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Sample records for local structural bias

  1. Local bias-induced phase transitions

    DOE PAGES

    Seal, Katyayani; Baddorf, Arthur P.; Jesse, Stephen; ...

    2008-11-27

    Electrical bias-induced phase transitions underpin a wide range of applications from data storage to energy generation and conversion. The mechanisms behind these transitions are often quite complex and in many cases are extremely sensitive to local defects that act as centers for local transformations or pinning. Furthermore, using ferroelectrics as an example, we review methods for probing bias-induced phase transitions and discuss the current limitations and challenges for extending the methods to field-induced phase transitions and electrochemical reactions in energy storage, biological and molecular systems.

  2. Local gravitational redshifts can bias cosmological measurements

    NASA Astrophysics Data System (ADS)

    Wojtak, Radosław; Davis, Tamara M.; Wiis, Jophiel

    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.

  3. 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.

  4. Investigating bias in squared regression structure coefficients

    PubMed Central

    Nimon, Kim F.; Zientek, Linda R.; Thompson, Bruce

    2015-01-01

    The importance of structure coefficients and analogs of regression weights for analysis within the general linear model (GLM) has been well-documented. The purpose of this study was to investigate bias in squared structure coefficients in the context of multiple regression and to determine if a formula that had been shown to correct for bias in squared Pearson correlation coefficients and coefficients of determination could be used to correct for bias in squared regression structure coefficients. Using data from a Monte Carlo simulation, this study found that squared regression structure coefficients corrected with Pratt's formula produced less biased estimates and might be more accurate and stable estimates of population squared regression structure coefficients than estimates with no such corrections. While our findings are in line with prior literature that identified multicollinearity as a predictor of bias in squared regression structure coefficients but not coefficients of determination, the findings from this study are unique in that the level of predictive power, number of predictors, and sample size were also observed to contribute bias in squared regression structure coefficients. PMID:26217273

  5. Investigating bias in squared regression structure coefficients.

    PubMed

    Nimon, Kim F; Zientek, Linda R; Thompson, Bruce

    2015-01-01

    The importance of structure coefficients and analogs of regression weights for analysis within the general linear model (GLM) has been well-documented. The purpose of this study was to investigate bias in squared structure coefficients in the context of multiple regression and to determine if a formula that had been shown to correct for bias in squared Pearson correlation coefficients and coefficients of determination could be used to correct for bias in squared regression structure coefficients. Using data from a Monte Carlo simulation, this study found that squared regression structure coefficients corrected with Pratt's formula produced less biased estimates and might be more accurate and stable estimates of population squared regression structure coefficients than estimates with no such corrections. While our findings are in line with prior literature that identified multicollinearity as a predictor of bias in squared regression structure coefficients but not coefficients of determination, the findings from this study are unique in that the level of predictive power, number of predictors, and sample size were also observed to contribute bias in squared regression structure coefficients.

  6. Morphology in autism spectrum disorders: local processing bias and language.

    PubMed

    Vulchanova, Mila; Talcott, Joel B; Vulchanov, Valentin; Stankova, Margarita; Eshuis, Hendrik

    2012-01-01

    We conducted a detailed study of a case of linguistic talent in the context of autism spectrum disorder, specifically Asperger syndrome. I.A. displays language strengths at the level of morphology and syntax. Yet, despite this grammar advantage, processing of figurative language and inferencing based on context presents a problem for him. The morphology advantage for I.A. is consistent with the weak central coherence (WCC) account of autism. From this account, the presence of a local processing bias is evident in the ways in which autistic individuals solve common problems, such as assessing similarities between objects and finding common patterns, and may therefore provide an advantage in some cognitive tasks compared to typical individuals. We extend the WCC account to language and provide evidence for a connection between the local processing bias and the acquisition of morphology and grammar.

  7. Precision measurement of the local bias of dark matter halos

    SciTech Connect

    Lazeyras, Titouan; Wagner, Christian; Schmidt, Fabian; Baldauf, Tobias E-mail: cwagner@mpa-garching.mpg.de E-mail: fabians@mpa-garching.mpg.de

    2016-02-01

    We present accurate measurements of the linear, quadratic, and cubic local bias of dark matter halos, using curved 'separate universe' N-body simulations which effectively incorporate an infinite-wavelength overdensity. This can be seen as an exact implementation of the peak-background split argument. We compare the results with the linear and quadratic bias measured from the halo-matter power spectrum and bispectrum, and find good agreement. On the other hand, the standard peak-background split applied to the Sheth and Tormen (1999) and Tinker et al. (2008) halo mass functions matches the measured linear bias parameter only at the level of 10%. The prediction from the excursion set-peaks approach performs much better, which can be attributed to the stochastic moving barrier employed in the excursion set-peaks prediction. We also provide convenient fitting formulas for the nonlinear bias parameters b{sub 2}(b{sub 1}) and b{sub 3}(b{sub 1}), which work well over a range of redshifts.

  8. OPTIMIZATION BIAS IN ENERGY-BASED STRUCTURE PREDICTION.

    PubMed

    Petrella, Robert J

    2013-12-01

    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.

  9. Prism adaptation reverses the local processing bias in patients with right temporo-parietal junction lesions

    PubMed Central

    Rafal, Robert D.; List, Alexandra

    2009-01-01

    Lesions to the right temporo-parietal cortex commonly result in hemispatial neglect. Lesions to the same area are also associated with hyperattention to local details of a scene and difficulty perceiving the global structure. This local processing bias is an important factor contributing to neglect and may contribute to the higher prevalence of the disorder following right compared with left hemisphere strokes. In recent years, visuomotor adaptation to rightward-shifting prisms has been introduced as a promising treatment for hemispatial neglect. Explanations for these improvements have generally described a leftward realignment of attention, however, the present investigation provides evidence that prism adaptation reduces the local processing bias. Five patients with right temporal-parietal junction lesions were asked to identify the global or local levels of hierarchical figures before and after visuomotor adaptation to rightward-shifting prisms. Prior to prism adaptation the patients had difficulty ignoring the local elements when identifying the global component. Following prism adaptation, however, this pattern was reversed, with greater global interference during local level identification. The results suggest that prism adaptation may improve non-spatially lateralized deficits that contribute to the neglect syndrome. PMID:19416951

  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. 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.

  13. 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.

  14. 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.

  15. 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…

  16. Exposure to an urban environment alters the local bias of a remote culture.

    PubMed

    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 British participants in the Ebbinghaus illusion and in a similarity-matching task with hierarchical figures. Critically, we measured the effect of exposure to an urban environment on local bias in the Himba. Even a brief exposure to an urban environment caused a shift in processing style: the local bias was reduced in traditional Himba who had visited a local town and even more reduced in urbanised Himba who had moved to that town on a permanent basis. We therefore propose that exposure to an urban environment contributes to the global bias found in Western and Japanese populations.

  17. 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.

  18. Biasing and the search for primordial non-Gaussianity beyond the local type

    NASA Astrophysics Data System (ADS)

    Gleyzes, Jérôme; de Putter, Roland; Green, Daniel; Doré, Olivier

    2017-04-01

    Primordial non-Gaussianity encodes valuable information about the physics of inflation, including the spectrum of particles and interactions. Significant improvements in our understanding of non-Gaussanity beyond Planck require information from large-scale structure. The most promising approach to utilize this information comes from the scale-dependent bias of halos. For local non-Gaussanity, the improvements available are well studied but the potential for non-Gaussianity beyond the local type, including equilateral and quasi-single field inflation, is much less well understood. In this paper, we forecast the capabilities of large-scale structure surveys to detect general non-Gaussianity through galaxy/halo power spectra. We study how non-Gaussanity can be distinguished from a general biasing model and where the information is encoded. For quasi-single field inflation, significant improvements over Planck are possible in some regions of parameter space. We also show that the multi-tracer technique can significantly improve the sensitivity for all non-Gaussianity types, providing up to an order of magnitude improvement for equilateral non-Gaussianity over the single-tracer measurement.

  19. 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.

  20. Recursive estimators of mean-areal and local bias in precipitation products that account for conditional bias

    NASA Astrophysics Data System (ADS)

    Zhang, Yu; Seo, Dong-Jun

    2017-03-01

    This paper presents novel formulations of Mean field bias (MFB) and local bias (LB) correction schemes that incorporate conditional bias (CB) penalty. These schemes are based on the operational MFB and LB algorithms in the National Weather Service (NWS) Multisensor Precipitation Estimator (MPE). By incorporating CB penalty in the cost function of exponential smoothers, we are able to derive augmented versions of recursive estimators of MFB and LB. Two extended versions of MFB algorithms are presented, one incorporating spatial variation of gauge locations only (MFB-L), and the second integrating both gauge locations and CB penalty (MFB-X). These two MFB schemes and the extended LB scheme (LB-X) are assessed relative to the original MFB and LB algorithms (referred to as MFB-O and LB-O, respectively) through a retrospective experiment over a radar domain in north-central Texas, and through a synthetic experiment over the Mid-Atlantic region. The outcome of the former experiment indicates that introducing the CB penalty to the MFB formulation leads to small, but consistent improvements in bias and CB, while its impacts on hourly correlation and Root Mean Square Error (RMSE) are mixed. Incorporating CB penalty in LB formulation tends to improve the RMSE at high rainfall thresholds, but its impacts on bias are also mixed. The synthetic experiment suggests that beneficial impacts are more conspicuous at low gauge density (9 per 58,000 km2), and tend to diminish at higher gauge density. The improvement at high rainfall intensity is partly an outcome of the conservativeness of the extended LB scheme. This conservativeness arises in part from the more frequent presence of negative eigenvalues in the extended covariance matrix which leads to no, or smaller incremental changes to the smoothed rainfall amounts.

  1. Asymmetric bias in user guided segmentations of brain structures

    NASA Astrophysics Data System (ADS)

    Styner, Martin; Smith, Rachel G.; Graves, Michael M.; Mosconi, Matthew W.; Peterson, Sarah; White, Scott; Blocher, Joe; El-Sayed, Mohammed; Hazlett, Heather C.

    2007-03-01

    Brain morphometric studies often incorporate comparative asymmetry analyses of left and right hemispheric brain structures. In this work we show evidence that common methods of user guided structural segmentation exhibit strong left-right asymmetric biases and thus fundamentally influence any left-right asymmetry analyses. We studied several structural segmentation methods with varying degree of user interaction from pure manual outlining to nearly fully automatic procedures. The methods were applied to MR images and their corresponding left-right mirrored images from an adult and a pediatric study. Several expert raters performed the segmentations of all structures. The asymmetric segmentation bias is assessed by comparing the left-right volumetric asymmetry in the original and mirrored datasets, as well as by testing each sides volumetric differences to a zero mean standard t-tests. The structural segmentations of caudate, putamen, globus pallidus, amygdala and hippocampus showed a highly significant asymmetric bias using methods with considerable manual outlining or landmark placement. Only the lateral ventricle segmentation revealed no asymmetric bias due to the high degree of automation and a high intensity contrast on its boundary. Our segmentation methods have been adapted in that they are applied to only one of the hemispheres in an image and its left-right mirrored image. Our work suggests that existing studies of hemispheric asymmetry without similar precautions should be interpreted in a new, skeptical light. Evidence of an asymmetric segmentation bias is novel and unknown to the imaging community. This result seems less surprising to the visual perception community and its likely cause is differences in perception of oppositely curved 3D structures.

  2. Estimating the Bias of Local Polynomial Approximation Methods Using the Peano Kernel

    SciTech Connect

    Blair, J.; Machorro, E.; Luttman, A.

    2013-03-01

    The determination of uncertainty of an estimate requires both the variance and the bias of the estimate. Calculating the variance of local polynomial approximation (LPA) estimates is straightforward. We present a method, using the Peano Kernel Theorem, to estimate the bias of LPA estimates and show how this can be used to optimize the LPA parameters in terms of the bias-variance tradeoff. Figures of merit are derived and values calculated for several common methods. The results in the literature are expanded by giving bias error bounds that are valid for all lengths of the smoothing interval, generalizing the currently available asymptotic results that are only valid in the limit as the length of this interval goes to zero.

  3. 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.

  4. Localized structures in convective experiments

    NASA Astrophysics Data System (ADS)

    Burguete, J.; Mancini, H.

    2014-01-01

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

  5. 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.

  6. 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.; ...

    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

  7. Directional biases in phylogenetic structure quantification: a Mediterranean case study

    PubMed Central

    Molina-Venegas, Rafael; Roquet, Cristina

    2014-01-01

    Recent years have seen an increasing effort to incorporate phylogenetic hypotheses to the study of community assembly processes. The incorporation of such evolutionary information has been eased by the emergence of specialized software for the automatic estimation of partially resolved supertrees based on published phylogenies. Despite this growing interest in the use of phylogenies in ecological research, very few studies have attempted to quantify the potential biases related to the use of partially resolved phylogenies and to branch length accuracy, and no work has examined how tree shape may affect inference of community phylogenetic metrics. In this study, using a large plant community and elevational dataset, we tested the influence of phylogenetic resolution and branch length information on the quantification of phylogenetic structure; and also explored the impact of tree shape (stemminess) on the loss of accuracy in phylogenetic structure quantification due to phylogenetic resolution. For this purpose, we used 9 sets of phylogenetic hypotheses of varying resolution and branch lengths to calculate three indices of phylogenetic structure: the mean phylogenetic distance (NRI), the mean nearest taxon distance (NTI) and phylogenetic diversity (stdPD) metrics. The NRI metric was the less sensitive to phylogenetic resolution, stdPD showed an intermediate sensitivity, and NTI was the most sensitive one; NRI was also less sensitive to branch length accuracy than NTI and stdPD, the degree of sensitivity being strongly dependent on the dating method and the sample size. Directional biases were generally towards type II errors. Interestingly, we detected that tree shape influenced the accuracy loss derived from the lack of phylogenetic resolution, particularly for NRI and stdPD. We conclude that well-resolved molecular phylogenies with accurate branch length information are needed to identify the underlying phylogenetic structure of communities, and also that

  8. Ion flow and sheath structure near positively biased electrodes

    NASA Astrophysics Data System (ADS)

    Hood, R.; Scheiner, B.; Baalrud, S. D.; Hopkins, M. M.; Barnat, E. V.; Yee, B. T.; Merlino, R. L.; Skiff, F.

    2016-11-01

    What effect does a dielectric material surrounding a small positively biased electrode have on the ion flow and sheath structure near the electrode? Measurements of the ion velocity distribution function and plasma potential near positively biased electrodes were made using laser-induced fluorescence and an emissive probe. The results were compared with 2D particle-in-cell simulations. Both measurements and simulations showed that when the positive electrode was surrounded by the dielectric material, ions were accelerated toward the electrode to approximately 0.5 times the ion sound speed before being deflected radially by the electron sheath potential barrier of the electrode. The axial potential profile in this case contained a virtual cathode. In comparison, when the dielectric material was removed from around the electrode, both the ion flow and virtual cathode depth near the electrode were dramatically reduced. These measurements suggest that the ion presheath from the dielectric material surrounding the electrode may enclose the electron sheath of the electrode, resulting in a virtual cathode that substantially influences the ion flow profile in the region.

  9. 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

  10. Ion flow and sheath structure near positively biased electrodes

    NASA Astrophysics Data System (ADS)

    Hood, Ryan; Scheiner, Brett; Baalrud, Scott; Hopkins, Matthew; Barnat, Ed; Yee, Benjamin; Merlino, Robert; Skiff, Fred

    2016-10-01

    Measurements of the ion velocity distribution function (IVDF) and plasma potential were made near small positively biased electrodes using laser-induced fluorescence (LIF) and an emissive probe. The effect of dielectric around the electrode was tested and compared with a 2D particle-in-cell (PIC) simulation. Both measurements and simulation reveal that if the electrode is embedded within a surrounding dielectric, ions are accelerated toward the electrode to approximately 0.5 times the ion sound speed before being deflected radially by the electron sheath potential barrier. The axial potential profile in this case contains a virtual cathode. In comparison, when the surrounding dielectric is removed, both the ion flow and virtual cathode depth are dramatically reduced. These measurements suggest that the ion presheath from the dielectric may enclose the electron sheath of the electrode resulting in a virtual cathode that substantially influences the local ion flow profile. This research was supported by the Office of Fusion Energy Sciences at the U.S. Department of Energy under contract DE-AC04-94SL85000.

  11. Color Representation Is Retinotopically Biased but Locally Intermingled in Mouse V1

    PubMed Central

    Aihara, Shuhei; Yoshida, Takashi; Hashimoto, Takayuki; Ohki, Kenichi

    2017-01-01

    Dichromatic vision is common in many mammals. However, color processing in the primary visual cortex (V1) of dichromatic mammals is relatively unknown compared to the trichromatic primates. In this study, we investigated the functional organization of color processing in mouse V1. The mouse retina has a graded expression pattern of two opsins along its dorsoventral axis. However, it is not clear whether and how this expression pattern is reflected in the cortical representation at local (several hundred microns) and areal (V1) level. Using in vivo two-photon calcium (Ca2+) imaging and wide-field Ca2+ imaging, we revealed that V1 neurons responded to S (UV)- and M (green)-opsin isolating stimuli with slightly biased color preference depending on retinotopic position in V1. This was consistent with the distribution of retinal opsins. At the cellular level, preferences for S- and M-opsin isolating stimuli were intermingled in a local region encompassing several hundred microns. These results suggest that functional organizations of color information are locally intermingled, but slightly biased depending on the retinotopic position in mouse V1.

  12. 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

  13. 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.

  14. 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.

  15. Mapping the Similarities of Spectra: Global and Locally-biased Approaches to SDSS Galaxies

    NASA Astrophysics Data System (ADS)

    Lawlor, David; Budavári, Tamás; Mahoney, Michael W.

    2016-12-01

    We present a novel approach to studying the diversity of galaxies. It is based on a novel spectral graph technique, that of locally-biased semi-supervised eigenvectors. Our method introduces new coordinates that summarize an entire spectrum, similar to but going well beyond the widely used Principal Component Analysis (PCA). Unlike PCA, however, this technique does not assume that the Euclidean distance between galaxy spectra is a good global measure of similarity. Instead, we relax that condition to only the most similar spectra, and we show that doing so yields more reliable results for many astronomical questions of interest. The global variant of our approach can identify very finely numerous astronomical phenomena of interest. The locally-biased variants of our basic approach enable us to explore subtle trends around a set of chosen objects. The power of the method is demonstrated in the Sloan Digital Sky Survey Main Galaxy Sample, by illustrating that the derived spectral coordinates carry an unprecedented amount of information.

  16. 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

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

    PubMed

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

    2015-04-07

    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.

  18. Removing Orientation-Induced Localization Biases in Single-Molecule Microscopy Using a Broadband Metasurface Mask

    PubMed Central

    Backlund, Mikael P.; Arbabi, Amir; Petrov, Petar N.; Arbabi, Ehsan; Saurabh, Saumya; Faraon, Andrei; Moerner, W. E.

    2016-01-01

    Nanoscale localization of single molecules is a crucial function in several advanced microscopy techniques, including single-molecule tracking and wide-field super-resolution imaging 1. To date, a central consideration of such techniques is how to optimize the precision of molecular localization. However, as these methods continue to push toward the nanometre size scale, an increasingly important concern is the localization accuracy. In particular, single fluorescent molecules emit with an anisotropic radiation pattern of an oscillating electric dipole, which can cause significant localization biases using common estimators 2-5. Here we present the theory and experimental demonstration of a solution to this problem based on azimuthal filtering in the Fourier plane of the microscope. We do so using a high efficiency dielectric metasurface polarization/phase device composed of nanoposts with sub-wavelength spacing 6. The method is demonstrated both on fluorophores embedded in a polymer matrix, and in dL5 protein complexes that bind Malachite green 7, 8. PMID:27574529

  19. 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.

  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. Exchange bias in ferrite hollow nanoparticles originated by complex internal magnetic structure

    NASA Astrophysics Data System (ADS)

    De Biasi, Emilio; Lima, Enio, Jr.; Vargas, Jose M.; Zysler, Roberto D.; Arbiol, Jordi; Ibarra, Alfonso; Goya, Gerardo F.; Ibarra, M. Ricardo

    2015-10-01

    Iron-oxide hollow nanospheres (HNS) may present unusual magnetic behavior as a consequence of their unique morphology. Here, we report the unusual magnetic behavior of HNS that are 9 nm in diameter. The magnetic properties of HNS originate in their complex magnetic structure, as evidenced by Mössbauer spectroscopy and magnetization measurements. We observe a bias in the hysteresis when measured at very low temperature in the field cooling protocol (10 kOe). In addition, dc (static) and ac (dynamic) magnetization measurements against temperature and applied field reveal a frustrated order of the system below 10 K. High-resolution transmission electron microscopy (HRTEM) studies reveal that the HNS are composed of small crystalline clusters of about 2 nm in diameter, which behave as individual magnetic entities. Micromagnetic simulations (using conjugate gradient in order to minimize the total energy of the system) reproduce the experimentally observed magnetic behavior. The model considers the hollow particles as constituted by small ordered clusters embedded in an antiferromagnetic environment (spins localized outside the clusters). In addition, the surface spins (in both inner and outer surfaces of the HNS) are affected by a local surface anisotropy. The strong effective magnetic anisotropy field of the clusters induces the bias observed when the system is cooled in the presence of a magnetic external field. This effect propagates through the exchange interaction into the entire particle.

  2. Localized structure of Euglena bioconvection

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  3. Bias assisted scanning probe microscopy direct write lithography enables local oxygen enrichment of lanthanum cuprates thin films

    SciTech Connect

    Lavini, Francesco; Yang, Nan; Vasudevan, Rama K.; Strelcov, Evgheni; Jesse, Stephen; Okatan, Mahmut Baris; Kravchenko, Ivan I.; Di Castro, Daniele; Kalinin, Sergei V.; Balestrino, Giuseppe; Foglietti, Vittorio; Aruta, Carmela

    2015-01-01

    Here, scanning probe bias techniques have been used as a method to locally dope thin epitaxial films of La2CuO4 (LCO) fabricated by pulsed laser deposition. The local electrochemical oxidation of LCO very efficiently introduces interstitial oxygen defects in the thin film. Details on the influence of the tip voltage bias and environmental conditions on the surface morphology have been investigated. The results show that a local uptake of oxygen occurs in the oxidized films.

  4. Drawing Firmer Conclusions: Autistic Children Show No Evidence of a Local Processing Bias in a Controlled Copying Task

    ERIC Educational Resources Information Center

    Smith, Alastair D.; Kenny, Lorcan; Rudnicka, Anna; Briscoe, Josie; Pellicano, Elizabeth

    2016-01-01

    Drawing tasks are frequently used to test competing theories of visuospatial skills in autism. Yet, methodological differences between studies have led to inconsistent findings. To distinguish between accounts based on local bias or global deficit, we present a simple task that has previously revealed dissociable local/global impairments in…

  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.

  6. 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

  7. 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.

  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; ...

    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. MRI tissue classification and bias field estimation based on coherent local intensity clustering: a unified energy minimization framework.

    PubMed

    Li, Chunming; Xu, Chenyang; Anderson, Adam W; Gore, John C

    2009-01-01

    This paper presents a new energy minimization method for simultaneous tissue classification and bias field estimation of magnetic resonance (MR) images. We first derive an important characteristic of local image intensities--the intensities of different tissues within a neighborhood form separable clusters, and the center of each cluster can be well approximated by the product of the bias within the neighborhood and a tissue-dependent constant. We then introduce a coherent local intensity clustering (CLIC) criterion function as a metric to evaluate tissue classification and bias field estimation. An integration of this metric defines an energy on a bias field, membership functions of the tissues, and the parameters that approximate the true signal from the corresponding tissues. Thus, tissue classification and bias field estimation are simultaneously achieved by minimizing this energy. The smoothness of the derived optimal bias field is ensured by the spatially coherent nature of the CLIC criterion function. As a result, no extra effort is needed to smooth the bias field in our method. Moreover, the proposed algorithm is robust to the choice of initial conditions, thereby allowing fully automatic applications. Our algorithm has been applied to high field and ultra high field MR images with promising results.

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

    NASA Astrophysics Data System (ADS)

    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.

  12. 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

  13. 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.

  14. Densest Local Structures of Uniaxial Ellipsoids

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  15. 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).

  16. Not a Copernican observer: biased peculiar velocity statistics in the local Universe

    NASA Astrophysics Data System (ADS)

    Hellwing, Wojciech A.; Nusser, Adi; Feix, Martin; Bilicki, Maciej

    2017-01-01

    We assess the effect of the local large scale structure on the estimation of two-point statistics of the observed radial peculiar velocities of galaxies. A large N-body simulation is used to examine these statistics from the perspective of random observers as well as "Local Group (LG)-like" observers conditioned to reside in an environment resembling the observed universe within 20 Mpc. The local environment systematically distorts the shape and amplitude of velocity statistics with respect to ensemble-averaged measurements made by a Copernican (random) observer. The Virgo cluster has the most significant impact, introducing large systematic deviations in all the statistics. For a simple "top-hat" selection function, an idealized survey extending to ˜160h-1 Mpc or deeper is needed to completely mitigate the effects of the local environment. Using shallower catalogues leads to systematic deviations of the order of 50 to 200% depending on the scale considered. For a flat redshift distribution similar to the one of the CosmicFlows-3 survey, the deviations are even more prominent in both the shape and amplitude at all separations considered (≲100h^{-1} Mpc). Conclusions based on statistics calculated without taking into account the impact of the local environment should be revisited.

  17. Local statistical interpretation for water structure

    NASA Astrophysics Data System (ADS)

    Sun, Qiang

    2013-05-01

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

  18. 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.

  19. 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.

  20. Deterministic weak localization in periodic structures.

    PubMed

    Tian, C; Larkin, A

    2005-12-09

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

  1. 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.

  2. 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…

  3. Deeper than Shallow: Evidence for Structure-Based Parsing Biases in Second-Language Sentence Processing

    ERIC Educational Resources Information Center

    Witzel, Jeffrey; Witzel, Naoko; Nicol, Janet

    2012-01-01

    This study examines the reading patterns of native speakers (NSs) and high-level (Chinese) nonnative speakers (NNSs) on three English sentence types involving temporarily ambiguous structural configurations. The reading patterns on each sentence type indicate that both NSs and NNSs were biased toward specific structural interpretations. These…

  4. Alcohol-attentional bias and motivational structure as independent predictors of social drinkers' alcohol consumption.

    PubMed

    Fadardi, Javad Salehi; Cox, W Miles

    2008-10-01

    Prior studies aimed at explaining cognitive-motivational reasons for drinking have focused on either cognitive or motivational factors, but not on both. This study examined the ability of both alcohol-attentional bias and motivational structure to predict alcohol consumption. Participants were university students (N=87) who completed a battery of tests, including the Personal Concerns Inventory (a measure of adaptive and maladaptive motivation), an alcohol Stroop test (a measure of alcohol-attentional bias), and an alcohol-use inventory. Regression, moderation, and mediation analyses showed that (a) maladaptive motivation and alcohol-attentional bias were positive predictors of alcohol consumption after participants' age, gender, and executive cognitive functioning had been controlled, and (b) maladaptive motivation and alcohol-attentional bias independently predicted alcohol consumption. The implications of the results for both theory and practice are discussed.

  5. Charge transfer-induced magnetic exchange bias and electron localization in (111)- and (001)-oriented LaNiO3/LaMnO3 superlattices

    NASA Astrophysics Data System (ADS)

    Wei, Haoming; Barzola-Quiquia, Jose Luis; Yang, Chang; Patzig, Christian; Höche, Thomas; Esquinazi, Pablo; Grundmann, Marius; Lorenz, Michael

    2017-03-01

    High-quality lattice-matched LaNiO3/LaMnO3 superlattices with monolayer terrace structure have been grown on both (111)- and (001)-oriented SrTiO3 substrates by pulsed laser deposition. In contrast to the previously reported experiments, a magnetic exchange bias is observed that reproducibly occurs in both (111)- and (001)-oriented superlattices with the thin single layers of 5 and 7 unit cells, respectively. The exchange bias is theoretically explained by charge transfer-induced magnetic moments at Ni atoms. Furthermore, magnetization data at low temperature suggest two magnetic phases in the superlattices, with Néel temperature around 10 K. Electrical transport measurements reveal a metal-insulator transition with strong localization of electrons in the superlattices with the thin LaNiO3 layers of 4 unit cells, in which the electrical transport is dominated by two-dimensional variable range hopping.

  6. Introduction: Dissipative localized structures in extended systems

    NASA Astrophysics Data System (ADS)

    Tlidi, Mustapha; Taki, Majid; Kolokolnikov, Theodore

    2007-09-01

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

  7. Interface electronic structure in a metal/ferroelectric heterostructure under applied bias

    NASA Astrophysics Data System (ADS)

    Rault, J. E.; Agnus, G.; Maroutian, T.; Pillard, V.; Lecoeur, Ph.; Niu, G.; Vilquin, B.; Silly, M. G.; Bendounan, A.; Sirotti, F.; Barrett, N.

    2013-04-01

    The effective barrier height between an electrode and a ferroelectric (FE) depends on both macroscopic electrical properties and microscopic chemical and electronic structure. The behavior of a prototypical electrode/FE/electrode structure, Pt/BaTiO3/Nb-doped SrTiO3, under in-situ bias voltage is investigated using x-ray photoelectron spectroscopy. The full band alignment is measured and is supported by transport measurements. Barrier heights depend on interface chemistry and on the FE polarization. A differential response of the core levels to applied bias as a function of the polarization state is observed, consistent with Callen charge variations near the interface.

  8. Polarization properties of localized structures in VCSELs

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  9. Tuning structure and roughness in exchange biased NiO/permalloy bilayers

    NASA Astrophysics Data System (ADS)

    Thomas, Luc; Negulescu, Béatrice; Dumont, Yves; Tessier, Michel; Keller, Niels; Wack, André; Guyot, Marcel

    2003-05-01

    Polycrystalline NiO thin films have been grown by pulsed laser deposition on quartz substrates. These films exhibit a strong texture, which can be tuned by changing deposition parameters such as substrate temperature or oxygen partial pressure. By varying the deposition temperature from room temperature up to 900 °C, (220), (111), and (200) textured films are prepared. In the temperature zones separating these orientations, competition between different growth directions leads to smaller crystallites, characterized by broader diffraction lines. Surface roughness measured by atomic force microscopy is strongly correlated with these structural features. Roughness is minimum for highly textured samples (about 7Å for 500 Å thick films), and it exhibits two peaks in the intermediate zones, with maximum values of about 40 Å. In order to correlate exchange bias with these structural features, 100 Å thick FeNi layers were deposited by rf sputtering on top of the 500 Å thick NiO films. Hysteresis loops were measured at 10 K by superconducting quantum interference device magnetometry after the samples were cooled in a 100 Oe magnetic field. Exchange bias is maximum for (111) oriented samples. No clear correlation between exchange bias and surface roughness is observed at low temperature. Exchange bias temperature dependence strongly depends upon NiO films deposition temperature. The blocking temperature, for which the exchange bias vanishes, varies between 150 K for (220) oriented samples and 250 K for (111) textured samples, and it exceeds room temperature for (200) films.

  10. Parietal structure and function explain human variation in working memory biases of visual attention.

    PubMed

    Soto, David; Rotshtein, Pia; Kanai, Ryota

    2014-04-01

    Recent research indicates that human attention appears inadvertently biased by items that match the contents of working memory (WM). WM-biases can lead to attentional costs when the memory content matches goal-irrelevant items and to attentional benefits when it matches the sought target. Here we used functional and structural MRI data to determine the neural basis of human variation in WM biases. We asked whether human variation in WM-benefits and WM-costs merely reflects the process of attentional capture by the contents of WM or whether variation in WM biases may be associated with distinct forms of cognitive control over internal WM signals based on selection goals. Human ability to use WM contents to facilitate selection was positively correlated with gray matter volume in the left superior posterior parietal cortex (PPC), while the ability to overcome interference by WM-matching distracters was associated with the left inferior PPC in the anterior IPS. Functional activity in the left PPC, measured by functional MRI, also predicted the magnitude of WM-costs on selection. Both structure and function of left PPC mediate the expression of WM biases in human visual attention.

  11. MR image segmentation and bias field estimation based on coherent local intensity clustering with total variation regularization.

    PubMed

    Tu, Xiaoguang; Gao, Jingjing; Zhu, Chongjing; Cheng, Jie-Zhi; Ma, Zheng; Dai, Xin; Xie, Mei

    2016-12-01

    Though numerous segmentation algorithms have been proposed to segment brain tissue from magnetic resonance (MR) images, few of them consider combining the tissue segmentation and bias field correction into a unified framework while simultaneously removing the noise. In this paper, we present a new unified MR image segmentation algorithm whereby tissue segmentation, bias correction and noise reduction are integrated within the same energy model. Our method is presented by a total variation term introduced to the coherent local intensity clustering criterion function. To solve the nonconvex problem with respect to membership functions, we add auxiliary variables in the energy function such as Chambolle's fast dual projection method can be used and the optimal segmentation and bias field estimation can be achieved simultaneously throughout the reciprocal iteration. Experimental results show that the proposed method has a salient advantage over the other three baseline methods on either tissue segmentation or bias correction, and the noise is significantly reduced via its applications on highly noise-corrupted images. Moreover, benefiting from the fast convergence of the proposed solution, our method is less time-consuming and robust to parameter setting.

  12. 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.

  13. Observation selection bias in contact prediction and its implications for structural bioinformatics

    PubMed Central

    Orlando, G.; Raimondi, D.; Vranken, W. F.

    2016-01-01

    Next Generation Sequencing is dramatically increasing the number of known protein sequences, with related experimentally determined protein structures lagging behind. Structural bioinformatics is attempting to close this gap by developing approaches that predict structure-level characteristics for uncharacterized protein sequences, with most of the developed methods relying heavily on evolutionary information collected from homologous sequences. Here we show that there is a substantial observational selection bias in this approach: the predictions are validated on proteins with known structures from the PDB, but exactly for those proteins significantly more homologs are available compared to less studied sequences randomly extracted from Uniprot. Structural bioinformatics methods that were developed this way are thus likely to have over-estimated performances; we demonstrate this for two contact prediction methods, where performances drop up to 60% when taking into account a more realistic amount of evolutionary information. We provide a bias-free dataset for the validation for contact prediction methods called NOUMENON. PMID:27857150

  14. Population structure with localized haplotype clusters.

    PubMed

    Browning, Sharon R; Weir, Bruce S

    2010-08-01

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

  15. 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...

  16. Correlation between substrate bias, growth process and structural properties of phosphorus incorporated tetrahedral amorphous carbon films

    NASA Astrophysics Data System (ADS)

    Liu, Aiping; Zhu, Jiaqi; Han, Jiecai; Wu, Huaping; Jia, Zechun

    2007-09-01

    We investigate the growth process and structural properties of phosphorus incorporated tetrahedral amorphous carbon (ta-C:P) films which are deposited at different substrate biases by filtered cathodic vacuum arc technique with PH 3 as the dopant source. The films are characterized by X-ray photoelectron spectroscopy (XPS), atomic force microscopy, Raman spectroscopy, residual stress measurement, UV/VIS/NIR absorption spectroscopy and temperature-dependent conductivity measurement. The atomic fraction of phosphorus in the films as a function of substrate bias is obtained by XPS analysis. The optimum bias for phosphorus incorporation is about -80 V. Raman spectra show that the amorphous structures of all samples with atomic-scaled smooth surface are not remarkably changed when PH 3 is implanted, but some small graphitic crystallites are formed. Moreover, phosphorus impurities and higher-energetic impinging ions are favorable for the clustering of sp 2 sites dispersed in sp 3 skeleton and increase the level of structural ordering for ta-C:P films, which further releases the compressive stress and enhances the conductivity of the films. Our analysis establishes an interrelationship between microstructure, stress state, electrical properties, and substrate bias, which helps to understand the deposition mechanism of ta-C:P films.

  17. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    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 SiO2/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.

  19. 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.

  20. 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.

  1. Drifting localized structures in doubly diffusive convection

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  2. Automatic Tool for Local Assembly Structures

    SciTech Connect

    2016-10-11

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

  3. Frequency based localization of structural discrepancies

    NASA Technical Reports Server (NTRS)

    Shepard, G. D.; Milani, J.

    1988-01-01

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

  4. A discriminative Ramachandran potential of mean force aimed at minimizing secondary structure bias.

    PubMed

    Koppole, Sampath; Schaefer, Michael

    2012-03-15

    We introduce PMF*, a novel potential of mean force (PMF) for the Ramachandran ϕ/Ψ dihedral plot of the 20 standard amino acids and assess its relevance to the conformation of polypeptides by scoring structures in the protein data bank and decoy datasets. The new energy function is a linear combination of the conventional, unreferenced PMF and the ΔPMF relative to the free energy of all amino acids in the parameterization set of structures, effectively removing their respective biases toward α-helix and β-strand. It is shown that low-resolution crystal structures, NMR structures, and theoretical models have on average significantly higher energies than high-resolution crystal structures; also PMF* is more discriminative for structure quality than the individual PMF and ΔPMF energy functions. PMF* may be well suited for use as a restraint energy term in the refinement of experimental structures and theoretical models.

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

    PubMed Central

    2014-01-01

    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. PMID:25593550

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

    PubMed

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

    2014-01-01

    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/cm(2)) 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.

  7. Clustering of Local Group Distances: Publication Bias or Correlated Measurements? IV. The Galactic Center

    NASA Astrophysics Data System (ADS)

    de Grijs, Richard; Bono, Giuseppe

    2016-11-01

    Aiming at deriving a statistically well-justified Galactic Center distance, R 0, and reducing any occurrence of publication bias, we compiled the most comprehensive and most complete database of Galactic Center distances available to date, containing 273 new or revised R 0 estimates published since records began in 1918 October until 2016 June. We separate our R 0 compilation into direct and indirect distance measurements. The latter include a large body of estimates that rely on centroid determinations for a range of tracer populations, as well as measurements based on kinematic observations of objects at the solar circle, combined with a mass and/or rotational model of the Milky Way. Careful assessment of the Galactic Center distances resulting from orbital modeling and statistical parallax measurements in the Galactic nucleus yields our final Galactic Center distance recommendation of {R}0=8.3+/- 0.2 {{(statistical)}}+/- 0.4 {{(systematic)}} {kpc}. The centroid-based distances are in good agreement with this recommendation. Neither the direct measurements nor the post-1990 centroid-based distance determinations suggest that publication bias may be important. The kinematics-based distance estimates are affected by significantly larger uncertainties, but they can be used to constrain the Galaxy’s rotation velocity at the solar galactocentric distance, {{{\\Theta }}}0. Our results imply that the International-Astronomical-Union-recommended Galactic Center distance ({R}0{IAU}=8.5 {kpc}) needs a downward adjustment, while its {{{\\Theta }}}0 recommendation ({{{\\Theta }}}0=220 km s-1) requires a substantial upward revision.

  8. The Structure of the Local Hot Bubble

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  9. Identifying and removing structural biases in climate models with history matching

    NASA Astrophysics Data System (ADS)

    Williamson, Daniel; Blaker, Adam T.; Hampton, Charlotte; Salter, James

    2015-09-01

    We describe the method of history matching, a method currently used to help quantify parametric uncertainty in climate models, and argue for its use in identifying and removing structural biases in climate models at the model development stage. We illustrate the method using an investigation of the potential to improve upon known ocean circulation biases in a coupled non-flux-adjusted climate model (the third Hadley Centre Climate Model; HadCM3). In particular, we use history matching to investigate whether or not the behaviour of the Antarctic Circumpolar Current (ACC), which is known to be too strong in HadCM3, represents a structural bias that could be corrected using the model parameters. We find that it is possible to improve the ACC strength using the parameters and observe that doing this leads to more realistic representations of the sub-polar and sub-tropical gyres, sea surface salinities (both globally and in the North Atlantic), sea surface temperatures in the sinking regions in the North Atlantic and in the Southern Ocean, North Atlantic Deep Water flows, global precipitation, wind fields and sea level pressure. We then use history matching to locate a region of parameter space predicted not to contain structural biases for ACC and SSTs that is around 1 % of the original parameter space. We explore qualitative features of this space and show that certain key ocean and atmosphere parameters must be tuned carefully together in order to locate climates that satisfy our chosen metrics. Our study shows that attempts to tune climate model parameters that vary only a handful of parameters relevant to a given process at a time will not be as successful or as efficient as history matching.

  10. The antiferromagnetic structures of IrMn3 and their influence on exchange-bias

    PubMed Central

    Kohn, A.; Kovács, A.; Fan, R.; McIntyre, G. J.; Ward, R. C. C.; Goff, J. P.

    2013-01-01

    We have determined the magnetic structures of single-crystal thin-films of IrMn3 for the crystallographic phases of chemically-ordered L12, and for chemically-disordered face-centred-cubic, which is the phase typically chosen for information-storage devices. For the chemically-ordered L12 thin-film, we find the same triangular magnetic structure as reported for the bulk material. We determine the magnetic structure of the chemically-disordered face-centred-cubic alloy for the first time, which differs from theoretical predictions, with magnetic moments tilted away from the crystal diagonals towards the face-planes. We study the influence of these two antiferromagnetic structures on the exchange-bias properties of an epitaxial body-centred-cubic Fe layer showing that magnetization reversal mechanism and bias-field in the ferromagnetic layer is altered significantly. We report a change of reversal mechanism from in-plane nucleation of 90° domain-walls when coupled to the newly reported cubic structure towards a rotational process, including an out-of-plane magnetization component when coupled to the L12 triangular structure. PMID:23934541

  11. Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor Interactions

    PubMed Central

    Toal, Siobhan; Schweitzer-Stenner, Reinhard

    2014-01-01

    The discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet perform complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue-level conformational ensembles. Multiple lines of evidence gathered over the last 15 years strongly suggest that amino acids residues display unique and restricted conformational preferences in the unfolded state of peptides and proteins, contrary to one of the basic assumptions of the canonical random coil model. To fully understand residue level order/disorder, however, one has to gain a quantitative, experimentally based picture of conformational distributions and to determine the physical basis underlying residue-level conformational biases. Here, we review the experimental, computational and bioinformatic evidence for conformational preferences of amino acid residues in (mostly short) peptides that can be utilized as suitable model systems for unfolded states of peptides and proteins. In this context particular attention is paid to the alleged high polyproline II preference of alanine. We discuss how these conformational propensities may be modulated by peptide solvent interactions and so called nearest-neighbor interactions. The relevance of conformational propensities for the protein folding problem and the understanding of IDPs is briefly discussed. PMID:25062017

  12. 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.

  13. A "looming bias" in spatial hearing? Effects of acoustic intensity and spectrum on categorical sound source localization.

    PubMed

    McCarthy, Lisa; Olsen, Kirk N

    2017-01-01

    Continuous increases of acoustic intensity (up-ramps) can indicate a looming (approaching) sound source in the environment, whereas continuous decreases of intensity (down-ramps) can indicate a receding sound source. From psychoacoustic experiments, an "adaptive perceptual bias" for up-ramp looming tonal stimuli has been proposed (Neuhoff, 1998). This theory postulates that (1) up-ramps are perceptually salient because of their association with looming and potentially threatening stimuli in the environment; (2) tonal stimuli are perceptually salient because of an association with single and potentially threatening biological sound sources in the environment, relative to white noise, which is more likely to arise from dispersed signals and nonthreatening/nonbiological sources (wind/ocean). In the present study, we extrapolated the "adaptive perceptual bias" theory and investigated its assumptions by measuring sound source localization in response to acoustic stimuli presented in azimuth to imply looming, stationary, and receding motion in depth. Participants (N = 26) heard three directions of intensity change (up-ramps, down-ramps, and steady state, associated with looming, receding, and stationary motion, respectively) and three levels of acoustic spectrum (a 1-kHz pure tone, the tonal vowel /ә/, and white noise) in a within-subjects design. We first hypothesized that if up-ramps are "perceptually salient" and capable of eliciting adaptive responses, then they would be localized faster and more accurately than down-ramps. This hypothesis was supported. However, the results did not support the second hypothesis. Rather, the white-noise and vowel conditions were localized faster and more accurately than the pure-tone conditions. These results are discussed in the context of auditory and visual theories of motion perception, auditory attentional capture, and the spectral causes of spatial ambiguity.

  14. 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.

  15. Giant exchange bias in Mn2FeGa with hexagonal structure

    NASA Astrophysics Data System (ADS)

    Liu, Z. H.; Zhang, Y. J.; Zhang, H. G.; Zhang, X. J.; Ma, X. Q.

    2016-07-01

    In this study, we present the experimental observation that polycrystalline Mn2+xFe1-xGa (x = -0.2, 0, 0.2, 0.4) compounds can be synthesized to be D019-type (Ni3Sn-type) hexagonal structure with space group P63/mmc. A giant exchange bias field up to 1.32 kOe was achieved in hexagonal Mn2FeGa alloy at 5 K. A cluster glass state is confirmed by ac susceptibility measurement under different driving frequencies. Interestingly, robust horizontal and vertical shifts in magnetic hysteresis loop were simultaneously observed at 5 K under high cooling field up to 90 kOe. The large exchange bias is originated from the large exchange anisotropy between cluster glass phase and ferrimagnetic matrix. The vertical shift is thought to be attributed to the incomplete reversal of frozen cluster spins.

  16. 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.

  17. Hα-FUV Flux Ratios of Local Volume Galaxies: Effects of Systematic Biases on Upper IMF Constraints

    NASA Astrophysics Data System (ADS)

    Johnson, Lent C.; Weisz, D. R.; Johnson, B. D.; Skillman, E. D.; LVL Team

    2011-01-01

    Recent observational evidence has shown that dwarf galaxies exhibit lower Hα-FUV flux ratios than typical star-forming galaxies. While this fact has been interpreted as evidence for a variable upper IMF, these results are subject to systematics due to imperfect internal dust attenuation corrections and other biases. Using observations of 127 Local Volume star-forming galaxies derived from the LVL and SDSS datasets, we explore how different internal dust corrections and sample completeness can affect the resulting physical interpretation. We also examine the susceptibility of our Hα-FUV ratio distribution and correlation analyses to biases that result from our choice of independent parameter (e.g., stellar mass, R-band surface brightness). We then apply our understanding of these factors to test the possibility that the observed ratio distribution could be the result of age effects. Using model star formation histories, we can explain the distribution of Hα-FUV ratios without invoking variations in the upper IMF.

  18. The progesterone derivative dydrogesterone abrogates murine stress-triggered abortion by inducing a Th2 biased local immune response.

    PubMed

    Joachim, Ricarda; Zenclussen, Ana Claudia; Polgar, Beata; Douglas, Alison J; Fest, Stefan; Knackstedt, Maike; Klapp, Burghard F; Arck, Petra Clara

    2003-11-01

    Stress is known to induce abortions in mice and humans, putatively via increased levels of abortogenic Th1 cytokines and a decrease of progesterone. Adequate levels of progesterone exert an antiabortive response through binding to the progesterone-receptor, which induces the release of progesterone-induced blocking factor (PIBF) from lymphocytes. PIBF is highly pregnancy-protective by induction of a Th2 biased immune activity. The aim of this study was to investigate the effect of the progesterone derivative dydrogesterone (6-dehydro-retroprogesterone) in stress-triggered murine abortion. DBA/2J-mated CBA/J female mice were randomized in different groups: two groups were treated with different dydrogesterone dosages in a single injection before exposure to sound stress on Day 5 of pregnancy, one group was exposed to stress without dydrogesterone treatment, the fourth group received no stress and no dydrogesterone. On gestation Day 13, a highly elevated abortion rate was detected in stressed mice compared to control mice. Stressed animals presented lower levels of progesterone and PIBF in plasma and a reduced staining intensity of progesterone receptor at the feto-maternal interface. Injection of dydrogesterone abrogated the effect of stress on the abortion rate. Further, dydrogesterone increased levels of plasma PIBF in stressed mice, but did not affect progesterone levels. Interestingly, dydrogesterone dramatically increased the percentage of IL-4 positive decidual immune cells in stressed mice. Our data suggest that dydrogesterone abrogates stress-triggered abortion by inducing a Th2 biased local immune response.

  19. 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

  20. 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

    2014-12-02

    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.

  1. 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.

  2. Female-biased sex difference in vasotocin-immunoreactive neural structures in the developing quail brain.

    PubMed

    Aste, Nicoletta; Yoshioka, Naoki; Sakamoto, Emiko; Saito, Noboru

    2016-11-01

    The bed nucleus of the stria terminalis pars medialis (BSTM), medial preoptic nucleus (POM), and lateral septal region (LS) exhibit more vasotocin-immunoreactive (VT-ir) neural structures in male than in female adult quail. VT-ir cells and fibers in these regions are sensitive to gonadal steroids only in males. The insensitivity of adult female VT-ir neural structures to sex steroids is attributed to estradiol exposure during a critical period in embryonic life. Although the VT-ir system has been intensively examined in adult quail, information is limited in embryos and juveniles. Therefore, we herein investigated the development of VT-immunoreactive neural structures from embryonic day (E) 9 to adulthood with a particular focus on the BSTM, POM and LS of both sexes. VT-ir neural structures were more evident in female than in male embryos from E9 (BSTM and POM) and E11 (LS). This sex difference disappeared between E15 and post-hatch day 1 in the BSTM and POM, and during the first week of life in the LS. Male-biased sex differences in VT-ir structures appeared at puberty. Female-biased sexual dimorphism in the density of the VT-ir structures of BSTM was reflected by the stronger expression of VT mRNA in females than in males. However, the density of VT mRNA somata was comparable in the two sexes. The exposure of male embryos to estradiol resulted in the feminization of VT-ir neural structures in the BSTM, but not in the POM or LS at E11. Collectively, these results suggest that sex differences in VT-ir neural structures changes drastically throughout quail life. In embryos, endogenous estradiol may stimulate the expression of VT in females, resulting in a robust sex difference in VT-ir cells and fibers in favor of this sex.

  3. 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

  4. 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.

  5. 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 E-mail: matteorf@stanford.edu E-mail: zvlah@stanford.edu

    2015-09-01

    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 σ{sub 8} = 0.9. For the lowest mass bin, we find percent level agreement up to k≅ 0.3 h Mpc{sup −1} for the one-loop two-point functions, and up to k≅ 0.15 h Mpc{sup −1} for the tree-level three-point functions, with the k-reach decreasing with higher mass bins. 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.

  6. 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.

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

    DOE PAGES

    Angulo, Raul; Fasiello, Matteo; Senatore, Leonardo; ...

    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

  8. Structure-Based Discovery of New Antagonist and Biased Agonist Chemotypes for the Kappa Opioid Receptor.

    PubMed

    Zheng, Zhong; Huang, Xi-Ping; Mangano, Thomas J; Zou, Rodger; Chen, Xin; Zaidi, Saheem A; Roth, Bryan L; Stevens, Raymond C; Katritch, Vsevolod

    2017-04-13

    The ongoing epidemics of opioid overdose raises an urgent need for effective antiaddiction therapies and addiction-free painkillers. The κ-opioid receptor (KOR) has emerged as a promising target for both indications, raising demand for new chemotypes of KOR antagonists as well as G-protein-biased agonists. We employed the crystal structure of the KOR-JDTic complex and ligand-optimized structural templates to perform virtual screening of available compound libraries for new KOR ligands. The prospective virtual screening campaign yielded a high 32% hit rate, identifying novel fragment-like and lead-like chemotypes of KOR ligands. A round of optimization resulted in 11 new submicromolar KOR binders (best Ki = 90 nM). Functional assessment confirmed at least two compounds as potent KOR antagonists, while compound 81 was identified as a potent Gi biased agonist for KOR with minimal β-arrestin recruitment. These results support virtual screening as an effective tool for discovery of new lead chemotypes with therapeutically relevant functional profiles.

  9. How Category Structure Influences the Perception of Object Similarity: The Atypicality Bias

    PubMed Central

    Tanaka, James William; Kantner, Justin; Bartlett, Marni

    2011-01-01

    Why do some faces appear more similar than others? Beyond structural factors, we speculate that similarity is governed by the organization of faces located in a multi-dimensional face space. To test this hypothesis, we morphed a typical face with an atypical face. If similarity judgments are guided purely by their physical properties, the morph should be perceived to be equally similar to its typical parent as its atypical parent. However, contrary to the structural prediction, our results showed that the morph face was perceived to be more similar to the atypical face than the typical face. Our empirical studies show that the atypicality bias is not limited to faces, but extends to other object categories (birds) whose members share common shape properties. We also demonstrate atypicality bias is malleable and can change subject to category learning and experience. Collectively, the empirical evidence indicates that perceptions of face and object similarity are affected by the distribution of stimuli in a face or object space. In this framework, atypical stimuli are located in a sparser region of the space where there is less competition for recognition and therefore, these representations capture a broader range of inputs. In contrast, typical stimuli are located in a denser region of category space where there is increased competition for recognition and hence, these representation draw a more restricted range of face inputs. These results suggest that the perceived likeness of an object is influenced by the organization of surrounding exemplars in the category space. PMID:22685441

  10. 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

  11. NiO/Fe(001): Magnetic anisotropy, exchange bias, and interface structure

    SciTech Connect

    Mlynczak, E.; Luches, P.

    2013-06-21

    The magnetic and structural properties of NiO/Fe epitaxial bilayers grown on MgO(001) were studied using magnetooptic Kerr effect (MOKE) and conversion electron Moessbauer spectroscopy (CEMS). The bilayers were prepared under ultra high vacuum conditions using molecular beam epitaxy with oblique deposition. Two systems were compared: one showing the exchange bias (100ML-NiO/24ML-Fe), ML stands for a monolayer, and another where the exchange bias was not observed (50ML-NiO/50ML-Fe). For both, the magnetic anisotropy was found to be complex, yet dominated by the growth-induced uniaxial anisotropy. The training effect was observed for the 100ML-NiO/24ML-Fe system and quantitatively described using the spin glass model. The composition and magnetic state of the interfacial Fe layers were studied using {sup 57}Fe-CEMS. An iron oxide phase (Fe{sup 3+}{sub 4}Fe{sup 2+}{sub 1}O{sub 7}), as thick as 31 A, was identified at the NiO/Fe interface in the as-deposited samples. The ferrimagnetic nature of the interfacial iron oxide film explains the complex magnetic anisotropy observed in the samples.

  12. NiO/Fe(001): Magnetic anisotropy, exchange bias, and interface structure

    NASA Astrophysics Data System (ADS)

    Młyńczak, E.; Luches, P.; Valeri, S.; Korecki, J.

    2013-06-01

    The magnetic and structural properties of NiO/Fe epitaxial bilayers grown on MgO(001) were studied using magnetooptic Kerr effect (MOKE) and conversion electron Mössbauer spectroscopy (CEMS). The bilayers were prepared under ultra high vacuum conditions using molecular beam epitaxy with oblique deposition. Two systems were compared: one showing the exchange bias (100ML-NiO/24ML-Fe), ML stands for a monolayer, and another where the exchange bias was not observed (50ML-NiO/50ML-Fe). For both, the magnetic anisotropy was found to be complex, yet dominated by the growth-induced uniaxial anisotropy. The training effect was observed for the 100ML-NiO/24ML-Fe system and quantitatively described using the spin glass model. The composition and magnetic state of the interfacial Fe layers were studied using 57Fe-CEMS. An iron oxide phase (Fe3+4Fe2+1O7), as thick as 31 Å, was identified at the NiO/Fe interface in the as-deposited samples. The ferrimagnetic nature of the interfacial iron oxide film explains the complex magnetic anisotropy observed in the samples.

  13. 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.

  14. Reduction of model structure bias in the prediction of critical source areas

    NASA Astrophysics Data System (ADS)

    Frey, M.; Stamm, C.; Schneider, M. K.; Reichert, P.

    2009-04-01

    Effective mitigation strategies to reduce the contamination of surface waters by agrochemicals rely on an accurate identification of critical source areas (CSA). We used a spatially distributed hydrological model to identify CSA in a small agricultural catchment in Switzerland. Since the knowledge about model parameters is coarse, prior predictions of CSA involve large uncertainties. We investigated to which degree river discharge data can constrain parameter values and improve the prediction. Thereby, we combined the prior knowledge used for the prior prediction with additional river discharge data within a Bayesian inference approach. In order to consider the effect of uncertainty in input data and in the model structure we formulated the likelihood function with an autoregressive error model additive to the river discharge calculated by the deterministic hydrological model. The additional information gained from river discharge data slightly reduced the width of some of the marginal parameter distributions and the prediction uncertainty for high or low-risk areas. However, the analysis of the statistical assumptions of the inference process revealed deficits in the model structure. Thus the base flow during dry periods tended to be overestimated. By making the percolation process water table dependent the base flow prediction could be improved. These improvements in model structure significantly reduced the model structure bias and thus improved the statistical basis of the probabilistic CSA prediction. Furthermore, the improved model structure led to a large constraint of the CSA prediction uncertainty.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

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

    PubMed Central

    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

  1. 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

  2. Structures of Local Rearrangements in Soft Colloidal Glasses

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

    We image local structural rearrangements in soft colloidal glasses under small periodic perturbations induced by thermal cycling. Local structural entropy S2 positively correlates with observed rearrangements in colloidal glasses. The high S2 values of the rearranging clusters in glasses indicate that fragile regions in glasses are structurally less correlated, similar to structural defects in crystalline solids. Slow-evolving high S2 spots are capable of predicting local rearrangements long before the relaxations occur, while fluctuation-created high S2 spots best correlate with local deformations right before the rearrangement events. Local free volumes are also found to correlate with particle rearrangements at extreme values, although the ability to identify relaxation sites is substantially lower than S2. Our experiments provide an efficient structural identifier for the fragile regions in glasses and highlight the important role of structural correlations in the physics of glasses.

  3. Berkson's bias, selection bias, and missing data.

    PubMed

    Westreich, Daniel

    2012-01-01

    Although Berkson's bias is widely recognized in the epidemiologic literature, it remains underappreciated as a model of both selection bias and bias due to missing data. Simple causal diagrams and 2 × 2 tables illustrate how Berkson's bias connects to collider bias and selection bias more generally, and show the strong analogies between Berksonian selection bias and bias due to missing data. In some situations, considerations of whether data are missing at random or missing not at random are less important than the causal structure of the missing data process. Although dealing with missing data always relies on strong assumptions about unobserved variables, the intuitions built with simple examples can provide a better understanding of approaches to missing data in real-world situations.

  4. 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.

  5. Is local selection so widespread in river organisms? Fractal geometry of river networks leads to high bias in outlier detection.

    PubMed

    Fourcade, Yoan; Chaput-Bardy, Audrey; Secondi, Jean; Fleurant, Cyril; Lemaire, Christophe

    2013-04-01

    Identifying local adaptation is crucial in conservation biology to define ecotypes and establish management guidelines. Local adaptation is often inferred from the detection of loci showing a high differentiation between populations, the so-called FST outliers. Methods of detection of loci under selection are reputed to be robust in most spatial population models. However, using simulations we showed that FST outlier tests provided a high rate of false-positives (up to 60%) in fractal environments such as river networks. Surprisingly, the number of sampled demes was correlated with parameters of population genetic structure, such as the variance of FST s, and hence strongly influenced the rate of outliers. This unappreciated property of river networks therefore needs to be accounted for in genetic studies on adaptation and conservation of river organisms.

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

    PubMed

    Bordeu, Ignacio; Clerc, Marcel G

    2015-10-01

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

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

    PubMed Central

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

    1999-01-01

    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. PMID:10097396

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

    PubMed

    Zacharias, Jan; Knapp, Ernst Walter

    2013-11-01

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

  9. The effect of sex-biased dispersal on opposite-sexed spatial genetic structure and inbreeding risk.

    PubMed

    Blyton, Michaela D J; Banks, Sam C; Peakall, Rod

    2015-04-01

    Natal sex-biased dispersal has long been thought to reduce the risk of inbreeding by spatially separating opposite-sexed kin. Yet, comprehensive and quantitative evaluations of this hypothesis are lacking. In this study, we quantified the effectiveness of sex-biased dispersal as an inbreeding avoidance strategy by combining spatially explicit simulations and empirical data. We quantified the extent of kin clustering by measuring the degree of spatial autocorrelation among opposite-sexed individuals (FM structure). This allowed us to systematically explore how the extent of sex-biased dispersal, generational overlap, and mate searching distance, influenced both kin clustering, and the resulting inbreeding in the absence of complementary inbreeding avoidance strategies. Simulations revealed that when sex-biased dispersal was limited, positive FM genetic structure developed quickly and increased as the mate searching distance decreased or as generational overlap increased. Interestingly, complete long-range sex-biased dispersal did not prevent the development of FM genetic structure when generations overlapped. We found a very strong correlation between FM genetic structure and both FIS under random mating, and pedigree-based measures of inbreeding. Thus, we show that the detection of FM genetic structure can be a strong indicator of inbreeding risk. Empirical data for two species with different life history strategies yielded patterns congruent with our simulations. Our study illustrates a new application of spatial genetic autocorrelation analysis that offers a framework for quantifying the risk of inbreeding that is easily extendable to other species. Furthermore, our findings provide other researchers with a context for interpreting observed patterns of opposite-sexed spatial genetic structure.

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

    PubMed

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

    2013-12-01

    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. This study used Monte Carlo data simulation techniques to evaluate sample size requirements for common applied SEMs. Across a series of simulations, we systematically varied key model properties, including number of indicators and factors, magnitude of factor loadings and path coefficients, and amount of missing data. We investigated how changes in these parameters affected sample size requirements with respect to statistical power, bias in the parameter estimates, and overall solution propriety. Results revealed a range of sample size requirements (i.e., from 30 to 460 cases), meaningful patterns of association between parameters and sample size, and highlight the limitations of commonly cited rules-of-thumb. The broad "lessons learned" for determining SEM sample size requirements are discussed.

  11. 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.

  12. Matching structural densities from different biophysical origins with gain and bias.

    PubMed

    Wriggers, Willy; Alamo, Lorenzo; Padrón, Raúl

    2011-03-01

    The registration of volumetric structures in real space involves geometric and density transformations that align a target map and a probe map in the best way possible. Many computational docking strategies exist for finding the geometric transformations that superimpose maps, but the problem of finding an optimal density transformation, for the purposes of difference calculations or segmentation, has received little attention in the literature. We report results based on simulated and experimental electron microscopy maps, showing that a single scale factor (gain) may be insufficient when it comes to minimizing the density discrepancy between an aligned target and probe. We propose an affine transformation, with gain and bias, that is parameterized by known surface isovalues and by an interactive centering of the "cancellation peak" in the surface thresholded difference map histogram. The proposed approach minimizes discrepancies across a wide range of interior densities. Owing to having only two parameters, it avoids overfitting and requires only minimal knowledge of the probe and target maps. The linear transformation also preserves phases and relative amplitudes in Fourier space. The histogram matching strategy was implemented in the newly revised volhist tool of the Situs package, version 2.6.

  13. 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.

  14. 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.

  15. 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

  16. Biased allosteric modulation at the CaS receptor engendered by structurally diverse calcimimetics

    PubMed Central

    Cook, A E; Mistry, S N; Gregory, K J; Furness, S G B; Sexton, P M; Scammells, P J; Conigrave, A D; Christopoulos, A; Leach, K

    2015-01-01

    BACKGROUND AND PURPOSE Clinical use of cinacalcet in hyperparathyroidism is complicated by its tendency to induce hypocalcaemia, arising partly from activation of calcium-sensing receptors (CaS receptors) in the thyroid and stimulation of calcitonin release. CaS receptor allosteric modulators that selectively bias signalling towards pathways that mediate desired effects [e.g. parathyroid hormone (PTH) suppression] rather than those mediating undesirable effects (e.g. elevated serum calcitonin), may offer better therapies. EXPERIMENTAL APPROACH We characterized the ligand-biased profile of novel calcimimetics in HEK293 cells stably expressing human CaS receptors, by monitoring intracellular calcium (Ca2+i) mobilization, inositol phosphate (IP)1 accumulation, ERK1/2 phosphorylation (pERK1/2) and receptor expression. KEY RESULTS Phenylalkylamine calcimimetics were biased towards allosteric modulation of Ca2+i mobilization and IP1 accumulation. S,R-calcimimetic B was biased only towards IP1 accumulation. R,R-calcimimetic B and AC-265347 were biased towards IP1 accumulation and pERK1/2. Nor-calcimimetic B was unbiased. In contrast to phenylalkylamines and calcimimetic B analogues, AC-265347 did not promote trafficking of a loss-of-expression, naturally occurring, CaS receptor mutation (G670E). CONCLUSIONS AND IMPLICATIONS The ability of R,R-calcimimetic B and AC-265347 to bias signalling towards pERK1/2 and IP1 accumulation may explain their suppression of PTH levels in vivo at concentrations that have no effect on serum calcitonin levels. The demonstration that AC-265347 promotes CaS receptor receptor signalling, but not trafficking reveals a novel profile of ligand-biased modulation at CaS receptors The identification of allosteric modulators that bias CaS receptor signalling towards distinct intracellular pathways provides an opportunity to develop desirable biased signalling profiles in vivo for mediating selective physiological responses. PMID:25220431

  17. 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; ...

    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

  18. 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.

  19. Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.

    PubMed

    Ezkurdia, Iakes; del Pozo, Angela; Frankish, Adam; Rodriguez, Jose Manuel; Harrow, Jennifer; Ashman, Keith; Valencia, Alfonso; Tress, Michael L

    2012-09-01

    Advances in high-throughput mass spectrometry are making proteomics an increasingly important tool in genome annotation projects. Peptides detected in mass spectrometry experiments can be used to validate gene models and verify the translation of putative coding sequences (CDSs). Here, we have identified peptides that cover 35% of the genes annotated by the GENCODE consortium for the human genome as part of a comprehensive analysis of experimental spectra from two large publicly available mass spectrometry databases. We detected the translation to protein of "novel" and "putative" protein-coding transcripts as well as transcripts annotated as pseudogenes and nonsense-mediated decay targets. We provide a detailed overview of the population of alternatively spliced protein isoforms that are detectable by peptide identification methods. We found that 150 genes expressed multiple alternative protein isoforms. This constitutes the largest set of reliably confirmed alternatively spliced proteins yet discovered. Three groups of genes were highly overrepresented. We detected alternative isoforms for 10 of the 25 possible heterogeneous nuclear ribonucleoproteins, proteins with a key role in the splicing process. Alternative isoforms generated from interchangeable homologous exons and from short indels were also significantly enriched, both in human experiments and in parallel analyses of mouse and Drosophila proteomics experiments. Our results show that a surprisingly high proportion (almost 25%) of the detected alternative isoforms are only subtly different from their constitutive counterparts. Many of the alternative splicing events that give rise to these alternative isoforms are conserved in mouse. It was striking that very few of these conserved splicing events broke Pfam functional domains or would damage globular protein structures. This evidence of a strong bias toward subtle differences in CDS and likely conserved cellular function and structure is remarkable and

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    NASA Astrophysics Data System (ADS)

    Yan, Zhi-Zhong; Zhang, Chuanzeng

    2012-03-01

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

  2. 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

  3. 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.

  4. Local structural modeling for implementation of optimal active damping

    NASA Astrophysics Data System (ADS)

    Blaurock, Carl A.; Miller, David W.

    1993-09-01

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

  5. 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.

  6. 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

  7. 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.

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

    PubMed

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

    2015-12-01

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

  9. Local structure preserving sparse coding for infrared target recognition

    PubMed Central

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

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Zhu, Xiubin

    2014-12-01

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

  11. 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

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

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

    PubMed Central

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

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  16. 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.

  17. Effect of substrate bias on the structural and electrical properties of sputtered Mo thin films on flexible substrates.

    PubMed

    Xu, Jiaxiong

    2016-07-04

    The metal molybdenum (Mo) thin films deposited on flexible substrates can act as the contact electrode of flexible Cu(In,Ga)Se2 or Cu2ZnSn(S,Se)4 solar cells. In this work, in order to enhance the structural and electrical characteristics of flexible Mo thin films, a negative substrate bias was applied during the direct current sputtering of Mo thin films. The flexible substrates used for growing the Mo films were stainless steel foils and polyimides. The characteristics of Mo thin films were studied by x-ray diffraction and sheet resistance measurements. The measured results reveal that an optimal value of negative substrate bias can be found for improving the electrical and structural characteristics of Mo thin films on flexible substrates. The minimum sheet resistances of Mo thin films are 2.50 Ω/sq and 2.73 Ω/sq for the stainless steel foil and polyimide substrates, respectively.

  18. Observation of pure inverse spin Hall effect in ferromagnetic metals via ferromagnetic/antiferromagnetic exchange-bias structures

    NASA Astrophysics Data System (ADS)

    Wu, H.; Wan, C. H.; Yuan, Z. H.; Zhang, X.; Jiang, J.; Zhang, Q. T.; Wen, Z. C.; Han, X. F.

    2015-08-01

    We report that the spin current generated by the spin Seebeck effect (SSE) in yttrium iron garnet (YIG) can be detected by a ferromagnetic metal (NiFe). By using the ferromagnetic/antiferromagnetic (FM/AFM) exchange bias structure (NiFe/IrMn), the inverse spin Hall effect (ISHE) and planar Nernst effect (PNE) of NiFe can be unambiguously separated, allowing us to observe a pure ISHE signal. After eliminating the in-plane temperature gradient in NiFe, we can even observe a pure ISHE signal without PNE from NiFe itself. It is worth noting that a large spin Hall angle (0.098) of NiFe is obtained, which is comparable with Pt. This work provides a kind of FM/AFM exchange bias structure to detect the spin current by charge signals, and highlights that ISHE in ferromagnetic metals can be used in spintronic research and applications.

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

    PubMed Central

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

    2011-01-01

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

  20. Renormalized halo bias

    SciTech Connect

    Assassi, Valentin; Baumann, Daniel; Green, Daniel; Zaldarriaga, Matias E-mail: dbaumann@damtp.cam.ac.uk E-mail: matiasz@ias.edu

    2014-08-01

    This paper provides a systematic study of renormalization in models of halo biasing. Building on work of McDonald, we show that Eulerian biasing is only consistent with renormalization if non-local terms and higher-derivative contributions are included in the biasing model. We explicitly determine the complete list of required bias parameters for Gaussian initial conditions, up to quartic order in the dark matter density contrast and at leading order in derivatives. At quadratic order, this means including the gravitational tidal tensor, while at cubic order the velocity potential appears as an independent degree of freedom. Our study naturally leads to an effective theory of biasing in which the halo density is written as a double expansion in fluctuations and spatial derivatives. We show that the bias expansion can be organized in terms of Galileon operators which aren't renormalized at leading order in derivatives. Finally, we discuss how the renormalized bias parameters impact the statistics of halos.

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

    PubMed

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

    2014-01-01

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

  2. 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

  3. 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.

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

    PubMed

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

    2011-02-11

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

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

    SciTech Connect

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

    2014-10-20

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

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. Enhanced optical second-harmonic generation from the current-biased graphene/SiO2/Si(001) structure.

    PubMed

    An, Yong Q; Nelson, Florence; Lee, Ji Ung; Diebold, Alain C

    2013-05-08

    We find that optical second-harmonic generation (SHG) in reflection from a chemical-vapor-deposition graphene monolayer transferred onto a SiO2/Si(001) substrate is enhanced about 3 times by the flow of direct current electric current in graphene. Measurements of rotational-anisotropy SHG revealed that the current-induced SHG from the current-biased graphene/SiO2/Si(001) structure undergoes a phase inversion as the measurement location on graphene is shifted laterally along the current flow direction. The enhancement is due to current-associated charge trapping at the graphene/SiO2 interface, which introduces a vertical electric field across the SiO2/Si interface that produces electric field-induced SHG. The phase inversion is due to the positive-to-negative polarity switch in the current direction of the trapped charges at the current-biased graphene/SiO2 interface.

  14. Influences of consolidation processes on local paper structure

    NASA Astrophysics Data System (ADS)

    Sung, Yongjoo

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

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

    PubMed

    Shi, Yunfeng; Falk, Michael L

    2005-08-26

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

  16. Predictive Methods for Dense Polymer Networks: Combating Bias with Bio-Based Structures

    DTIC Science & Technology

    2016-03-16

    Briefing Charts 3. DATES COVERED (From - To) 24 February 2016 – 18 March 2016 4. TITLE AND SUBTITLE Predictive methods for dense polymer networks...PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NO. Air Force Research Laboratory (AFMC) AFRL/RQRP 10 E. Saturn...unlimited. PA Clearance 16152 Integrity  Service  Excellence Predictive methods for dense polymer networks: Combating bias with bio-based

  17. How does the cosmic large-scale structure bias the Hubble diagram?

    NASA Astrophysics Data System (ADS)

    Fleury, Pierre; Clarkson, Chris; Maartens, Roy

    2017-03-01

    The Hubble diagram is one of the cornerstones of observational cosmology. It is usually analysed assuming that, on average, the underlying relation between magnitude and redshift matches the prediction of a Friedmann-Lemaître-Robertson-Walker model. However, the inhomogeneity of the Universe generically biases these observables, mainly due to peculiar velocities and gravitational lensing, in a way that depends on the notion of average used in theoretical calculations. In this article, we carefully derive the notion of average which corresponds to the observation of the Hubble diagram. We then calculate its bias at second-order in cosmological perturbations, and estimate the consequences on the inference of cosmological parameters, for various current and future surveys. We find that this bias deeply affects direct estimations of the evolution of the dark-energy equation of state. However, errors in the standard inference of cosmological parameters remain smaller than observational uncertainties, even though they reach percent level on some parameters; they reduce to sub-percent level if an optimal distance indicator is used.

  18. Underreporting in traffic accident data, bias in parameters and the structure of injury severity models.

    PubMed

    Yamamoto, Toshiyuki; Hashiji, Junpei; Shankar, Venkataraman N

    2008-07-01

    Injury severities in traffic accidents are usually recorded on ordinal scales, and statistical models have been applied to investigate the effects of driver factors, vehicle characteristics, road geometrics and environmental conditions on injury severity. The unknown parameters in the models are in general estimated assuming random sampling from the population. Traffic accident data however suffer from underreporting effects, especially for lower injury severities. As a result, traffic accident data can be regarded as outcome-based samples with unknown population shares of the injury severities. An outcome-based sample is overrepresented by accidents of higher severities. As a result, outcome-based samples result in biased parameters which skew our inferences on the effect of key safety variables such as safety belt usage. The pseudo-likelihood function for the case with unknown population shares, which is the same as the conditional maximum likelihood for the case with known population shares, is applied in this study to examine the effects of severity underreporting on the parameter estimates. Sequential binary probit models and ordered-response probit models of injury severity are developed and compared in this study. Sequential binary probit models assume that the factors determining the severity change according to the level of the severity itself, while ordered-response probit models assume that the same factors correlate across all levels of severity. Estimation results suggest that the sequential binary probit models outperform the ordered-response probit models, and that the coefficient estimates for lap and shoulder belt use are biased if underreporting is not considered. Mean parameter bias due to underreporting can be significant. The findings show that underreporting on the outcome dimension may induce bias in inferences on a variety of factors. In particular, if underreporting is not accounted for, the marginal impacts of a variety of factors appear

  19. Polar-biased localization of the cold stress-induced RNA helicase, CrhC, in the Cyanobacterium Anabaena sp. strain PCC 7120.

    PubMed

    El-Fahmawi, Bassam; Owttrim, George W

    2003-11-01

    Shift of the filamentous cyanobacterium, Anabaena sp. strain PCC 7120, from 30 degrees C to 20 degrees C induces expression of a cold shock response gene encoding the RNA helicase CrhC. Subcellular localization using cellular fractionation and membrane purification indicated that CrhC is localized to the plasma membrane with no evidence of a soluble-cytoplasmic form. Treatment of spheroplasts with trypsin and membrane fractions with various denaturing agents identified CrhC as an integral membrane protein associated with the cytoplasmic face of the plasma membrane. Immunoelectron microscopy confirmed the plasma membrane association of CrhC. Interestingly, a higher specific labelling was observed at the cell poles on the septa between adjacent cells within cell filaments. On a per cell area basis, CrhC localization to the cell pole was 3.5- and >1000-fold higher than to the lateral portion of the plasma membrane or cytoplasm respectively. In addition, CrhC also localizes to new cell poles forming within a dividing cell. Polar-biased localization of the CrhC RNA helicase implies a role in RNA metabolism that is plasma membrane associated and preferentially occurs at the cell poles during cyanobacterial response to cold stress.

  20. 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.

  1. Local Function Conservation in Sequence and Structure Space

    PubMed Central

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

    2008-01-01

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

  2. Local function conservation in sequence and structure space.

    PubMed

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

    2008-07-04

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

  3. Effects of substrate bias on structure and mechanical properties of (AlCrNbSiTiV)N coatings

    NASA Astrophysics Data System (ADS)

    Huang, Ping-Kang; Yeh, Jien-Wei

    2009-06-01

    AlCrNbSiTiV nitride films were deposited by reactive radio-frequency magnetron sputtering and the effects of substrate bias on the chemical composition, structure and mechanical properties of the deposited films were investigated. AlCrNbSiTiV nitride films exhibit a single FCC NaCl-type structure and have the stoichiometric nitride ratio of (Al, Cr, Nb, Si, Ti, V)50N50. The deposition rate decreases with increasing substrate bias due to resputtering effects and densification of films, which also leads to less obvious columnar structure, reduced grain size, smaller surface roughness and transition of preferred orientation from the (1 1 1) plane to the (2 0 0) plane. The nitride film deposited at -100 V exhibits the maximum compressive stress around 4.5 GPa and attains a peak hardness and an elastic modulus of 42 GPa and 350 GPa, respectively, which fall in the superhard grade. Moreover, the film keeps its hardness at the superhard grade even after its residual compressive stress was partially released by annealing at 1073 K for 5 h. The structural evolution mechanism and strengthening mechanism are both discussed.

  4. Stabilizing hierarchical compensation for locally controlled large flexible structures

    NASA Technical Reports Server (NTRS)

    Das, B.; Balas, M.

    1989-01-01

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

  5. Models of models: filtering and bias rings in depiction of knowledge structures and their implications for design.

    PubMed

    Revell, Kirsten M A; Stanton, Neville A

    2012-01-01

    Mental models are poorly specified in three ways: in their defining criteria, their source and the bias to which they have been subjected. Literature from psychology, HCI and human factors sources was reviewed to determine the utility of 'mental models' as a design tool. The definitions and theories offered by key contributors to the notion of mental models were compared. Schematics, representing both the knowledge structures proposed in cognitive processing, as well as the layers of bias evident when forming or accessing mental models, were constructed. Fundamental similarities and differences in the use of this notion, as well as ambiguities in definition, were highlighted graphically. The need for specificity in the use of mental models was emphasised as essential for pragmatic application in design. The use of graphical comparison was proposed as a means of identifying the risk of bias and a means to categorise approaches to mental model research. Practitioner Summary: Mental models are considered significant in user centred design. To apply this notion pragmatically, its definition and methods of construction and access need to be sufficiently specified. This article offers a graphical method to compare existing research in mental models, highlighting similarities, differences and ambiguities.

  6. Non-collinear magnetism and exchange bias at the FM NiFe/AFM NiMn interface: local spin density FLAPW study

    NASA Astrophysics Data System (ADS)

    Nakamura, K.; Freeman, A. J.; Wang, D.-S.; Zhong, L.; Fernandez-de-Castro, J.

    2001-03-01

    Magnetism at interfaces, such as the exchange bias between ferromagnetic (FM) and antiferromagnetic (AFM) materials, has attracted great attention because of technological applications. In order to investigate magnetic structures at the FM/AFM interface, we have implemented the FLAPW (E. Wimmer, H. Krakauer, M. Weinert and A.J. Freeman, PRB 24, 864(1981)) methodologies including non-collinear magnetism, in which the magnetic moment direction as well as the magnitude can vary continuously all over space. We first demonstrate this approach to determine the structure of a magnetic structure at an interface between FM NiFe and AFM NiMn. Although both bulk systems each show collinear FM and AFM structures, we found that a perpendicular magnetic orientation at their interface is energetically favorable, where the magnetic moments of the FM NiFe tend to lie perpendicular to those of AFM NiMn.

  7. 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.

  8. 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…

  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. Tunable Surface Structuration of Silicon by Metal Assisted Chemical Etching with Pt Nanoparticles under Electrochemical Bias.

    PubMed

    Torralba, Encarnación; Le Gall, Sylvain; Lachaume, Raphaël; Magnin, Vincent; Harari, Joseph; Halbwax, Mathieu; Vilcot, Jean-Pierre; Cachet-Vivier, Christine; Bastide, Stéphane

    2016-11-16

    An in-depth study of metal assisted chemical etching (MACE) of p-type c-Si in HF/H2O2 aqueous solutions using Pt nanoparticles as catalysts is presented. Combination of cyclic voltammetry, open circuit measurements, chronoamperometry, impedance spectroscopy, and 2D band bending modeling of the metal/semiconductor/electrolyte interfaces at the nanoscale and under different etching conditions allows gaining physical insights into this system. Additionally, in an attempt to mimic the etching conditions, the modeling has been performed with a positively biased nanoparticle buried in the Si substrate. Following these findings, the application of an external polarization during etching is introduced as a novel efficient approach for achieving straightforward control of the pore morphology by acting upon the band bending at the Si/electrolyte junction. In this way, nanostructures ranging from straight mesopores to cone-shaped macropores are obtained as the Si sample is biased from negative to positive potentials. Remarkably, macroscopic cone-shaped pores in the 1-5 μm size range with a high aspect ratio (L/W ∼ 1.6) are obtained by this method. This morphology leads to a reduction of the surface reflectance below 5% over the entire VIS-NIR domain, which outperforms macrostructures made by state of the art texturization techniques for Si solar cells.

  11. Eliminating Bias

    EPA Pesticide Factsheets

    Learn how to eliminate bias from monitoring systems by instituting appropriate installation, operation, and quality assurance procedures. Provides links to download An Operator's Guide to Eliminating Bias in CEM Systems.

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

    NASA Astrophysics Data System (ADS)

    Knobloch, E.

    2008-04-01

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

  13. 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

  14. 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.

  15. Local magnetic structure determination using polarized neutron holography

    NASA Astrophysics Data System (ADS)

    Szakál, Alex; Markó, Márton; Cser, László

    2015-05-01

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

  16. 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

  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. Functional implications of local DNA structures in regulatory motifs.

    PubMed

    Xiang, Qian

    2013-01-01

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

  19. 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.

  20. Training effects and the microscopic magnetic structure of exchange biased Co/CoO bilayers.

    SciTech Connect

    Berger, A.; Dahlberg, E. D.; Felcher, G. P.; Hill, B. K.; te Velthius, S. G. E.

    1999-09-01

    Exchange bias of a partially oxidized thin film of ferromagnetic Co was studied by magnetization measurements and polarized neutron reflectivity (PNR). The magnetization curve shows strong effects of training with cycling of the magnetic field. Reflectivity measurements with the field parallel to the cooling field showed the onset of spin-dependent diffuse scattering--off the specular reflection--after a training cycle. Such scattering, of the Yoneda type, is due to misaligned Co domains possibly close to the Co/CoO interface. Subjecting the field cooled Co/CoO pair to a field perpendicular to the cooling field causes a rotation of the magnetization. PNR measurements confirmed earlier susceptibility studies by indicating that the rotation of the magnetization is reversible in fields up to 400 Oe. The rotation of the magnetization of Co is uniform across the film thickness.

  1. 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.

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

    PubMed

    Overduin, S D; Patey, G N

    2015-09-07

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

  3. Recognition of Local DNA Structures by p53 Protein.

    PubMed

    Brázda, Václav; Coufal, Jan

    2017-02-10

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

  4. Recognition of Local DNA Structures by p53 Protein

    PubMed Central

    Brázda, Václav; Coufal, Jan

    2017-01-01

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

  5. Intergroup bias.

    PubMed

    Hewstone, Miles; Rubin, Mark; Willis, Hazel

    2002-01-01

    This chapter reviews the extensive literature on bias in favor of in-groups at the expense of out-groups. We focus on five issues and identify areas for future research: (a) measurement and conceptual issues (especially in-group favoritism vs. out-group derogation, and explicit vs. implicit measures of bias); (b) modern theories of bias highlighting motivational explanations (social identity, optimal distinctiveness, uncertainty reduction, social dominance, terror management); (c) key moderators of bias, especially those that exacerbate bias (identification, group size, status and power, threat, positive-negative asymmetry, personality and individual differences); (d) reduction of bias (individual vs. intergroup approaches, especially models of social categorization); and (e) the link between intergroup bias and more corrosive forms of social hostility.

  6. 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.

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

    PubMed

    Kim, Keonwook; Kim, Youngwoong

    2015-02-06

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

  8. 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

  9. 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.

  10. 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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1998-03-01

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

  13. Alfvénic localized structures in partially ionized plasmas

    NASA Astrophysics Data System (ADS)

    Borhanian, Jafar; Rezaei, Arash

    2017-02-01

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

  14. The local spiral structure of the Milky Way.

    PubMed

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

    2016-09-01

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

  15. 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

  16. Attention Orienting in Response to Non-conscious Hierarchical Arrows: Individuals with Higher Autistic Traits Differ in Their Global/Local Bias

    PubMed Central

    Laycock, Robin; Chan, Daniel; Crewther, Sheila G.

    2017-01-01

    One aspect of the social communication impairments that characterize autism spectrum disorder (ASD) include reduced use of often subtle non-verbal social cues. People with ASD, and those with self-reported sub-threshold autistic traits, also show impairments in rapid visual processing of stimuli unrelated to social or emotional properties. Hence, this study sought to investigate whether perceptually non-conscious visual processing is related to autistic traits. A neurotypical sample of thirty young adults completed the Subthreshold Autism Trait Questionnaire and a Posner-like attention cueing task. Continuous Flash Suppression (CFS) was employed to render incongruous hierarchical arrow cues perceptually invisible prior to consciously presented targets. This was achieved via a 10 Hz masking stimulus presented to the dominant eye that suppressed information presented to the non-dominant eye. Non-conscious arrows consisted of local arrow elements pointing in one direction, and forming a global arrow shape pointing in the opposite direction. On each trial, the cue provided either a valid or invalid cue for the spatial location of the subsequent target, depending on which level (global or local) received privileged attention. A significant autism-trait group by global cue validity interaction indicated a difference in the extent of non-conscious local/global cueing between groups. Simple effect analyses revealed that whilst participants with lower autistic traits showed a global arrow cueing effect, those with higher autistic traits demonstrated a small local arrow cueing effect. These results suggest that non-conscious processing biases in local/global attention may be related to individual differences in autistic traits. PMID:28149288

  17. Effect of negative bias voltage on CrN films deposited by arc ion plating. II. Film composition, structure, and properties

    SciTech Connect

    Wang Qimin; Kim, Kwang Ho

    2008-09-15

    Chromium nitride (CrN) films were deposited on Si wafers by arc ion plating at various negative bias voltages and several groups of N{sub 2}/Ar gas flux ratios and chamber gas pressures. The authors systematically investigated the influence of negative bias voltage on the synthesis, composition, microstructure, and properties of the arc ion plating (AIP) CrN films. In this article, the authors investigated the influence of negative bias voltage on the chemical composition, structure, and mechanical properties of the CrN films. The results showed that the chemical composition and phase structure of the AIP CrN films were greatly altered by application of negative bias voltage. Due to the selective resputtering effect, substoichiometric CrN films were obtained. With increase in bias voltages, the main phases in the films transformed from Cr+CrN to Cr{sub 2}N at low N{sub 2}/Ar flow ratios, whereas the films at high N{sub 2}/Ar flow ratios retained the CrN phase structure. The CrN films experienced texture transformation from CrN (200) to CrN (220), and Cr{sub 2}N (300) to Cr{sub 2}N(300)+Cr{sub 2}N(110). Increase in negative bias voltage also resulted in microstructure evolution of coarse columnar grains{yields}fine columnar grains{yields}quasiamorphous microstructure{yields}recrystallized structures. From the experimental results, the authors proposed a new structure zone model based on enhanced bombardment of incident ions by application of negative bias voltage. The influence of negative bias voltage on the microhardness and residual stresses of the films and the inherent mechanisms were also explored.

  18. What is the difference between OASIS and OPERA? Roughly five pixels: orthographic structure biases the perceived length of letter strings.

    PubMed

    Chetail, Fabienne; Content, Alain

    2014-01-01

    A thorough understanding of monosyllabic-word-recognition processes, in contrast with multisyllabic-word processing, has accumulated over the past decades. One fundamental challenge regarding multisyllabic words concerns their parsing into smaller units and the nature of the cues determining the parsing. We propose that the organization of consonant and vowel letters provides powerful cues for parsing, and we present data from a new task showing that a word's orthographic structure, as determined by the number of vowel-letter clusters, influences estimations of its length. Words were briefly presented on a computer screen, and participants had to estimate word length by drawing a line on the screen with the mouse. In three experiments, participants estimated words comprising fewer orthographic units as shorter than words comprising more units even though the words matched for number of letters. Further results demonstrated that the length bias was driven by orthographic information and not by phonological structure.

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

    PubMed Central

    Kumar, Sushant; Clarke, Declan; Gerstein, Mark

    2016-01-01

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

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

    PubMed

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

    2012-05-01

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

  1. Cosmic structure and dynamics of the local Universe

    NASA Astrophysics Data System (ADS)

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

    2012-11-01

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

  2. 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.

  3. 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).

  4. 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.

  5. CONDENSED MATTER: ELECTRONIC STRUCTURE, ELECTRICAL, MAGNETIC, AND OPTICAL PROPERTIES Electronic Transport Calculations Using Maximally-Localized Wannier Functions

    NASA Astrophysics Data System (ADS)

    Wang, Neng-Ping

    2011-01-01

    I present a method to calculate the ballistic transport properties of atomic-scale structures under bias. The electronic structure of the system is calculated using the Kohn-Sham scheme of density functional theory (DFT). The DFT eigenvectors are then transformed into a set of maximally localized Wannier functions (MLWFs) [N. Marzari and D. Vanderbilt, Phys. Rev. B 56 (1997) 12847]. The MLWFs are used as a minimal basis set to obtain the Hamitonian matrices of the scattering region and the adjacent leads, which are needed for transport calculation using the nonequilibrium Green's function formalism. The coupling of the scattering region to the semi-infinite leads is described by the self-energies of the leads. Using the nonequilibrium Green's function method, one calculates self-consistently the charge distribution of the system under bias and evaluates the transmission and current through the system. To solve the Poisson equation within the scheme of MLWFs I introduce a computationally efficient method. The method is applied to a molecular hydrogen contact in two transition metal monatomic wires (Cu and Pt). It is found that for Pt the I-V characteristics is approximately linear dependence, however, for Cu the I-V characteristics manifests a linear dependence at low bias voltages and exhibits apparent nonlinearity at higher bias voltages. I have also calculated the transmission in the zero bias voltage limit for a single CO molecule adsorbed on Cu and Pt monatomic wires. While a chemical scissor effect occurs for the Cu monatomic wire with an adsorbed CO molecule, it is absent for the Pt monatomic wire due to the contribution of d-orbitals at the Fermi energy.

  6. 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

  7. Structural damage localization using wavelet-based silhouette statistics

    NASA Astrophysics Data System (ADS)

    Jung, Uk; Koh, Bong-Hwan

    2009-04-01

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

  8. Local Structure of Cerium in Aluminophosphate and Silicophosphate Glasses

    SciTech Connect

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

    2011-12-31

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

  9. Local Structure of Cerium in Aluminophosphate and Silicophosphate Glasses

    SciTech Connect

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

    2011-09-20

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

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Localization and structure of carbonaceous deposits on reforming catalysts

    SciTech Connect

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

    1990-12-01

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

  15. Electronic-structure calculation for metals by local optimization

    NASA Astrophysics Data System (ADS)

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

    1989-03-01

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

  16. 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.

  17. The local electronic structure of alpha-Li3N.

    PubMed

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

    2008-07-28

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

  18. 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

  19. 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.

  20. 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.

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2001-09-01

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

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

    NASA Astrophysics Data System (ADS)

    Wasti, Sambid; Taylor, Mark

    2012-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Wasti, Sambid; Taylor, Mark

    2011-10-01

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

  6. 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.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    Bahlmann, Claus; Li, Xianlin; Okada, Kazunori

    2006-03-01

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

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

    PubMed

    Conradson, S; Espinosa, F; Villella, P

    2001-03-01

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

  10. 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

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

    PubMed

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

    1990-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  13. 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

  14. 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.…

  15. 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,…

  16. Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences

    PubMed Central

    2016-01-01

    X-ray crystallography has been applied to the structural analysis of a series of tetrapeptides that were previously assessed for catalytic activity in an atroposelective bromination reaction. Common to the series is a central Pro-Xaa sequence, where Pro is either l- or d-proline, which was chosen to favor nucleation of canonical β-turn secondary structures. Crystallographic analysis of 35 different peptide sequences revealed a range of conformational states. The observed differences appear not only in cases where the Pro-Xaa loop-region is altered, but also when seemingly subtle alterations to the flanking residues are introduced. In many instances, distinct conformers of the same sequence were observed, either as symmetry-independent molecules within the same unit cell or as polymorphs. Computational studies using DFT provided additional insight into the analysis of solid-state structural features. Select X-ray crystal structures were compared to the corresponding solution structures derived from measured proton chemical shifts, 3J-values, and 1H–1H-NOESY contacts. These findings imply that the conformational space available to simple peptide-based catalysts is more diverse than precedent might suggest. The direct observation of multiple ground state conformations for peptides of this family, as well as the dynamic processes associated with conformational equilibria, underscore not only the challenge of designing peptide-based catalysts, but also the difficulty in predicting their accessible transition states. These findings implicate the advantages of low-barrier interconversions between conformations of peptide-based catalysts for multistep, enantioselective reactions. PMID:28029251

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

    NASA Astrophysics Data System (ADS)

    Ding, Jun

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

  18. Local Tomography and the Jordan Structure of Quantum Theory

    NASA Astrophysics Data System (ADS)

    Barnum, Howard; Wilce, Alexander

    2014-02-01

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

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

    NASA Technical Reports Server (NTRS)

    Dong, Stanley B.

    1989-01-01

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

  20. Imaging biological structures with fluorescence photoactivation localization microscopy.

    PubMed

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

    2009-01-01

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

  1. The local structure of topological charge fluctuations in QCD

    SciTech Connect

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

    2002-06-01

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

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

    SciTech Connect

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

    2008-12-01

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

  3. Embrittlement and Flow Localization in Reactor Structural Materials

    SciTech Connect

    Xianglin Wu; Xiao Pan; James Stubbins

    2006-10-06

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

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

    NASA Astrophysics Data System (ADS)

    Taghavian, Fatemeh; Salehi, Mostafa; Teimouri, Mehdi

    2017-02-01

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

  5. Mapping Milky Way and Local Volume Structure With LSST

    NASA Astrophysics Data System (ADS)

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

    2010-01-01

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

  6. Peculiar velocities into the next generation: cosmological parameters from large surveys without bias from non-linear structure

    NASA Astrophysics Data System (ADS)

    Abate, Alexandra; Bridle, Sarah; Teodoro, Luis F. A.; Warren, Michael S.; Hendry, Martin

    2008-10-01

    We investigate methods to best estimate the normalization of the mass density fluctuation power spectrum (σ8) using peculiar velocity data from a survey like the six-degree Field Galaxy Velocity Survey (6dFGSv). We focus on two potential problems: (i) biases from non-linear growth of structure and (ii) the large number of velocities in the survey. Simulations of ΛCDM-like models are used to test the methods. We calculate the likelihood from a full covariance matrix of velocities averaged in grid cells. This simultaneously reduces the number of data points and smoothes out non-linearities which tend to dominate on small scales. We show how the averaging can be taken into account in the predictions in a practical way, and show the effect of the choice of cell size. We find that a cell size can be chosen that significantly reduces the non-linearities without significantly increasing the error bars on cosmological parameters. We compare our results with those from a principal components analysis following Watkins et al. and Feldman et al. to select a set of optimal moments constructed from linear combinations of the peculiar velocities that are least sensitive to the non-linear scales. We conclude that averaging in grid cells performs equally well. We find that for a survey such as 6dFGSv we can estimate σ8 with less than 3 per cent bias from non-linearities. The expected error on σ8 after marginalizing over Ωm is approximately 16 per cent.

  7. 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.

  8. 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.

  9. Analysis of stability improvement in ZnO thin film transistor with dual-gate structure under negative bias stress

    NASA Astrophysics Data System (ADS)

    Yun, Ho-Jin; Kim, Young-Su; Jeong, Kwang-Seok; Kim, Yu-Mi; Yang, Seung-dong; Lee, Hi-Deok; Lee, Ga-Won

    2014-01-01

    In this study, we fabricated dual-gate zinc oxide thin film transistors (ZnO TFTs) without additional processes and analyzed their stability characteristics under a negative gate bias stress (NBS) by comparison with conventional bottom-gate structures. The dual-gate device shows superior electrical parameters, such as subthreshold swing (SS) and on/off current ratio. NBS of VGS = -20 V with VDS = 0 was applied, resulting in a negative threshold voltage (Vth) shift. After applying stress for 1000 s, the Vth shift is 0.60 V in a dual-gate ZnO TFT, while the Vth shift is 2.52 V in a bottom-gate ZnO TFT. The stress immunity of the dual-gate device is caused by the change in field distribution in the ZnO channel by adding another gate as the technology computer aided design (TCAD) simulation shows. Additionally, in flicker noise analysis, a lower noise level with a different mechanism is observed in the dual-gate structure. This can be explained by the top side of the ZnO film having a larger crystal and fewer grain boundaries than the bottom side, which is revealed by the enhanced SS and XRD results. Therefore, the improved stability of the dual-gate ZnO TFT is greatly related to the E-field cancellation effect and crystal quality of the ZnO film.

  10. Structure and local charging of electromigrated Au nanocontacts.

    PubMed

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

    2017-02-03

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

  11. Structure and local charging of electromigrated Au nanocontacts

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

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

    PubMed

    Jagla, E A

    2007-10-01

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

  13. 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.

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

    PubMed

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

    2015-06-01

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

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

    PubMed Central

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

    2009-01-01

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

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

    SciTech Connect

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

    1998-12-10

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

  17. 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.

  18. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    NASA Astrophysics Data System (ADS)

    Deych, Lev; Yamilov, Alexey; Lisyansky, Alexander

    2000-11-01

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

  1. The local electronic structure of α-Li3N

    SciTech Connect

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

    2008-07-28

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

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

    NASA Technical Reports Server (NTRS)

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

    1976-01-01

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

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Manimala, James Mathew

    in locally dissipative AM with various damped oscillator microstructures was studied using mechanical lattice models. The presence of damping was represented by a complex effective-mass. Analytical transmissibilities and numerical verifications were obtained for Kelvin-Voigt-type, Maxwell-type and Zener-type oscillators. Although peak attenuation at resonance is diminished, broadband attenuation was found to be achievable without increasing mass ratio, obviating the bandgap width limitations of locally resonant AM. Static and frequency-dependent measures of optimal damping that maximize the attenuation characteristics were established. A transitional value for the excitation frequency was identified within the locally resonant bandgap, above which there always exists an optimal amount of damping that renders the attenuation for the dissipative AM greater than that for the locally resonant case. AM with nonlinear stiffnesses were also investigated. For a base-excited two degree of freedom system consisting of a master structure and a Duffing-type oscillator, approximate transmissibility was derived, verified using simulations and compared to its equivalent damped model. Analytical solutions for dispersion curve shifts in nonlinear chains with linear resonators and in linear chains with nonlinear oscillators were obtained using perturbation analysis and first order approximations for cubic hardening and softening cases. Amplitude-activated alterations in bandgap width and the possibility of phenomena such as branch curling and overtaking were observed. Device implications of nonlinear AM as amplitude-dependent filters and direction-biased waveguides were examined using simulations.

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

    PubMed Central

    Lee, Hui Sun; Im, Wonpil

    2012-01-01

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

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

    PubMed

    Hobbs, Bruce E; Ord, Alison

    2012-04-28

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

    Walrath, Jenna Cherie

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

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

    PubMed

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

    2009-11-11

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

  11. Spatial-temporal structures of human alpha rhythms: theory, microcurrent sources, multiscale measurements, and global binding of local networks.

    PubMed

    Nunez, P L; Wingeier, B M; Silberstein, R B

    2001-07-01

    A theoretical framework supporting experimental measures of dynamic properties of human EEG is proposed with emphasis on distinct alpha rhythms. Robust relationships between measured dynamics and cognitive or behavioral conditions are reviewed, and proposed physiological bases for EEG at cellular levels are considered. Classical EEG data are interpreted in the context of a conceptual framework that distinguishes between locally and globally dominated dynamic processes, as estimated with coherence or other measures of phase synchronization. Macroscopic (scalp) potentials generated by cortical current sources are described at three spatial scales, taking advantage of the columnar structure of neocortex. New EEG data demonstrate that both globally coherent and locally dominated behavior can occur within the alpha band, depending on narrow band frequency, spatial measurement scale, and brain state. Quasi-stable alpha phase structures consistent with global standing waves are observed. At the same time, alpha and theta phase locking between cortical regions during mental calculations is demonstrated, consistent with neural network formation. The brain-binding problem is considered in the context of EEG dynamic behavior that generally exhibits both of these local and global aspects. But specific experimental designs and data analysis methods may severely bias physiological interpretations in either local or global directions.

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

    PubMed

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

    2016-11-01

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

  13. 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.

  14. 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

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  16. Journal bias or author bias?

    PubMed

    Harris, Ian

    2016-01-01

    I read with interest the comment by Mark Wilson in the Indian Journal of Medical Ethics regarding bias and conflicts of interest in medical journals. Wilson targets one journal (the New England Journal of Medicine: NEJM) and one particular "scandal" to make his point that journals' decisions on publication are biased by commercial conflicts of interest (CoIs). It is interesting that he chooses the NEJM which, by his own admission, had one of the strictest CoI policies and had published widely on this topic. The feeling is that if the NEJM can be guilty, they can all be guilty.

  17. Local structure analysis of materials for increased energy efficiency

    NASA Astrophysics Data System (ADS)

    Medling, Scott

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

  18. 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

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

    PubMed

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

    2016-02-26

    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.

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

    PubMed

    Levy, Roger P; Keller, Frank

    2013-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

  2. 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.

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

    PubMed Central

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

    2010-01-01

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

  4. 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)

  5. 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.

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

    NASA Astrophysics Data System (ADS)

    Liu, Hao; Li, Ti-Pei

    2009-03-01

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

  7. The suppressed negative bias illumination-induced instability in In-Ga-Zn-O thin film transistors with fringe field structure

    NASA Astrophysics Data System (ADS)

    Chen, Yu-Chun; Chang, Ting-Chang; Li, Hung-Wei; Hsieh, Tien-Yu; Chen, Te-Chih; Wu, Chang-Pei; Chou, Cheng-Hsu; Chung, Wang-Cheng; Chang, Jung-Fang; Tai, Ya-Hsiang

    2012-11-01

    This study investigates the suppressed negative gate bias illumination stress (NBIS) -induced instability of via-type amorphous indium-gallium-zinc-oxide (a-IGZO) thin film transistors (TFTs) with fringe field (FF) structures. The less negative threshold voltage shifts of devices after NBIS are showed when device has larger FF structures. This finding is attributed to more dispersive distribution of photo-generated holes in the width direction of a-IGZO during NBIS, which reduce the hole trapping phenomenon in the front channel interface. The a-IGZO TFT with FF structure is expected to be an effective method to increase the electrical reliability of devices after NBIS.

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

    DTIC Science & Technology

    2015-06-01

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

  9. 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.

  10. 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.

  11. An Approximate Bayesian Computation Approach to Overcome Biases That Arise When Using Amplified Fragment Length Polymorphism Markers to Study Population Structure

    PubMed Central

    Foll, Matthieu; Beaumont, Mark A.; Gaggiotti, Oscar

    2008-01-01

    There is great interest in using amplified fragment length polymorphism (AFLP) markers because they are inexpensive and easy to produce. It is, therefore, possible to generate a large number of markers that have a wide coverage of species genomes. Several statistical methods have been proposed to study the genetic structure using AFLPs but they assume Hardy–Weinberg equilibrium and do not estimate the inbreeding coefficient, FIS. A Bayesian method has been proposed by Holsinger and colleagues that relaxes these simplifying assumptions but we have identified two sources of bias that can influence estimates based on these markers: (i) the use of a uniform prior on ancestral allele frequencies and (ii) the ascertainment bias of AFLP markers. We present a new Bayesian method that avoids these biases by using an implementation based on the approximate Bayesian computation (ABC) algorithm. This new method estimates population-specific FIS and FST values and offers users the possibility of taking into account the criteria for selecting the markers that are used in the analyses. The software is available at our web site (http://www-leca.ujf-grenoble.fr/logiciels.htm). Finally, we provide advice on how to avoid the effects of ascertainment bias. PMID:18505879

  12. Structural features of multiple nifH-like sequences and very biased codon usage in nitrogenase genes of Clostridium pasteurianum.

    PubMed Central

    Chen, K C; Chen, J S; Johnson, J L

    1986-01-01

    The structural gene (nifH1) encoding the nitrogenase iron protein of Clostridium pasteurianum has been cloned and sequenced. It is located on a 4-kilobase EcoRI fragment (cloned into pBR325) that also contains a portion of nifD and another nifH-like sequence (nifH2). C. pasteurianum nifH1 encodes a polypeptide (273 amino acids) identical to that of the isolated iron protein, indicating that the smaller size of the C. pasteurianum iron protein does not result from posttranslational processing. The 5' flanking region of nifH1 or nifH2 does not contain the nif promoter sequences found in several gram-negative bacteria. Instead, a sequence resembling the Escherichia coli consensus promoter (TTGACA-N17-TATAAT) is present before C. pasteurianum nifH2, and a TATAAT sequence is present before C pasteurianum nifH1. Codon usage in nifH1, nifH2, and nifD (partial) is very biased. A preference for A or U in the third position of the codons is seen. nifH2 could encode a protein of 272 amino acid residues, which differs from the iron protein (nifH1 product) in 23 amino acid residues (8%). Another nifH-like sequence (nifH3) is located on a nonadjacent EcoRI fragment and has been partially sequenced. C. pasteurianum nifH2 and nifH3 may encode proteins having several amino acids that are conserved in other proteins but not in C. pasteurianum iron protein, suggesting a possible role for the multiple nifH-like sequences of C. pasteurianum in the evolution of nifH. Among the nine sequenced iron proteins, only the C. pasteurianum protein lacks a conserved lysine residue which is near the extended C terminus of the other iron proteins. The absence of this positive charge in the C. pasteurianum iron protein might affect the cross-reactivity of the protein in heterologous systems. Images PMID:3457003

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

    PubMed

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

    2013-02-21

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

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

    NASA Astrophysics Data System (ADS)

    Mishra, Ashutosh; Ninama, Samrath; Trivedi, Apurva

    2014-09-01

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

  15. Photoconductivity and photoluminescence under bias in GaInNAs/GaAs MQW p-i-n structures

    NASA Astrophysics Data System (ADS)

    Khalil, Hagir M.; Royall, Ben; Mazzucato, Simone; Balkan, Naci

    2012-09-01

    The low temperature photoluminescence under bias (PLb) and the photoconductivity (PC) of a p-i-n GaInNAs/GaAs multiple quantum well sample have been investigated. Under optical excitation with photons of energy greater than the GaAs bandgap, PC and PLb results show a number of step-like increases when the sample is reverse biased. The nature of these steps, which depends upon the temperature, exciting wavelength and intensity and the number of quantum wells (QWs) in the device, is explained in terms of thermionic emission and negative charge accumulation due to the low confinement of holes in GaInNAs QWs. At high temperature, thermal escape from the wells becomes much more dominant and the steps smear out.

  16. Photoconductivity and photoluminescence under bias in GaInNAs/GaAs MQW p-i-n structures.

    PubMed

    Khalil, Hagir M; Royall, Ben; Mazzucato, Simone; Balkan, Naci

    2012-09-28

    The low temperature photoluminescence under bias (PLb) and the photoconductivity (PC) of a p-i-n GaInNAs/GaAs multiple quantum well sample have been investigated. Under optical excitation with photons of energy greater than the GaAs bandgap, PC and PLb results show a number of step-like increases when the sample is reverse biased. The nature of these steps, which depends upon the temperature, exciting wavelength and intensity and the number of quantum wells (QWs) in the device, is explained in terms of thermionic emission and negative charge accumulation due to the low confinement of holes in GaInNAs QWs. At high temperature, thermal escape from the wells becomes much more dominant and the steps smear out.

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

    ERIC Educational Resources Information Center

    Levy, Roger P.; Keller, Frank

    2013-01-01

    Probabilistic expectations and memory limitations are central factors governing the real-time comprehension of natural language, but how the two factors interact remains poorly understood. One respect in which the two factors have come into theoretical conflict is the documentation of both "locality" effects, in which having more dependents…

  18. Influence of the substrate bias voltage on the crystallographic structure and mechanical properties of Ti6Al4V coatings deposited by rf magnetron

    NASA Astrophysics Data System (ADS)

    Alfonso, J. E.; Pacheco, Fernando; Castro P., Alvaro; Torres, J.

    2005-08-01

    Physical and mechanical properties of pure titanium are improved when the material is mixed with aluminum and vanadium at specific concentrations. Specifically, the alloy composed by 90% of titanium, 6% of aluminum and 4% of vanadium (Ti-6Al-4V) is highly resistant to fatigue and corrosion titanium and their alloys can be deposited by two techniques: Chemical Vapor Deposition (CVD) and Physical Vapor Deposition (PVD). However, some problems are generated when carbonated steel substrates are used under the CVD technique, mainly because those substrates lost its carbon as a result of the high substrate temperature used during the deposition process. Alternatively, PVD (magnetron sputtering, ion plating) is a low temperature substrate process and also has the advantage that substrate bias can promote structure refinement through resputtering effects.Substrate bias influence on the crystalline structure of Ti6Al4V thin films prepared by rf magnetron sputtering are presented in this work. Samples were grown onto common glass and AISI 420 steel substrates using a Ti6Al4V (99.9 %) target. Substrate bias was varied from -100 V to -200 V. Samples were characterized by X-ray Diffraction (XRD), Energy Dispersive X-ray Spectroscopy (EDXS), Scanning Electron Microscopy (SEM), and Atomic Force Microscopy (AFM). Thin films stoichiometry were studied by EDX in agreement with the Ti-6Al-4V target. Finally, the studies of the mechanical behavior of the films on steel showed that the hardness increased 1100 Knoop when the bias voltage is raised to -160 V.

  19. CONDENSED MATTER: ELECTRONIC STRUCTURE, ELECTRICAL, MAGNETIC, AND OPTICAL PROPERTIES: Intraband dynamics and terahertz emission in biased semiconductor superlattices coupled to double far-infrared pulses

    NASA Astrophysics Data System (ADS)

    Li, Min; Mi, Xian-Wu

    2009-12-01

    This paper studies both the intraband polarization and terahertz emission of a semiconductor superlattice in combined dc and ac electric fields by using the superposition of two identical time delayed and phase shifted optical pulses. By adjusting the delay between these two optical pulses, our results show that the intraband polarization is sensitive to the time delay. The peak values appear again for the terahertz emission intensity due to the superposition of two optical pulses. The emission lines of terahertz blueshift and redshift in different ac electric fields and dynamic localization appears. The emission lines of THz only appear to blueshift when the biased superlattice is driven by a single optical pulse. Due to excitonic dynamic localization, the terahertz emission intensity decays with time in different dc and ac electric fields. These are features of this superlattice which distinguish it from a superlattice generated by a single optical pulse to drive it.

  20. 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.

  1. 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.

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

    PubMed

    Biondini, Gino; Li, Sitai; Mantzavinos, Dionyssios

    2016-12-01

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

  3. Oscillation structure of localized perturbations in modulationally unstable media

    NASA Astrophysics Data System (ADS)

    Biondini, Gino; Li, Sitai; Mantzavinos, Dionyssios

    2016-12-01

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

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

    PubMed

    Wu, Peter I-Kung; Edelman, Elazer R

    2008-09-18

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

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  7. 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.

  8. Electrical Effect in Silver-Point Realization Due to Cell Structure and Bias Voltage Based on Resistance Measurement Using AC and DC Bridges

    NASA Astrophysics Data System (ADS)

    Widiatmo, J. V.; Harada, K.; Yamazawa, K.; Tamba, J.; Arai, M.

    2015-08-01

    Electrical effects related to insulating leakage represent one of the major factors contributing to uncertainties in measurements using high-temperature standard platinum resistance thermometers (HTSPRTs), especially during the realization of the silver freezing point (). This work is focused on the evaluation of the differences in resistance measurements observed when using AC resistance bridges and DC resistance bridges, hereafter, termed the AC-DC differences, as the result of various electrical effects. The magnitude of the AC-DC difference in several silver-point cells is demonstrated with several HTSPRTs. The effect of the cell structure on the AC-DC difference is evaluated by exchanging some components, part by part, within a silver-point cell. Then, the effect of the bias voltage applied to the heat pipe within the silver-point furnace is evaluated. Through the analysis of the experimental results and comparison with the reports in the literature, the importance of evaluating the AC-DC difference as a means to characterize the underlying electrical effects is discussed, considering that applying a negative bias condition to the furnace with respect to the high-temperature SPRT can minimize the AC-DC difference. Concluding recommendations are proposed on the components used in silver-point cells and the application of a bias voltage to the measurement circuit to minimize the effects of the electrical leakage.

  9. MRI tissue segmentation incorporating a bias field modulated smoothness prior

    NASA Astrophysics Data System (ADS)

    Song, Enmin; Cardenas, Valerie A.; Sacrey, Diana; Blumenfeld, Robert; Weiner, Michael W.; Studholme, Colin

    2003-05-01

    This paper examines a refinement to probabilistic intensity based tissue segmentation methods, which makes use of knowledge derived from an MRI bias field estimate. Intensity based labeling techniques have employed local smoothness priors to reduce voxel level tissue labeling errors, by making use of the assumption that, within uniform regions of tissue, a voxel should be highly likely to have a similar tissue assignment to its neighbors. Increasing the size of this neighborhood provides more robustness to noise, but reduces the ability to describe small structures. However, when intensity bias due to RF field inhomogeneity is present within the MRI data, local contrast to noise may vary across the image. We therefore propose an approach to refining the labeling by making use of the bias field estimate, to adapt the neighborhood size applied to reduce local labeling errors. We explore the use of a radially symmetric Gaussian weighted neighborhood, and the use of the mean and median of the adapted region probabilities, to refine local probabilistic labeling. The approach is evaluated using the Montreal brainweb MRI simulator as a gold standard providing known gray, white and CSF tissue segmentation. These results show that the method is capable of improving the local tissue labeling in areas most influenced by inhomogeneity. The method appears most promising in its application to regional tissue volume analysis or higher field MRI data where bias field inhomogeneity can be significant.

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

    PubMed

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

    2015-10-20

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

  11. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

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

  13. 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…

  14. 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

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

    PubMed

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

    2005-11-01

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

  16. Deformed relativity symmetries and the local structure of spacetime

    NASA Astrophysics Data System (ADS)

    Letizia, Marco; Liberati, Stefano

    2017-02-01

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

  17. Light Localization by Defects in Optically Induced Photonic Structures

    NASA Astrophysics Data System (ADS)

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

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

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Gades, Heinrich; Mitus, Antoni C.

    1991-08-01

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

  20. 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.

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

    DOE PAGES

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

    2016-06-30

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

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

    PubMed

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

    2016-07-20

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

  3. 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.

  4. Structural Damage Detection Using Frequency Domain Error Localization.

    DTIC Science & Technology

    1994-12-01

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

  5. Input clustering and the microscale structure of local circuits

    PubMed Central

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

    2014-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Ransom, Jonathan B.

    1989-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  8. Magnetic structures at the ferromagnetic NiFe and antiferromagnetic NiMn interface in exchange-biased films: Role of noncollinear magnetism and roughness

    NASA Astrophysics Data System (ADS)

    Nakamura, Kohji; Freeman, A. J.; Wang, Ding-Sheng; Zhong, Lieping; Fernandez-de-Castro, Juan

    2002-01-01

    The magnetic structures at the compensated ferromagnetic/antiferromagnetic (FM/AFM) interface of exchange bias FM NiFe/AFM NiMn films were determined with first-principles full-potential linearized augmented plane-wave calculations including noncollinear magnetism. The results predict that the magnetic moments of the FM NiFe layer lie perpendicular to those of the AFM NiMn layer. The intra-atomic noncollinear magnetism that arises near the interface is found to play an important role in stabilizing the perpendicular coupling that leads to a large biquadratic exchange energy (BEE). The BEE is large enough to require formation of a magnetic domain wall (with an estimated thickness ~370 Å) in the AFM NiMn layers, which may account for the observed large coercivity and exchange bias. We also discuss magnetic structures at a rough FM/AFM interface-as simulated in model calculations with the inclusion of line step defects-which may contribute to a unidirectional magnetic anisotropy.

  9. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  11. 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.

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

    PubMed

    Schudoma, Christian; Larhlimi, Abdelhalim; Walther, Dirk

    2011-07-01

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

  13. 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

  14. 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…

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

    SciTech Connect

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

    2015-01-01

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

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

    PubMed

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

    2017-02-23

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

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

    DTIC Science & Technology

    1992-04-01

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

  18. Characterizing and understanding systematic biases in the vertical structure of clouds in CMIP5/CFMIP2 models

    NASA Astrophysics Data System (ADS)

    Cesana, G.; Waliser, D. E.

    2016-10-01

    From a traditional low-, middle-, and high-cloud "layered" perspective as well as a more detailed "level" perspective (40 levels), we compare the vertical distribution of clouds in 12 general circulation models (GCMs) against the GCM-Oriented Cloud-Aerosols Lidar and Infrared Pathfinder Satellite Observations Cloud Product (CALIPSO-GOCCP) using a satellite simulator approach. The layered perspective shows that models exhibit the similar regional biases: an overestimate (underestimate) of high clouds over oceans (continents) in the tropics and a strong underestimate of low clouds over stratocumulus regions. Although high clouds are too infrequent on average, the level perspective reveals that high-level clouds fill too many upper levels of the column when present (geometrically too thick), suggesting an overestimation of the cloud overlap. Compositing by dynamical regimes and large-scale relative humidity shows that the models tend to have too many high-level clouds in moist environments and too few boundary layer clouds in dry environments regardless of dynamical regimes.

  19. 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.

  20. 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.

  1. 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…

  2. 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).

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

    PubMed

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

    2010-01-05

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

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

    NASA Astrophysics Data System (ADS)

    Zheng, D.; Ni, S.

    2015-12-01

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

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

    SciTech Connect

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

    2013-01-01

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

  6. 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…

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

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

    PubMed

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

    2016-06-01

    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 entered into a principal-component analysis. Only one factor, consisting of the Shepard's tabletops and Square-diamond illusions, was found to have reduced susceptibility as a function of autistic traits. Given that only two illusions were affected and that these illusions depend mostly on the processing of within-object relational properties, we conclude there is something distinct about autistic-like perceptual functioning but not in ways predicted by a preference of local over global elements.

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

    PubMed

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

    2007-01-01

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

  10. 33 CFR 208.10 - Local flood protection works; maintenance and operation of structures and facilities.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

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

  11. 33 CFR 208.10 - Local flood protection works; maintenance and operation of structures and facilities.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

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

  12. 33 CFR 208.10 - Local flood protection works; maintenance and operation of structures and facilities.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

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

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

    SciTech Connect

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

    2013-04-30

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

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

    PubMed

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

    2009-06-24

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-10-01

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

  16. The membrane-water interface region of membrane proteins: structural bias and the anti-snorkeling effect.

    PubMed

    Liang, Jie; Adamian, Larisa; Jackups, Ronald

    2005-07-01

    Membrane proteins have important roles in many cellular processes. Computational analysis of their sequences and structures has provided much insight into the organizing principles of transmembrane helices. In a recent study, the membrane-water interface region was examined in detail for the first time. The results have revealed that this interface region has an important role in constraining protein secondary structure. This study raises new questions and opens up new directions for studying membrane proteins.

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

    PubMed Central

    Vagenende, Vincent; Trout, Bernhardt L.

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Haynes, Colin; Todd, Michael

    2015-03-01

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

  19. Bias field tunable magnetic configuration and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm length

    NASA Astrophysics Data System (ADS)

    Adhikari, K.; Choudhury, S.; Mandal, R.; Barman, S.; Otani, Y.; Barman, A.

    2017-01-01

    Ferromagnetic nano-cross structures promise exotic static magnetic configurations and very rich and tunable magnetization dynamics leading towards potential applications in magnetic logic and communication devices. Here, we report an experimental study of external magnetic field tunable static magnetic configurations and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm lengths (L). Broadband ferromagnetic resonance measurements showed a strong variation in the number of spin-wave (SW) modes and mode frequencies (f) with bias field magnitude (H). Simulated static magnetic configurations and SW mode profiles explain the rich variation of the SW spectra, including mode softening, mode crossover, mode splitting, and mode merging. Such variation of SW spectra is further modified by the size of the nano-cross. Remarkably, with decreasing arm length of nano-cross structures, the onion magnetization ground state becomes more stable. Calculated magnetostatic field distributions support the above observations and revealed the non-collective nature of the dynamics in closely packed nano-cross structures. The latter is useful for their possible applications in magnetic storage and memory devices.

  20. 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.

  1. 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.

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

    PubMed

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

    2017-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  4. 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

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

    NASA Astrophysics Data System (ADS)

    Ozkaya, Efe; Yilmaz, Cetin

    2017-02-01

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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2017-01-11

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

  8. 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.

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

    PubMed

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

    2010-03-01

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

  10. 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.

  11. 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.

  12. 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.

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

    PubMed

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

    2014-05-27

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

  14. 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.

  15. Memory effect of a single-walled carbon nanotube on nitride-oxide structure under various bias conditions.

    SciTech Connect

    Park, H.; Shin, H.; Kim, J. H.; Hong, S.; Xu, J.; Materials Science Division; Brown Univ.; Kookmin Univ.

    2010-01-11

    We report on the memory effect of single-walled carbon nanotubes (SWNTs) placed on a nitride-oxide layer structure designed as a charge storage medium. The conductance of the SWNT was modulated by the injected charge in the nitride-oxide interface and the polarities of injected charges were then detected. A large on/off-state current ratio (>10{sup 4}) was obtained at a small program/erase voltage range (<3 V). We also studied the effect of a half-selected cell on the conductance of the SWNTs to identify the issues with cross-point memory architecture.

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

    PubMed

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

    2010-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Hara, Kazuo; Shimbo, Masashi; Matsumoto, Yuji

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

  18. Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: implications for understanding the mechanistic basis of the male mutation bias.

    PubMed

    Lercher, M J; Williams, E J; Hurst, L D

    2001-11-01

    The sex chromosomes and autosomes spend different times in the germ line of the two sexes. If cell division is mutagenic and if the sexes differ in number of cell divisions, then we expect that sequences on the X and Y chromosomes and autosomes should mutate at different rates. Tests of this hypothesis for several mammalian species have led to conflicting results. At the same time, recent evidence suggests that the chromosomal location of genes on autosomes affects their rate of evolution at synonymous sites. This suggests a mutagenic source different from germ cell replication. To correctly interpret the previous estimates of male mutation bias, it is crucial to understand the degree and range of this local similarity. With a carefully chosen randomization protocol, local similarity in synonymous rates of evolution can be detected in human-rodent and mouse-rat comparisons. However, the synonymous-site similarity in the mouse-rat comparison remains weak. Simulations suggest that this difference between the mouse-human and the mouse-rat comparisons is not artifactual and that there is therefore a difference between humans and rodents in the local patterns of mutation or selection on synonymous sites (conversely, we show that the previously reported absence of a local similarity in nonsynonymous rates of evolution in the human-rodent comparison was a methodological artifact). We show that linkage effects have a long-range component: not one in a million random genomes shows such levels of autosomal heterogeneity. The heterogeneity is so great that more autosomes than expected by chance have rates of synonymous evolution comparable with that of the X chromosome. As autosomal heterogeneity cannot be owing to different times spent in the germ line, this demonstrates that the dominant determiner of synonymous rates of evolution is not, as has been conjectured, the time spent in the male germ line.

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

    PubMed Central

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1991-06-01

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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    PubMed

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

    2003-06-01

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

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

    PubMed Central

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

    2016-01-01

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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

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

    PubMed

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

    2013-04-26

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

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

    PubMed

    Taylor, Paul J; Donald, Ian

    2007-06-01

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

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

    SciTech Connect

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

    2009-02-27

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

  17. 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…

  18. 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.

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

    USGS Publications Warehouse

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

    2016-01-01

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

  20. 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

  1. 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.

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

    ERIC Educational Resources Information Center

    Miller, Donald R.

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

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

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Xiao, Yi

    2016-10-01

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

  4. 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.

  5. 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.; ...

    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

  6. 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.

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

    PubMed

    Yang, Nan; Silverberg, Jesse L

    2017-04-04

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

  8. 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.

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

    PubMed

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

    2011-07-13

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2005-11-01

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

  12. 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.

  13. 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'…

  14. Oaths and hypothetical bias.

    PubMed

    Stevens, T H; Tabatabaei, Maryam; Lass, Daniel

    2013-09-30

    Results from experiments using an oath to eliminate hypothetical bias in stated preference valuation are presented. An oath has several potential advantages relative to other methods for reducing hypothetical bias. Our empirical results suggest that with an oath, mean hypothetical payments are not different from mean actual payments and that when controlling for experimental participants' characteristics using regression analyses, the oath eliminated hypothetical bias.

  15. Recalibrating Academic Bias

    ERIC Educational Resources Information Center

    Yancey, George

    2012-01-01

    Whether political and/or religious academic bias exists is a question with important ramifications for the educational institutions. Those arguing for the presence of such bias contend that political conservatives and the highly religious in academia are marginalized and face discrimination. The question of academic bias tends to be cast in a…

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

    NASA Astrophysics Data System (ADS)

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

    2001-12-01

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

  17. 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.

  18. 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.

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

    SciTech Connect

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

    1995-06-01

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

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

    PubMed Central

    Lee, Hui Sun; Im, Wonpil

    2013-01-01

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

  1. 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.

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

    PubMed Central

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

    2009-01-01

    Glass patterns are moirés created from a sparse random dot field paired with its spatially-shifted copy. Because discrimination of these patterns is not based on local features, they have been used extensively to study global integration processes. Here, we investigated whether 4–5.5 month old infants are sensitive to the global structure of Glass patterns by measuring Visual Evoked Potentials (VEPs). Although we found strong responses to the appearance of the constituent dots, we found sensitivity to the global structure of the Glass patterns in the infants only over a very limited range of spatial separation. In contrast, we observed robust responses in the infants when we connected the dot pairs of the Glass pattern with lines. Moreover, both infants and adults showed differential responses to exchanges between line patterns portraying different global structures. A control study varying luminance contrast in adults suggests that infant sensitivity to global structure is not primarily limited by reduced element visibility. Together our results suggest that the insensitivity to structure in conventional Glass patterns is due to inefficiencies in extracting the local orientation cues generated by the dot pairs. Once the local orientations are made unambiguous or when the interpolation span is small, infants can integrate these signals over the image. PMID:19642888

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

    NASA Astrophysics Data System (ADS)

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

    1994-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Viet Ha, Nguyen; Golinval, Jean-Claude

    2010-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2005-04-01

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

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

    PubMed

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

    2007-07-14

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

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

    PubMed

    Zhang, Xiao-Long; Lin, Xiao-Li

    2010-09-01

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

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

    NASA Astrophysics Data System (ADS)

    Ponedel, Benjamin C.; Knobloch, Edgar

    2016-11-01

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

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

    PubMed

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

    2014-06-16

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

  12. 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

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

    PubMed

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

    2007-09-21

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

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

    PubMed Central

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

    2015-01-01

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

  15. 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.

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

    DOE PAGES

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

    2015-10-01

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

  17. 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.

  18. 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

  19. Probing Local Structures in ZrO2 Nanocrystals Using EXAFS

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

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

  20. "Catching" Social Bias.

    PubMed

    Skinner, Allison L; Meltzoff, Andrew N; Olson, Kristina R

    2017-02-01

    Identifying the origins of social bias is critical to devising strategies to overcome prejudice. In two experiments, we tested the hypothesis that young children can catch novel social biases from brief exposure to biased nonverbal signals demonstrated by adults. Our results are consistent with this hypothesis. In Experiment 1, we found that children who were exposed to a brief video depicting nonverbal bias in favor of one individual over another subsequently explicitly preferred, and were more prone to behave prosocially toward, the target of positive nonverbal signals. Moreover, in Experiment 2, preschoolers generalized such bias to other individuals. The spread of bias observed in these experiments lays a critical foundation for understanding the way that social biases may develop and spread early in childhood.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  4. 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

  5. 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.

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

    SciTech Connect

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

    2016-02-14

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

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

    SciTech Connect

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

    2016-02-14

    We report a detailed study of the local composition and structure of a model, bi-phasic nanoglass with nominal stoichiometry Cu{sub 55}Nb{sub 45}. Three dimensional atom probe data suggest a nanoscale-phase-separated glassy structure having well defined Cu-rich and Nb-rich regions with a characteristic length scale of ≈3 nm. However, extended x-ray absorption fine structure analysis indicates subtle differences in the local environments of Cu and Nb. While the Cu atoms displayed a strong tendency to cluster and negligible structural order beyond the first coordination shell, the Nb atoms had a larger fraction of unlike neighbors (higher chemical order) and a distinctly better-ordered structural environment (higher topological order). This provides the first experimental indication that metallic glass formation may occur due to frustration arising from the competition between chemical ordering and clustering. These observations are complemented by classical as well as ab initio molecular dynamics simulations. Our study indicates that these nanoscale phase-separated glasses are quite distinct from the single phase nanoglasses (studied by Gleiter and others) in the following three respects: (i) they contain at least two structurally and compositionally distinct, nanodispersed, glassy phases, (ii) these phases are separated by comparatively sharp inter-phase boundaries, and (iii) thermally induced crystallization occurs via a complex, multi-step mechanism. Such materials, therefore, appear to constitute a new class of disordered systems that may be called a composite nanoglass.

  8. 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.

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

    PubMed Central

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

    2008-01-01

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

  10. 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.

  11. Electrical biasing and voltage contrast imaging in a focused ion beam system

    SciTech Connect

    Campbell, A.N.; Soden, J.M.; Rife, J.L.; Lee, R.G.

    1995-09-01

    We present two new techniques that enhance conventional focused ion beam (FIB) system capabilities for integrated circuit (IC) analysis: in situ electrical biasing and voltage contrast imaging. We have used in situ electrical biasing to enable a number of advanced failure analysis applications including (1) real time evaluation of device electrical behavior during milling and deposition, (2) verification of IC functional modifications without removal from the FIB system, and (3) ultraprecision control for cross sectioning of deep submicron structures, such as programmed amorphous silicon antifuses. We have also developed FIB system voltage contrast imaging that can be used for a variety of failure analysis applications. The use of passive voltage contrast imaging for defect localization and for navigation on planarized devices will be illustrated. In addition, we describe new, biased voltage contrast imaging techniques and provide examples of their application to the failure analysis of complex ICs. We discuss the necessary changes in system operating parameters to perform biased voltage contrast imaging.

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

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

    PubMed

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

    2013-03-26

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

  14. 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.

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

    SciTech Connect

    Ross, M

    2008-08-15

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

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

    SciTech Connect

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

    2009-09-15

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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    SciTech Connect

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

    2014-05-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

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

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

    SciTech Connect

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

    2008-01-01

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

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

    PubMed

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

    2004-11-12

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

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

    DTIC Science & Technology

    2009-07-01

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

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

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

    PubMed Central

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

    2004-01-01

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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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…

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

    PubMed

    Khalajhedayati, Amirhossein; Rupert, Timothy J

    2015-06-01

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

  20. 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.