S.

    1997-03-31

    The reasons for sex biases in congenital anomalies that arise before structural or hormonal dimorphisms are established has long been unclear. A review of such disorders shows that patterning and tissue anomalies are female biased, and structural findings are more common in males. This suggests different gender dependent susceptibilities to developmental disturbances, with female vulnerabilities focused on early blastogenesis/determination, while males are more likely to involve later organogenesis/morphogenesis. A dual origin for some anomalies explains paradoxical reductions of sex biases with greater severity (i.e., multiple rather than single malformations), presumably as more severe events increase the involvement of an otherwise minor process with opposite biases to those of the primary mechanism. The cause for these sex differences is unknown, but early dimorphisms, such as differences in growth or presence of H-Y antigen, may be responsible. This model provides a useful rationale for understanding and classifying sex-biased congenital anomalies. 42 refs., 7 tabs.

  13. 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.

  14. Structural Biomechanics Modulate Intramuscular Distribution of Locally Delivered Drugs

    PubMed Central

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

    2008-01-01

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

  15. 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.

  16. Amorphous FeCoSiB for exchange bias coupled and decoupled magnetoelectric multilayer systems: Real-structure and magnetic properties

    SciTech Connect

    Hrkac, V.; Strobel, J.; Kienle, L.; Lage, E.; Köppel, G.; McCord, J.; Quandt, E.; Meyners, D.

    2014-10-07

    The effect of field annealing for exchanged biased multilayer films is studied with respect to the resultant structural and magnetic film properties. The presented multilayer stacks comprise repeating sequences of Ta/Cu/(1 1 1) textured antiferromagnetic Mn₇₀Ir₃₀ /amorphous ferromagnetic Fe₇₀.₂Co₇.₈Si₂B₁₀. Within the ferromagnetic layers crystalline filaments are observed. An additional Ta layer between the antiferromagnet and ferromagnet is used in order to investigate and separate the influence of the common Mn₇₀Ir₃₀/Fe₇₀.₂Co₇.₈Si₁₂B₁₀ interface on the occurring filaments and structural changes. In situ and ex situ transmission electron microscopy is used for a comprehensive structure characterization of multilayer stacks for selected temperature stages. Up to 250 °C, the multilayers are structurally unaltered and preserve the as-deposited condition. A deliberate increase to 350 °C exhibits different crystallization processes for the films, depending on the presence of crystal nuclei within the amorphous ferromagnetic layer. The influence of volume-to-surface ratio of the multilayer stacks to the crystallization process is emphasized by the comparison of in situ and ex situ investigations as the respective specimen thickness is changed. Complementary magnetic studies reveal a defined exchange bias obtained at the first annealing step and a decrease of total anisotropy field with partial crystallization after the subsequent annealing at 350 °C.

  17. 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.

  18. Geometric biases in power-spectrum measurements

    NASA Astrophysics Data System (ADS)

    Samushia, L.; Branchini, E.; Percival, W. J.

    2015-10-01

    The observed distribution of galaxies has local transverse isotropy around the line of sight (LOS) with respect to the observer. The difference in the statistical clustering signal along and across the LOS encodes important information about the geometry of the Universe, its expansion rate and the rate of growth of structure within it. Because the LOS varies across a survey, the standard fast Fourier transform (FFT) based methods of measuring the anisotropic power spectrum (APS) cannot be used for surveys with wide observational footprint, other than to measure the monopole moment. We derive a simple analytic formula to quantify the bias for higher order Legendre moments, and we demonstrate that it is scale independent for a simple survey model, and depends only on the observed area. We derive a similar numerical correction formula for recently proposed alternative estimators of the APS that are based on summing over galaxies rather than using an FFT, and can therefore incorporate a varying LOS. We demonstrate that their bias depends on scale but not on the observed area. For a quadrupole the bias is always less than 1 per cent for k > 0.01 h Mpc^{-1} at z > 0.32. For a hexadecapole the bias is below 5 per cent for k > 0.05 h Mpc^{-1} at z > 0.32.

  19. Localization of wood floor structure by infrared thermography

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

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

  20. 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

  1. Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity.

    PubMed

    Qi, Yueying; Xu, Wenjing; Xing, Tian; Zhao, Mingming; Li, Nana; Yan, Li; Xia, Guangmin; Wang, Mengcheng

    2015-01-01

    Synonymous codon usage bias (SCUB) is the nonuniform usage of codons, occurring often in nearly all organisms. Our previous study found that SCUB is correlated with intron number, is unequal among exons in the plant nuclear genome, and mirrors evolutionary specialization. However, whether this rule exists in the plastid genome has not been addressed. Here, we present an analysis of SCUB in the plastid genomes of 25 species from lower to higher plants (algae, bryophytes, pteridophytes, gymnosperms, and spermatophytes). We found NNA and NNT (A- and T-ending codons) are preferential in the plastid genomes of all plants. Interestingly, this preference is heterogeneous among taxonomies of plants, with the strongest preference in bryophytes and the weakest in pteridophytes, suggesting an association between SCUB and plant evolution. In addition, SCUB frequencies are consistent among genes with varied introns and among exons, indicating that the bias of NNA and NNT is unrelated to either intron number or exon position. Further, SCUB is associated with DNA methylation-induced conversion of cytosine to thymine in the vascular plants but not in algae or bryophytes. These data demonstrate that these SCUB profiles in the plastid genome are distinctly different compared with the nuclear genome.

  2. Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity

    PubMed Central

    Qi, Yueying; Xu, Wenjing; Xing, Tian; Zhao, Mingming; Li, Nana; Yan, Li; Xia, Guangmin; Wang, Mengcheng

    2015-01-01

    Synonymous codon usage bias (SCUB) is the nonuniform usage of codons, occurring often in nearly all organisms. Our previous study found that SCUB is correlated with intron number, is unequal among exons in the plant nuclear genome, and mirrors evolutionary specialization. However, whether this rule exists in the plastid genome has not been addressed. Here, we present an analysis of SCUB in the plastid genomes of 25 species from lower to higher plants (algae, bryophytes, pteridophytes, gymnosperms, and spermatophytes). We found NNA and NNT (A- and T-ending codons) are preferential in the plastid genomes of all plants. Interestingly, this preference is heterogeneous among taxonomies of plants, with the strongest preference in bryophytes and the weakest in pteridophytes, suggesting an association between SCUB and plant evolution. In addition, SCUB frequencies are consistent among genes with varied introns and among exons, indicating that the bias of NNA and NNT is unrelated to either intron number or exon position. Further, SCUB is associated with DNA methylation–induced conversion of cytosine to thymine in the vascular plants but not in algae or bryophytes. These data demonstrate that these SCUB profiles in the plastid genome are distinctly different compared with the nuclear genome. PMID:25922569

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

    PubMed

    Kumar, Prasun; Bansal, Manju

    2015-05-01

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

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

    PubMed

    Kumar, Prasun; Bansal, Manju

    2015-05-01

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

  5. Possibilities of structural engineering in multilayer vacuum-arc ZrN/CrN coatings by varying the nanolayer thickness and application of a bias potential

    NASA Astrophysics Data System (ADS)

    Sobol', O. V.; Andreev, A. A.; Gorban', V. F.; Stolbovoy, V. A.; Melekhov, A. A.; Postelnyk, A. A.

    2016-07-01

    The possibility of attaining an superhard state in multilayer vacuum-arc ZrN/CrN coatings with a layer thickness of about 20 nm has been established. It has been shown that the application of a constant negative potential for structural engineering during deposition leads to the formation of solid solutions due to mixing of interfaces. The hardness of these systems exceeds 30 GPa. The application of a pulsed high-voltage bias potential at which the ordering of atoms stimulated by elevated mobility is observed makes it possible to suppress the mixing of the interfaces and to attain elevated hardness (up to 42 GPa) for nanometer layer thicknesses.

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

    PubMed

    Conway, Patrick; DiMaio, Frank

    2016-08-01

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

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

    PubMed

    Conway, Patrick; DiMaio, Frank

    2016-08-01

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

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

    ERIC Educational Resources Information Center

    Salthouse, Timothy A.

    2004-01-01

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

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

    PubMed

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

    1999-02-15

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

  11. Local genetic structure in a clonal dioecious angiosperm.

    PubMed

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

    2005-04-01

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

  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. 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.; Lu, D.; Frenkel, A. I.

    2016-06-30

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

  14. Zero-bias features and ``Shapiro-like'' steps in the current-voltage characteristics of an SN structure.

    NASA Astrophysics Data System (ADS)

    Roshchin, Igor V.; Shnirman, Alexander

    2000-03-01

    Using the tunneling Hamiltonian method proposed by Hekking and Nazarov(F. W. J. Hekking and Y. V. Nazarov, Physical Review B 49), 6847 (1994) we consider contribution of the Andreev reflection to the current through SN interfaces. Application of an external ac field results in steps in the current-voltage characteristics at Vn = nπ hbar /2e. Shape of the steps is determined by the shape of the dc current zero-bias conductance peak (ZBCP) arising due to the multiple Andreev reflections. We discuss the influence of temperature, strength, and sign of the electron-electron interaction and other parameters of the normal metal on the ZBCP and the steps. Experimental parameters of a highly-doped n^+-InAs are used to obtain estimates for proposed experiments.

  15. 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.

  16. 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.

  17. Gene structure and chromosomal localization of plasma kallikrein

    SciTech Connect

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

    1991-02-12

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

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

    NASA Astrophysics Data System (ADS)

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

    1999-10-01

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

  19. Local structure and electrical switching in chalcogenide glasses

    NASA Astrophysics Data System (ADS)

    Murugavel, S.; Asokan, S.

    1998-08-01

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

  20. 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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

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

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

    PubMed Central

    Keeling, M J

    1999-01-01

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

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

    PubMed

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

    2010-12-23

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

  5. Twin Masks of Spiral Structure? A Local Perspective

    NASA Astrophysics Data System (ADS)

    Steiman-Cameron, Thomas Y.

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

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

    SciTech Connect

    Goldsmith, L.H.

    1980-09-01

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

  7. 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.

  8. 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

  9. Exchange bias and magnetic properties induced by intrinsic structural distortion in CaMn{sub 3}O{sub 6} nanoribbons

    SciTech Connect

    Yu, J. Y. Huang, K.; Wu, H. Y.; Feng, Y.; Tang, Z.; Zhang, L.; Wang, L.

    2014-01-13

    Single-crystalline CaMn{sub 3}O{sub 6} nanoribbons have been synthesized by a molten-salt method. To explore the origin of the magnetism of nanosized antiferromagnetic (AFM) manganites, a comparative study has been conducted for CaMn{sub 3}O{sub 6} (CMO-1) and post-growth vacuum annealed (CMO-2) nanoribbons. A lattice expansion resulting from oxygen release during vacuum annealing is observed. Correspondingly, AFM ordering in CMO-2 is further suppressed, and ferromagnetism and spin-glass (SG)-like behavior are significantly enhanced, which are presumed attributable to the intrinsic structural distortions induced by oxygen vacancies. In this case, side and surface effects are not decisive factors. In addition, this study provided observations of the exchange bias effect in manganite nanoribbons with an AFM-SG-like-ferromagnetic (FM) structure, as compared with the typical AFM-core-FM-shell.

  10. 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

  11. 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…

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

    PubMed

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

    2015-09-01

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

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

    PubMed

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

    2015-09-01

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

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

    DOE PAGES

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  16. Event representations constrain the structure of language: Sign language as a window into universally accessible linguistic biases.

    PubMed

    Strickland, Brent; Geraci, Carlo; Chemla, Emmanuel; Schlenker, Philippe; Kelepir, Meltem; Pfau, Roland

    2015-05-12

    According to a theoretical tradition dating back to Aristotle, verbs can be classified into two broad categories. Telic verbs (e.g., "decide," "sell," "die") encode a logical endpoint, whereas atelic verbs (e.g., "think," "negotiate," "run") do not, and the denoted event could therefore logically continue indefinitely. Here we show that sign languages encode telicity in a seemingly universal way and moreover that even nonsigners lacking any prior experience with sign language understand these encodings. In experiments 1-5, nonsigning English speakers accurately distinguished between telic (e.g., "decide") and atelic (e.g., "think") signs from (the historically unrelated) Italian Sign Language, Sign Language of the Netherlands, and Turkish Sign Language. These results were not due to participants' inferring that the sign merely imitated the action in question. In experiment 6, we used pseudosigns to show that the presence of a salient visual boundary at the end of a gesture was sufficient to elicit telic interpretations, whereas repeated movement without salient boundaries elicited atelic interpretations. Experiments 7-10 confirmed that these visual cues were used by all of the sign languages studied here. Together, these results suggest that signers and nonsigners share universally accessible notions of telicity as well as universally accessible "mapping biases" between telicity and visual form. PMID:25918419

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

    PubMed Central

    2011-01-01

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

  18. Local spatial structure of forest biomass and its consequences for remote sensing of carbon stocks

    NASA Astrophysics Data System (ADS)

    Réjou-Méchain, M.; Muller-Landau, H. C.; Detto, M.; Thomas, S. C.; Le Toan, T.; Saatchi, S. S.; Barreto-Silva, J. S.; Bourg, N. A.; Bunyavejchewin, S.; Butt, N.; Brockelman, W. Y.; Cao, M.; Cárdenas, D.; Chiang, J.-M.; Chuyong, G. B.; Clay, K.; Condit, R.; Dattaraja, H. S.; Davies, S. J.; Duque, A.; Esufali, S.; Ewango, C.; Fernando, R. H. S.; Fletcher, C. D.; Gunatilleke, I. A. U. N.; Hao, Z.; Harms, K. E.; Hart, T. B.; Hérault, B.; Howe, R. W.; Hubbell, S. P.; Johnson, D. J.; Kenfack, D.; Larson, A. J.; Lin, L.; Lin, Y.; Lutz, J. A.; Makana, J.-R.; Malhi, Y.; Marthews, T. R.; McEwan, R. W.; McMahon, S. M.; McShea, W. J.; Muscarella, R.; Nathalang, A.; Noor, N. S. M.; Nytch, C. J.; Oliveira, A. A.; Phillips, R. P.; Pongpattananurak, N.; Punchi-Manage, R.; Salim, R.; Schurman, J.; Sukumar, R.; Suresh, H. S.; Suwanvecho, U.; Thomas, D. W.; Thompson, J.; Uríarte, M.; Valencia, R.; Vicentini, A.; Wolf, A. T.; Yap, S.; Yuan, Z.; Zartman, C. E.; Zimmerman, J. K.; Chave, J.

    2014-12-01

    Advances in forest carbon mapping have the potential to greatly reduce uncertainties in the global carbon budget and to facilitate effective emissions mitigation strategies such as REDD+ (Reducing Emissions from Deforestation and Forest Degradation). Though broad-scale mapping is based primarily on remote sensing data, the accuracy of resulting forest carbon stock estimates depends critically on the quality of field measurements and calibration procedures. The mismatch in spatial scales between field inventory plots and larger pixels of current and planned remote sensing products for forest biomass mapping is of particular concern, as it has the potential to introduce errors, especially if forest biomass shows strong local spatial variation. Here, we used 30 large (8-50 ha) globally distributed permanent forest plots to quantify the spatial variability in aboveground biomass density (AGBD in Mg ha-1) at spatial scales ranging from 5 to 250 m (0.025-6.25 ha), and to evaluate the implications of this variability for calibrating remote sensing products using simulated remote sensing footprints. We found that local spatial variability in AGBD is large for standard plot sizes, averaging 46.3% for replicate 0.1 ha subplots within a single large plot, and 16.6% for 1 ha subplots. AGBD showed weak spatial autocorrelation at distances of 20-400 m, with autocorrelation higher in sites with higher topographic variability and statistically significant in half of the sites. We further show that when field calibration plots are smaller than the remote sensing pixels, the high local spatial variability in AGBD leads to a substantial "dilution" bias in calibration parameters, a bias that cannot be removed with standard statistical methods. Our results suggest that topography should be explicitly accounted for in future sampling strategies and that much care must be taken in designing calibration schemes if remote sensing of forest carbon is to achieve its promise.

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

    PubMed

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

    2009-07-01

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

  20. Susceptibility to Optical Illusions Varies as a Function of the Autism-Spectrum Quotient but Not in Ways Predicted by Local-Global Biases

    ERIC Educational Resources Information Center

    Chouinard, Philippe A.; Unwin, Katy L.; Landry, Oriane; Sperandio, Irene

    2016-01-01

    Individuals with autism spectrum disorder and those with autistic tendencies in non-clinical groups are thought to have a perceptual style privileging local details over global integration. We used 13 illusions to investigate this perceptual style in typically developing adults with various levels of autistic traits. Illusory susceptibility was…

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

    PubMed

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

    2010-01-01

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

  2. The Threshold of Embedded M Collider Bias and Confounding Bias

    ERIC Educational Resources Information Center

    Kelcey, Benjamin; Carlisle, Joanne

    2011-01-01

    Of particular import to this study, is collider bias originating from stratification on retreatment variables forming an embedded M or bowtie structural design. That is, rather than assume an M structural design which suggests that "X" is a collider but not a confounder, the authors adopt what they consider to be a more reasonable position and…

  3. 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).

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

    PubMed Central

    Levin, Igor; Vanderah, Terrell

    2008-01-01

    The functional responses (e.g., dielectric, magnetic, catalytic, etc.) of many industrially-relevant materials are controlled by their local structure—a term that refers to the atomic arrangements on a scale ranging from atomic (sub-nanometer) to several nanometers. Thus, accurate knowledge of local structure is central to understanding the properties of nanostructured materials, thereby placing the problem of determining atomic positions on the nanoscale—the so-called “nanostructure problem”—at the center of modern materials development. Today, multiple experimental techniques exist for probing local atomic arrangements; nonetheless, finding accurate comprehensive, and robust structural solutions for the nanostructured materials still remains a formidable challenge because any one of these methods yields only a partial view of the local structure. The primary goal of this 2-day NIST-sponsored workshop was to bring together experts in the key experimental and theoretical areas relevant to local-structure determination to devise a strategy for the collaborative effort required to develop a comprehensive measurement solution on the local scale. The participants unanimously agreed that solving the nanostructure problem—an ultimate frontier in materials characterization—necessitates a coordinated interdisciplinary effort that transcends the existing capabilities of any single institution, including national laboratories, centers, and user facilities. The discussions converged on an institute dedicated to local structure determination as the most viable organizational platform for successfully addressing the nanostructure problem. The proposed “institute” would provide an intellectual infrastructure for local structure determination by (1) developing and maintaining relevant computer software integrated in an open-source global optimization framework (Fig. 2), (2) connecting industrial and academic users with experts in measurement techniques, (3

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

    NASA Astrophysics Data System (ADS)

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

    2009-08-01

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

  6. Dependence of BiFeO3 thickness on exchange bias in BiFeO3/ Co2FeAl multiferroic structures

    NASA Astrophysics Data System (ADS)

    Zhang, X.; Zhang, D. L.; Wang, Y. H.; Miao, J.; Xu, X. G.; Jiang, Y.

    2011-01-01

    We have grown BiFeO3 (BFO) thin films with different thickness on Si/SiO2/Ti/Pt(111) substrates by pulsed laser deposition. Half-metallic Co2FeAl (CFA) films with a thickness of 5 nm were then grown on the BFO films by magnetron sputtering. Through the magnetic hysteresis loops of the BFO/CFA heterostructure, we observe a direct correlation between the thickness of the BFO film and exchange bias (EB) field. The EB field exhibits fluctuation behavior with a cyclical BFO thickness of 60 nm, which is close to the spiral modulation wavelength (62 nm) of BFO. It indicates the influence of spiral modulation on the EB in the BFO/CFA multiferroic structure.

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

    NASA Astrophysics Data System (ADS)

    Horváth, Ivan

    2005-03-01

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

  8. Improving CMB non-Gaussianity estimators using tracers of local structure

    SciTech Connect

    Mead, James M. G.; King, Lindsay; Lewis, Antony

    2011-01-15

    Local non-Gaussianity causes correlations between large-scale perturbation modes and the small-scale power. The large-scale CMB signal has contributions from the integrated Sachs-Wolfe (ISW) effect, which does not correlate with the small-scale power. If this ISW contribution can be removed, the sensitivity to local non-Gaussianity is improved. Gravitational lensing and galaxy counts can be used to trace the ISW contribution; in particular, we show that the CMB lensing potential is highly correlated with the ISW signal. We construct a nearly optimal estimator for the local non-Gaussianity parameter f{sub NL} and investigate to what extent we can use this to decrease the variance on f{sub NL}. We show that the variance can be decreased by up to 20% at Planck sensitivity using galaxy counts. CMB lensing is a good bias-independent ISW tracer for future more sensitive observations, though the fractional decrease in variance is small if good polarization data are also available.

  9. Genetic structure and rabies spread potential in raccoons: the role of landscape barriers and sex-biased dispersal.

    PubMed

    Côté, Héloïse; Garant, Dany; Robert, Karine; Mainguy, Julien; Pelletier, Fanie

    2012-06-01

    Identifying natural barriers to movements of hosts associated with infectious diseases is essential for developing effective control strategies. Raccoon rabies variant (RRV) is a zoonosis of concern for humans because its main vector, the raccoon (Procyon lotor), is found near residential areas. In Québec, Canada, all cases of RRV found in raccoons since 2006 were detected on the eastern side of the Richelieu River, suggesting that this river acts as a barrier to gene flow and thus the potential for RRV to spread. The objectives of this study were to characterize the genetic structure of raccoon populations and assess the effect of the Richelieu River on the population structure in southern Québec, Canada. We also evaluated whether RRV spread potential differed between sex and at a larger spatial scale. Our analyses revealed a weak signal of genetic differentiation among individuals located on each side of the Richelieu River. At a larger spatial scale, genetic structuring was weak. Our results suggest that rivers might not always efficiently restrain raccoon movements and spread of RRV. We suggest that the difference in genetic structure found between sexes can be partly explained by male movements during the breeding season in winter, when ice bridges allow passage over most rivers in Québec.

  10. Genetic structure and rabies spread potential in raccoons: the role of landscape barriers and sex-biased dispersal.

    PubMed

    Côté, Héloïse; Garant, Dany; Robert, Karine; Mainguy, Julien; Pelletier, Fanie

    2012-06-01

    Identifying natural barriers to movements of hosts associated with infectious diseases is essential for developing effective control strategies. Raccoon rabies variant (RRV) is a zoonosis of concern for humans because its main vector, the raccoon (Procyon lotor), is found near residential areas. In Québec, Canada, all cases of RRV found in raccoons since 2006 were detected on the eastern side of the Richelieu River, suggesting that this river acts as a barrier to gene flow and thus the potential for RRV to spread. The objectives of this study were to characterize the genetic structure of raccoon populations and assess the effect of the Richelieu River on the population structure in southern Québec, Canada. We also evaluated whether RRV spread potential differed between sex and at a larger spatial scale. Our analyses revealed a weak signal of genetic differentiation among individuals located on each side of the Richelieu River. At a larger spatial scale, genetic structuring was weak. Our results suggest that rivers might not always efficiently restrain raccoon movements and spread of RRV. We suggest that the difference in genetic structure found between sexes can be partly explained by male movements during the breeding season in winter, when ice bridges allow passage over most rivers in Québec. PMID:25568059

  11. Genetic structure and rabies spread potential in raccoons: the role of landscape barriers and sex-biased dispersal

    PubMed Central

    Côté, Héloïse; Garant, Dany; Robert, Karine; Mainguy, Julien; Pelletier, Fanie

    2012-01-01

    Identifying natural barriers to movements of hosts associated with infectious diseases is essential for developing effective control strategies. Raccoon rabies variant (RRV) is a zoonosis of concern for humans because its main vector, the raccoon (Procyon lotor), is found near residential areas. In Québec, Canada, all cases of RRV found in raccoons since 2006 were detected on the eastern side of the Richelieu River, suggesting that this river acts as a barrier to gene flow and thus the potential for RRV to spread. The objectives of this study were to characterize the genetic structure of raccoon populations and assess the effect of the Richelieu River on the population structure in southern Québec, Canada. We also evaluated whether RRV spread potential differed between sex and at a larger spatial scale. Our analyses revealed a weak signal of genetic differentiation among individuals located on each side of the Richelieu River. At a larger spatial scale, genetic structuring was weak. Our results suggest that rivers might not always efficiently restrain raccoon movements and spread of RRV. We suggest that the difference in genetic structure found between sexes can be partly explained by male movements during the breeding season in winter, when ice bridges allow passage over most rivers in Québec. PMID:25568059

  12. Local spatial structure of forest biomass and its consequences for remote sensing of carbon stocks

    NASA Astrophysics Data System (ADS)

    Réjou-Méchain, M.; Muller-Landau, H. C.; Detto, M.; Thomas, S. C.; Le Toan, T.; Saatchi, S. S.; Barreto-Silva, J. S.; Bourg, N. A.; Bunyavejchewin, S.; Butt, N.; Brockelman, W. Y.; Cao, M.; Cárdenas, D.; Chiang, J.-M.; Chuyong, G. B.; Clay, K.; Condit, R.; Dattaraja, H. S.; Davies, S. J.; Duque, A.; Esufali, S.; Ewango, C.; Fernando, R. H. S.; Fletcher, C. D.; Gunatilleke, I. A. U. N.; Hao, Z.; Harms, K. E.; Hart, T. B.; Hérault, B.; Howe, R. W.; Hubbell, S. P.; Johnson, D. J.; Kenfack, D.; Larson, A. J.; Lin, L.; Lin, Y.; Lutz, J. A.; Makana, J.-R.; Malhi, Y.; Marthews, T. R.; McEwan, R. W.; McMahon, S. M.; McShea, W. J.; Muscarella, R.; Nathalang, A.; Noor, N. S. M.; Nytch, C. J.; Oliveira, A. A.; Phillips, R. P.; Pongpattananurak, N.; Punchi-Manage, R.; Salim, R.; Schurman, J.; Sukumar, R.; Suresh, H. S.; Suwanvecho, U.; Thomas, D. W.; Thompson, J.; Uríarte, M.; Valencia, R.; Vicentini, A.; Wolf, A. T.; Yap, S.; Yuan, Z.; Zartman, C. E.; Zimmerman, J. K.; Chave, J.

    2014-04-01

    Advances in forest carbon mapping have the potential to greatly reduce uncertainties in the global carbon budget and to facilitate effective emissions mitigation strategies such as REDD+. Though broad scale mapping is based primarily on remote sensing data, the accuracy of resulting forest carbon stock estimates depends critically on the quality of field measurements and calibration procedures. The mismatch in spatial scales between field inventory plots and larger pixels of current and planned remote sensing products for forest biomass mapping is of particular concern, as it has the potential to introduce errors, especially if forest biomass shows strong local spatial variation. Here, we used 30 large (8-50 ha) globally distributed permanent forest plots to quantify the spatial variability in aboveground biomass (AGB) at spatial grains ranging from 5 to 250 m (0.025-6.25 ha), and we evaluate the implications of this variability for calibrating remote sensing products using simulated remote sensing footprints. We found that the spatial sampling error in AGB is large for standard plot sizes, averaging 46.3% for 0.1 ha subplots and 16.6% for 1 ha subplots. Topographically heterogeneous sites showed positive spatial autocorrelation in AGB at scales of 100 m and above; at smaller scales, most study sites showed negative or nonexistent spatial autocorrelation in AGB. We further show that when field calibration plots are smaller than the remote sensing pixels, the high local spatial variability in AGB leads to a substantial "dilution" bias in calibration parameters, a bias that cannot be removed with current statistical methods. Overall, our results suggest that topography should be explicitly accounted for in future sampling strategies and that much care must be taken in designing calibration schemes if remote sensing of forest carbon is to achieve its promise.

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

    SciTech Connect

    Zemla, A T

    2006-02-13

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

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

    NASA Astrophysics Data System (ADS)

    Singh, Harishchandra; Yadav, A. K.

    2016-05-01

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

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

    SciTech Connect

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

    2010-11-19

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

  16. Investigating the shape bias in typically developing children and children with autism spectrum disorders.

    PubMed

    Potrzeba, Emily R; Fein, Deborah; Naigles, Letitia

    2015-01-01

    Young typically developing (TD) children have been observed to utilize word learning strategies such as the noun bias and shape bias; these improve their efficiency in acquiring and categorizing novel terms. Children using the shape bias extend object labels to new objects of the same shape; thus, the shape bias prompts the categorization of object words based on the global characteristic of shape over local, discrete details. Individuals with autism spectrum disorders (ASDs) frequently attend to minor details of objects rather than their global structure. Therefore, children with ASD may not use shape bias to acquire new words. Previous research with children with ASD has provided evidence that they parallel TD children in showing a noun bias, but not a shape bias (Tek et al., 2008). However, this sample was small and individual and item differences were not investigated in depth. In an extension of Tek et al. (2008) with twice the sample size and a wider developmental timespan, we tested 32 children with ASD and 35 TD children in a longitudinal study across 20 months using the intermodal preferential looking paradigm. Children saw five triads of novel objects (target, shape-match, color-match) in both NoName and Name trials; those who looked longer at the shape-match during the Name trials than the NoName trials demonstrated a shape bias. The TD group showed a significant shape bias at all visits, beginning at 20 months of age while the language-matched ASD group did not show a significant shape bias at any visit. Within the ASD group, though, some children did show a shape bias; these children had larger vocabularies concurrently and longitudinally. Degree of shape bias elicitation varied by item, but did not seem related to perceptual complexity. We conclude that shape does not appear to be an organizing factor for word learning by children with ASD. PMID:25954219

  17. Investigating the shape bias in typically developing children and children with autism spectrum disorders

    PubMed Central

    Potrzeba, Emily R.; Fein, Deborah; Naigles, Letitia

    2015-01-01

    Young typically developing (TD) children have been observed to utilize word learning strategies such as the noun bias and shape bias; these improve their efficiency in acquiring and categorizing novel terms. Children using the shape bias extend object labels to new objects of the same shape; thus, the shape bias prompts the categorization of object words based on the global characteristic of shape over local, discrete details. Individuals with autism spectrum disorders (ASDs) frequently attend to minor details of objects rather than their global structure. Therefore, children with ASD may not use shape bias to acquire new words. Previous research with children with ASD has provided evidence that they parallel TD children in showing a noun bias, but not a shape bias (Tek et al., 2008). However, this sample was small and individual and item differences were not investigated in depth. In an extension of Tek et al. (2008) with twice the sample size and a wider developmental timespan, we tested 32 children with ASD and 35 TD children in a longitudinal study across 20 months using the intermodal preferential looking paradigm. Children saw five triads of novel objects (target, shape-match, color-match) in both NoName and Name trials; those who looked longer at the shape-match during the Name trials than the NoName trials demonstrated a shape bias. The TD group showed a significant shape bias at all visits, beginning at 20 months of age while the language-matched ASD group did not show a significant shape bias at any visit. Within the ASD group, though, some children did show a shape bias; these children had larger vocabularies concurrently and longitudinally. Degree of shape bias elicitation varied by item, but did not seem related to perceptual complexity. We conclude that shape does not appear to be an organizing factor for word learning by children with ASD. PMID:25954219

  18. The evolution of galaxies at constant number density: a less biased view of star formation, quenching, and structural formation

    NASA Astrophysics Data System (ADS)

    Ownsworth, Jamie R.; Conselice, Christopher J.; Mundy, Carl J.; Mortlock, Alice; Hartley, William G.; Duncan, Kenneth; Almaini, Omar

    2016-09-01

    Due to significant galaxy contamination and impurity in stellar mass selected samples (up to 95 per cent from z = 0-3), we examine the star formation history, quenching time-scales, and structural evolution of galaxies using a constant number density selection with data from the United Kingdom Infra-Red Deep Sky Survey Ultra-Deep Survey field. Using this methodology, we investigate the evolution of galaxies at a variety of number densities from z = 0-3. We find that samples chosen at number densities ranging from 3 × 10-4 to 10-5 galaxies Mpc-3 (corresponding to z ˜ 0.5 stellar masses of M* = 1010.95-11.6 M0) have a star-forming blue fraction of ˜50 per cent at z ˜ 2.5, which evolves to a nearly 100 per cent quenched red and dead population by z ˜ 1. We also see evidence for number density downsizing, such that the galaxies selected at the lowest densities (highest masses) become a homogeneous red population before those at higher number densities. Examining the evolution of the colours for these systems furthermore shows that the formation redshift of galaxies selected at these number densities is zform > 3. The structural evolution through size and Sérsic index fits reveal that while there remains evolution in terms of galaxies becoming larger and more concentrated in stellar mass at lower redshifts, the magnitude of the change is significantly smaller than for a mass-selected sample. We also find that changes in size and structure continues at z < 1, and is coupled strongly to passivity evolution. We conclude that galaxy structure is driving the quenching of galaxies, such that galaxies become concentrated before they become passive.

  19. Impact of Gate and Passivation Structures on Current Collapse of AlGaN/GaN High-Electron-Mobility Transistors under Off-State-Bias Stress

    NASA Astrophysics Data System (ADS)

    Tajima, Masafumi; Hashizume, Tamotsu

    2011-06-01

    Using a dual-gate structure, we have investigated the impact of gate-stress position on the current collapse behavior of AlGaN/GaN high-electron-mobility transistors (HEMTs) without surface passivation. When the gate-bias stress under the off state was applied to the additional gate between the main gate and the drain electrode, we observed a marked increase in on-resistance (RON). On the other hand, the off-state stress on the main gate itself caused a decrease in drain saturation current as well as an increase in RON. The calculation of electric field at the AlGaN surface showed that the field peaks existed at the gate edges on both the drain and source sides, probably causing electron charging at the AlGaN surface near both gate-edge areas. These results indicated that the off-state gate stress induces “virtual gates” in the gate edges expanding in both the drain and source directions. The impacts of device structures on the current collapse have been characterized, using Schottky-gate HEMTs with and without surface passivation and metal-oxide-semiconductor (MOS) gate HEMTs. The surface passivation and MOS-gate structure was effective in mitigating current collapse, which was explained in terms of surface state density, electric field strength, and gate leakage current.

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

    PubMed

    Dehmer, Matthias; Emmert-Streib, Frank

    2008-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-01-01

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

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

    PubMed

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

    2015-10-13

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

  3. 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

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

    NASA Astrophysics Data System (ADS)

    Yang, Yue

    2016-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  6. 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.

  7. 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.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2009-06-01

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

  12. Divertor bias experiments

    NASA Astrophysics Data System (ADS)

    Staebler, G. M.

    1994-06-01

    Electrical biasing of the divertor target plates has recently been implemented on several tokamaks. The results of these experiments to date will be reviewed in this paper. The bias electrode configuration is unique in each experiment. The effects of biasing on the scrape-off layer (SOL) plasma also differ. By comparing results between machines, and using theoretical models, an understanding of the basic physics of biasing begins to emerge. Divertor biasing has been demonstrated to have a strong influence on the particle and energy transport within the SOL. The ability to externally control the SOL plasma with biasing has promising applications to future tokamak reactors.

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

    NASA Astrophysics Data System (ADS)

    Lu, Wen; Liu, Hai-yan

    2007-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Schroer, Bert

    2015-02-01

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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  19. Cognitive Biases Questionnaire for Psychosis

    PubMed Central

    Peters, Emmanuelle R.

    2014-01-01

    Objective: The Cognitive Biases Questionnaire for psychosis (CBQp) was developed to capture 5 cognitive distortions (jumping to conclusions, intentionalising, catastrophising, emotional reasoning, and dichotomous thinking), which are considered important for the pathogenesis of psychosis. Vignettes were adapted from the Cognitive Style Test (CST),1 relating to “Anomalous Perceptions” and “Threatening Events” themes. Method: Scale structure, reliability, and validity were investigated in a psychosis group, and CBQp scores were compared with those of depressed and healthy control samples. Results: The CBQp showed good internal consistency and test-retest reliability. The 5 biases were not independent, with a 2-related factor scale providing the best fit. This structure suggests that the CBQp assesses a general thinking bias rather than distinct cognitive errors, while Anomalous Perception and Threatening Events theme scores can be used separately. Total CBQp scores showed good convergent validity with the CST, but individual biases were not related to existing tasks purporting to assess similar reasoning biases. Psychotic and depressed populations scored higher than healthy controls, and symptomatic psychosis patients scored higher than their nonsymptomatic counterparts, with modest relationships between CBQp scores and symptom severity once emotional disorders were partialled out. Anomalous Perception theme and Intentionalising bias scores showed some specificity to psychosis. Conclusions: Overall, the CBQp has good psychometric properties, although it is likely that it measures a different construct to existing tasks, tentatively suggested to represent a bias of interpretation rather than reasoning, judgment or decision-making processes. It is a potentially useful tool in both research and clinical arenas. PMID:23413104

  20. Symmetry as Bias: Rediscovering Special Relativity

    NASA Technical Reports Server (NTRS)

    Lowry, Michael R.

    1992-01-01

    This paper describes a rational reconstruction of Einstein's discovery of special relativity, validated through an implementation: the Erlanger program. Einstein's discovery of special relativity revolutionized both the content of physics and the research strategy used by theoretical physicists. This research strategy entails a mutual bootstrapping process between a hypothesis space for biases, defined through different postulated symmetries of the universe, and a hypothesis space for physical theories. The invariance principle mutually constrains these two spaces. The invariance principle enables detecting when an evolving physical theory becomes inconsistent with its bias, and also when the biases for theories describing different phenomena are inconsistent. Structural properties of the invariance principle facilitate generating a new bias when an inconsistency is detected. After a new bias is generated. this principle facilitates reformulating the old, inconsistent theory by treating the latter as a limiting approximation. The structural properties of the invariance principle can be suitably generalized to other types of biases to enable primal-dual learning.

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

    PubMed

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

    2016-06-01

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

  2. 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.

  3. Vertical structure and physical processes of the Madden-Julian Oscillation: Biases and uncertainties at short range

    SciTech Connect

    Xavier, Prince K.; Petch, Jon C.; Klingaman, Nicholas P.; Woolnough, Steve J.; Jiang, Xianan; Waliser, Duane E.; Caian, Mihaela; Cole, Jason; Hagos, Samson M.; Hannay, Cecile; Kim, Daehyun; Miyakawa, Tomoki; Pritchard, Michael S.; Roehrig, Romain; Shindo, Eiki; Vitart, Frederic; Wang, Hailan

    2015-05-26

    We present an analysis of diabatic heating and moistening processes from 12 to 36 h lead time forecasts from 12 Global Circulation Models as part of the “Vertical structure and physical processes of the Madden-Julian Oscillation (MJO)” project. A lead time of 12–36 h is chosen to constrain the large-scale dynamics and thermodynamics to be close to observations while avoiding being too close to the initial spin-up of the models as they adjust to being driven from the Years of Tropical Convection (YOTC) analysis. A comparison of the vertical velocity and rainfall with the observations and YOTC analysis suggests that the phases of convection associated with the MJO are constrained in most models at this lead time although the rainfall in the suppressed phase is typically overestimated. Although the large-scale dynamics is reasonably constrained, moistening and heating profiles have large intermodel spread. In particular, there are large spreads in convective heating and moistening at midlevels during the transition to active convection. Radiative heating and cloud parameters have the largest relative spread across models at upper levels during the active phase. A detailed analysis of time step behavior shows that some models show strong intermittency in rainfall and differences in the precipitation and dynamics relationship between models. In conclusion, the wealth of model outputs archived during this project is a very valuable resource for model developers beyond the study of the MJO. Additionally, the findings of this study can inform the design of process model experiments, and inform the priorities for field experiments and future observing systems.

  4. Vertical structure and physical processes of the Madden-Julian Oscillation: Biases and uncertainties at short range

    DOE PAGES

    Xavier, Prince K.; Petch, Jon C.; Klingaman, Nicholas P.; Woolnough, Steve J.; Jiang, Xianan; Waliser, Duane E.; Caian, Mihaela; Cole, Jason; Hagos, Samson M.; Hannay, Cecile; et al

    2015-05-26

    We present an analysis of diabatic heating and moistening processes from 12 to 36 h lead time forecasts from 12 Global Circulation Models as part of the “Vertical structure and physical processes of the Madden-Julian Oscillation (MJO)” project. A lead time of 12–36 h is chosen to constrain the large-scale dynamics and thermodynamics to be close to observations while avoiding being too close to the initial spin-up of the models as they adjust to being driven from the Years of Tropical Convection (YOTC) analysis. A comparison of the vertical velocity and rainfall with the observations and YOTC analysis suggests thatmore » the phases of convection associated with the MJO are constrained in most models at this lead time although the rainfall in the suppressed phase is typically overestimated. Although the large-scale dynamics is reasonably constrained, moistening and heating profiles have large intermodel spread. In particular, there are large spreads in convective heating and moistening at midlevels during the transition to active convection. Radiative heating and cloud parameters have the largest relative spread across models at upper levels during the active phase. A detailed analysis of time step behavior shows that some models show strong intermittency in rainfall and differences in the precipitation and dynamics relationship between models. In conclusion, the wealth of model outputs archived during this project is a very valuable resource for model developers beyond the study of the MJO. Additionally, the findings of this study can inform the design of process model experiments, and inform the priorities for field experiments and future observing systems.« less

  5. Assessment of bias correction under transient climate change

    NASA Astrophysics Data System (ADS)

    Van Schaeybroeck, Bert; Vannitsem, Stéphane

    2015-04-01

    Calibration of climate simulations is necessary since large systematic discrepancies are generally found between the model climate and the observed climate. Recent studies have cast doubt upon the common assumption of the bias being stationary when the climate changes. This led to the development of new methods, mostly based on linear sensitivity of the biases as a function of time or forcing (Kharin et al. 2012). However, recent studies uncovered more fundamental problems using both low-order systems (Vannitsem 2011) and climate models, showing that the biases may display complicated non-linear variations under climate change. This last analysis focused on biases derived from the equilibrium climate sensitivity, thereby ignoring the effect of the transient climate sensitivity. Based on the linear response theory, a general method of bias correction is therefore proposed that can be applied on any climate forcing scenario. The validity of the method is addressed using twin experiments with a climate model of intermediate complexity LOVECLIM (Goosse et al., 2010). We evaluate to what extent the bias change is sensitive to the structure (frequency) of the applied forcing (here greenhouse gases) and whether the linear response theory is valid for global and/or local variables. To answer these question we perform large-ensemble simulations using different 300-year scenarios of forced carbon-dioxide concentrations. Reality and simulations are assumed to differ by a model error emulated as a parametric error in the wind drag or in the radiative scheme. References [1] H. Goosse et al., 2010: Description of the Earth system model of intermediate complexity LOVECLIM version 1.2, Geosci. Model Dev., 3, 603-633. [2] S. Vannitsem, 2011: Bias correction and post-processing under climate change, Nonlin. Processes Geophys., 18, 911-924. [3] V.V. Kharin, G. J. Boer, W. J. Merryfield, J. F. Scinocca, and W.-S. Lee, 2012: Statistical adjustment of decadal predictions in a changing

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

    PubMed

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

    2007-12-28

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

  7. 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.

  8. 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.

  9. Local Structural Analysis of Half-Metallic Ferromagnet CrO2

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    NASA Astrophysics Data System (ADS)

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

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

  13. 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.

  14. 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.

  15. 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.

  16. 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

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

    SciTech Connect

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

    1998-04-01

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

  18. 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…

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

    PubMed

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

    2016-05-25

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

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

    ERIC Educational Resources Information Center

    Griffin, Robert J.; Dunwoody, Sharon

    1995-01-01

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

  1. 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.

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

    PubMed

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

    2016-07-20

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

  3. Demonstrating the Correspondence Bias

    ERIC Educational Resources Information Center

    Howell, Jennifer L.; Shepperd, James A.

    2011-01-01

    Among the best-known and most robust biases in person perception is the correspondence bias--the tendency for people to make dispositional, rather than situational, attributions for an actor's behavior. The correspondence bias appears in virtually every social psychology textbook and in many introductory psychology textbooks, yet the authors'…

  4. Bias in Grading

    ERIC Educational Resources Information Center

    Malouff, John

    2008-01-01

    Bias in grading can be conscious or unconscious. The author describes different types of bias, such as those based on student attractiveness or performance in prior courses, and a variety of methods of reducing bias, including keeping students anonymous during grading and using detailed criteria for subjective grading.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

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

    SciTech Connect

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

    2007-02-02

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

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

    NASA Astrophysics Data System (ADS)

    Campo, Matteo; Speck, Thomas

    2016-08-01

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

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

    PubMed

    Feig, Michael

    2016-07-25

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

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

    SciTech Connect

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

    2006-09-01

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

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

    PubMed

    Feig, Michael

    2016-07-25

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

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

    NASA Astrophysics Data System (ADS)

    Dill, Robert; Klemann, Volker

    2015-04-01

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

  15. 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

  16. Queries for Bias Testing

    NASA Technical Reports Server (NTRS)

    Gordon, Diana F.

    1992-01-01

    Selecting a good bias prior to concept learning can be difficult. Therefore, dynamic bias adjustment is becoming increasingly popular. Current dynamic bias adjustment systems, however, are limited in their ability to identify erroneous assumptions about the relationship between the bias and the target concept. Without proper diagnosis, it is difficult to identify and then remedy faulty assumptions. We have developed an approach that makes these assumptions explicit, actively tests them with queries to an oracle, and adjusts the bias based on the test results.

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

    PubMed Central

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

    2014-01-01

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

  18. Biases in Visual, Auditory, and Audiovisual Perception of Space.

    PubMed

    Odegaard, Brian; Wozny, David R; Shams, Ladan

    2015-12-01

    Localization of objects and events in the environment is critical for survival, as many perceptual and motor tasks rely on estimation of spatial location. Therefore, it seems reasonable to assume that spatial localizations should generally be accurate. Curiously, some previous studies have reported biases in visual and auditory localizations, but these studies have used small sample sizes and the results have been mixed. Therefore, it is not clear (1) if the reported biases in localization responses are real (or due to outliers, sampling bias, or other factors), and (2) whether these putative biases reflect a bias in sensory representations of space or a priori expectations (which may be due to the experimental setup, instructions, or distribution of stimuli). Here, to address these questions, a dataset of unprecedented size (obtained from 384 observers) was analyzed to examine presence, direction, and magnitude of sensory biases, and quantitative computational modeling was used to probe the underlying mechanism(s) driving these effects. Data revealed that, on average, observers were biased towards the center when localizing visual stimuli, and biased towards the periphery when localizing auditory stimuli. Moreover, quantitative analysis using a Bayesian Causal Inference framework suggests that while pre-existing spatial biases for central locations exert some influence, biases in the sensory representations of both visual and auditory space are necessary to fully explain the behavioral data. How are these opposing visual and auditory biases reconciled in conditions in which both auditory and visual stimuli are produced by a single event? Potentially, the bias in one modality could dominate, or the biases could interact/cancel out. The data revealed that when integration occurred in these conditions, the visual bias dominated, but the magnitude of this bias was reduced compared to unisensory conditions. Therefore, multisensory integration not only improves the

  19. Biases in Visual, Auditory, and Audiovisual Perception of Space.

    PubMed

    Odegaard, Brian; Wozny, David R; Shams, Ladan

    2015-12-01

    Localization of objects and events in the environment is critical for survival, as many perceptual and motor tasks rely on estimation of spatial location. Therefore, it seems reasonable to assume that spatial localizations should generally be accurate. Curiously, some previous studies have reported biases in visual and auditory localizations, but these studies have used small sample sizes and the results have been mixed. Therefore, it is not clear (1) if the reported biases in localization responses are real (or due to outliers, sampling bias, or other factors), and (2) whether these putative biases reflect a bias in sensory representations of space or a priori expectations (which may be due to the experimental setup, instructions, or distribution of stimuli). Here, to address these questions, a dataset of unprecedented size (obtained from 384 observers) was analyzed to examine presence, direction, and magnitude of sensory biases, and quantitative computational modeling was used to probe the underlying mechanism(s) driving these effects. Data revealed that, on average, observers were biased towards the center when localizing visual stimuli, and biased towards the periphery when localizing auditory stimuli. Moreover, quantitative analysis using a Bayesian Causal Inference framework suggests that while pre-existing spatial biases for central locations exert some influence, biases in the sensory representations of both visual and auditory space are necessary to fully explain the behavioral data. How are these opposing visual and auditory biases reconciled in conditions in which both auditory and visual stimuli are produced by a single event? Potentially, the bias in one modality could dominate, or the biases could interact/cancel out. The data revealed that when integration occurred in these conditions, the visual bias dominated, but the magnitude of this bias was reduced compared to unisensory conditions. Therefore, multisensory integration not only improves the

  20. 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.

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

    DOE PAGES

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

    2015-10-01

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

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

    PubMed

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

  4. 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

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

  6. Gender Bias in Lebanese Language Classes

    ERIC Educational Resources Information Center

    Mougharbel, Ghada M.; Bahous, Rima

    2010-01-01

    Gender bias, though often implicit and unnoticed, exists in many forms and in different situations. The purpose of this study is to investigate whether gender bias exists in Lebanese language classrooms. Semi-structured interviews, questionnaires, and nonparticipant observational techniques were used for data collection. Results reveal…

  7. Analysis of phylogeny and codon usage bias and relationship of GC content, amino acid composition with expression of the structural nif genes.

    PubMed

    Mondal, Sunil Kanti; Kundu, Sudip; Das, Rabindranath; Roy, Sujit

    2016-08-01

    Bacteria and archaea have evolved with the ability to fix atmospheric dinitrogen in the form of ammonia, catalyzed by the nitrogenase enzyme complex which comprises three structural genes nifK, nifD and nifH. The nifK and nifD encodes for the beta and alpha subunits, respectively, of component 1, while nifH encodes for component 2 of nitrogenase. Phylogeny based on nifDHK have indicated that Cyanobacteria is closer to Proteobacteria alpha and gamma but not supported by the tree based on 16SrRNA. The evolutionary ancestor for the different trees was also different. The GC1 and GC2% analysis showed more consistency than GC3% which appeared to below for Firmicutes, Cyanobacteria and Euarchaeota while highest in Proteobacteria beta and clearly showed the proportional effect on the codon usage with a few exceptions. Few genes from Firmicutes, Euryarchaeota, Proteobacteria alpha and delta were found under mutational pressure. These nif genes with low and high GC3% from different classes of organisms showed similar expected number of codons. Distribution of the genes and codons, based on codon usage demonstrated opposite pattern for different orientation of mirror plane when compared with each other. Overall our results provide a comprehensive analysis on the evolutionary relationship of the three structural nif genes, nifK, nifD and nifH, respectively, in the context of codon usage bias, GC content relationship and amino acid composition of the encoded proteins and exploration of crucial statistical method for the analysis of positive data with non-constant variance to identify the shape factors of codon adaptation index.

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

    NASA Astrophysics Data System (ADS)

    Kim, Juhyung; Terry, Paul W.

    2010-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  10. 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.

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

    PubMed

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

    2014-08-28

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

  12. 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.

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

    SciTech Connect

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

    2014-01-28

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

  14. 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

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

    SciTech Connect

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

    2006-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    PubMed

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

    2016-02-14

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

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

    PubMed

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

    2016-06-01

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

  19. Switching of perpendicular exchange bias in Pt/Co/Pt/α-Cr{sub 2}O{sub 3}/Pt layered structure using magneto-electric effect

    SciTech Connect

    Toyoki, Kentaro; Shiratsuchi, Yu Kobane, Atsushi; Harimoto, Shotaro; Onoue, Satoshi; Nomura, Hikaru; Nakatani, Ryoichi

    2015-05-07

    Switching of the perpendicular exchange bias polarity using a magneto-electric (ME) effect of α-Cr{sub 2}O{sub 3} was investigated. From the change in the exchange bias field with the electric field during the ME field cooling, i.e., the simultaneous application of both magnetic and electric fields during the cooling, we determined the threshold electric field to switch the perpendicular exchange bias polarity. It was found that the threshold electric field was inversely proportional to the magnetic field indicating that the EH product was constant. The high EH product was required to switch the exchange bias for the film possessing the high exchange anisotropy energy density, which suggests that the energy gain by the ME effect has to overcome the interfacial exchange coupling energy to reverse the interfacial antiferromagnetic spin.

  20. 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.

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

    PubMed

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

    2013-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Shimada, Ryoko; Sakai, Hitomi

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

  3. 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.

  4. 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.

  5. 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.

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

    PubMed Central

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

    2010-01-01

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

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

    SciTech Connect

    Liakh, Dmitry I

    2014-01-01

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

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

    SciTech Connect

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

    2015-06-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Weeks, John D.

    2002-10-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1987-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    SciTech Connect

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

    2012-03-07

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

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

    PubMed

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

    2012-07-28

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

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

    PubMed

    Bonyár, Attila

    2016-08-01

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

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

    SciTech Connect

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

    2007-04-01

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

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

    SciTech Connect

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

    2006-09-25

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

  19. 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.

  20. 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.

  1. 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.

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

    NASA Astrophysics Data System (ADS)

    Ciambella, J.; Vestroni, F.

    2015-03-01

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

  3. 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.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2012-07-01

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

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

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

    PubMed Central

    2015-01-01

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

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

    PubMed Central

    Kim, Youngwoong; Kim, Keonwook

    2015-01-01

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

  10. 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

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

    PubMed

    Kim, Youngwoong; Kim, Keonwook

    2015-01-01

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

  12. 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

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

    NASA Astrophysics Data System (ADS)

    Qiu, Xiangyun

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

  14. Bias field tailored plasmonic nano-electrode for high-power terahertz photonic devices

    PubMed Central

    Moon, Kiwon; Lee, Il-Min; Shin, Jun-Hwan; Lee, Eui Su; Kim, Namje; Lee, Won-Hui; Ko, Hyunsung; Han, Sang-Pil; Park, Kyung Hyun

    2015-01-01

    Photoconductive antennas with nano-structured electrodes and which show significantly improved performances have been proposed to satisfy the demand for compact and efficient terahertz (THz) sources. Plasmonic field enhancement was previously considered the dominant mechanism accounting for the improvements in the underlying physics. However, we discovered that the role of plasmonic field enhancement is limited and near-field distribution of bias field should be considered as well. In this paper, we clearly show that the locally enhanced bias field due to the size effect is much more important than the plasmonic enhanced absorption in the nano-structured electrodes for the THz emitters. Consequently, an improved nano-electrode design is presented by tailoring bias field distribution and plasmonic enhancement. Our findings will pave the way for new perspectives in the design and analysis of plasmonic nano-structures for more efficient THz photonic devices. PMID:26347288

  15. Bias field tailored plasmonic nano-electrode for high-power terahertz photonic devices.

    PubMed

    Moon, Kiwon; Lee, Il-Min; Shin, Jun-Hwan; Lee, Eui Su; Kim, Namje; Lee, Won-Hui; Ko, Hyunsung; Han, Sang-Pil; Park, Kyung Hyun

    2015-01-01

    Photoconductive antennas with nano-structured electrodes and which show significantly improved performances have been proposed to satisfy the demand for compact and efficient terahertz (THz) sources. Plasmonic field enhancement was previously considered the dominant mechanism accounting for the improvements in the underlying physics. However, we discovered that the role of plasmonic field enhancement is limited and near-field distribution of bias field should be considered as well. In this paper, we clearly show that the locally enhanced bias field due to the size effect is much more important than the plasmonic enhanced absorption in the nano-structured electrodes for the THz emitters. Consequently, an improved nano-electrode design is presented by tailoring bias field distribution and plasmonic enhancement. Our findings will pave the way for new perspectives in the design and analysis of plasmonic nano-structures for more efficient THz photonic devices. PMID:26347288

  16. 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.

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

    PubMed

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

    2015-07-30

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  19. 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

  20. 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…

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

    PubMed

    Lerman-Sinkoff, Dov B; Barch, Deanna M

    2016-01-01

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

  2. 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

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

    PubMed

    Lerman-Sinkoff, Dov B; Barch, Deanna M

    2016-01-01

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

  4. Local Structure, Electronic Behavior, and Electrocatalytic Reactivity of CO-Reduced Platinum-Iron Oxide Nanoparticles

    SciTech Connect

    Duchesne, Paul N.; Chen, Guangxu; Zheng, Nanfeng; Zhang, Peng

    2014-02-18

    A series of platinum–iron oxide nanoparticles was synthesized using a “clean” CO-reduction method that employed different ratios of Pt-Fe precursor salts in oleylamine at elevated temperatures. High-resolution transmission electron microscopy (HRTEM) and energy-dispersive X-ray spectroscopy (EDS) studies revealed that nearly monodisperse (i.e., with relative standard deviations of less than 15%) nanoparticles with mean diameters of 3.5–4.4 nm and varied elemental compositions (Pt54Fe46 Pt70Fe30, and Pt87Fe13) were obtained. X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) measurements at the Pt L3- and Fe K-edges revealed that these nanoparticles all consisted of a Pt core with amorphous iron oxide on the surface. Furthermore, it was observed that the local structure (e.g., Pt–Pt bond distance and coordination number) and electronic behavior of the Pt–FeO nanoparticles (e.g., Pt d electron density and Fe valence state) are dependent on the Pt-Fe precursor ratios used in their synthesis. Quantum mechanical ab initio calculations were employed to interpret the results from X-ray spectroscopy and help elucidate the relationships between local structure and electronic properties in the nanoparticle samples. Finally, the surface reactivity of these nanoparticles in the oxygen reduction reaction (ORR) was explored, demonstrating higher electrocatalytic activity for all three platinum–iron oxide samples in comparison with a commercial Pt catalyst. The surface reactivity was also found to be sensitive to the Pt-Fe ratios of the nanoparticles and could be correlated with their local structure and electronic behavior.

  5. Interpretation biases in paranoia.

    PubMed

    Savulich, George; Freeman, Daniel; Shergill, Sukhi; Yiend, Jenny

    2015-01-01

    Information in the environment is frequently ambiguous in meaning. Emotional ambiguity, such as the stare of a stranger, or the scream of a child, encompasses possible good or bad emotional consequences. Those with elevated vulnerability to affective disorders tend to interpret such material more negatively than those without, a phenomenon known as "negative interpretation bias." In this study we examined the relationship between vulnerability to psychosis, measured by trait paranoia, and interpretation bias. One set of material permitted broadly positive/negative (valenced) interpretations, while another allowed more or less paranoid interpretations, allowing us to also investigate the content specificity of interpretation biases associated with paranoia. Regression analyses (n=70) revealed that trait paranoia, trait anxiety, and cognitive inflexibility predicted paranoid interpretation bias, whereas trait anxiety and cognitive inflexibility predicted negative interpretation bias. In a group comparison those with high levels of trait paranoia were negatively biased in their interpretations of ambiguous information relative to those with low trait paranoia, and this effect was most pronounced for material directly related to paranoid concerns. Together these data suggest that a negative interpretation bias occurs in those with elevated vulnerability to paranoia, and that this bias may be strongest for material matching paranoid beliefs. We conclude that content-specific biases may be important in the cause and maintenance of paranoid symptoms.

  6. Global localization of 3D anatomical structures by pre-filtered Hough forests and discrete optimization.

    PubMed

    Donner, René; Menze, Bjoern H; Bischof, Horst; Langs, Georg

    2013-12-01

    The accurate localization of anatomical landmarks is a challenging task, often solved by domain specific approaches. We propose a method for the automatic localization of landmarks in complex, repetitive anatomical structures. The key idea is to combine three steps: (1) a classifier for pre-filtering anatomical landmark positions that (2) are refined through a Hough regression model, together with (3) a parts-based model of the global landmark topology to select the final landmark positions. During training landmarks are annotated in a set of example volumes. A classifier learns local landmark appearance, and Hough regressors are trained to aggregate neighborhood information to a precise landmark coordinate position. A non-parametric geometric model encodes the spatial relationships between the landmarks and derives a topology which connects mutually predictive landmarks. During the global search we classify all voxels in the query volume, and perform regression-based agglomeration of landmark probabilities to highly accurate and specific candidate points at potential landmark locations. We encode the candidates' weights together with the conformity of the connecting edges to the learnt geometric model in a Markov Random Field (MRF). By solving the corresponding discrete optimization problem, the most probable location for each model landmark is found in the query volume. We show that this approach is able to consistently localize the model landmarks despite the complex and repetitive character of the anatomical structures on three challenging data sets (hand radiographs, hand CTs, and whole body CTs), with a median localization error of 0.80 mm, 1.19 mm and 2.71 mm, respectively. PMID:23664450

  7. Global localization of 3D anatomical structures by pre-filtered Hough Forests and discrete optimization

    PubMed Central

    Donner, René; Menze, Bjoern H.; Bischof, Horst; Langs, Georg

    2013-01-01

    The accurate localization of anatomical landmarks is a challenging task, often solved by domain specific approaches. We propose a method for the automatic localization of landmarks in complex, repetitive anatomical structures. The key idea is to combine three steps: (1) a classifier for pre-filtering anatomical landmark positions that (2) are refined through a Hough regression model, together with (3) a parts-based model of the global landmark topology to select the final landmark positions. During training landmarks are annotated in a set of example volumes. A classifier learns local landmark appearance, and Hough regressors are trained to aggregate neighborhood information to a precise landmark coordinate position. A non-parametric geometric model encodes the spatial relationships between the landmarks and derives a topology which connects mutually predictive landmarks. During the global search we classify all voxels in the query volume, and perform regression-based agglomeration of landmark probabilities to highly accurate and specific candidate points at potential landmark locations. We encode the candidates’ weights together with the conformity of the connecting edges to the learnt geometric model in a Markov Random Field (MRF). By solving the corresponding discrete optimization problem, the most probable location for each model landmark is found in the query volume. We show that this approach is able to consistently localize the model landmarks despite the complex and repetitive character of the anatomical structures on three challenging data sets (hand radiographs, hand CTs, and whole body CTs), with a median localization error of 0.80 mm, 1.19 mm and 2.71 mm, respectively. PMID:23664450

  8. 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.

  9. The effect of static and dynamic spatially structured disturbances on a locally dispersing population.

    PubMed

    Hiebeler, David E; Morin, Benjamin R

    2007-05-01

    Previous models of locally dispersing populations have shown that in the presence of spatially structured fixed habitat heterogeneity, increasing local spatial autocorrelation in habitat generally has a beneficial effect on such populations, increasing equilibrium population density. It has also been shown that with large-scale disturbance events which simultaneously affect contiguous blocks of sites, increasing spatial autocorrelation in the disturbances has a harmful effect, decreasing equilibrium population density. Here, spatial population models are developed which include both of these spatially structured exogenous influences, to determine how they interact with each other and with the endogenously generated spatial structure produced by the population dynamics. The models show that when habitat is fragmented and disturbance occurs at large spatial scales, the population cannot persist no matter how large its birth rate, an effect not seen in previous simpler models of this type. The behavior of the model is also explored when the local autocorrelation of habitat heterogeneity and disturbance events are equal, i.e. the two effects occur at the same spatial scale. When this scale parameter is very small, habitat fragmentation prevents the population from persisting because sites attempting to reproduce will drop most of their offspring on unsuitable sites; when the parameter is very large, large-scale disturbance events drive the population to extinction. Population levels reach their maximum at intermediate values of the scale parameter, and the critical values in the model show that the population will persist most easily at these intermediate scales of spatial influences. The models are investigated via spatially explicit stochastic simulations, traditional (infinite-dispersal) and improved (local-dispersal) mean-field approximations, and pair approximations.

  10. Demographic History, Population Structure, and Local Adaptation in Alpine Populations of Cardamine impatiens and Cardamine resedifolia

    PubMed Central

    Ometto, Lino; Li, Mingai; Bresadola, Luisa; Barbaro, Enrico; Neteler, Markus; Varotto, Claudio

    2015-01-01

    Species evolution depends on numerous and distinct forces, including demography and natural selection. For example, local adaptation and population structure affect the evolutionary history of species living along environmental clines. This is particularly relevant in plants, which are often characterized by limited dispersal ability and the need to respond to abiotic and biotic stress factors specific to the local environment. Here we study the demographic history and the possible existence of local adaptation in two related species of Brassicaceae, Cardamine impatiens and Cardamine resedifolia, which occupy separate habitats along the elevation gradient. Previous genome-wide analyses revealed the occurrence of distinct selective pressures in the two species, with genes involved in cold response evolving particularly fast in C. resedifolia. In this study we surveyed patterns of molecular evolution and genetic variability in a set of 19 genes, including neutral and candidate genes involved in cold response, across 10 populations each of C. resedifolia and C. impatiens from the Italian Alps (Trentino). We inferred the population structure and demographic history of the two species, and tested the occurrence of signatures of local adaptation in these genes. The results indicate that, despite a slightly higher population differentiation in C. resedifolia than in C. impatiens, both species are only weakly structured and that populations sampled at high altitude experience less gene flow than low-altitude ones. None of the genes showed signatures of positive selection, suggesting that they do not seem to play relevant roles in the current evolutionary processes of adaptation to alpine environments of these species. PMID:25933225

  11. 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.

  12. 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.

  13. Effects of Anions on Local Structure of Al and Si in Aluminosilicates.

    PubMed

    Miyazaki; Yokoyama

    1999-06-15

    Three kinds of amorphous aluminosilicates were synthesized by coprecipitation of silicic acid with aluminum hydroxide in the presence of different inorganic ions: sulfate, chloride, and nitrate. Although the bulk composition of the aluminosilicates obtained was not affected by anion species, their DTA spectra were significantly different, suggesting that their structures also differ. The local structure of Al and Si in the aluminosilicates was studied in detail by 27Al and 29Si MAS NMR. From the 27Al MAS NMR spectra and comparison between 29Si HD- and CP-MAS NMR spectra, it was concluded that the aluminosilicate obtained in the presence of sulfate ions has only a montmorillonite-like structure, whereas in the cases of chloride and nitrate, the solids are composed of three phases: aluminum hydroxide, silica, and the montmorillonite-like aluminosilicate. The difference in the local structure of Al and Si in the aluminosilicates was explained by the difference in interaction between the anions and aluminum ions. Copyright 1999 Academic Press.

  14. Effects of anions on local structure of Al and Si in aluminosilicates

    SciTech Connect

    Miyazaki, Akane; Yokoyama, Takushi

    1999-06-15

    Three kinds of amorphous aluminosilicates were synthesized by coprecipitation of silicic acid with aluminum hydroxide in the presence of different inorganic ions: sulfate, chloride, and nitrate. Although the bulk composition of the aluminosilicates obtained was not affected by anion species, their DTA spectra were significantly different, suggesting that their structures also differ. The local structure of Al and Si in the aluminosilicates was studied in detail by {sup 27}Al and {sup 29}Si MAS NMR. From the {sup 27}Al MAS NMR spectra and comparison between {sup 29}Si HD- and CP-MAS NMR spectra, it was concluded that the aluminosilicate obtained in the presence of sulfate ions has only a montmorillonite-like structure, whereas in the cases of chloride and nitrate, the solids are composed of three phases: aluminum hydroxide, silica, and the montmorillonite-like aluminosilicate. The difference in the local structure of Al and Si in the aluminosilicates was explained by the difference in interaction between the anions and aluminum ions.

  15. 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.

  16. Local structure of Ge quantum dots determined by combined numerical analysis of EXAFS and XANES data.

    PubMed

    Zhang, Yuanpeng; Ersoy, Osman; Karatutlu, Ali; Little, William; Sapelkin, Andrei

    2016-01-01

    The sensitivity of X-ray absorption near-edge structure (XANES) to the local symmetry has been investigated in small (∼4 nm) matrix-free Ge quantum dots. The FDMNES package was used to calculate the theoretical XANES spectra that were compared with the experimental data of as-prepared and annealed nanoparticles. It was found that XANES data for an as-prepared sample can only be adequately described if the second coordination shell of the diamond-type structural model is included in the FDMNES calculations. This is in contrast to the extended X-ray absorption fine-structure data that show only the first-shell signal. These results suggest that, despite the high degree of disorder and a large surface-to-volume ratio, as-prepared small Ge quantum dots retain the diamond-type symmetry beyond the first shell. Furthermore, we utilized this sensitivity of XANES to the local symmetry to study annealed Ge quantum dots and found evidence for significant structural distortion which we attribute to the existence of surface disorder in the annealed oxygen-free Ge quantum dots. PMID:26698071

  17. Diversity, population structure, and evolution of local peach cultivars in China identified by simple sequence repeats.

    PubMed

    Shen, Z J; Ma, R J; Cai, Z X; Yu, M L; Zhang, Z

    2015-01-15

    The fruit peach originated in China and has a history of domestication of more than 4000 years. Numerous local cultivars were selected during the long course of cultivation, and a great morphological diversity exists. To study the diversity and genetic background of local peach cultivars in China, a set of 158 accessions from different ecological regions, together with 27 modern varieties and 10 wild accessions, were evaluated using 49 simple sequence repeats (SSRs) covering the peach genome. Broad diversity was also observed in local cultivars at the SSR level. A total of 648 alleles were amplified with an average of 13.22 observed alleles per locus. The number of genotypes detected ranged from 9 (UDP96015) to 58 (BPPCT008) with an average of 27.00 genotypes per marker. Eight subpopulations divided by STRUCTURE basically coincided with the dendrogram of genetic relationships and could be explained by the traditional groups. The 8 subpopulations were juicy honey peach, southwestern peach I, wild peach, Buddha peach + southwestern peach II, northern peach, southern crisp peach, ornamental peach, and Prunus davidiana + P. kansuensis. Most modern varieties carried the genetic backgrounds of juicy honey peach and southwestern peach I, while others carried diverse genetic backgrounds, indicating that local cultivars were partly used in modern breeding programs. Based on the traditional evolution pathway, a modified pathway for the development of local peach cultivars in China was proposed using the genetic background of subpopulations that were identified by SSRs. Current status and prospects of utilization of Chinese local peach cultivars were also discussed according to the SSR information.

  18. In situ localization of mRNAs coding for mouse testicular structural genes

    SciTech Connect

    Hecht, N.B. ); Penshow, J.D. )

    1987-11-01

    In situ hybridization histochemistry has been used to localize mRNA transcripts of five nuclear and cytoplasmic structural genes in the mouse testis. The mRNAs for three nuclear structural proteins involved in chromatin transformation during spermatogenesis (the two protamine variants of the mouse and one of the testis-specific proteins) are restricted solely to postmeiotic germ cells. In contrast, mRNAs for two other structural proteins, actin and {alpha} tubulin, are detected throughout spermatogenesis. Although present in premeiotic, meiotic, and postmeiotic cell types, the mRNA levels of actin and {alpha} tubulin differ considerably during spermiogenesis, the haploid phase of spermatogenesis. Actin mRNA levels decrease markedly as the male gamete differentiates during spermiogenesis whereas {alpha}-tubulin mRNAs are equally abundant in the haploid round and elongating spermatids.

  19. 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.

  20. 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.

  1. G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design.

    PubMed

    Lee, Hui Sun; Im, Wonpil

    2016-04-01

    Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G-LoSA. G-LoSA aligns protein local structures in a sequence order independent way and provides a GA-score, a chemical feature-based and size-independent structure similarity score. Our benchmark validation shows the robust performance of G-LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure-centric comparative biology studies. In particular, G-LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G-LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer-aided drug design. We hope that G-LoSA can be a useful computational method for exploring interesting biological problems through large-scale comparison of protein local structures and facilitating drug discovery research and development. G-LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/. PMID:26813336

  2. Localized heuristic inverse quantitative structure activity relationship with bulk descriptors using numerical gradients.

    PubMed

    Stålring, Jonna; Almeida, Pedro R; Carlsson, Lars; Helgee Ahlberg, Ernst; Hasselgren, Catrin; Boyer, Scott

    2013-08-26

    State-of-the-art quantitative structure-activity relationship (QSAR) models are often based on nonlinear machine learning algorithms, which are difficult to interpret. From a pharmaceutical perspective, QSARs are used to enhance the chemical design process. Ultimately, they should not only provide a prediction but also contribute to a mechanistic understanding and guide modifications to the chemical structure, promoting compounds with desirable biological activity profiles. Global ranking of descriptor importance and inverse QSAR have been used for these purposes. This paper introduces localized heuristic inverse QSAR, which provides an assessment of the relative ability of the descriptors to influence the biological response in an area localized around the predicted compound. The method is based on numerical gradients with parameters optimized using data sets sampled from analytical functions. The heuristic character of the method reduces the computational requirements and makes it applicable not only to fragment based methods but also to QSARs based on bulk descriptors. The application of the method is illustrated on congeneric QSAR data sets, and it is shown that the predicted influential descriptors can be used to guide structural modifications that affect the biological response in the desired direction. The method is implemented into the AZOrange Open Source QSAR package. The current implementation of localized heuristic inverse QSAR is a step toward a generally applicable method for elucidating the structure activity relationship specifically for a congeneric region of chemical space when using QSARs based on bulk properties. Consequently, this method could contribute to accelerating the chemical design process in pharmaceutical projects, as well as provide information that could enhance the mechanistic understanding for individual scaffolds.

  3. 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.

  4. Structural and electronic properties of trans-polyacetylene under local strain

    NASA Astrophysics Data System (ADS)

    Ketabi, S. A.

    2016-06-01

    A theoretical study is presented to investigate the structural and electronic properties of trans-polyacetylene (trans-PA) molecule under local strain. The influence of a local bending or compression of the space between neighboring carbon atoms on the band gap of the molecule was studied. Making use of an effective difference equation based on tight-binding procedure the band structure of trans-PA has been calculated. Our results indicate that the energy gap of the strained molecule modified significantly which affects the electronic properties of the molecule. We found that the size of the molecular gap is proportional to the bending angle so that for the bending perpendicular to π-orbitals plane the band gap reduced drastically and for the parallel one the band gap gradually increased. Furthermore, the current-voltage characteristics of the strained trans-PA molecule are studied. We found that under the local strain the threshold voltage for the current flow through the bent molecule decreased (increased) depending on the bending is perpendicular (parallel) to the molecule plane.

  5. 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.

  6. 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.

  7. Jumping to conclusions, a lack of belief flexibility and delusional conviction in psychosis: a longitudinal investigation of the structure, frequency, and relatedness of reasoning biases.

    PubMed

    So, Suzanne H; Freeman, Daniel; Dunn, Graham; Kapur, Shitij; Kuipers, Elizabeth; Bebbington, Paul; Fowler, David; Garety, Philippa A

    2012-02-01

    Two reasoning biases, jumping to conclusions (JTC) and belief inflexibility, have been found to be associated with delusions. We examined these biases and their relationship with delusional conviction in a longitudinal cohort of people with schizophrenia-spectrum psychosis. We hypothesized that JTC, lack of belief flexibility, and delusional conviction would form distinct factors, and that JTC and lack of belief flexibility would predict less change in delusional conviction over time. Two hundred seventy-three patients with delusions were assessed over twelve months of a treatment trial (Garety et al., 2008). Forty-one percent of the sample had 100% conviction in their delusions, 50% showed a JTC bias, and 50%-75% showed a lack of belief flexibility. Delusional conviction, JTC, and belief flexibility formed distinct factors although conviction was negatively correlated with belief flexibility. Conviction declined slightly over the year in this established psychosis group, whereas the reasoning biases were stable. There was little evidence that reasoning predicted the slight decline in conviction. The degree to which people believe their delusions, their ability to think that they may be mistaken and to consider alternative explanations, and their hastiness in decision making are three distinct processes although belief flexibility and conviction are related. In this established psychosis sample, reasoning biases changed little in response to medication or psychological therapy. Required now is examination of these processes in psychosis groups where there is greater change in delusion conviction, as well as tests of the effects on delusions when these reasoning biases are specifically targeted. PMID:21910515

  8. Political bias is tenacious.

    PubMed

    Ditto, Peter H; Wojcik, Sean P; Chen, Eric Evan; Grady, Rebecca Hofstein; Ringel, Megan M

    2015-01-01

    Duarte et al. are right to worry about political bias in social psychology but they underestimate the ease of correcting it. Both liberals and conservatives show partisan bias that often worsens with cognitive sophistication. More non-liberals in social psychology is unlikely to speed our convergence upon the truth, although it may broaden the questions we ask and the data we collect.

  9. Investigating Test Bias.

    ERIC Educational Resources Information Center

    Hoepfner, Ralph; Strickland, Guy P.

    This study investigates the question of test bias to develop an index of the appropriateness of a test to a particular socioeconomic or racial-ethnic group. Bias is defined as an item by race interaction in an analysis-of-variance design. The sample of 172 third graders at two integrated schools in a large California school district, included 26…

  10. Sampler bias -- Phase 1

    SciTech Connect

    Blanchard, R.J.

    1995-03-07

    This documents Phase 1 determinations on sampler induced bias for four sampler types used in tank characterization. Each sampler, grab sampler or bottle-on-a-string, auger sampler, sludge sampler and universal sampler, is briefly discussed and their physical limits noted. Phase 2 of this document will define additional testing and analysis to further define Sampler Bias.

  11. Localized structures and front propagation in the Lengyel-Epstein model

    SciTech Connect

    Jensen, O.; Pannbacker, V.O.; Mosekilde, E.; Dewel, G.; Borckmans, P. Service de Chimie-Physique, Code Postal 231 Universite Libre de Bruxelles, 1050 Brussels )

    1994-08-01

    Pattern selection, localized structure formation, and front propagation are analyzed within the framework of a model for the chlorine dioxide--iodine--malonic acid reaction that represents a key to understanding recently obtained Turing structures. This model is distinguished from previously studied, simple reaction-diffusion models by producing a strongly subcritical transition to stripes. The wave number for the modes of maximum linear gain is calculated and compared with the dominant wave number for the finally selected, stationary structures grown from the homogeneous steady state or developed behind a traveling front. The speed of propagation for a front between the homogeneous steady state and a one-dimensional (1D) Turing structure is obtained. This velocity shows a characteristic change in behavior at the crossover between the subcritical and supercritical regimes for the Turing bifurcation. In the subcritical regime there is an interval where the front velocity vanishes as a result of a pinning of the front to the underlying structure. In 2D, two different nucleation mechanisms for hexagonal structures are illustrated on the Lengyel-Epstein and the Brusselator model. Finally, the observation of 1D and 2D spirals with Turing-induced cores is reported.

  12. Local weighting of nanometric track structure properties in macroscopic voxel geometries for particle beam treatment planning

    NASA Astrophysics Data System (ADS)

    Alexander, F.; Villagrasa, C.; Rabus, H.; Wilkens, J. J.

    2015-12-01

    The research project BioQuaRT within the European Metrology Research Programme aimed at correlating ion track structure characteristics with the biological effects of radiation and developed measurement and simulation techniques for determining ion track structure on different length scales from about 2 nm to about 10 μm. Within this framework, we investigated methods to translate track-structure quantities derived on a nanometre scale to macroscopic dimensions. Here we make use of parameterizations that link the energy of the projectile to the ionization pattern of the track using nanodosimetric ionization cluster size distributions. They were defined with data generated by simulations of ion tracks in liquid water using the Geant4 Monte Carlo toolkit with the Geant4-DNA processes. For the clinical situation with a mixed radiation field, where particles of various energies hit a cell from several directions, we have to find macroscopic relevant mean values. They can be determined by appropriate local weighting functions for the identified parameterization. We show that a stopping power weighted mean value of the mentioned track structure properties can describe the overall track structure in a cell exposed to a mixed radiation field. The parameterization, together with the presented stopping power weighting approach, show how nanometric track structure properties could be integrated into treatment planning systems without the need to perform time consuming simulations on the nanometer level for each individual patient.

  13. The local structure of SrLaGaO 4:Cr 3+ crystal

    NASA Astrophysics Data System (ADS)

    Zeng, Ti-Xian; Chen, Jia-Jun; Zhao, Bei-Jun; Zhu, Shi-Fu; Huang, Yi; Chen, Tai-Hong

    2008-07-01

    The local tetragonal distortion in the vicinity of substitutional Cr 3+ impurities in SrLaGaO 4 crystal was determined by fitting the calculated optical spectra and EPR parameter to the experimental values based on Zhao's semi-SCF d-orbit wave functions model of free Cr 3+ ions, the point-charge crystal field model and Macfarlane's perturbation loop method. This paper found that the local structures of SrLaGaO 4 were: R⊥‧=0.1907 nm and R∥‧=0.2237 nm (where R⊥‧ and R∥‧ denoted Cr 3+-O 2- distances perpendicular to and parallel with the C4 axis). The results agreed well with the experimental findings.

  14. Boundary-locality and perturbative structure of entanglement spectra in gapped systems.

    PubMed

    Alba, Vincenzo; Haque, Masudul; Läuchli, Andreas M

    2012-06-01

    The entanglement between two parts of a many-body system can be characterized in detail by the entanglement spectrum. Focusing on gapped phases of several one-dimensional systems, we show how this spectrum is dominated by contributions from the boundary between the parts. This contradicts the view of an "entanglement Hamiltonian" as a bulk entity. The boundary-local nature of the entanglement spectrum is clarified through its hierarchical level structure, through the combination of two single-boundary spectra to form a two-boundary spectrum, and finally through consideration of dominant eigenfunctions of the entanglement Hamiltonian. We show consequences of boundary-locality for perturbative calculations of the entanglement spectrum.

  15. The crystal structure of human adenylate kinase 6: An adenylate kinase localized to the cell nucleus.

    PubMed

    Ren, Hui; Wang, Liya; Bennett, Matthew; Liang, Yuhe; Zheng, Xiaofeng; Lu, Fei; Li, Lanfen; Nan, Jie; Luo, Ming; Eriksson, Staffan; Zhang, Chuanmao; Su, Xiao-Dong

    2005-01-11

    Adenylate kinases (AKs) play important roles in nucleotide metabolism in all organisms and in cellular energetics by means of phosphotransfer networks in eukaryotes. The crystal structure of a human AK named AK6 was determined by in-house sulfur single-wavelength anomalous dispersion phasing methods and refined to 2.0-A resolution with a free R factor of 21.8%. Sequence analyses revealed that human AK6 belongs to a distinct subfamily of AKs present in all eukaryotic organisms sequenced so far. Enzymatic assays show that human AK6 has properties similar with other AKs, particularly with AK5. Fluorescence microscopy showed that human AK6 is localized predominantly to the nucleus of HeLa cells. The identification of a nuclear-localized AK sheds light on nucleotide metabolism in the nucleus and the energetic communication between mitochondria and nucleus by means of phosphotransfer networks.

  16. 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.

  17. Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

    PubMed Central

    Montano, Valeria; Didelot, Xavier; Foll, Matthieu; Linz, Bodo; Reinhardt, Richard; Suerbaum, Sebastian; Moodley, Yoshan; Jensen, Jeffrey D.

    2015-01-01

    Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g., transcription elongation factor NusA and tumor necrosis factor alpha-inducing protein Tipα) and hitherto unknown functional genes. PMID:25995212

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

    PubMed Central

    Gao, Zhen; Gao, Fei; Zhang, Baile

    2016-01-01

    We experimentally demonstrate that multiple high-order spoof localized surface plasmons (spoof-LSPs) modes can be supported on a complementary metallic spiral structure, which were absent in the previously reported spoof-LSPs modes. Through exact numerical simulations and near-field imaging experiments, we directly observe these high-order spoof-LSPs modes at microwave frequencies. We also show that these higher-order spoof-LSPs modes exhibit larger frequency shifts caused by the local environmental refractive index change than the previously reported low-order spoof-LSPs modes. Hence the complementary MSS may find potential applications as plasmonic sensor in the microwave and terahertz frequencies. PMID:27079658

  19. Gas phase structures and charge localization in small aluminum oxide anions: Infrared photodissociation spectroscopy and electronic structure calculations.

    PubMed

    Song, Xiaowei; Fagiani, Matias R; Gewinner, Sandy; Schöllkopf, Wieland; Asmis, Knut R; Bischoff, Florian A; Berger, Fabian; Sauer, Joachim

    2016-06-28

    We use cryogenic ion trap vibrational spectroscopy in combination with quantum chemical calculations to study the structure of mono- and dialuminum oxide anions. The infrared photodissociation spectra of D2-tagged AlO1-4 (-) and Al2O3-6 (-) are measured in the region from 400 to 1200 cm(-1). Structures are assigned based on a comparison to simulated harmonic and anharmonic IR spectra derived from electronic structure calculations. The monoaluminum anions contain an even number of electrons and exhibit an electronic closed-shell ground state. The Al2O3-6 (-) anions are oxygen-centered radicals. As a result of a delicate balance between localization and delocalization of the unpaired electron, only the BHLYP functional is able to qualitatively describe the observed IR spectra of all species with the exception of AlO3 (-). Terminal Al-O stretching modes are found between 1140 and 960 cm(-1). Superoxo and peroxo stretching modes are found at higher (1120-1010 cm(-1)) and lower energies (850-570 cm(-1)), respectively. Four modes in-between 910 and 530 cm(-1) represent the IR fingerprint of the common structural motif of dialuminum oxide anions, an asymmetric four-member Al-(O)2-Al ring. PMID:27369513

  20. Gas phase structures and charge localization in small aluminum oxide anions: Infrared photodissociation spectroscopy and electronic structure calculations

    NASA Astrophysics Data System (ADS)

    Song, Xiaowei; Fagiani, Matias R.; Gewinner, Sandy; Schöllkopf, Wieland; Asmis, Knut R.; Bischoff, Florian A.; Berger, Fabian; Sauer, Joachim

    2016-06-01

    We use cryogenic ion trap vibrational spectroscopy in combination with quantum chemical calculations to study the structure of mono- and dialuminum oxide anions. The infrared photodissociation spectra of D2-tagged AlO1-4- and Al2O3-6- are measured in the region from 400 to 1200 cm-1. Structures are assigned based on a comparison to simulated harmonic and anharmonic IR spectra derived from electronic structure calculations. The monoaluminum anions contain an even number of electrons and exhibit an electronic closed-shell ground state. The Al2O3-6- anions are oxygen-centered radicals. As a result of a delicate balance between localization and delocalization of the unpaired electron, only the BHLYP functional is able to qualitatively describe the observed IR spectra of all species with the exception of AlO3-. Terminal Al-O stretching modes are found between 1140 and 960 cm-1. Superoxo and peroxo stretching modes are found at higher (1120-1010 cm-1) and lower energies (850-570 cm-1), respectively. Four modes in-between 910 and 530 cm-1 represent the IR fingerprint of the common structural motif of dialuminum oxide anions, an asymmetric four-member Al-(O)2-Al ring.