Visualizing nD Point Clouds as Topological Landscape Profiles to Guide Local Data Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oesterling, Patrick; Heine, Christian; Weber, Gunther H.

2012-05-04

Analyzing high-dimensional point clouds is a classical challenge in visual analytics. Traditional techniques, such as projections or axis-based techniques, suffer from projection artifacts, occlusion, and visual complexity.We propose to split data analysis into two parts to address these shortcomings. First, a structural overview phase abstracts data by its density distribution. This phase performs topological analysis to support accurate and non-overlapping presentation of the high-dimensional cluster structure as a topological landscape profile. Utilizing a landscape metaphor, it presents clusters and their nesting as hills whose height, width, and shape reflect cluster coherence, size, and stability, respectively. A second local analysis phasemore » utilizes this global structural knowledge to select individual clusters or point sets for further, localized data analysis. Focusing on structural entities significantly reduces visual clutter in established geometric visualizations and permits a clearer, more thorough data analysis. In conclusion, this analysis complements the global topological perspective and enables the user to study subspaces or geometric properties, such as shape.« less

Structural analysis of strontium in human teeth treated with surface pre-reacted glass-ionomer filler eluate by using extended X-ray absorption fine structure analysis.

PubMed

Uo, Motohiro; Wada, Takahiro; Asakura, Kiyotaka

2017-03-31

The bioactive effects of strontium released from surface pre-reacted glass-ionomer (S-PRG) fillers may aid in caries prevention. In this study, the local structure of strontium taken up by teeth was estimated by extended X-ray absorption fine structure analysis. Immersing teeth into S-PRG filler eluate increased the strontium content in enamel and dentin by more than 100 times. The local structure of strontium in enamel and dentin stored in distilled water was the same as that in synthetic strontium-containing hydroxyapatite (SrHAP). Moreover, the local structure of strontium in enamel and dentin after immersion in the S-PRG filler eluate was also similar to that of SrHAP. After immersion in the S-PRG filler eluate, strontium was suggested to be incorporated into the hydroxyapatite (HAP) of enamel and dentin at the calcium site in HAP.

Local Structure and Short-Range Order in a NiCoCr Solid Solution Alloy

DOE PAGES

Zhang, F. X.; Zhao, Shijun; Jin, Ke; ...

2017-05-19

Multi-element solid solution alloys are intrinsically disordered on the atomic scale, and many of their advanced properties originate from the unique local structural characteristics. We measured the local structure of a NiCoCr solid solution alloy with X-ray/neutron total scattering and extended X-ray absorption fine structure (EXAFS) techniques. The atomic pair distribution function analysis (PDF) did not exhibit distinct structural distortion. But, EXAFS analysis suggested that the Cr atoms are favorably bonded with Ni and Co in the solid solution alloys. This short-range order (SRO) plays a role in the distinct low values of electrical and thermal conductivities in Ni-based solidmore » solution alloys when Cr is incorporated. Both the long-range and local structures of the NiCoCr alloy upon Ni ion irradiation were studied and an irradiation-induced enhancement of SRO was found.« less

Effects of local vibrations on the dynamics of space truss structures

NASA Technical Reports Server (NTRS)

Warnaar, Dirk B.; Mcgowan, Paul E.

1987-01-01

The paper discusses the influence of local member vibrations on the dynamics of repetitive space truss structures. Several focus problems wherein local member vibration modes are in the frequency range of the global truss modes are discussed. Special attention is given to defining methods that can be used to identify the global modes of a truss structure amidst many local modes. Significant interactions between the motions of local member vibrations and the global behavior are shown to occur in truss structures when: (1) the natural frequencies of the individual members for clamped-clamped boundary conditions are in the vicinity of the global truss frequency; and (2) the total mass of the individual members represents a large portion of the mass of the whole structure. The analysis is carried out with a structural analysis code which uses exact member theory. The modeling detail required using conventional finite element codes to adequately represent such a class of problems is examined. The paper concludes with some practical considerations for the design and dynamic testing of structures which might exhibit such behavior.

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

PubMed

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

2008-11-15

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

Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface

PubMed Central

2012-01-01

Background Despite computational challenges, elucidating conformations that a protein system assumes under physiologic conditions for the purpose of biological activity is a central problem in computational structural biology. While these conformations are associated with low energies in the energy surface that underlies the protein conformational space, few existing conformational search algorithms focus on explicitly sampling low-energy local minima in the protein energy surface. Methods This work proposes a novel probabilistic search framework, PLOW, that explicitly samples low-energy local minima in the protein energy surface. The framework combines algorithmic ingredients from evolutionary computation and computational structural biology to effectively explore the subspace of local minima. A greedy local search maps a conformation sampled in conformational space to a nearby local minimum. A perturbation move jumps out of a local minimum to obtain a new starting conformation for the greedy local search. The process repeats in an iterative fashion, resulting in a trajectory-based exploration of the subspace of local minima. Results and conclusions The analysis of PLOW's performance shows that, by navigating only the subspace of local minima, PLOW is able to sample conformations near a protein's native structure, either more effectively or as well as state-of-the-art methods that focus on reproducing the native structure for a protein system. Analysis of the actual subspace of local minima shows that PLOW samples this subspace more effectively that a naive sampling approach. Additional theoretical analysis reveals that the perturbation function employed by PLOW is key to its ability to sample a diverse set of low-energy conformations. This analysis also suggests directions for further research and novel applications for the proposed framework. PMID:22759582

Structural Analysis of the Redesigned Ice/Frost Ramp Bracket

NASA Technical Reports Server (NTRS)

Phillips, D. R.; Dawicke, D. S.; Gentz, S. J.; Roberts, P. W.; Raju, I. S.

2007-01-01

This paper describes the interim structural analysis of a redesigned Ice/Frost Ramp bracket for the Space Shuttle External Tank (ET). The proposed redesigned bracket consists of mounts for attachment to the ET wall, supports for the electronic/instrument cables and propellant repressurization lines that run along the ET, an upper plate, a lower plate, and complex bolted connections. The eight nominal bolted connections are considered critical in the summarized structural analysis. Each bolted connection contains a bolt, a nut, four washers, and a non-metallic spacer and block that are designed for thermal insulation. A three-dimensional (3D) finite element model of the bracket is developed using solid 10-node tetrahedral elements. The loading provided by the ET Project is used in the analysis. Because of the complexities associated with accurately modeling the bolted connections in the bracket, the analysis is performed using a global/local analysis procedure. The finite element analysis of the bracket identifies one of the eight bolted connections as having high stress concentrations. A local area of the bracket surrounding this bolted connection is extracted from the global model and used as a local model. Within the local model, the various components of the bolted connection are refined, and contact is introduced along the appropriate interfaces determined by the analysts. The deformations from the global model are applied as boundary conditions to the local model. The results from the global/local analysis show that while the stresses in the bolts are well within yield, the spacers fail due to compression. The primary objective of the interim structural analysis is to show concept viability for static thermal testing. The proposed design concept would undergo continued design optimization to address the identified analytical assumptions and concept shortcomings, assuming successful thermal testing.

Distortion of Local Atomic Structures in Amorphous Ge-Sb-Te Phase Change Materials

NASA Astrophysics Data System (ADS)

Hirata, A.; Ichitsubo, T.; Guan, P. F.; Fujita, T.; Chen, M. W.

2018-05-01

The local atomic structures of amorphous Ge-Sb-Te phase-change materials have yet to be clarified and the rapid crystal-amorphous phase change resulting in distinct optical contrast is not well understood. We report the direct observation of local atomic structures in amorphous Ge2Sb2Te5 using "local" reverse Monte Carlo modeling dedicated to an angstrom-beam electron diffraction analysis. The results corroborated the existence of local structures with rocksalt crystal-like topology that were greatly distorted compared to the crystal symmetry. This distortion resulted in the breaking of ideal octahedral atomic environments, thereby forming local disordered structures that basically satisfied the overall amorphous structure factor. The crystal-like distorted octahedral structures could be the main building blocks in the formation of the overall amorphous structure of Ge-Sb-Te.

Structural-change localization and monitoring through a perturbation-based inverse problem.

PubMed

Roux, Philippe; Guéguen, Philippe; Baillet, Laurent; Hamze, Alaa

2014-11-01

Structural-change detection and characterization, or structural-health monitoring, is generally based on modal analysis, for detection, localization, and quantification of changes in structure. Classical methods combine both variations in frequencies and mode shapes, which require accurate and spatially distributed measurements. In this study, the detection and localization of a local perturbation are assessed by analysis of frequency changes (in the fundamental mode and overtones) that are combined with a perturbation-based linear inverse method and a deconvolution process. This perturbation method is applied first to a bending beam with the change considered as a local perturbation of the Young's modulus, using a one-dimensional finite-element model for modal analysis. Localization is successful, even for extended and multiple changes. In a second step, the method is numerically tested under ambient-noise vibration from the beam support with local changes that are shifted step by step along the beam. The frequency values are revealed using the random decrement technique that is applied to the time-evolving vibrations recorded by one sensor at the free extremity of the beam. Finally, the inversion method is experimentally demonstrated at the laboratory scale with data recorded at the free end of a Plexiglas beam attached to a metallic support.

Global/local stress analysis of composite panels

NASA Technical Reports Server (NTRS)

Ransom, Jonathan B.; Knight, Norman F., Jr.

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.

A local structure model for network analysis

DOE PAGES

Casleton, Emily; Nordman, Daniel; Kaiser, Mark

2017-04-01

The statistical analysis of networks is a popular research topic with ever widening applications. Exponential random graph models (ERGMs), which specify a model through interpretable, global network features, are common for this purpose. In this study we introduce a new class of models for network analysis, called local structure graph models (LSGMs). In contrast to an ERGM, a LSGM specifies a network model through local features and allows for an interpretable and controllable local dependence structure. In particular, LSGMs are formulated by a set of full conditional distributions for each network edge, e.g., the probability of edge presence/absence, depending onmore » neighborhoods of other edges. Additional model features are introduced to aid in specification and to help alleviate a common issue (occurring also with ERGMs) of model degeneracy. Finally, the proposed models are demonstrated on a network of tornadoes in Arkansas where a LSGM is shown to perform significantly better than a model without local dependence.« less

A local structure model for network analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Casleton, Emily; Nordman, Daniel; Kaiser, Mark

The statistical analysis of networks is a popular research topic with ever widening applications. Exponential random graph models (ERGMs), which specify a model through interpretable, global network features, are common for this purpose. In this study we introduce a new class of models for network analysis, called local structure graph models (LSGMs). In contrast to an ERGM, a LSGM specifies a network model through local features and allows for an interpretable and controllable local dependence structure. In particular, LSGMs are formulated by a set of full conditional distributions for each network edge, e.g., the probability of edge presence/absence, depending onmore » neighborhoods of other edges. Additional model features are introduced to aid in specification and to help alleviate a common issue (occurring also with ERGMs) of model degeneracy. Finally, the proposed models are demonstrated on a network of tornadoes in Arkansas where a LSGM is shown to perform significantly better than a model without local dependence.« less

Local Influence Analysis of Nonlinear Structural Equation Models

ERIC Educational Resources Information Center

Lee, Sik-Yum; Tang, Nian-Sheng

2004-01-01

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

Local kernel nonparametric discriminant analysis for adaptive extraction of complex structures

NASA Astrophysics Data System (ADS)

Li, Quanbao; Wei, Fajie; Zhou, Shenghan

2017-05-01

The linear discriminant analysis (LDA) is one of popular means for linear feature extraction. It usually performs well when the global data structure is consistent with the local data structure. Other frequently-used approaches of feature extraction usually require linear, independence, or large sample condition. However, in real world applications, these assumptions are not always satisfied or cannot be tested. In this paper, we introduce an adaptive method, local kernel nonparametric discriminant analysis (LKNDA), which integrates conventional discriminant analysis with nonparametric statistics. LKNDA is adept in identifying both complex nonlinear structures and the ad hoc rule. Six simulation cases demonstrate that LKNDA have both parametric and nonparametric algorithm advantages and higher classification accuracy. Quartic unilateral kernel function may provide better robustness of prediction than other functions. LKNDA gives an alternative solution for discriminant cases of complex nonlinear feature extraction or unknown feature extraction. At last, the application of LKNDA in the complex feature extraction of financial market activities is proposed.

Performance Analysis of Local Ensemble Kalman Filter

NASA Astrophysics Data System (ADS)

Tong, Xin T.

2018-03-01

Ensemble Kalman filter (EnKF) is an important data assimilation method for high-dimensional geophysical systems. Efficient implementation of EnKF in practice often involves the localization technique, which updates each component using only information within a local radius. This paper rigorously analyzes the local EnKF (LEnKF) for linear systems and shows that the filter error can be dominated by the ensemble covariance, as long as (1) the sample size exceeds the logarithmic of state dimension and a constant that depends only on the local radius; (2) the forecast covariance matrix admits a stable localized structure. In particular, this indicates that with small system and observation noises, the filter error will be accurate in long time even if the initialization is not. The analysis also reveals an intrinsic inconsistency caused by the localization technique, and a stable localized structure is necessary to control this inconsistency. While this structure is usually taken for granted for the operation of LEnKF, it can also be rigorously proved for linear systems with sparse local observations and weak local interactions. These theoretical results are also validated by numerical implementation of LEnKF on a simple stochastic turbulence in two dynamical regimes.

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

DOEpatents

Zemla, Adam T [Brentwood, CA

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.

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

NASA Astrophysics Data System (ADS)

Belianinov, Alex; Ganesh, Panchapakesan; Lin, Wenzhi; Sales, Brian C.; Sefat, Athena S.; Jesse, Stephen; Pan, Minghu; Kalinin, Sergei V.

2014-12-01

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1-xSex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.

Analysis of multifunctional piezoelectric metastructures for low-frequency bandgap formation and energy harvesting

NASA Astrophysics Data System (ADS)

Sugino, C.; Erturk, A.

2018-05-01

Vibration-based energy harvesting is a growing field for generating low-power electricity to use in wireless electronic devices, such as the sensor networks used in structural health monitoring applications. Locally resonant metastructures, which are structures that comprise locally resonant metamaterial components, enable bandgap formation at wavelengths much longer than the lattice size, for critical applications such as low-frequency vibration attenuation in flexible structures. This work aims to bridge the domains of energy harvesting and locally resonant metamaterials to form multifunctional structures that exhibit both low-power electricity generation and vibration attenuation capabilities. A fully coupled electromechanical modeling framework is developed for two characteristic systems and their modal analysis is presented. Simulations are performed to explore the vibration and electrical power frequency response maps for varying electrical load resistance, and optimal loading conditions are presented. Case studies are presented to understand the interaction of bandgap formation and energy harvesting capabilities of this new class of multifunctional energy-harvesting locally resonant metastructures. It is shown that useful energy can be harvested from locally resonant metastructures without significantly diminishing their dramatic vibration attenuation in the locally resonant bandgap. Thus, integrating energy harvesters into a locally resonant metastructure enables a new potential for multifunctional locally resonant metastructures that can host self-powered sensors.

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

Analysis of local bond-orientational order for liquid gallium at ambient pressure: Two types of cluster structures.

PubMed

Chen, Lin-Yuan; Tang, Ping-Han; Wu, Ten-Ming

2016-07-14

In terms of the local bond-orientational order (LBOO) parameters, a cluster approach to analyze local structures of simple liquids was developed. In this approach, a cluster is defined as a combination of neighboring seeds having at least nb local-orientational bonds and their nearest neighbors, and a cluster ensemble is a collection of clusters with a specified nb and number of seeds ns. This cluster analysis was applied to investigate the microscopic structures of liquid Ga at ambient pressure (AP). The liquid structures studied were generated through ab initio molecular dynamics simulations. By scrutinizing the static structure factors (SSFs) of cluster ensembles with different combinations of nb and ns, we found that liquid Ga at AP contained two types of cluster structures, one characterized by sixfold orientational symmetry and the other showing fourfold orientational symmetry. The SSFs of cluster structures with sixfold orientational symmetry were akin to the SSF of a hard-sphere fluid. On the contrary, the SSFs of cluster structures showing fourfold orientational symmetry behaved similarly as the anomalous SSF of liquid Ga at AP, which is well known for exhibiting a high-q shoulder. The local structures of a highly LBOO cluster whose SSF displayed a high-q shoulder were found to be more similar to the structure of β-Ga than those of other solid phases of Ga. More generally, the cluster structures showing fourfold orientational symmetry have an inclination to resemble more to β-Ga.

Layerwise Mechanics and Finite Elements for Smart Composite Structures with Piezoelectric Actuators and Sensors

NASA Technical Reports Server (NTRS)

Saravanos, Dimitris A.; Heyliger, Paul R.; Hopkins, Dale A.

1996-01-01

Recent developments on layerwise mechanics for the analysis of composite laminates and structures with piezoelectric actuators and sensors are reviewed. The mechanics implement layerwise representations of displacements and electric potential, and can model both the global and local electromechanical response of smart composite structures. The corresponding finite-element implementations for the static and dynamic analysis of smart piezoelectric composite structures are also summarized. Select application illustrate the accuracy, robustness and capability of the developed mechanics to capture the global and local dynamic response of thin and/or thick laminated piezoelectric plates.

Global-local methodologies and their application to nonlinear analysis

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.

1989-01-01

An assessment is made of the potential of different global-local analysis strategies for predicting the nonlinear and postbuckling responses of structures. Two postbuckling problems of composite panels are used as benchmarks and the application of different global-local methodologies to these benchmarks is outlined. The key elements of each of the global-local strategies are discussed and future research areas needed to realize the full potential of global-local methodologies are identified.

Local linear discriminant analysis framework using sample neighbors.

PubMed

Fan, Zizhu; Xu, Yong; Zhang, David

2011-07-01

The linear discriminant analysis (LDA) is a very popular linear feature extraction approach. The algorithms of LDA usually perform well under the following two assumptions. The first assumption is that the global data structure is consistent with the local data structure. The second assumption is that the input data classes are Gaussian distributions. However, in real-world applications, these assumptions are not always satisfied. In this paper, we propose an improved LDA framework, the local LDA (LLDA), which can perform well without needing to satisfy the above two assumptions. Our LLDA framework can effectively capture the local structure of samples. According to different types of local data structure, our LLDA framework incorporates several different forms of linear feature extraction approaches, such as the classical LDA and principal component analysis. The proposed framework includes two LLDA algorithms: a vector-based LLDA algorithm and a matrix-based LLDA (MLLDA) algorithm. MLLDA is directly applicable to image recognition, such as face recognition. Our algorithms need to train only a small portion of the whole training set before testing a sample. They are suitable for learning large-scale databases especially when the input data dimensions are very high and can achieve high classification accuracy. Extensive experiments show that the proposed algorithms can obtain good classification results.

Decentralized control experiments on NASA's flexible grid

NASA Technical Reports Server (NTRS)

Ozguner, U.; Yurkowich, S.; Martin, J., III; Al-Abbass, F.

1986-01-01

Methods arising from the area of decentralized control are emerging for analysis and control synthesis for large flexible structures. In this paper the control strategy involves a decentralized model reference adaptive approach using a variable structure control. Local models are formulated based on desired damping and response time in a model-following scheme for various modal configurations. Variable structure controllers are then designed employing co-located angular rate and position feedback. In this scheme local control forces the system to move on a local sliding mode in some local error space. An important feature of this approach is that the local subsystem is made insensitive to dynamical interactions with other subsystems once the sliding surface is reached. Experiments based on the above have been performed for NASA's flexible grid experimental apparatus. The grid is designed to admit appreciable low-frequency structural dynamics, and allows for implementation of distributed computing components, inertial sensors, and actuation devices. A finite-element analysis of the grid provides the model for control system design and simulation; results of several simulations are reported on here, and a discussion of application experiments on the apparatus is presented.

On structural identifiability analysis of the cascaded linear dynamic systems in isotopically non-stationary 13C labelling experiments.

PubMed

Lin, Weilu; Wang, Zejian; Huang, Mingzhi; Zhuang, Yingping; Zhang, Siliang

2018-06-01

The isotopically non-stationary 13C labelling experiments, as an emerging experimental technique, can estimate the intracellular fluxes of the cell culture under an isotopic transient period. However, to the best of our knowledge, the issue of the structural identifiability analysis of non-stationary isotope experiments is not well addressed in the literature. In this work, the local structural identifiability analysis for non-stationary cumomer balance equations is conducted based on the Taylor series approach. The numerical rank of the Jacobian matrices of the finite extended time derivatives of the measured fractions with respect to the free parameters is taken as the criterion. It turns out that only one single time point is necessary to achieve the structural identifiability analysis of the cascaded linear dynamic system of non-stationary isotope experiments. The equivalence between the local structural identifiability of the cascaded linear dynamic systems and the local optimum condition of the nonlinear least squares problem is elucidated in the work. Optimal measurements sets can then be determined for the metabolic network. Two simulated metabolic networks are adopted to demonstrate the utility of the proposed method. Copyright © 2018 Elsevier Inc. All rights reserved.

Health promotion activities in annual reports of local governments: 'Health for All' targets as a tool for content analysis.

PubMed

Andersson, Camilla M; Bjärås, Gunilla E M; Tillgren, Per; Ostenson, Claes-Göran

2003-09-01

This article presents an instrument to study the annual reporting of health promotion activities in local governments within the three intervention municipalities of the Stockholm Diabetes Prevention Program (SDPP). The content of health promotion activities are described and the strengths, weaknesses and relevance of the method to health promotion discussed. A content analysis of local governmental reports from 1995-2000 in three Swedish municipalities. A matrix with WHO's 38 'Health for All' (HFA) targets from 1991 was used when coding the local health promotion activities. There are many public health initiatives within the local governmental structure even if they are not always addressed as health promotion. The main focuses in the local governmental reports were environmental issues, unemployment, social care and welfare. Local governmental reports were found to be a useful source of information that could provide knowledge about the priorities and organizational capacities for health promotion within local authorities. Additionally the HFA targets were an effective tool to identify and categorize systematically local health promotion activities in the annual reports of local governments. Identifying local health promotion initiatives by local authorities may ease the development of a health perspective and joint actions within the existing political and administrative structure. This paper provides a complementary method of attaining and structuring information about the local community for developments in health promotion.

Localized variations in electronic structure of AlGaN/GaN heterostructures grown by molecular-beam epitaxy

NASA Astrophysics Data System (ADS)

Smith, K. V.; Yu, E. T.; Elsass, C. R.; Heying, B.; Speck, J. S.

2001-10-01

Local electronic properties in a molecular-beam-epitaxy-grown AlxGa1-xN/GaN heterostructure field-effect transistor epitaxial layer structure are probed using depth-resolved scanning capacitance microscopy. Theoretical analysis of contrast observed in scanning capacitance images acquired over a range of bias voltages is used to assess the possible structural origins of local inhomogeneities in electronic structure, which are shown to be concentrated in areas where Ga droplets had formed on the surface during growth. Within these regions, there are significant variations in the local electronic structure that are attributed to variations in both AlxGa1-xN layer thickness and Al composition. Increased charge trapping is also observed in these regions.

Atomistic cluster alignment method for local order mining in liquids and glasses

NASA Astrophysics Data System (ADS)

Fang, X. W.; Wang, C. Z.; Yao, Y. X.; Ding, Z. J.; Ho, K. M.

2010-11-01

An atomistic cluster alignment method is developed to identify and characterize the local atomic structural order in liquids and glasses. With the “order mining” idea for structurally disordered systems, the method can detect the presence of any type of local order in the system and can quantify the structural similarity between a given set of templates and the aligned clusters in a systematic and unbiased manner. Moreover, population analysis can also be carried out for various types of clusters in the system. The advantages of the method in comparison with other previously developed analysis methods are illustrated by performing the structural analysis for four prototype systems (i.e., pure Al, pure Zr, Zr35Cu65 , and Zr36Ni64 ). The results show that the cluster alignment method can identify various types of short-range orders (SROs) in these systems correctly while some of these SROs are difficult to capture by most of the currently available analysis methods (e.g., Voronoi tessellation method). Such a full three-dimensional atomistic analysis method is generic and can be applied to describe the magnitude and nature of noncrystalline ordering in many disordered systems.

Perturbation Selection and Local Influence Analysis for Nonlinear Structural Equation Model

ERIC Educational Resources Information Center

Chen, Fei; Zhu, Hong-Tu; Lee, Sik-Yum

2009-01-01

Local influence analysis is an important statistical method for studying the sensitivity of a proposed model to model inputs. One of its important issues is related to the appropriate choice of a perturbation vector. In this paper, we develop a general method to select an appropriate perturbation vector and a second-order local influence measure…

LCS-TA to identify similar fragments in RNA 3D structures.

PubMed

Wiedemann, Jakub; Zok, Tomasz; Milostan, Maciej; Szachniuk, Marta

2017-10-23

In modern structural bioinformatics, comparison of molecular structures aimed to identify and assess similarities and differences between them is one of the most commonly performed procedures. It gives the basis for evaluation of in silico predicted models. It constitutes the preliminary step in searching for structural motifs. In particular, it supports tracing the molecular evolution. Faced with an ever-increasing amount of available structural data, researchers need a range of methods enabling comparative analysis of the structures from either global or local perspective. Herein, we present a new, superposition-independent method which processes pairs of RNA 3D structures to identify their local similarities. The similarity is considered in the context of structure bending and bonds' rotation which are described by torsion angles. In the analyzed RNA structures, the method finds the longest continuous segments that show similar torsion within a user-defined threshold. The length of the segment is provided as local similarity measure. The method has been implemented as LCS-TA algorithm (Longest Continuous Segments in Torsion Angle space) and is incorporated into our MCQ4Structures application, freely available for download from http://www.cs.put.poznan.pl/tzok/mcq/ . The presented approach ties torsion-angle-based method of structure analysis with the idea of local similarity identification by handling continuous 3D structure segments. The first method, implemented in MCQ4Structures, has been successfully utilized in RNA-Puzzles initiative. The second one, originally applied in Euclidean space, is a component of LGA (Local-Global Alignment) algorithm commonly used in assessing protein models submitted to CASP. This unique combination of concepts implemented in LCS-TA provides a new perspective on structure quality assessment in local and quantitative aspect. A series of computational experiments show the first results of applying our method to comparison of RNA 3D models. LCS-TA can be used for identifying strengths and weaknesses in the prediction of RNA tertiary structures.

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

PubMed

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.

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

DOE PAGES

Belianinov, Alex; Panchapakesan, G.; Lin, Wenzhi; ...

2014-12-02

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1 x Sex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signaturemore » and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.« less

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belianinov, Alex, E-mail: belianinova@ornl.gov; Ganesh, Panchapakesan; Lin, Wenzhi

2014-12-01

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe{sub 0.55}Se{sub 0.45} (T{sub c} = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe{sub 1−x}Se{sub x} structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified bymore » their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.« less

Local structure studies of materials using pair distribution function analysis

NASA Astrophysics Data System (ADS)

Peterson, Joseph W.

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

Disruptions of brain structural network in end-stage renal disease patients with long-term hemodialysis and normal-appearing brain tissues.

PubMed

Chou, Ming-Chung; Ko, Chih-Hung; Chang, Jer-Ming; Hsieh, Tsyh-Jyi

2018-05-04

End-stage renal disease (ESRD) patients on hemodialysis were demonstrated to exhibit silent and invisible white-matter alterations which would likely lead to disruptions of brain structural networks. Therefore, the purpose of this study was to investigate the disruptions of brain structural network in ESRD patients. Thiry-three ESRD patients with normal-appearing brain tissues and 29 age- and gender-matched healthy controls were enrolled in this study and underwent both cognitive ability screening instrument (CASI) assessment and diffusion tensor imaging (DTI) acquisition. Brain structural connectivity network was constructed using probabilistic tractography with automatic anatomical labeling template. Graph-theory analysis was performed to detect the alterations of node-strength, node-degree, node-local efficiency, and node-clustering coefficient in ESRD patients. Correlational analysis was performed to understand the relationship between network measures, CASI score, and dialysis duration. Structural connectivity, node-strength, node-degree, and node-local efficiency were significantly decreased, whereas node-clustering coefficient was significantly increased in ESRD patients as compared with healthy controls. The disrupted local structural networks were generally associated with common neurological complications of ESRD patients, but the correlational analysis did not reveal significant correlation between network measures, CASI score, and dialysis duration. Graph-theory analysis was helpful to investigate disruptions of brain structural network in ESRD patients with normal-appearing brain tissues. Copyright © 2018. Published by Elsevier Masson SAS.

A generative, probabilistic model of local protein structure.

PubMed

Boomsma, Wouter; Mardia, Kanti V; Taylor, Charles C; Ferkinghoff-Borg, Jesper; Krogh, Anders; Hamelryck, Thomas

2008-07-01

Despite significant progress in recent years, protein structure prediction maintains its status as one of the prime unsolved problems in computational biology. One of the key remaining challenges is an efficient probabilistic exploration of the structural space that correctly reflects the relative conformational stabilities. Here, we present a fully probabilistic, continuous model of local protein structure in atomic detail. The generative model makes efficient conformational sampling possible and provides a framework for the rigorous analysis of local sequence-structure correlations in the native state. Our method represents a significant theoretical and practical improvement over the widely used fragment assembly technique by avoiding the drawbacks associated with a discrete and nonprobabilistic approach.

Time-delayed feedback control of breathing localized structures in a three-component reaction-diffusion system.

PubMed

Gurevich, Svetlana V

2014-10-28

The dynamics of a single breathing localized structure in a three-component reaction-diffusion system subjected to time-delayed feedback is investigated. It is shown that variation of the delay time and the feedback strength can lead either to stabilization of the breathing or to delay-induced periodic or quasi-periodic oscillations of the localized structure. A bifurcation analysis of the system in question is provided and an order parameter equation is derived that describes the dynamics of the localized structure in the vicinity of the Andronov-Hopf bifurcation. With the aid of this equation, the boundaries of the stabilization domains as well as the dependence of the oscillation radius on delay parameters can be explicitly derived, providing a robust mechanism to control the behaviour of the breathing localized structure in a straightforward manner. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Translocality, Network Structure, and Music Worlds: Underground Metal in the United Kingdom.

PubMed

Emms, Rachel; Crossley, Nick

2018-02-01

Translocal music worlds are often defined as networks of local music worlds. However, their networked character and more especially their network structure is generally assumed rather than concretely mapped and explored. Formal social network analysis (SNA) is beginning to attract interest in music sociology but it has not previously been used to explore a translocal music world. In this paper, drawing upon a survey of the participation of 474 enthusiasts in 148 live music events, spread across 6 localities, we use SNA to explore a significant "slice" of the network structure of the U.K.'s translocal underground heavy metal world. Translocality is generated in a number of ways, we suggest, but one way, the way we focus upon, involves audiences traveling between localities to attend gigs and festivals. Our analysis of this network uncovers a core-periphery structure which, we further find, maps onto locality. Not all live events enjoy equal standing in our music world and some localities are better placed to capture more prestigious events, encouraging inward travel. The identification of such structures, and the inequality they point to, is, we believe, one of several benefits of using SNA to analyze translocal music worlds. © 2018 Canadian Sociological Association/La Société canadienne de sociologie.

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

PubMed

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

2016-07-20

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

Local structure-based image decomposition for feature extraction with applications to face recognition.

PubMed

Qian, Jianjun; Yang, Jian; Xu, Yong

2013-09-01

This paper presents a robust but simple image feature extraction method, called image decomposition based on local structure (IDLS). It is assumed that in the local window of an image, the macro-pixel (patch) of the central pixel, and those of its neighbors, are locally linear. IDLS captures the local structural information by describing the relationship between the central macro-pixel and its neighbors. This relationship is represented with the linear representation coefficients determined using ridge regression. One image is actually decomposed into a series of sub-images (also called structure images) according to a local structure feature vector. All the structure images, after being down-sampled for dimensionality reduction, are concatenated into one super-vector. Fisher linear discriminant analysis is then used to provide a low-dimensional, compact, and discriminative representation for each super-vector. The proposed method is applied to face recognition and examined using our real-world face image database, NUST-RWFR, and five popular, publicly available, benchmark face image databases (AR, Extended Yale B, PIE, FERET, and LFW). Experimental results show the performance advantages of IDLS over state-of-the-art algorithms.

Precision and accuracy in smFRET based structural studies—A benchmark study of the Fast-Nano-Positioning System

NASA Astrophysics Data System (ADS)

Nagy, Julia; Eilert, Tobias; Michaelis, Jens

2018-03-01

Modern hybrid structural analysis methods have opened new possibilities to analyze and resolve flexible protein complexes where conventional crystallographic methods have reached their limits. Here, the Fast-Nano-Positioning System (Fast-NPS), a Bayesian parameter estimation-based analysis method and software, is an interesting method since it allows for the localization of unknown fluorescent dye molecules attached to macromolecular complexes based on single-molecule Förster resonance energy transfer (smFRET) measurements. However, the precision, accuracy, and reliability of structural models derived from results based on such complex calculation schemes are oftentimes difficult to evaluate. Therefore, we present two proof-of-principle benchmark studies where we use smFRET data to localize supposedly unknown positions on a DNA as well as on a protein-nucleic acid complex. Since we use complexes where structural information is available, we can compare Fast-NPS localization to the existing structural data. In particular, we compare different dye models and discuss how both accuracy and precision can be optimized.

Dynamic nuclear polarization enhanced nuclear magnetic resonance and electron spin resonance studies of hydration and local water dynamics in micelle and vesicle assemblies.

PubMed

McCarney, Evan R; Armstrong, Brandon D; Kausik, Ravinath; Han, Songi

2008-09-16

We present a unique analysis tool for the selective detection of local water inside soft molecular assemblies (hydrophobic cores, vesicular bilayers, and micellar structures) suspended in bulk water. Through the use of dynamic nuclear polarization (DNP), the (1)H NMR signal of water is amplified, as it interacts with stable radicals that possess approximately 658 times higher spin polarization. We utilized stable nitroxide radicals covalently attached along the hydrophobic tail of stearic acid molecules that incorporate themselves into surfactant-based micelle or vesicle structures. Here, we present a study of local water content and fluid viscosity inside oleate micelles and vesicles and Triton X-100 micelles to serve as model systems for soft molecular assemblies. This approach is unique because the amplification of the NMR signal is performed in bulk solution and under ambient conditions with site-specific spin labels that only detect the water that is directly interacting with the localized spin labels. Continuous wave (cw) electron spin resonance (ESR) analysis provides rotational dynamics of the spin-labeled molecular chain segments and local polarity parameters that can be related to hydration properties, whereas we show that DNP-enhanced (1)H NMR analysis of fluid samples directly provides translational water dynamics and permeability of the local environment probed by the spin label. Our technique therefore has the potential to become a powerful analysis tool, complementary to cw ESR, to study hydration characteristics of surfactant assemblies, lipid bilayers, or protein aggregates, where water dynamics is a key parameter of their structure and function. In this study, we find that there is significant penetration of water inside the oleate micelles with a higher average local water viscosity (approximately 1.8 cP) than in bulk water, and Triton X-100 micelles and oleate vesicle bilayers mostly exclude water while allowing for considerable surfactant chain motion and measurable water permeation through the soft structure.

Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations

PubMed Central

Szczurek, Aleksander; Klewes, Ludger; Xing, Jun; Gourram, Amine; Birk, Udo; Knecht, Hans; Dobrucki, Jurek W.; Mai, Sabine

2017-01-01

Abstract Advanced light microscopy is an important tool for nanostructure analysis of chromatin. In this report we present a general concept for Single Molecule localization Microscopy (SMLM) super-resolved imaging of DNA-binding dyes based on modifying the properties of DNA and the dye. By careful adjustment of the chemical environment leading to local, reversible DNA melting and hybridization control over the fluorescence signal of the DNA-binding dye molecules can be introduced. We postulate a transient binding as the basis for our variation of binding-activated localization microscopy (BALM). We demonstrate that several intercalating and minor-groove binding DNA dyes can be used to register (optically isolate) only a few DNA-binding dye signals at a time. To highlight this DNA structure fluctuation-assisted BALM (fBALM), we applied it to measure, for the first time, nanoscale differences in nuclear architecture in model ischemia with an anticipated structural resolution of approximately 50 nm. Our data suggest that this approach may open an avenue for the enhanced microscopic analysis of chromatin nano-architecture and hence the microscopic analysis of nuclear structure aberrations occurring in various pathological conditions. It may also become possible to analyse nuclear nanostructure differences in different cell types, stages of development or environmental stress conditions. PMID:28082388

Understanding Your Local Economy: Economic Base Analysis and Local Development Strategies. Community Economics.

ERIC Educational Resources Information Center

Weber, Bruce A.; And Others

Community decision makers selecting an economic development strategy most appropriate for their local community must begin with an understanding of how their local economy functions, what its economic base is, and how changes in that base may affect local economic structure and performance. The economic base approach emphasizes the roles of…

The Energy Landscape Analysis of Cancer Mutations in Protein Kinases

PubMed Central

Dixit, Anshuman; Verkhivker, Gennady M.

2011-01-01

The growing interest in quantifying the molecular basis of protein kinase activation and allosteric regulation by cancer mutations has fueled computational studies of allosteric signaling in protein kinases. In the present study, we combined computer simulations and the energy landscape analysis of protein kinases to characterize the interplay between oncogenic mutations and locally frustrated sites as important catalysts of allostetric kinase activation. While structurally rigid kinase core constitutes a minimally frustrated hub of the catalytic domain, locally frustrated residue clusters, whose interaction networks are not energetically optimized, are prone to dynamic modulation and could enable allosteric conformational transitions. The results of this study have shown that the energy landscape effect of oncogenic mutations may be allosteric eliciting global changes in the spatial distribution of highly frustrated residues. We have found that mutation-induced allosteric signaling may involve a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. The presented study has demonstrated that activation cancer mutations may affect the thermodynamic equilibrium between kinase states by allosterically altering the distribution of locally frustrated sites and increasing the local frustration in the inactive form, while eliminating locally frustrated sites and restoring structural rigidity of the active form. The energy landsape analysis of protein kinases and the proposed role of locally frustrated sites in activation mechanisms may have useful implications for bioinformatics-based screening and detection of functional sites critical for allosteric regulation in complex biomolecular systems. PMID:21998754

Closed-form solutions in stress-driven two-phase integral elasticity for bending of functionally graded nano-beams

NASA Astrophysics Data System (ADS)

Barretta, Raffaele; Fabbrocino, Francesco; Luciano, Raimondo; Sciarra, Francesco Marotti de

2018-03-01

Strain-driven and stress-driven integral elasticity models are formulated for the analysis of the structural behaviour of fuctionally graded nano-beams. An innovative stress-driven two-phases constitutive mixture defined by a convex combination of local and nonlocal phases is presented. The analysis reveals that the Eringen strain-driven fully nonlocal model cannot be used in Structural Mechanics since it is ill-posed and the local-nonlocal mixtures based on the Eringen integral model partially resolve the ill-posedeness of the model. In fact, a singular behaviour of continuous nano-structures appears if the local fraction tends to vanish so that the ill-posedness of the Eringen integral model is not eliminated. On the contrary, local-nonlocal mixtures based on the stress-driven theory are mathematically and mechanically appropriate for nanosystems. Exact solutions of inflected functionally graded nanobeams of technical interest are established by adopting the new local-nonlocal mixture stress-driven integral relation. Effectiveness of the new nonlocal approach is tested by comparing the contributed results with the ones corresponding to the mixture Eringen theory.

Characterization of the Bm61 of the Bombyx mori nucleopolyhedrovirus.

PubMed

Shen, Hongxing; Chen, Keping; Yao, Qin; Zhou, Yang

2009-07-01

orf61 (bm61) of Bombyx mori Nucleopolyhedrovirus (BmNPV) is a highly conserved baculovirus gene, suggesting that it performs an important role in the virus life cycle whose function is unknown. In this study, we describe the characterization of bm61. Quantitative polymerase chain reaction (qPCR) and western blot analysis demonstrated that bm61 was expressed as a late gene. Immunofluorescence analysis by confocal microscopy showed that BM61 protein was localized on nuclear membrane and in intranuclear ring zone of infected cells. Structure localization of the BM61 in BV and ODV by western analysis demonstrated that BM61 was the protein of both BV and ODV. In addition, our data indicated that BM61 was a late structure protein localized in nucleus.

Layerwise mechanics and finite element for the dynamic analysis of piezoelectric composite plates

NASA Technical Reports Server (NTRS)

Saravanos, Dimitris A.; Heyliger, Paul R.; Hopkins, Dale A.

1996-01-01

Laminate and structural mechanics for the analysis of laminated composite plate structures with piezoelectric actuators and sensors are presented. The theories implement layerwise representations of displacements and electric potential, and can model both the global and local electromechanical response of smart composite laminates. Finite-element formulations are developed for the quasi-static and dynamic analysis of smart composite structures containing piezoelectric layers. Comparisons with an exact solution illustrate the accuracy, robustness and capability of the developed mechanics to capture the global and local response of thin and/or thick laminated piezoelectric plates. Additional correlations and numerical applications demonstrate the unique capabilities of the mechanics in analyzing the static and free-vibration response of composite plates with distributed piezoelectric actuators and sensors.

Transmission electron microscopy: direct observation of crystal structure in refractory ceramics.

PubMed

Shaw, T M; Thomas, G

1978-11-10

Using high-resolution multibeam interference techniques in the transmission electron microscope, images have been obtained that make possible a real-space structure analysis of a beryllium-silicon-nitrogen compound. The results illustrate the usefulness of lattice imaging in the analysis of local crystal structure in these technologically promising ceramic materials.

Investigation of podosome ring protein arrangement using localization microscopy images.

PubMed

Staszowska, Adela D; Fox-Roberts, Patrick; Foxall, Elizabeth; Jones, Gareth E; Cox, Susan

2017-02-15

Podosomes are adhesive structures formed on the plasma membrane abutting the extracellular matrix of macrophages, osteoclasts, and dendritic cells. They consist of an f-actin core and a ring structure composed of integrins and integrin-associated proteins. The podosome ring plays a major role in adhesion to the underlying extracellular matrix, but its detailed structure is poorly understood. Recently, it has become possible to study the nano-scale structure of podosome rings using localization microscopy. Unlike traditional microscopy images, localization microscopy images are reconstructed using discrete points, meaning that standard image analysis methods cannot be applied. Here, we present a pipeline for podosome identification, protein position calculation, and creating a podosome ring model for use with localization microscopy data. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Structure identification methods for atomistic simulations of crystalline materials

DOE PAGES

Stukowski, Alexander

2012-05-28

Here, we discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.

Holographic Reconstruction of Photoelectron Diffraction and Its Circular Dichroism for Local Structure Probing

NASA Astrophysics Data System (ADS)

Matsui, Fumihiko; Matsushita, Tomohiro; Daimon, Hiroshi

2018-06-01

The local atomic structure around a specific element atom can be recorded as a photoelectron diffraction pattern. Forward focusing peaks and diffraction rings around them indicate the directions and distances from the photoelectron emitting atom to the surrounding atoms. The state-of-the-art holography reconstruction algorithm enables us to image the local atomic arrangement around the excited atom in a real space. By using circularly polarized light as an excitation source, the angular momentum transfer from the light to the photoelectron induces parallax shifts in these diffraction patterns. As a result, stereographic images of atomic arrangements are obtained. These diffraction patterns can be used as atomic-site-resolved probes for local electronic structure investigation in combination with spectroscopy techniques. Direct three-dimensional atomic structure visualization and site-specific electronic property analysis methods are reviewed. Furthermore, circular dichroism was also found in valence photoelectron and Auger electron diffraction patterns. The investigation of these new phenomena provides hints for the development of new techniques for local structure probing.

Surface plasmon resonances of arbitrarily shaped nanometallic structures in the small-screening-length limit

PubMed Central

Giannini, Vincenzo; Maier, Stefan A.; Craster, Richard V.

2016-01-01

According to the hydrodynamic Drude model, surface plasmon resonances of metallic nanostructures blueshift owing to the non-local response of the metal’s electron gas. The screening length characterizing the non-local effect is often small relative to the overall dimensions of the metallic structure, which enables us to derive a coarse-grained non-local description using matched asymptotic expansions; a perturbation theory for the blueshifts of arbitrary-shaped nanometallic structures is then developed. The effect of non-locality is not always a perturbation and we present a detailed analysis of the ‘bonding’ modes of a dimer of nearly touching nanowires where the leading-order eigenfrequencies and eigenmode distributions are shown to be a renormalization of those predicted assuming a local metal permittivity. PMID:27493575

Sensitivity analysis of a wing aeroelastic response

NASA Technical Reports Server (NTRS)

Kapania, Rakesh K.; Eldred, Lloyd B.; Barthelemy, Jean-Francois M.

1991-01-01

A variation of Sobieski's Global Sensitivity Equations (GSE) approach is implemented to obtain the sensitivity of the static aeroelastic response of a three-dimensional wing model. The formulation is quite general and accepts any aerodynamics and structural analysis capability. An interface code is written to convert one analysis's output to the other's input, and visa versa. Local sensitivity derivatives are calculated by either analytic methods or finite difference techniques. A program to combine the local sensitivities, such as the sensitivity of the stiffness matrix or the aerodynamic kernel matrix, into global sensitivity derivatives is developed. The aerodynamic analysis package FAST, using a lifting surface theory, and a structural package, ELAPS, implementing Giles' equivalent plate model are used.

Humans make efficient use of natural image statistics when performing spatial interpolation.

PubMed

D'Antona, Anthony D; Perry, Jeffrey S; Geisler, Wilson S

2013-12-16

Visual systems learn through evolution and experience over the lifespan to exploit the statistical structure of natural images when performing visual tasks. Understanding which aspects of this statistical structure are incorporated into the human nervous system is a fundamental goal in vision science. To address this goal, we measured human ability to estimate the intensity of missing image pixels in natural images. Human estimation accuracy is compared with various simple heuristics (e.g., local mean) and with optimal observers that have nearly complete knowledge of the local statistical structure of natural images. Human estimates are more accurate than those of simple heuristics, and they match the performance of an optimal observer that knows the local statistical structure of relative intensities (contrasts). This optimal observer predicts the detailed pattern of human estimation errors and hence the results place strong constraints on the underlying neural mechanisms. However, humans do not reach the performance of an optimal observer that knows the local statistical structure of the absolute intensities, which reflect both local relative intensities and local mean intensity. As predicted from a statistical analysis of natural images, human estimation accuracy is negligibly improved by expanding the context from a local patch to the whole image. Our results demonstrate that the human visual system exploits efficiently the statistical structure of natural images.

Energy localization and frequency analysis in the locust ear.

PubMed

Malkin, Robert; McDonagh, Thomas R; Mhatre, Natasha; Scott, Thomas S; Robert, Daniel

2014-01-06

Animal ears are exquisitely adapted to capture sound energy and perform signal analysis. Studying the ear of the locust, we show how frequency signal analysis can be performed solely by using the structural features of the tympanum. Incident sound waves generate mechanical vibrational waves that travel across the tympanum. These waves shoal in a tsunami-like fashion, resulting in energy localization that focuses vibrations onto the mechanosensory neurons in a frequency-dependent manner. Using finite element analysis, we demonstrate that two mechanical properties of the locust tympanum, distributed thickness and tension, are necessary and sufficient to generate frequency-dependent energy localization.

Summary of Research Report

NASA Technical Reports Server (NTRS)

Elishakoff, Isaac

1998-01-01

Ten papers, published in various publications, on buckling, and the effects of imperfections on various structures are presented. These papers are: (1) Buckling mode localization in elastic plates due to misplacement in the stiffner location; (2) On vibrational imperfection sensitivity on Augusti's model structure in the vicinity of a non-linear static state; (3) Imperfection sensitivity due to elastic moduli in the Roorda Koiter frame; (4) Buckling mode localization in a multi-span periodic structure with a disorder in a single span; (5) Prediction of natural frequency and buckling load variability due to uncertainty in material properties by convex modeling; (6) Derivation of multi-dimensional ellipsoidal convex model for experimental data; (7) Passive control of buckling deformation via Anderson localization phenomenon; (8)Effect of the thickness and initial im perfection on buckling on composite cylindrical shells: asymptotic analysis and numerical results by BOSOR4 and PANDA2; (9) Worst case estimation of homology design by convex analysis; (10) Buckling of structures with uncertain imperfections - Personal perspective.

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

A simulation for gravity fine structure recovery from low-low GRAVSAT SST data

NASA Technical Reports Server (NTRS)

Estes, R. H.; Lancaster, E. R.

1976-01-01

Covariance error analysis techniques were applied to investigate estimation strategies for the low-low SST mission for accurate local recovery of gravitational fine structure, considering the aliasing effects of unsolved for parameters. A 5 degree by 5 degree surface density block representation of the high order geopotential was utilized with the drag-free low-low GRAVSAT configuration in a circular polar orbit at 250 km altitude. Recovery of local sets of density blocks from long data arcs was found not to be feasible due to strong aliasing effects. The error analysis for the recovery of local sets of density blocks using independent short data arcs demonstrated that the estimation strategy of simultaneously estimating a local set of blocks covered by data and two "buffer layers" of blocks not covered by data greatly reduced aliasing errors.

A study of self organized criticality in ion temperature gradient mode driven gyrokinetic turbulence

NASA Astrophysics Data System (ADS)

Mavridis, M.; Isliker, H.; Vlahos, L.; Görler, T.; Jenko, F.; Told, D.

2014-10-01

An investigation on the characteristics of self organized criticality (Soc) in ITG mode driven turbulence is made, with the use of various statistical tools (histograms, power spectra, Hurst exponents estimated with the rescaled range analysis, and the structure function method). For this purpose, local non-linear gyrokinetic simulations of the cyclone base case scenario are performed with the GENE software package. Although most authors concentrate on global simulations, which seem to be a better choice for such an investigation, we use local simulations in an attempt to study the locally underlying mechanisms of Soc. We also study the structural properties of radially extended structures, with several tools (fractal dimension estimate, cluster analysis, and two dimensional autocorrelation function), in order to explore whether they can be characterized as avalanches. We find that, for large enough driving temperature gradients, the local simulations exhibit most of the features of Soc, with the exception of the probability distribution of observables, which show a tail, yet they are not of power-law form. The radial structures have the same radial extent at all temperature gradients examined; radial motion (transport) though appears only at large temperature gradients, in which case the radial structures can be interpreted as avalanches.

A study of self organized criticality in ion temperature gradient mode driven gyrokinetic turbulence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mavridis, M.; Isliker, H.; Vlahos, L.

2014-10-15

An investigation on the characteristics of self organized criticality (Soc) in ITG mode driven turbulence is made, with the use of various statistical tools (histograms, power spectra, Hurst exponents estimated with the rescaled range analysis, and the structure function method). For this purpose, local non-linear gyrokinetic simulations of the cyclone base case scenario are performed with the GENE software package. Although most authors concentrate on global simulations, which seem to be a better choice for such an investigation, we use local simulations in an attempt to study the locally underlying mechanisms of Soc. We also study the structural properties ofmore » radially extended structures, with several tools (fractal dimension estimate, cluster analysis, and two dimensional autocorrelation function), in order to explore whether they can be characterized as avalanches. We find that, for large enough driving temperature gradients, the local simulations exhibit most of the features of Soc, with the exception of the probability distribution of observables, which show a tail, yet they are not of power-law form. The radial structures have the same radial extent at all temperature gradients examined; radial motion (transport) though appears only at large temperature gradients, in which case the radial structures can be interpreted as avalanches.« less

Failure analysis of thick composite cylinders under external pressure

NASA Technical Reports Server (NTRS)

Caiazzo, A.; Rosen, B. W.

1992-01-01

Failure of thick section composites due to local compression strength and overall structural instability is treated. Effects of material nonlinearity, imperfect fiber architecture, and structural imperfections upon anticipated failure stresses are determined. Comparisons with experimental data for a series of test cylinders are described. Predicting the failure strength of composite structures requires consideration of stability and material strength modes of failure using linear and nonlinear analysis techniques. Material strength prediction requires the accurate definition of the local multiaxial stress state in the material. An elasticity solution for the linear static analysis of thick anisotropic cylinders and rings is used herein to predict the axisymmetric stress state in the cylinders. Asymmetric nonlinear behavior due to initial cylinder out of roundness and the effects of end closure structure are treated using finite element methods. It is assumed that local fiber or ply waviness is an important factor in the initiation of material failure. An analytical model for the prediction of compression failure of fiber composites, which includes the effects of fiber misalignments, matrix inelasticity, and multiaxial applied stresses is used for material strength calculations. Analytical results are compared to experimental data for a series of glass and carbon fiber reinforced epoxy cylinders subjected to external pressure. Recommendations for pretest characterization and other experimental issues are presented. Implications for material and structural design are discussed.

Structural evolution across the insulator-metal transition in oxygen-deficient BaTiO 3-δ studied using neutron total scattering and Rietveld analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeong, I.-K.; Lee, Seunghun; Jeong, Se-Young

2011-08-29

Oxygen-deficient BaTiO 3-δ exhibits an insulator-metal transition with increasing δ. We performed neutron total scattering measurements to study structural evolution across an insulator-metal transition in BaTiO 3-δ. Despite its significant impact on resistivity, slight oxygen reduction (δ=0.09) caused only a small disturbance on the local doublet splitting of Ti-O bond. This finding implies that local polarization is well preserved under marginal electric conduction. In the highly oxygen-deficient metallic state (δ=0.25), however, doublet splitting of the Ti-O bond became smeared. The smearing of the local Ti-O doublet is complemented with long-range structural analysis and demonstrates that the metallic conduction in themore » highly oxygen-reduced BaTiO 3-δ is due to the appearance of nonferroelectric cubic lattice.« less

State Size and Government Level Matter Most: A Structural Equation Model of Local Health Department Policy Behaviors.

PubMed

Meyerson, Beth E; Sayegh, M Aaron

2016-01-01

To explore relationships between local health department policy behaviors, levels of government activity, policy focus areas, and selected health department characteristics. Cross-sectional analysis of secondary data from the 2013 National Association of County & City Health Officials (NACCHO) Profile Survey. Local health departments throughout the United States. A total of 2000 local health departments responding to the 2013 Profile Survey of Local Health Departments. Survey data were gathered by the NACCHO. Secondary analysis of reported policy behaviors for the 2013 NACCHO Profile Survey. A structural equation model tested effects on and between state population size, rurality, census region and policy focus, and the latent variables of policy behavior formed from a confirmatory factor analysis. Policy behaviors, levels of government activity (local, state, and federal), policy focus areas, and selected local health department characteristics. The majority (85.1%) of health departments reported at least one of the possible policy behaviors. State population size increased the probability of local policy behavior, and local behavior increased the probability of state policy behavior. State size increased the likelihood of federal policy behavior and the focus on tobacco, emergency preparedness, and obesity/chronic disease. However, the more rural a state was, the more likely policy behavior was at the state and federal levels and not at local levels. Specific policy behaviors mattered less than the level of government activity. Size of state and rurality of health departments influence the government level of policy behavior.

Modeling of Local BEAM Structure for Evaluation of MMOD Impacts to Support Development of a Health Monitoring System

NASA Technical Reports Server (NTRS)

Lyle, Karen H.; Vassilakos, Gregory J.

2015-01-01

This report summarizes initial modeling of the local response of the Bigelow Expandable Activity Module (BEAM) to micrometeorite and orbital debris (MMOD) impacts using a structural, non-linear, transient dynamic finite element code. Complementary test results for a local BEAM structure are presented for both hammer and projectile impacts. Review of these data provided guidance for the transient dynamic model development. The local model is intended to support predictions using the global BEAM model, described in a companion report. Two types of local models were developed. One mimics the simplified Soft-Goods (fabric envelop) part of the BEAM NASTRAN model delivered by the project. The second investigates through-the-thickness modeling challenges for MMOD-type impacts. Both the testing and the analysis summaries contain lessons learned and areas for future efforts.

The wave attenuation mechanism of the periodic local resonant metamaterial

NASA Astrophysics Data System (ADS)

Chang, I.-Ling; Liang, Zhen-Xian; Kao, Hao-Wei; Chang, Shih-Hsiang; Yang, Chih-Ying

2018-01-01

This research discusses the wave propagation behavior and attenuation mechanism of the elastic metamaterial with locally resonant sub-structure. The dispersion relation of the single resonance system, i.e., periodic spring mass system with sub-structure, could be derived based on lattice dynamics and the band gap could be easily identified. The dynamically equivalent properties, i.e., mass and elastic property, of the single resonance system are derived and found to be frequency dependent. Negative effective properties are found in the vicinity of the local resonance. It is examined whether the band gap always coincides with the frequency range of negative effective properties. The wave attenuation mechanism and the characteristic dynamic behavior of the elastic metamaterial are also studied from the energy point of view. From the analysis, it is clarified that the coupled Bragg-resonance band gap is much wider than the narrow-banded local resonance and the corresponding effective material properties at band gap could be either positive or negative. However, the band gap is totally overlapping with the frequency range of negative effective properties for the metamaterial with band gap purely caused by local resonance. The presented analysis can be extended to other forms of elastic metamaterials involving periodic resonator structures.

The crystal structure and morphology of NiO-YSZ composite that prepared from local zircon concentrate of Bangka Island

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rahmawati, F., E-mail: fitria@mipa.uns.ac.id; Apriyani, K.; Heraldy, E.

2016-03-29

In order to increase the economic value of local zircon concentrate from Bangka Island, NiO-YSZ was synthesized from Zirconia, ZrO{sub 2} that was prepared from local zircon concentrate. The NiO-YSZ composite was synthesized by solid state reaction method. XRD analysis equipped with Le Bail refinement was carried out to analyze the crystal structure and cell parameters of the prepared materials. The result showed that zirconia was crystallized in tetragonal structure with a space group of P42/NMC. Yttria-Stabilized-Zirconia (YSZ) was prepared by doping 8% mol yttrium oxide into zirconia and then sintered at 1250°C for 3 hours. Doping of 8% molmore » Yttria allowed phase transformation of zirconia from tetragonal into the cubic structure. Meanwhile, the composite of NiO-YSZ consists of two crystalline phases, i.e. the NiO with cubic structure and the YSZ with cubic structure. SEM analysis of the prepared materials shows that the addition of NiO into YSZ allows the morphology to become more roughness with larger grain size.« less

The polarized Debye sheath effect on Kadomtsev-Petviashvili electrostatic structures in strongly coupled dusty plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shahmansouri, M.; Alinejad, H.

2015-04-15

We give a theoretical investigation on the dynamics of nonlinear electrostatic waves in a strongly coupled dusty plasma with strong electrostatic interaction between dust grains in the presence of the polarization force (i.e., the force due to the polarized Debye sheath). Adopting a reductive perturbation method, we derived a three-dimensional Kadomtsev-Petviashvili equation that describes the evolution of weakly nonlinear electrostatic localized waves. The energy integral equation is used to study the existence domains of the localized structures. The analysis provides the localized structure existence region, in terms of the effects of strong interaction between the dust particles and polarization force.

Study of improved modeling and solution procedures for nonlinear analysis. [aircraft-like structures

NASA Technical Reports Server (NTRS)

Kamat, M. P.

1979-01-01

An evaluation of the ACTION computer code on an aircraft like structure is presented. This computer program proved adequate in predicting gross response parameters in structures which undergo severe localized cross sectional deformations.

Localization of multiple defects using the compact phased array (CPA) method

NASA Astrophysics Data System (ADS)

Senyurek, Volkan Y.; Baghalian, Amin; Tashakori, Shervin; McDaniel, Dwayne; Tansel, Ibrahim N.

2018-01-01

Array systems of transducers have found numerous applications in detection and localization of defects in structural health monitoring (SHM) of plate-like structures. Different types of array configurations and analysis algorithms have been used to improve the process of localization of defects. For accurate and reliable monitoring of large structures by array systems, a high number of actuator and sensor elements are often required. In this study, a compact phased array system consisting of only three piezoelectric elements is used in conjunction with an updated total focusing method (TFM) for localization of single and multiple defects in an aluminum plate. The accuracy of the localization process was greatly improved by including wave propagation information in TFM. Results indicated that the proposed CPA approach can locate single and multiple defects with high accuracy while decreasing the processing costs and the number of required transducers. This method can be utilized in critical applications such as aerospace structures where the use of a large number of transducers is not desirable.

The politics of local hospital reform: a case study of hospital reorganization following the 2002 Norwegian hospital reform.

PubMed

Tjerbo, Trond

2009-11-20

The Norwegian hospital reform of 2002 was an attempt to make restructuring of hospitals easier by removing politicians from the decision-making processes. To facilitate changes seen as necessary but politically difficult, the central state took over ownership of the hospitals and stripped the county politicians of what had been their main responsibility for decades. This meant that decisions regarding hospital structure and organization were now being taken by professional administrators and not by politically elected representatives. The question raised here is whether this has had any effect on the speed of restructuring of the hospital sector. The empirical part is a case study of the restructuring process in Innlandet Hospital Trust (IHT), which was one of the largest enterprise established after the hospital reform and where the vision for restructuring was clearly set. Different sources of qualitative data are used in the analysis. These include interviews with key actors, observational data and document studies. The analysis demonstrates how the new professional leaders at first acted in accordance with the intentions of the hospital reform, but soon chose to avoid the more ambitious plans for restructuring the hospital structure and in fact reintroduced local politics into the decision-making process. The analysis further illustrates how local networks and engagement of political representatives from all levels of government complicated the decision-making process surrounding local structural reforms. Local political representatives teamed up with other actors and created powerful networks. At the same time, national politicians had incentives to involve themselves in the processes as supporters of the status quo. Because of the incentives that faced political actors and the controversial nature of major hospital reforms, the removal of local politicians and the centralization of ownership did not necessarily facilitate reforms in the hospital structure. Keeping politics at an arm's length may simply be unrealistic and further complicate the politics of local hospital reforms.

The politics of local hospital reform: a case study of hospital reorganization following the 2002 Norwegian hospital reform

PubMed Central

2009-01-01

Background The Norwegian hospital reform of 2002 was an attempt to make restructuring of hospitals easier by removing politicians from the decision-making processes. To facilitate changes seen as necessary but politically difficult, the central state took over ownership of the hospitals and stripped the county politicians of what had been their main responsibility for decades. This meant that decisions regarding hospital structure and organization were now being taken by professional administrators and not by politically elected representatives. The question raised here is whether this has had any effect on the speed of restructuring of the hospital sector. Method The empirical part is a case study of the restructuring process in Innlandet Hospital Trust (IHT), which was one of the largest enterprise established after the hospital reform and where the vision for restructuring was clearly set. Different sources of qualitative data are used in the analysis. These include interviews with key actors, observational data and document studies. Results The analysis demonstrates how the new professional leaders at first acted in accordance with the intentions of the hospital reform, but soon chose to avoid the more ambitious plans for restructuring the hospital structure and in fact reintroduced local politics into the decision-making process. The analysis further illustrates how local networks and engagement of political representatives from all levels of government complicated the decision-making process surrounding local structural reforms. Local political representatives teamed up with other actors and created powerful networks. At the same time, national politicians had incentives to involve themselves in the processes as supporters of the status quo. Conclusion Because of the incentives that faced political actors and the controversial nature of major hospital reforms, the removal of local politicians and the centralization of ownership did not necessarily facilitate reforms in the hospital structure. Keeping politics at an arm's length may simply be unrealistic and further complicate the politics of local hospital reforms. PMID:19930553

Advances in the REDCAT software package

PubMed Central

2013-01-01

Background Residual Dipolar Couplings (RDCs) have emerged in the past two decades as an informative source of experimental restraints for the study of structure and dynamics of biological macromolecules and complexes. The REDCAT software package was previously introduced for the analysis of molecular structures using RDC data. Here we report additional features that have been included in this software package in order to expand the scope of its analyses. We first discuss the features that enhance REDCATs user-friendly nature, such as the integration of a number of analyses into one single operation and enabling convenient examination of a structural ensemble in order to identify the most suitable structure. We then describe the new features which expand the scope of RDC analyses, performing exercises that utilize both synthetic and experimental data to illustrate and evaluate different features with regard to structure refinement and structure validation. Results We establish the seamless interaction that takes place between REDCAT, VMD, and Xplor-NIH in demonstrations that utilize our newly developed REDCAT-VMD and XplorGUI interfaces. These modules enable visualization of RDC analysis results on the molecular structure displayed in VMD and refinement of structures with Xplor-NIH, respectively. We also highlight REDCAT’s Error-Analysis feature in reporting the localized fitness of a structure to RDC data, which provides a more effective means of recognizing local structural anomalies. This allows for structurally sound regions of a molecule to be identified, and for any refinement efforts to be focused solely on locally distorted regions. Conclusions The newly engineered REDCAT software package, which is available for download via the WWW from http://ifestos.cse.sc.edu, has been developed in the Object Oriented C++ environment. Our most recent enhancements to REDCAT serve to provide a more complete RDC analysis suite, while also accommodating a more user-friendly experience, and will be of great interest to the community of researchers and developers since it hides the complications of software development. PMID:24098943

Multi-component quantitation of meso/nanostructural surfaces and its application to local chemical compositions of copper meso/nanostructures self-organized on silica

NASA Astrophysics Data System (ADS)

Huang, Chun-Yi; Chang, Hsin-Wei; Chang, Che-Chen

2018-03-01

Knowledge about the chemical compositions of meso/nanomaterials is fundamental to development of their applications in advanced technologies. Auger electron spectroscopy (AES) is an effective analysis method for the characterization of meso/nanomaterial structures. Although a few studies have reported the use of AES for the analysis of the local composition of these structures, none have explored in detail the validity of the meso/nanoanalysis results generated by the AES instrument. This paper addresses the limitations of AES and the corrections necessary to offset them for this otherwise powerful meso/nanoanalysis tool. The results of corrections made to the AES multi-point analysis of high-density copper-based meso/nanostructures provides major insights into their local chemical compositions and technological prospects, which the primitive composition output of the AES instrument failed to provide.

Disconnecting structure and dynamics in glassy thin films

PubMed Central

Sussman, Daniel M.; Cubuk, Ekin D.; Liu, Andrea J.

2017-01-01

Nanometrically thin glassy films depart strikingly from the behavior of their bulk counterparts. We investigate whether the dynamical differences between a bulk and thin film polymeric glass former can be understood by differences in local microscopic structure. Machine learning methods have shown that local structure can serve as the foundation for successful, predictive models of particle rearrangement dynamics in bulk systems. By contrast, in thin glassy films, we find that particles at the center of the film and those near the surface are structurally indistinguishable despite exhibiting very different dynamics. Next, we show that structure-independent processes, already present in bulk systems and demonstrably different from simple facilitated dynamics, are crucial for understanding glassy dynamics in thin films. Our analysis suggests a picture of glassy dynamics in which two dynamical processes coexist, with relative strengths that depend on the distance from an interface. One of these processes depends on local structure and is unchanged throughout most of the film, while the other is purely Arrhenius, does not depend on local structure, and is strongly enhanced near the free surface of a film. PMID:28928147

Automatic segmentation of solitary pulmonary nodules based on local intensity structure analysis and 3D neighborhood features in 3D chest CT images

NASA Astrophysics Data System (ADS)

Chen, Bin; Kitasaka, Takayuki; Honma, Hirotoshi; Takabatake, Hirotsugu; Mori, Masaki; Natori, Hiroshi; Mori, Kensaku

2012-03-01

This paper presents a solitary pulmonary nodule (SPN) segmentation method based on local intensity structure analysis and neighborhood feature analysis in chest CT images. Automated segmentation of SPNs is desirable for a chest computer-aided detection/diagnosis (CAS) system since a SPN may indicate early stage of lung cancer. Due to the similar intensities of SPNs and other chest structures such as blood vessels, many false positives (FPs) are generated by nodule detection methods. To reduce such FPs, we introduce two features that analyze the relation between each segmented nodule candidate and it neighborhood region. The proposed method utilizes a blob-like structure enhancement (BSE) filter based on Hessian analysis to augment the blob-like structures as initial nodule candidates. Then a fine segmentation is performed to segment much more accurate region of each nodule candidate. FP reduction is mainly addressed by investigating two neighborhood features based on volume ratio and eigenvector of Hessian that are calculates from the neighborhood region of each nodule candidate. We evaluated the proposed method by using 40 chest CT images, include 20 standard-dose CT images that we randomly chosen from a local database and 20 low-dose CT images that were randomly chosen from a public database: LIDC. The experimental results revealed that the average TP rate of proposed method was 93.6% with 12.3 FPs/case.

Local and average structures of BaTiO 3-Bi(Zn 1/2Ti 1/2)O 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Usher, Tedi-Marie; Iamsasri, Thanakorn; Forrester, Jennifer S.

The complex crystallographic structures of (1-x)BaTiO 3-xBi(Zn 1/2Ti 1/2)O 3 (BT-xBZT) are examined using high resolution synchrotron X-ray diffraction, neutron diffraction, and neutron pair distribution function (PDF) analyses. The short-range structures are characterized from the PDFs, and a combined analysis of the X-ray and neutron diffraction patterns is used to determine the long-range structures. Our results demonstrate that the structure appears different when averaged over different length scales. In all compositions, the local structures determined from the PDFs show local tetragonal distortions (i.e., c/a > 1). But, a box-car fitting analysis of the PDFs reveals variations at different length scales.more » For 0.80BT-0.20BZT and 0.90BT-0.10BZT, the tetragonal distortions decrease at longer atom-atom distances (e.g., 30 vs. 5 ). When the longest distances are evaluated (r > 40 ), the lattice parameters approach cubic. Neutron and X-ray diffraction yield further information about the long-range structure. Compositions 0.80BT-0.20BZT and 0.90BT-0.10BZT appear cubic by Bragg diffraction (no peak splitting), consistent with the PDFs at long distances. However, these patterns cannot be adequately fit using a cubic lattice model; modeling their structures with the P4mm space group allows for a better fit to the patterns because the space group allows for c-axis atomic displacements that occur at the local scale. Furthermore, for the compositions 0.92BT-0.08BZT and 0.94BT-0.06BZT, strong tetragonal distortions are observed at the local scale and a less-distorted tetragonal structure is observed at longer length scales. In Rietveld refinements, the latter is modeled using a tetragonal phase. Since the peak overlap in these two-phase compositions limits the ability to model the local-scale structures as tetragonal, it is approximated in the refinements as a cubic phase. These results demonstrate that alloying BT with BZT results in increased disorder and disrupts the long-range ferroelectric symmetry present in BT, while the large tetragonal distortion present in BZT persists at the local scale.« less

Local and average structures of BaTiO 3-Bi(Zn 1/2Ti 1/2)O 3

DOE PAGES

Usher, Tedi-Marie; Iamsasri, Thanakorn; Forrester, Jennifer S.; ...

2016-11-11

The complex crystallographic structures of (1-x)BaTiO 3-xBi(Zn 1/2Ti 1/2)O 3 (BT-xBZT) are examined using high resolution synchrotron X-ray diffraction, neutron diffraction, and neutron pair distribution function (PDF) analyses. The short-range structures are characterized from the PDFs, and a combined analysis of the X-ray and neutron diffraction patterns is used to determine the long-range structures. Our results demonstrate that the structure appears different when averaged over different length scales. In all compositions, the local structures determined from the PDFs show local tetragonal distortions (i.e., c/a > 1). But, a box-car fitting analysis of the PDFs reveals variations at different length scales.more » For 0.80BT-0.20BZT and 0.90BT-0.10BZT, the tetragonal distortions decrease at longer atom-atom distances (e.g., 30 vs. 5 ). When the longest distances are evaluated (r > 40 ), the lattice parameters approach cubic. Neutron and X-ray diffraction yield further information about the long-range structure. Compositions 0.80BT-0.20BZT and 0.90BT-0.10BZT appear cubic by Bragg diffraction (no peak splitting), consistent with the PDFs at long distances. However, these patterns cannot be adequately fit using a cubic lattice model; modeling their structures with the P4mm space group allows for a better fit to the patterns because the space group allows for c-axis atomic displacements that occur at the local scale. Furthermore, for the compositions 0.92BT-0.08BZT and 0.94BT-0.06BZT, strong tetragonal distortions are observed at the local scale and a less-distorted tetragonal structure is observed at longer length scales. In Rietveld refinements, the latter is modeled using a tetragonal phase. Since the peak overlap in these two-phase compositions limits the ability to model the local-scale structures as tetragonal, it is approximated in the refinements as a cubic phase. These results demonstrate that alloying BT with BZT results in increased disorder and disrupts the long-range ferroelectric symmetry present in BT, while the large tetragonal distortion present in BZT persists at the local scale.« less

X-ray circular dichroism signals: a unique probe of local molecular chirality

DOE PAGES

Zhang, Yu; Rouxel, Jeremy R.; Autschbach, Jochen; ...

2017-06-26

Core-resonant circular dichroism (CD) signals are induced by molecular chirality and vanish for achiral molecules and racemic mixtures. The highly localized nature of core excitations makes them ideal probes of local chirality within molecules. Simulations of the circular dichroism spectra of several molecular families illustrate how these signals vary with the electronic coupling to substitution groups, the distance between the X-ray chromophore and the chiral center, geometry, and chemical structure. As a result, clear insight into the molecular structure is obtained through analysis of the X-ray CD spectra.

X-ray circular dichroism signals: a unique probe of local molecular chirality

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yu; Rouxel, Jeremy R.; Autschbach, Jochen

Core-resonant circular dichroism (CD) signals are induced by molecular chirality and vanish for achiral molecules and racemic mixtures. The highly localized nature of core excitations makes them ideal probes of local chirality within molecules. Simulations of the circular dichroism spectra of several molecular families illustrate how these signals vary with the electronic coupling to substitution groups, the distance between the X-ray chromophore and the chiral center, geometry, and chemical structure. As a result, clear insight into the molecular structure is obtained through analysis of the X-ray CD spectra.

Thermoviscoplastic response of thin plates subjected to intense local heating

NASA Technical Reports Server (NTRS)

Byrom, Ted G.; Allen, David H.; Thornton, Earl A.

1992-01-01

A finite element method is employed to investigate the thermoviscoplastic response of a half-cylinder to intense localized transient heating. Thermoviscoplastic material behavior is characterized by the Bodner-Partom constitutive model. Structure geometry is modeled with a three-dimensional assembly of CST-DKT plate elements incorporating the large deflection von Karman assumptions. The paper compares the results of a dynamic analysis with a quasi-static analysis for the half-cylinder structure with a step-function transient temperature loading similar to that which may be encountered with shock wave interference on a hypersonic leading edge.

SCit: web tools for protein side chain conformation analysis.

PubMed

Gautier, R; Camproux, A-C; Tufféry, P

2004-07-01

SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit.

A two-step FEM-SEM approach for wave propagation analysis in cable structures

NASA Astrophysics Data System (ADS)

Zhang, Songhan; Shen, Ruili; Wang, Tao; De Roeck, Guido; Lombaert, Geert

2018-02-01

Vibration-based methods are among the most widely studied in structural health monitoring (SHM). It is well known, however, that the low-order modes, characterizing the global dynamic behaviour of structures, are relatively insensitive to local damage. Such local damage may be easier to detect by methods based on wave propagation which involve local high frequency behaviour. The present work considers the numerical analysis of wave propagation in cables. A two-step approach is proposed which allows taking into account the cable sag and the distribution of the axial forces in the wave propagation analysis. In the first step, the static deformation and internal forces are obtained by the finite element method (FEM), taking into account geometric nonlinear effects. In the second step, the results from the static analysis are used to define the initial state of the dynamic analysis which is performed by means of the spectral element method (SEM). The use of the SEM in the second step of the analysis allows for a significant reduction in computational costs as compared to a FE analysis. This methodology is first verified by means of a full FE analysis for a single stretched cable. Next, simulations are made to study the effects of damage in a single stretched cable and a cable-supported truss. The results of the simulations show how damage significantly affects the high frequency response, confirming the potential of wave propagation based methods for SHM.

Data analysis and detection methods for on-line health monitoring of bridge structures

DOT National Transportation Integrated Search

2002-06-01

Developing an efficient structural health monitoring (SHM) technique is important for reducing potential hazards posed : to the public by damaged civil structures. The ultimate goal of applying SHM is to real-time detect, localize, and quantify : the...

Local backbone structure prediction of proteins

PubMed Central

De Brevern, Alexandre G.; Benros, Cristina; Gautier, Romain; Valadié, Hélène; Hazout, Serge; Etchebest, Catherine

2004-01-01

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

Influence of local meshing size on stress intensity factor of orthopedic lag screw

NASA Astrophysics Data System (ADS)

Husain, M. N.; Daud, R.; Basaruddin, K. S.; Mat, F.; Bajuri, M. Y.; Arifin, A. K.

2017-09-01

Linear elastic fracture mechanics (LEFM) concept is generally used to study the influence of crack on the performance of structures. In order to study the LEFM concept on damaged structure, the usage of finite element analysis software is implemented to do the simulation of the structure. Mesh generation is one of the most crucial procedures in finite element method. For the structure that crack or damaged, it is very important to determine the accurate local meshing size at the crack tip of the crack itself in order to get the accurate value of stress intensity factor, KI. Pre crack will be introduced to the lag screw based on the von mises' stress result that had been performed in previous research. This paper shows the influence of local mesh arrangement on numerical value of the stress intensity factor, KI obtained by the displacement method. This study aims to simulate the effect of local meshing which is the singularity region on stress intensity factor, KI to the critical point of failure in screw. Five different set of wedges meshing size are introduced during the simulation of finite element analysis. The number of wedges used to simulate this research is 8, 10, 14, 16 and 20. There are three set of numerical equations used to validate the results which are brown and srawley, gross and brown and Tada equation. The result obtained from the finite element software (ANSYS APDL) has a positive agreement with the numerical analysis which is Brown and Srawley compared to other numerical formula. Radius of first row size of 0.014 and singularity element with 14 numbers of wedges is proved to be the best local meshing for this study.

Characterizing the correlations between local phase fractions of gas-liquid two-phase flow with wire-mesh sensor.

PubMed

Tan, C; Liu, W L; Dong, F

2016-06-28

Understanding of flow patterns and their transitions is significant to uncover the flow mechanics of two-phase flow. The local phase distribution and its fluctuations contain rich information regarding the flow structures. A wire-mesh sensor (WMS) was used to study the local phase fluctuations of horizontal gas-liquid two-phase flow, which was verified through comparing the reconstructed three-dimensional flow structure with photographs taken during the experiments. Each crossing point of the WMS is treated as a node, so the measurement on each node is the phase fraction in this local area. An undirected and unweighted flow pattern network was established based on connections that are formed by cross-correlating the time series of each node under different flow patterns. The structure of the flow pattern network reveals the relationship of the phase fluctuations at each node during flow pattern transition, which is then quantified by introducing the topological index of the complex network. The proposed analysis method using the WMS not only provides three-dimensional visualizations of the gas-liquid two-phase flow, but is also a thorough analysis for the structure of flow patterns and the characteristics of flow pattern transition. This article is part of the themed issue 'Supersensing through industrial process tomography'. © 2016 The Author(s).

Characterizing the correlations between local phase fractions of gas–liquid two-phase flow with wire-mesh sensor

PubMed Central

Liu, W. L.; Dong, F.

2016-01-01

Understanding of flow patterns and their transitions is significant to uncover the flow mechanics of two-phase flow. The local phase distribution and its fluctuations contain rich information regarding the flow structures. A wire-mesh sensor (WMS) was used to study the local phase fluctuations of horizontal gas–liquid two-phase flow, which was verified through comparing the reconstructed three-dimensional flow structure with photographs taken during the experiments. Each crossing point of the WMS is treated as a node, so the measurement on each node is the phase fraction in this local area. An undirected and unweighted flow pattern network was established based on connections that are formed by cross-correlating the time series of each node under different flow patterns. The structure of the flow pattern network reveals the relationship of the phase fluctuations at each node during flow pattern transition, which is then quantified by introducing the topological index of the complex network. The proposed analysis method using the WMS not only provides three-dimensional visualizations of the gas–liquid two-phase flow, but is also a thorough analysis for the structure of flow patterns and the characteristics of flow pattern transition. This article is part of the themed issue ‘Supersensing through industrial process tomography’. PMID:27185959

Structures and Dynamics Division research and technology plans, FY 1982

NASA Technical Reports Server (NTRS)

Bales, K. S.

1982-01-01

Computational devices to improve efficiency for structural calculations are assessed. The potential of large arrays of microprocessors operating in parallel for finite element analysis is defined, and the impact of specialized computer hardware on static, dynamic, thermal analysis in the optimization of structural analysis and design calculations is determined. General aviation aircraft crashworthiness and occupant survivability is also considered. Mechanics technology required for design coefficient, fault tolerant advanced composite aircraft components subject to combined loads, impact, postbuckling effects and local discontinuities are developed.

New Insight into the Local Structure of Hydrous Ferric Arsenate Using Full-Potential Multiple Scattering Analysis, Density Functional Theory Calculations, and Vibrational Spectroscopy.

PubMed

Wang, Shaofeng; Ma, Xu; Zhang, Guoqing; Jia, Yongfeng; Hatada, Keisuke

2016-11-15

Hydrous ferric arsenate (HFA) is an important arsenic-bearing precipitate in the mining-impacted environment and hydrometallurgical tailings. However, there is no agreement on its local atomic structure. The local structure of HFA was reprobed by employing a full-potential multiple scattering (FPMS) analysis, density functional theory (DFT) calculations, and vibrational spectroscopy. The FPMS simulations indicated that the coordination number of the As-Fe, Fe-As, or both in HFA was approximately two. The DFT calculations constructed a structure of HFA with the formula of Fe(HAsO 4 ) x (H 2 AsO 4 ) 1-x (OH) y ·zH 2 O. The presence of protonated arsenate in HFA was also evidenced by vibrational spectroscopy. The As and Fe K-edge X-ray absorption near-edge structure spectra of HFA were accurately reproduced by FPMS simulations using the chain structure, which was also a reasonable model for extended X-Ray absorption fine structure fitting. The FPMS refinements indicated that the interatomic Fe-Fe distance was approximately 5.2 Å, consistent with that obtained by Mikutta et al. (Environ. Sci. Technol. 2013, 47 (7), 3122-3131) using wavelet analysis. All of the results suggested that HFA was more likely to occur as a chain with AsO 4 tetrahedra and FeO 6 octahedra connecting alternately in an isolated bidentate-type fashion. This finding is of significance for understanding the fate of arsenic and the formation of ferric arsenate minerals in an acidic environment.

Phases and interfaces from real space atomically resolved data: Physics-based deep data image analysis

DOE PAGES

Vasudevan, Rama K.; Ziatdinov, Maxim; Jesse, Stephen; ...

2016-08-12

Advances in electron and scanning probe microscopies have led to a wealth of atomically resolved structural and electronic data, often with ~1–10 pm precision. However, knowledge generation from such data requires the development of a physics-based robust framework to link the observed structures to macroscopic chemical and physical descriptors, including single phase regions, order parameter fields, interfaces, and structural and topological defects. Here, we develop an approach based on a synergy of sliding window Fourier transform to capture the local analog of traditional structure factors combined with blind linear unmixing of the resultant 4D data set. This deep data analysismore » is ideally matched to the underlying physics of the problem and allows reconstruction of the a priori unknown structure factors of individual components and their spatial localization. We demonstrate the principles of this approach using a synthetic data set and further apply it for extracting chemical and physically relevant information from electron and scanning tunneling microscopy data. Furthermore, this method promises to dramatically speed up crystallographic analysis in atomically resolved data, paving the road toward automatic local structure–property determinations in crystalline and quasi-ordered systems, as well as systems with competing structural and electronic order parameters.« less

The CLAIR model: Extension of Brodmann areas based on brain oscillations and connectivity.

PubMed

Başar, Erol; Düzgün, Aysel

2016-05-01

Since the beginning of the last century, the localization of brain function has been represented by Brodmann areas, maps of the anatomic organization of the brain. They are used to broadly represent cortical structures with their given sensory-cognitive functions. In recent decades, the analysis of brain oscillations has become important in the correlation of brain functions. Moreover, spectral connectivity can provide further information on the dynamic connectivity between various structures. In addition, brain responses are dynamic in nature and structural localization is almost impossible, according to Luria (1966). Therefore, brain functions are very difficult to localize; hence, a combined analysis of oscillation and event-related coherences is required. In this study, a model termed as "CLAIR" is described to enrich and possibly replace the concept of the Brodmann areas. A CLAIR model with optimum function may take several years to develop, but this study sets out to lay its foundation. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Singularities in Optimal Structural Design

NASA Technical Reports Server (NTRS)

Patnaik, S. N.; Guptill, J. D.; Berke, L.

1992-01-01

Singularity conditions that arise during structural optimization can seriously degrade the performance of the optimizer. The singularities are intrinsic to the formulation of the structural optimization problem and are not associated with the method of analysis. Certain conditions that give rise to singularities have been identified in earlier papers, encompassing the entire structure. Further examination revealed more complex sets of conditions in which singularities occur. Some of these singularities are local in nature, being associated with only a segment of the structure. Moreover, the likelihood that one of these local singularities may arise during an optimization procedure can be much greater than that of the global singularity identified earlier. Examples are provided of these additional forms of singularities. A framework is also given in which these singularities can be recognized. In particular, the singularities can be identified by examination of the stress displacement relations along with the compatibility conditions and/or the displacement stress relations derived in the integrated force method of structural analysis.

Singularities in optimal structural design

NASA Technical Reports Server (NTRS)

Patnaik, S. N.; Guptill, J. D.; Berke, L.

1992-01-01

Singularity conditions that arise during structural optimization can seriously degrade the performance of the optimizer. The singularities are intrinsic to the formulation of the structural optimization problem and are not associated with the method of analysis. Certain conditions that give rise to singularities have been identified in earlier papers, encompassing the entire structure. Further examination revealed more complex sets of conditions in which singularities occur. Some of these singularities are local in nature, being associated with only a segment of the structure. Moreover, the likelihood that one of these local singularities may arise during an optimization procedure can be much greater than that of the global singularity identified earlier. Examples are provided of these additional forms of singularities. A framework is also given in which these singularities can be recognized. In particular, the singularities can be identified by examination of the stress displacement relations along with the compatibility conditions and/or the displacement stress relations derived in the integrated force method of structural analysis.

Buckling analysis for axially compressed flat plates, structural sections, and stiffened plates reinforced with laminated composites

NASA Technical Reports Server (NTRS)

Viswanathan, A. V.; Soong, T.; Miller, R. E., Jr.

1971-01-01

A classical buckling analysis is developed for stiffened, flat plates composed of a series of linked plate and beam elements. Plates are idealized as multilayered orthotropic elements. Structural beads and lips are idealized as beams. The loaded edges of the stiffened plate are simply-supported and the conditions at the unloaded edges can be prescribed arbitrarily. The plate and beam elements are matched along their common junctions for displacement continuity and force equilibrium in an exact manner. Offsets between elements are considered in the analysis. Buckling under uniaxial compressive load for plates, sections, and stiffened plates is investigated. Buckling loads are the lowest of all possible general and local failure modes, and the mode shape is used to determine whether buckling is a local or general instability. Numerical correlations with existing analysis and test data for plates, sections, and stiffened plates including boron-reinforced structures are discussed. In general correlations are reasonably good.

Buckling analysis for structural sections and stiffened plates reinforced with laminated composites.

NASA Technical Reports Server (NTRS)

Viswanathan, A. V.; Soong, T.-C.; Miller, R. E., Jr.

1972-01-01

A classical buckling analysis is developed for stiffened, flat plates composed of a series of linked flat plate and beam elements. Plates are idealized as multilayered orthotropic elements; structural beads and lips are idealized as beams. The loaded edges of the stiffened plate are simply supported and the conditions at the unloaded edges can be prescribed arbitrarily. The plate and beam elements are matched along their common junctions for displacement continuity and force equilibrium in an exact manner. Offsets between elements are considered in the analysis. Buckling under uniaxial compressive load for plates, sections and stiffened plates is investigated. Buckling loads are found as the lowest of all possible general and local failure modes and the mode shape is used to determine whether buckling is a local or general instability. Numerical correlations with existing analysis and test data for plates, sections and stiffened plates including boron-reinforced structures are discussed. In general, correlations are reasonably good.

Analysis of the local structure around Cr3+ centers in perovskite KMgF3 using both ab initio (DFT) and semi-empirical (SPM) calculations

NASA Astrophysics Data System (ADS)

Emül, Y.; Erbahar, D.; Açıkgöz, M.

2014-11-01

The local structure around Cr3+ centers in perovskite KMgF3 crystal have been investigated through the applications of both an ab-initio, density functional theory (DFT), and a semi empirical, superposition model (SPM), analyses. A supercell approach is used for DFT calculations. All the tetragonal (Cr3+-VMg and Cr3+-Li+), trigonal (Cr3+-VK), and CrF5O cluster centers have been considered with various structural models based on the previously suggested experimental inferences. The significant structural changes around the Cr3+ centers induced by Mg2+ or K+ vacancies and the Li substitution at those vacancy sites have been determined and discussed by means of charge distribution. This study provides insight on both the roles of Mg2+ and K+ vacancies and Li+ ion in the local structural properties around Cr3+ centers in KMgF3.

PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks

PubMed Central

Craveur, Pierrick; Joseph, Agnel Praveen; Jallu, Vincent

2017-01-01

This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license. PMID:29177113

Chlamydia trachomatis protein CT009 is a structural and functional homolog to the key morphogenesis component RodZ and interacts with division septal plane localized MreB

DOE PAGES

Kemege, Kyle E.; Hickey, John M.; Barta, Michael L.; ...

2014-11-10

Cell division in Chlamydiae is poorly understood as apparent homologs to most conserved bacterial cell division proteins are lacking and presence of elongation (rod shape) associated proteins indicate non-canonical mechanisms may be employed. The rod-shape determining protein MreB has been proposed as playing a unique role in chlamydial cell division. In other organisms, MreB is part of an elongation complex that requires RodZ for proper function. A recent study reported that the protein encoded by ORF CT009 interacts with MreB despite low sequence similarity to RodZ. The studies in this paper expand on those observations through protein structure, mutagenesis andmore » cellular localization analyses. Structural analysis indicated that CT009 shares high level of structural similarity to RodZ, revealing the conserved orientation of two residues critical for MreB interaction. Substitutions eliminated MreB protein interaction and partial complementation provided by CT009 in RodZ deficient Escherichia coli. Cellular localization analysis of CT009 showed uniform membrane staining in Chlamydia. This was in contrast to the localization of MreB, which was restricted to predicted septal planes. Finally, MreB localization to septal planes provides direct experimental observation for the role of MreB in cell division and supports the hypothesis that it serves as a functional replacement for FtsZ in Chlamydia.« less

Chlamydia trachomatis protein CT009 is a structural and functional homolog to the key morphogenesis component RodZ and interacts with division septal plane localized MreB

PubMed Central

Kemege, Kyle E.; Hickey, John M.; Barta, Michael L.; Wickstrum, Jason; Balwalli, Namita; Lovell, Scott; Battaile, Kevin P.; Hefty, P. Scott

2015-01-01

Summary Cell division in Chlamydiae is poorly understood as apparent homologs to most conserved bacterial cell division proteins are lacking and presence of elongation (rod shape) associated proteins indicate non-canonical mechanisms may be employed. The rod-shape determining protein MreB has been proposed as playing a unique role in chlamydial cell division. In other organisms, MreB is part of an elongation complex that requires RodZ for proper function. A recent study reported that the protein encoded by ORF CT009 interacts with MreB despite low sequence similarity to RodZ. The studies herein expand on those observations through protein structure, mutagenesis, and cellular localization analyses. Structural analysis indicated that CT009 shares high level of structural similarity to RodZ, revealing the conserved orientation of two residues critical for MreB interaction. Substitutions eliminated MreB protein interaction and partial complementation provided by CT009 in RodZ deficient E. coli. Cellular localization analysis of CT009 showed uniform membrane staining in Chlamydia. This was in contrast to the localization of MreB, which was restricted to predicted septal planes. MreB localization to septal planes provides direct experimental observation for the role of MreB in cell division and supports the hypothesis that it serves as a functional replacement for FtsZ in Chlamydia. PMID:25382739

Chlamydia trachomatis protein CT009 is a structural and functional homolog to the key morphogenesis component RodZ and interacts with division septal plane localized MreB.

PubMed

Kemege, Kyle E; Hickey, John M; Barta, Michael L; Wickstrum, Jason; Balwalli, Namita; Lovell, Scott; Battaile, Kevin P; Hefty, P Scott

2015-02-01

Cell division in Chlamydiae is poorly understood as apparent homologs to most conserved bacterial cell division proteins are lacking and presence of elongation (rod shape) associated proteins indicate non-canonical mechanisms may be employed. The rod-shape determining protein MreB has been proposed as playing a unique role in chlamydial cell division. In other organisms, MreB is part of an elongation complex that requires RodZ for proper function. A recent study reported that the protein encoded by ORF CT009 interacts with MreB despite low sequence similarity to RodZ. The studies herein expand on those observations through protein structure, mutagenesis and cellular localization analyses. Structural analysis indicated that CT009 shares high level of structural similarity to RodZ, revealing the conserved orientation of two residues critical for MreB interaction. Substitutions eliminated MreB protein interaction and partial complementation provided by CT009 in RodZ deficient Escherichia coli. Cellular localization analysis of CT009 showed uniform membrane staining in Chlamydia. This was in contrast to the localization of MreB, which was restricted to predicted septal planes. MreB localization to septal planes provides direct experimental observation for the role of MreB in cell division and supports the hypothesis that it serves as a functional replacement for FtsZ in Chlamydia. © 2014 John Wiley & Sons Ltd.

Multi-disciplinary optimization of aeroservoelastic systems

NASA Technical Reports Server (NTRS)

Karpel, Mordechay

1991-01-01

New methods were developed for efficient aeroservoelastic analysis and optimization. The main target was to develop a method for investigating large structural variations using a single set of modal coordinates. This task was accomplished by basing the structural modal coordinates on normal modes calculated with a set of fictitious masses loading the locations of anticipated structural changes. The following subject areas are covered: (1) modal coordinates for aeroelastic analysis with large local structural variations; and (2) time simulation of flutter with large stiffness changes.

VoroTop: Voronoi cell topology visualization and analysis toolkit

NASA Astrophysics Data System (ADS)

Lazar, Emanuel A.

2018-01-01

This paper introduces a new open-source software program called VoroTop, which uses Voronoi topology to analyze local structure in atomic systems. Strengths of this approach include its abilities to analyze high-temperature systems and to characterize complex structure such as grain boundaries. This approach enables the automated analysis of systems and mechanisms previously not possible.

Computational Methods for Structural Mechanics and Dynamics, part 1

NASA Technical Reports Server (NTRS)

Stroud, W. Jefferson (Editor); Housner, Jerrold M. (Editor); Tanner, John A. (Editor); Hayduk, Robert J. (Editor)

1989-01-01

The structural analysis methods research has several goals. One goal is to develop analysis methods that are general. This goal of generality leads naturally to finite-element methods, but the research will also include other structural analysis methods. Another goal is that the methods be amenable to error analysis; that is, given a physical problem and a mathematical model of that problem, an analyst would like to know the probable error in predicting a given response quantity. The ultimate objective is to specify the error tolerances and to use automated logic to adjust the mathematical model or solution strategy to obtain that accuracy. A third goal is to develop structural analysis methods that can exploit parallel processing computers. The structural analysis methods research will focus initially on three types of problems: local/global nonlinear stress analysis, nonlinear transient dynamics, and tire modeling.

Global and Local Stress Analyses of McDonnell Douglas Stitched/RFI Composite Wing Stub Box

NASA Technical Reports Server (NTRS)

Wang, John T.

1996-01-01

This report contains results of structural analyses performed in support of the NASA structural testing of an all-composite stitched/RFI (resin film infusion) wing stub box. McDonnell Douglas Aerospace Company designed and fabricated the wing stub box. The analyses used a global/local approach. The global model contains the entire test article. It includes the all-composite stub box, a metallic load-transition box and a metallic wing-tip extension box. The two metallic boxes are connected to the inboard and outboard ends of the composite wing stub box, respectively. The load-transition box was attached to a steel and concrete vertical reaction structure and a load was applied at the tip of the extension box to bend the wing stub box upward. The local model contains an upper cover region surrounding three stringer runouts. In that region, a large nonlinear deformation was identified by the global analyses. A more detailed mesh was used for the local model to obtain more accurate analysis results near stringer runouts. Numerous analysis results such as deformed shapes, displacements at selected locations, and strains at critical locations are included in this report.

SCit: web tools for protein side chain conformation analysis

PubMed Central

Gautier, R.; Camproux, A.-C.; Tufféry, P.

2004-01-01

SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit. PMID:15215438

Localizing Target Structures in Ultrasound Video

PubMed Central

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

2013-01-01

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

Deformation structure analysis of material at fatigue on the basis of the vector field

NASA Astrophysics Data System (ADS)

Kibitkin, Vladimir V.; Solodushkin, Andrey I.; Pleshanov, Vasily S.

2017-12-01

In the paper, spatial distributions of deformation, circulation, and shear amplitudes and shear angles are obtained from the displacement vector field measured by the DIC technique. This vector field and its characteristics of shears and vortices are given as an example of such approach. The basic formulae are also given. The experiment shows that honeycomb deformation structures can arise in the center of a macrovortex at developed plastic flow. The spatial distribution of local circulation and shears is discovered, which coincides with the deformation structure but their amplitudes are different. The analysis proves that the spatial distribution of shear angles is a result of maximum tangential and normal stresses. The anticlockwise circulation of most local vortices obeys the normal Gaussian law in the area of interest.

Influence of local demography on asymptotic and transient dynamics of a yellow-bellied marmot metapopulation.

PubMed

Ozgul, Arpat; Oli, Madan K; Armitage, Kenneth B; Blumstein, Daniel T; Van Vuren, Dirk H

2009-04-01

Despite recent advances in biodemography and metapopulation ecology, we still have limited understanding of how local demographic parameters influence short- and long-term metapopulation dynamics. We used long-term data from 17 local populations, along with the recently developed methods of matrix metapopulation modeling and transient sensitivity analysis, to investigate the influence of local demography on long-term (asymptotic) versus short-term (transient) dynamics of a yellow-bellied marmot metapopulation in Colorado. Both long- and short-term dynamics depended primarily on a few colony sites and were highly sensitive to changes in demography at these sites, particularly in survival of reproductive adult females. Interestingly, the relative importance of sites differed between long- and short-term dynamics; the spatial structure and local population sizes, while insignificant for asymptotic dynamics, were influential on transient dynamics. However, considering the spatial structure was uninformative about the relative influence of local demography on metapopulation dynamics. The vital rates that were the most influential on local dynamics were also the most influential on both long- and short-term metapopulation dynamics. Our results show that an explicit consideration of local demography is essential for a complete understanding of the dynamics and persistence of spatially structured populations.

Introducing Fe 2+ into Nickel-Iron Layered Double Hydroxide: Local Structure Modulated Water Oxidation Activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cai, Zhao; Zhou, Daojin; Wang, Maoyu

Exploring materials with regulated local structures and understanding how the atomic motifs govern the reactivity and durability of catalysts are a critical challenge for designing advanced catalysts. Here we report the tuning of the local atomic structure of nickel–iron layered double hydroxides (NiFe–LDHs) by partially substituting Ni 2+ with Fe 2+ to introduce Fe–O–Fe moieties. These Fe 2+–containing NiFe–LDHs exhibit enhanced oxygen evolution reaction (OER) activity with an ultralow overpotential of 195 mV at the current density of 10 mA/cm 2, which is among the best OER catalytic performance reported to date. In–situ X–ray absorption, Raman, and electrochemical analysis jointlymore » reveal that the Fe–O–Fe motifs could stabilize high–valent metal sites at low overpotentials, thereby enhancing the OER activity. Lastly, these results reveal the importance of tuning the local atomic structure for designing high efficiency electrocatalysts.« less

Locating damage using integrated global-local approach with wireless sensing system and single-chip impedance measurement device.

PubMed

Lin, Tzu-Hsuan; Lu, Yung-Chi; Hung, Shih-Lin

2014-01-01

This study developed an integrated global-local approach for locating damage on building structures. A damage detection approach with a novel embedded frequency response function damage index (NEFDI) was proposed and embedded in the Imote2.NET-based wireless structural health monitoring (SHM) system to locate global damage. Local damage is then identified using an electromechanical impedance- (EMI-) based damage detection method. The electromechanical impedance was measured using a single-chip impedance measurement device which has the advantages of small size, low cost, and portability. The feasibility of the proposed damage detection scheme was studied with reference to a numerical example of a six-storey shear plane frame structure and a small-scale experimental steel frame. Numerical and experimental analysis using the integrated global-local SHM approach reveals that, after NEFDI indicates the approximate location of a damaged area, the EMI-based damage detection approach can then identify the detailed damage location in the structure of the building.

Introducing Fe2+ into Nickel-Iron Layered Double Hydroxide: Local Structure Modulated Water Oxidation Activity.

PubMed

Cai, Zhao; Zhou, Daojin; Wang, Maoyu; Bak, Seongmin; Wu, Yueshen; Wu, Zishan; Tian, Yang; Xiong, Xuya; Li, Yaping; Liu, Wen; Siahrostami, Samira; Kuang, Yun; Yang, Xiao-Qing; Duan, Haohong; Feng, Zhenxing; Wang, Hailiang; Sun, Xiaoming

2018-06-11

Exploring materials with regulated local structures and understanding how the atomic motifs govern the reactivity and durability of catalysts are a critical challenge for designing advanced catalysts. Here we report the tuning of the local atomic structure of nickel-iron layered double hydroxides (NiFe-LDHs) by partially substituting Ni2+ with Fe2+ to introduce Fe-O-Fe moieties. These Fe2+-containing NiFe-LDHs exhibit enhanced oxygen evolution reaction (OER) activity with an ultralow overpotential of 195 mV at the current density of 10 mA/cm2, which is among the best OER catalytic performance reported to date. In-situ X-ray absorption, Raman, and electrochemical analysis jointly reveal that the Fe-O-Fe motifs could stabilize high-valent metal sites at low overpotentials, thereby enhancing the OER activity. These results reveal the importance of tuning the local atomic structure for designing high efficiency electrocatalysts. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Introducing Fe 2+ into Nickel-Iron Layered Double Hydroxide: Local Structure Modulated Water Oxidation Activity

DOE PAGES

Cai, Zhao; Zhou, Daojin; Wang, Maoyu; ...

2018-06-11

Exploring materials with regulated local structures and understanding how the atomic motifs govern the reactivity and durability of catalysts are a critical challenge for designing advanced catalysts. Here we report the tuning of the local atomic structure of nickel–iron layered double hydroxides (NiFe–LDHs) by partially substituting Ni 2+ with Fe 2+ to introduce Fe–O–Fe moieties. These Fe 2+–containing NiFe–LDHs exhibit enhanced oxygen evolution reaction (OER) activity with an ultralow overpotential of 195 mV at the current density of 10 mA/cm 2, which is among the best OER catalytic performance reported to date. In–situ X–ray absorption, Raman, and electrochemical analysis jointlymore » reveal that the Fe–O–Fe motifs could stabilize high–valent metal sites at low overpotentials, thereby enhancing the OER activity. Lastly, these results reveal the importance of tuning the local atomic structure for designing high efficiency electrocatalysts.« less

Atomic resolution holography.

PubMed

Hayashi, Kouichi

2014-11-01

Atomic resolution holography, such as X-ray fluorescence holography (XFH)[1] and photoelectron holography (PH), has the attention of researcher as an informative local structure analysis, because it provides three dimensional atomic images around specific elements within a range of a few nanometers. It can determine atomic arrangements around a specific element without any prior knowledge of structures. It is considered that the atomic resolution holographic is a third method of structural analysis at the atomic level after X-ray diffraction (XRD) and X-ray absorption fine structure (XAFS). As known by many researchers, XRD and XAFS are established methods that are widespread use in various fields. XRD and XAFS provide information on long-range translational periodicities and very local environments, respectively, whereas the atomic resolution holography gives 3D information on the local order and can visualize surrounding atoms with a large range of coordination shells. We call this feature "3D medium-range local structure observation".In addition to this feature, the atomic resolution holography is very sensitive to the displacement of atoms from their ideal positions, and one can obtain quantitative information about local lattice distortions by analyzing reconstructed atomic images[2] When dopants with different atomic radii from the matrix elements are present, the lattices around the dopants are distorted. However, using the conventional methods of structural analysis, one cannot determine the extent to which the local lattice distortions are preserved from the dopants. XFH is a good tool for solving this problem.Figure 1 shows a recent achievement on a relaxor ferroelectric of Pb(Mg1/3Nb2/3)O3 (PMN) using XFH. The structural studies of relaxor ferroelectrics have been carried out by X-ray or neutron diffractions, which suggested rhombohedral distortions of their lattices. However, their true pictures have not been obtained, yet. The Nb Kα holograms showed four separate Pb images, as shown in Fig.1. Using these images, we could obtain acute and obtuse rhombohedral structures of the crystal unit cells. Moreover, the Pb-Pb correlated images reconstructed from Pb Lα holograms showed a local structure of body center-like 2a0 ×2a0 × 2a0 superlattice, proving a rigid 3D network structural model combining the two kinds of rhombohedrons. This superstructure are believed to play an important role in the relaxor behaviour of PMN at atomic level[3].jmicro;63/suppl_1/i13/DFU047F1F1DFU047F1Fig. 1.3D images of the nearest Pb and O atoms around Nb in Pb(Mg1/3Nb2/3)O3. The cube represents 1/8 of the unit cell. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Mechanisms governing brittle fault mechanics - a multi-scale study from the Permian Khao-Kwang fold-and-thrust belt, Thailand

NASA Astrophysics Data System (ADS)

von Hagke, Christoph; Morley, Chris; Kanitpanyacharoen, Waruntorn

2017-04-01

Despite our qualitative understanding of factors contributing to thrust and detachment weakness such as mineralogy, pore fluid pressure, or efficiency of structure localization, it is difficult to assess the contribution of the individual factors. Here we present multi-scale analysis of a mixed clay / carbonate high displacement (kms of heave) thrust zone, where it is possible to study structures formed within a similar temperature and pressure regime, and thus only varying due to lithological contrasts. We mapped the well-exposed thrust zone in a large quarry at outcrop scale in five separate sections present along a strike-distance of 1 km. The thrust zone shows considerable variations in structural style, as well as localization within different clay and limestone horizons. Zones of low and high strain have been identified. We investigate these changes in macroscopic deformation style using Virtual Polarizing Microscopy, and the combined methods of Broad Ion Beam milling and Scanning Electron Microscopy in addition with XRD analysis. We characterize structural and mineralogical variations in the thrust zone at all scales, from outcrop down to nano-meters. Results show strain localization is heterogeneous, with strong variations along strike. Within the clay package, strain localizes along zones rich in organic matter. Microstructures are complex, and show multiple deformation events, including crack-seal processes and reworking of vein material. Pressure solution is dominant. XRD analysis shows mineralogical differences between zones of high and low strain within the shale-dominated package. However, highest strain does not only occur in the clay units, but partly is accommodated in the surrounding limestone.

Dynamics of localized structures in reaction-diffusion systems induced by delayed feedback

NASA Astrophysics Data System (ADS)

Gurevich, Svetlana V.

2013-05-01

We are interested in stability properties of a single localized structure in a three-component reaction-diffusion system subjected to the time-delayed feedback. We shall show that variation in the product of the delay time and the feedback strength leads to complex dynamical behavior of the system, including formation of target patterns, spontaneous motion, and spontaneous breathing as well as various complex structures, arising from combination of different oscillatory instabilities. In the case of spontaneous motion, we provide a bifurcation analysis of the delayed system and derive an order parameter equation for the position of the localized structure, explicitly describing its temporal evolution in the vicinity of the bifurcation point. This equation is a subject to a nonlinear delay differential equation, which can be transformed to the normal form of the pitchfork drift bifurcation.

Lack of congruence in species diversity indices and community structures of planktonic groups based on local environmental factors.

PubMed

Doi, Hideyuki; Chang, Kwang-Hyeon; Nishibe, Yuichiro; Imai, Hiroyuki; Nakano, Shin-ichi

2013-01-01

The importance of analyzing the determinants of biodiversity and community composition by using multiple trophic levels is well recognized; however, relevant data are lacking. In the present study, we investigated variations in species diversity indices and community structures of the plankton taxonomic groups-zooplankton, rotifers, ciliates, and phytoplankton-under a range of local environmental factors in pond ecosystems. For each planktonic group, we estimated the species diversity index by using linear models and analyzed the community structure by using canonical correspondence analysis. We showed that the species diversity indices and community structures varied among the planktonic groups and according to local environmental factors. The observed lack of congruence among the planktonic groups may have been caused by niche competition between groups with similar trophic guilds or by weak trophic interactions. Our findings highlight the difficulty of predicting total biodiversity within a system, based upon a single taxonomic group. Thus, to conserve the biodiversity of an ecosystem, it is crucial to consider variations in species diversity indices and community structures of different taxonomic groups, under a range of local conditions.

Multiple-wavelength neutron holography with pulsed neutrons

PubMed Central

Hayashi, Kouichi; Ohoyama, Kenji; Happo, Naohisa; Matsushita, Tomohiro; Hosokawa, Shinya; Harada, Masahide; Inamura, Yasuhiro; Nitani, Hiroaki; Shishido, Toetsu; Yubuta, Kunio

2017-01-01

Local structures around impurities in solids provide important information for understanding the mechanisms of material functions, because most of them are controlled by dopants. For this purpose, the x-ray absorption fine structure method, which provides radial distribution functions around specific elements, is most widely used. However, a similar method using neutron techniques has not yet been developed. If one can establish a method of local structural analysis with neutrons, then a new frontier of materials science can be explored owing to the specific nature of neutron scattering—that is, its high sensitivity to light elements and magnetic moments. Multiple-wavelength neutron holography using the time-of-flight technique with pulsed neutrons has great potential to realize this. We demonstrated multiple-wavelength neutron holography using a Eu-doped CaF2 single crystal and obtained a clear three-dimensional atomic image around trivalent Eu substituted for divalent Ca, revealing an interesting feature of the local structure that allows it to maintain charge neutrality. The new holography technique is expected to provide new information on local structures using the neutron technique. PMID:28835917

Multiple-wavelength neutron holography with pulsed neutrons.

PubMed

Hayashi, Kouichi; Ohoyama, Kenji; Happo, Naohisa; Matsushita, Tomohiro; Hosokawa, Shinya; Harada, Masahide; Inamura, Yasuhiro; Nitani, Hiroaki; Shishido, Toetsu; Yubuta, Kunio

2017-08-01

Local structures around impurities in solids provide important information for understanding the mechanisms of material functions, because most of them are controlled by dopants. For this purpose, the x-ray absorption fine structure method, which provides radial distribution functions around specific elements, is most widely used. However, a similar method using neutron techniques has not yet been developed. If one can establish a method of local structural analysis with neutrons, then a new frontier of materials science can be explored owing to the specific nature of neutron scattering-that is, its high sensitivity to light elements and magnetic moments. Multiple-wavelength neutron holography using the time-of-flight technique with pulsed neutrons has great potential to realize this. We demonstrated multiple-wavelength neutron holography using a Eu-doped CaF 2 single crystal and obtained a clear three-dimensional atomic image around trivalent Eu substituted for divalent Ca, revealing an interesting feature of the local structure that allows it to maintain charge neutrality. The new holography technique is expected to provide new information on local structures using the neutron technique.

Structural alphabets derived from attractors in conformational space

PubMed Central

2010-01-01

Background The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as 'states'. Collections of selected representatives for these states define Structural Alphabets, describing the most typical local conformations within protein structures. These alphabets form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis. Results A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness. Conclusions The density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics. PMID:20170534

Advanced fitness landscape analysis and the performance of memetic algorithms.

PubMed

Merz, Peter

2004-01-01

Memetic algorithms (MAs) have demonstrated very effective in combinatorial optimization. This paper offers explanations as to why this is so by investigating the performance of MAs in terms of efficiency and effectiveness. A special class of MAs is used to discuss efficiency and effectiveness for local search and evolutionary meta-search. It is shown that the efficiency of MAs can be increased drastically with the use of domain knowledge. However, effectiveness highly depends on the structure of the problem. As is well-known, identifying this structure is made easier with the notion of fitness landscapes: the local properties of the fitness landscape strongly influence the effectiveness of the local search while the global properties strongly influence the effectiveness of the evolutionary meta-search. This paper also introduces new techniques for analyzing the fitness landscapes of combinatorial problems; these techniques focus on the investigation of random walks in the fitness landscape starting at locally optimal solutions as well as on the escape from the basins of attractions of current local optima. It is shown for NK-landscapes and landscapes of the unconstrained binary quadratic programming problem (BQP) that a random walk to another local optimum can be used to explain the efficiency of recombination in comparison to mutation. Moreover, the paper shows that other aspects like the size of the basins of attractions of local optima are important for the efficiency of MAs and a local search escape analysis is proposed. These simple analysis techniques have several advantages over previously proposed statistical measures and provide valuable insight into the behaviour of MAs on different kinds of landscapes.

Density Functionals of Chemical Bonding

PubMed Central

Putz, Mihai V.

2008-01-01

The behavior of electrons in general many-electronic systems throughout the density functionals of energy is reviewed. The basic physico-chemical concepts of density functional theory are employed to highlight the energy role in chemical structure while its extended influence in electronic localization function helps in chemical bonding understanding. In this context the energy functionals accompanied by electronic localization functions may provide a comprehensive description of the global-local levels electronic structures in general and of chemical bonds in special. Becke-Edgecombe and author’s Markovian electronic localization functions are discussed at atomic, molecular and solid state levels. Then, the analytical survey of the main workable kinetic, exchange, and correlation density functionals within local and gradient density approximations is undertaken. The hierarchy of various energy functionals is formulated by employing both the parabolic and statistical correlation degree of them with the electronegativity and chemical hardness indices by means of quantitative structure-property relationship (QSPR) analysis for basic atomic and molecular systems. PMID:19325846

Blind identification of full-field vibration modes of output-only structures from uniformly-sampled, possibly temporally-aliased (sub-Nyquist), video measurements

NASA Astrophysics Data System (ADS)

Yang, Yongchao; Dorn, Charles; Mancini, Tyler; Talken, Zachary; Nagarajaiah, Satish; Kenyon, Garrett; Farrar, Charles; Mascareñas, David

2017-03-01

Enhancing the spatial and temporal resolution of vibration measurements and modal analysis could significantly benefit dynamic modelling, analysis, and health monitoring of structures. For example, spatially high-density mode shapes are critical for accurate vibration-based damage localization. In experimental or operational modal analysis, higher (frequency) modes, which may be outside the frequency range of the measurement, contain local structural features that can improve damage localization as well as the construction and updating of the modal-based dynamic model of the structure. In general, the resolution of vibration measurements can be increased by enhanced hardware. Traditional vibration measurement sensors such as accelerometers have high-frequency sampling capacity; however, they are discrete point-wise sensors only providing sparse, low spatial sensing resolution measurements, while dense deployment to achieve high spatial resolution is expensive and results in the mass-loading effect and modification of structure's surface. Non-contact measurement methods such as scanning laser vibrometers provide high spatial and temporal resolution sensing capacity; however, they make measurements sequentially that requires considerable acquisition time. As an alternative non-contact method, digital video cameras are relatively low-cost, agile, and provide high spatial resolution, simultaneous, measurements. Combined with vision based algorithms (e.g., image correlation or template matching, optical flow, etc.), video camera based measurements have been successfully used for experimental and operational vibration measurement and subsequent modal analysis. However, the sampling frequency of most affordable digital cameras is limited to 30-60 Hz, while high-speed cameras for higher frequency vibration measurements are extremely costly. This work develops a computational algorithm capable of performing vibration measurement at a uniform sampling frequency lower than what is required by the Shannon-Nyquist sampling theorem for output-only modal analysis. In particular, the spatio-temporal uncoupling property of the modal expansion of structural vibration responses enables a direct modal decoupling of the temporally-aliased vibration measurements by existing output-only modal analysis methods, yielding (full-field) mode shapes estimation directly. Then the signal aliasing properties in modal analysis is exploited to estimate the modal frequencies and damping ratios. The proposed method is validated by laboratory experiments where output-only modal identification is conducted on temporally-aliased acceleration responses and particularly the temporally-aliased video measurements of bench-scale structures, including a three-story building structure and a cantilever beam.

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

PubMed Central

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

2009-01-01

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

Fine-Scale Analysis Reveals Cryptic Landscape Genetic Structure in Desert Tortoises

PubMed Central

Latch, Emily K.; Boarman, William I.; Walde, Andrew; Fleischer, Robert C.

2011-01-01

Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We investigated fine-scale spatial patterns of genetic variation and gene flow in relation to features of the landscape in desert tortoise (Gopherus agassizii), using 859 tortoises genotyped at 16 microsatellite loci with associated data on geographic location, sex, elevation, slope, and soil type, and spatial relationship to putative barriers (power lines, roads). We used spatially explicit and non-explicit Bayesian clustering algorithms to partition the sample into discrete clusters, and characterize the relationships between genetic distance and ecological variables to identify factors with the greatest influence on gene flow at a local scale. Desert tortoises exhibit weak genetic structure at a local scale, and we identified two subpopulations across the study area. Although genetic differentiation between the subpopulations was low, our landscape genetic analysis identified both natural (slope) and anthropogenic (roads) landscape variables that have significantly influenced gene flow within this local population. We show that desert tortoise movements at a local scale are influenced by features of the landscape, and that these features are different than those that influence gene flow at larger scales. Our findings are important for desert tortoise conservation and management, particularly in light of recent translocation efforts in the region. More generally, our results indicate that recent landscape changes can affect gene flow at a local scale and that their effects can be detected almost immediately. PMID:22132143

Fine-scale analysis reveals cryptic landscape genetic structure in desert tortoises.

PubMed

Latch, Emily K; Boarman, William I; Walde, Andrew; Fleischer, Robert C

2011-01-01

Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We investigated fine-scale spatial patterns of genetic variation and gene flow in relation to features of the landscape in desert tortoise (Gopherus agassizii), using 859 tortoises genotyped at 16 microsatellite loci with associated data on geographic location, sex, elevation, slope, and soil type, and spatial relationship to putative barriers (power lines, roads). We used spatially explicit and non-explicit Bayesian clustering algorithms to partition the sample into discrete clusters, and characterize the relationships between genetic distance and ecological variables to identify factors with the greatest influence on gene flow at a local scale. Desert tortoises exhibit weak genetic structure at a local scale, and we identified two subpopulations across the study area. Although genetic differentiation between the subpopulations was low, our landscape genetic analysis identified both natural (slope) and anthropogenic (roads) landscape variables that have significantly influenced gene flow within this local population. We show that desert tortoise movements at a local scale are influenced by features of the landscape, and that these features are different than those that influence gene flow at larger scales. Our findings are important for desert tortoise conservation and management, particularly in light of recent translocation efforts in the region. More generally, our results indicate that recent landscape changes can affect gene flow at a local scale and that their effects can be detected almost immediately.

A class of covariate-dependent spatiotemporal covariance functions

PubMed Central

Reich, Brian J; Eidsvik, Jo; Guindani, Michele; Nail, Amy J; Schmidt, Alexandra M.

2014-01-01

In geostatistics, it is common to model spatially distributed phenomena through an underlying stationary and isotropic spatial process. However, these assumptions are often untenable in practice because of the influence of local effects in the correlation structure. Therefore, it has been of prolonged interest in the literature to provide flexible and effective ways to model non-stationarity in the spatial effects. Arguably, due to the local nature of the problem, we might envision that the correlation structure would be highly dependent on local characteristics of the domain of study, namely the latitude, longitude and altitude of the observation sites, as well as other locally defined covariate information. In this work, we provide a flexible and computationally feasible way for allowing the correlation structure of the underlying processes to depend on local covariate information. We discuss the properties of the induced covariance functions and discuss methods to assess its dependence on local covariate information by means of a simulation study and the analysis of data observed at ozone-monitoring stations in the Southeast United States. PMID:24772199

Fractal dimension based damage identification incorporating multi-task sparse Bayesian learning

NASA Astrophysics Data System (ADS)

Huang, Yong; Li, Hui; Wu, Stephen; Yang, Yongchao

2018-07-01

Sensitivity to damage and robustness to noise are critical requirements for the effectiveness of structural damage detection. In this study, a two-stage damage identification method based on the fractal dimension analysis and multi-task Bayesian learning is presented. The Higuchi’s fractal dimension (HFD) based damage index is first proposed, directly examining the time-frequency characteristic of local free vibration data of structures based on the irregularity sensitivity and noise robustness analysis of HFD. Katz’s fractal dimension is then presented to analyze the abrupt irregularity change of the spatial curve of the displacement mode shape along the structure. At the second stage, the multi-task sparse Bayesian learning technique is employed to infer the final damage localization vector, which borrow the dependent strength of the two fractal dimension based damage indication information and also incorporate the prior knowledge that structural damage occurs at a limited number of locations in a structure in the absence of its collapse. To validate the capability of the proposed method, a steel beam and a bridge, named Yonghe Bridge, are analyzed as illustrative examples. The damage identification results demonstrate that the proposed method is capable of localizing single and multiple damages regardless of its severity, and show superior robustness under heavy noise as well.

Determinants of community structure of zooplankton in heavily polluted river ecosystems

NASA Astrophysics Data System (ADS)

Xiong, Wei; Li, Jie; Chen, Yiyong; Shan, Baoqing; Wang, Weimin; Zhan, Aibin

2016-02-01

River ecosystems are among the most affected habitats globally by human activities, such as the release of chemical pollutants. However, it remains largely unknown how and to what extent many communities such as zooplankton are affected by these environmental stressors in river ecosystems. Here, we aim to determine major factors responsible for shaping community structure of zooplankton in heavily polluted river ecosystems. Specially, we use rotifers in the Haihe River Basin (HRB) in North China as a case study to test the hypothesis that species sorting (i.e. species are “filtered” by environmental factors and occur at environmental suitable sites) plays a key role in determining community structure at the basin level. Based on an analysis of 94 sites across the plain region of HRB, we found evidence that both local and regional factors could affect rotifer community structure. Interestingly, further analyses indicated that local factors played a more important role in determining community structure. Thus, our results support the species sorting hypothesis in highly polluted rivers, suggesting that local environmental constraints, such as environmental pollution caused by human activities, can be stronger than dispersal limitation caused by regional factors to shape local community structure of zooplankton at the basin level.

A Multiscale, Nonlinear, Modeling Framework Enabling the Design and Analysis of Composite Materials and Structures

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Arnold, Steven M.

2012-01-01

A framework for the multiscale design and analysis of composite materials and structures is presented. The ImMAC software suite, developed at NASA Glenn Research Center, embeds efficient, nonlinear micromechanics capabilities within higher scale structural analysis methods such as finite element analysis. The result is an integrated, multiscale tool that relates global loading to the constituent scale, captures nonlinearities at this scale, and homogenizes local nonlinearities to predict their effects at the structural scale. Example applications of the multiscale framework are presented for the stochastic progressive failure of a SiC/Ti composite tensile specimen and the effects of microstructural variations on the nonlinear response of woven polymer matrix composites.

A Multiscale, Nonlinear, Modeling Framework Enabling the Design and Analysis of Composite Materials and Structures

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Arnold, Steven M.

2011-01-01

A framework for the multiscale design and analysis of composite materials and structures is presented. The ImMAC software suite, developed at NASA Glenn Research Center, embeds efficient, nonlinear micromechanics capabilities within higher scale structural analysis methods such as finite element analysis. The result is an integrated, multiscale tool that relates global loading to the constituent scale, captures nonlinearities at this scale, and homogenizes local nonlinearities to predict their effects at the structural scale. Example applications of the multiscale framework are presented for the stochastic progressive failure of a SiC/Ti composite tensile specimen and the effects of microstructural variations on the nonlinear response of woven polymer matrix composites.

STRUCTURING EDUCATION FOR BUSINESS MANAGEMENT.

ERIC Educational Resources Information Center

WHITT, ROBERT L.

IN TERMS OF SERVICES RECEIVED, LOCAL SCHOOLS BENEFIT SUBSTANTIALLY FROM EDUCATIONAL BUSINESS MANAGEMENT. IN ORDER TO ISOLATE BUSINESS ADMINISTRATIVE PROBLEMS OF THE SCHOOL SYSTEM, AN ANALYSIS WAS CONDUCTED AT EACH OF 6 ADMINISTRATIVE SERVICE LEVELS--LOCAL (ATTENDANCE LEVEL), DISTRICT, AREA, REGIONAL, STATE, AND MULTI-STATE. AS A RESULT OF MERGED…

Regional and local species richness in an insular environment: Serpentine plants in California

USGS Publications Warehouse

Harrison, S.; Safford, H.D.; Grace, J.B.; Viers, J.H.; Davies, K.F.

2006-01-01

We asked how the richness of the specialized (endemic) flora of serpentine rock outcrops in California varies at both the regional and local scales. Our study had two goals: first, to test whether endemic richness is affected by spatial habitat structure (e.g., regional serpentine area, local serpentine outcrop area, regional and local measures of outcrop isolation), and second, to conduct this test in the context of a broader assessment of environmental influences (e.g., climate, soils, vegetation, disturbance) and historical influences (e.g., geologic age, geographic province) on local and regional species richness. We measured endemic and total richness and environmental variables in 109 serpentine sites (1000-m2 paired plots) in 78 serpentine-containing regions of the state. We used structural equation modeling (SEM) to simultaneously relate regional richness to regionalscale predictors, and local richness to both local-scale and regional-scale predictors. Our model for serpentine endemics explained 66% of the variation in local endemic richness based on local environment (vegetation, soils, rock cover) and on regional endemic richness. It explained 73% of the variation in regional endemic richness based on regional environment (climate and productivity), historical factors (geologic age and geographic province), and spatial structure (regional total area of serpentine, the only significant spatial variable in our analysis). We did not find a strong influence of spatial structure on species richness. However, we were able to distinguish local vs. regional influences on species richness to a novel extent, despite the existence of correlations between local and regional conditions. ?? 2006 by the Ecological Society of America.

Local structure and polarization resistance of Ce doped SrMnO{sub 3} using extended x-ray fine structure analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryu, Jiseung; Lee, Heesoo, E-mail: heesoo@pusan.ac.kr

2014-09-15

Changes to the local structure of Sr and Mn atoms in Sr{sub 1−x}Ce{sub x}MnO{sub 3} (SCM) according to increasing Ce content and the effect of the structural change on the polarization resistance of SCM were investigated. The reduction of manganese was confirmed by the absorption edge shift of the Mn K-edge toward lower energies. The noise of oscillation in extended X-ray absorption fine structure k{sup 3}χ data at Mn K-edge reveals the distortion of the local structure of Mn atoms, and the peak that indicates the bonding length of Mn-O, Sr/Ce, and -Mn decreased with the addition of Ce contentmore » in Fourier transformations of the Mn K-edge. The distortion of the local structure at Mn atoms was affected by the reduced manganese ions having larger ionic radii than Mn{sup 4+}. Meanwhile, few distortions of local atomic structures of Sr atoms occurred, and the average nearest neighboring distances of Sr-O and Sr-Mn are ∼2.13 Å and ∼2.95 Å, respectively. The average bonding lengths of the Ce-O and Ce-Mn increased because the ionic radius of substituted Ce ion with 12 coordination number is smaller than that of Sr ion, which leads the reduction of Mn ions and the distortion of local structure at the substituted A-site. Therefore, we reasoned that the distortion of the local atomic structure at Mn atoms in MnO{sub 6} and Ce atoms in A-site is one of the causes for interrupting oxygen ion transfers as a geometric factor, which results in an increase in the polarization resistance of SCM within the Ce composition range from 10 mol. % to 30 mol. %.« less

Quantification of micro-CT images of textile reinforcements

NASA Astrophysics Data System (ADS)

Straumit, Ilya; Lomov, Stepan V.; Wevers, Martine

2017-10-01

VoxTex software (KU Leuven) employs 3D image processing, which use the local directionality information, retrieved using analysis of local structure tensor. The processing results in a voxel 3D array, with each voxel carrying information on (1) material type (matrix; yarn/ply, with identification of the yarn/ply in the reinforcement architecture; void) and (2) fibre direction for fibrous yarns/plies. The knowledge of the material phase volume and known characterisation of the textile structure allows assigning to the voxels (3) fibre volume fraction. This basic voxel model can be further used for different type of the material analysis: Internal geometry and characterisation of defects; permeability; micromechanics; mesoFE voxel models. Apart from the voxel based analysis, approaches to reconstruction of the yarn paths are presented.

Alanine and proline content modulate global sensitivity to discrete perturbations in disordered proteins.

PubMed

Perez, Romel B; Tischer, Alexander; Auton, Matthew; Whitten, Steven T

2014-12-01

Molecular transduction of biological signals is understood primarily in terms of the cooperative structural transitions of protein macromolecules, providing a mechanism through which discrete local structure perturbations affect global macromolecular properties. The recognition that proteins lacking tertiary stability, commonly referred to as intrinsically disordered proteins (IDPs), mediate key signaling pathways suggests that protein structures without cooperative intramolecular interactions may also have the ability to couple local and global structure changes. Presented here are results from experiments that measured and tested the ability of disordered proteins to couple local changes in structure to global changes in structure. Using the intrinsically disordered N-terminal region of the p53 protein as an experimental model, a set of proline (PRO) and alanine (ALA) to glycine (GLY) substitution variants were designed to modulate backbone conformational propensities without introducing non-native intramolecular interactions. The hydrodynamic radius (R(h)) was used to monitor changes in global structure. Circular dichroism spectroscopy showed that the GLY substitutions decreased polyproline II (PP(II)) propensities relative to the wild type, as expected, and fluorescence methods indicated that substitution-induced changes in R(h) were not associated with folding. The experiments showed that changes in local PP(II) structure cause changes in R(h) that are variable and that depend on the intrinsic chain propensities of PRO and ALA residues, demonstrating a mechanism for coupling local and global structure changes. Molecular simulations that model our results were used to extend the analysis to other proteins and illustrate the generality of the observed PRO and alanine effects on the structures of IDPs. © 2014 Wiley Periodicals, Inc.

Alanine and proline content modulate global sensitivity to discrete perturbations in disordered proteins

PubMed Central

Perez, Romel B.; Tischer, Alexander; Auton, Matthew; Whitten, Steven T.

2014-01-01

Molecular transduction of biological signals is understood primarily in terms of the cooperative structural transitions of protein macromolecules, providing a mechanism through which discrete local structure perturbations affect global macromolecular properties. The recognition that proteins lacking tertiary stability, commonly referred to as intrinsically disordered proteins, mediate key signaling pathways suggests that protein structures without cooperative intramolecular interactions may also have the ability to couple local and global structure changes. Presented here are results from experiments that measured and tested the ability of disordered proteins to couple local changes in structure to global changes in structure. Using the intrinsically disordered N-terminal region of the p53 protein as an experimental model, a set of proline and alanine to glycine substitution variants were designed to modulate backbone conformational propensities without introducing non-native intramolecular interactions. The hydrodynamic radius (Rh) was used to monitor changes in global structure. Circular dichroism spectroscopy showed that the glycine substitutions decreased polyproline II (PPII) propensities relative to the wild type, as expected, and fluorescence methods indicated that substitution-induced changes in Rh were not associated with folding. The experiments showed that changes in local PPII structure cause changes in Rh that are variable and that depend on the intrinsic chain propensities of proline and alanine residues, demonstrating a mechanism for coupling local and global structure changes. Molecular simulations that model our results were used to extend the analysis to other proteins and illustrate the generality of the observed proline and alanine effects on the structures of intrinsically disordered proteins. PMID:25244701

Structural Evolution of Iron Antimonides from Amorphous Precursors to Crystalline Products Studied by Total Scattering Techniques.

PubMed

Bauers, Sage R; Wood, Suzannah R; Jensen, Kirsten M Ø; Blichfeld, Anders B; Iversen, Bo B; Billinge, Simon J L; Johnson, David C

2015-08-05

Homogeneous reaction precursors may be used to form several solid-state compounds inaccessible by traditional synthetic routes, but there has been little development of techniques that allow for a priori prediction of what may crystallize in a given material system. Here, the local structures of FeSbx designed precursors are determined and compared with the structural motifs of their crystalline products. X-ray total scattering and atomic pair distribution function (PDF) analysis are used to show that precursors that first nucleate a metastable FeSb3 compound share similar local structure to the product. Interestingly, precursors that directly crystallize to thermodynamically stable FeSb2 products also contain local structural motifs of the metastable phase, despite their compositional disagreement. While both crystalline phases consist of distorted FeSb6 octahedra with Sb shared between either two or three octahedra as required for stoichiometry, a corner-sharing arrangement indicative of AX3-type structures is the only motif apparent in the PDF of either precursor. Prior speculation was that local composition controlled which compounds nucleate from amorphous intermediates, with different compositions favoring different local arrangements and hence different products. This data suggests that local environments in these amorphous intermediates may not be very sensitive to overall composition. This can provide insight into potential metastable phases which may form in a material system, even with a precursor that does not crystallize to the kinetically stabilized product. Determination of local structure in homogeneous amorphous reaction intermediates from techniques such as PDF can be a valuable asset in the development of systematic methods to prepare targeted solid-state compounds from designed precursors.

Singularity in structural optimization

NASA Technical Reports Server (NTRS)

Patnaik, S. N.; Guptill, J. D.; Berke, L.

1993-01-01

The conditions under which global and local singularities may arise in structural optimization are examined. Examples of these singularities are presented, and a framework is given within which the singularities can be recognized. It is shown, in particular, that singularities can be identified through the analysis of stress-displacement relations together with compatibility conditions or the displacement-stress relations derived by the integrated force method of structural analysis. Methods of eliminating the effects of singularities are suggested and illustrated numerically.

Conformations of the HIV-1 protease: A crystal structure data set analysis.

PubMed

Palese, Luigi Leonardo

2017-11-01

The HIV protease is an important drug target for HIV/AIDS therapy, and its structure and function have been extensively investigated. This enzyme performs an essential role in viral maturation by processing specific cleavage sites in the Gag and Gag-Pol precursor polyproteins so as to release their mature forms. This 99 amino acid aspartic protease works as a homodimer, with the active site localized in a central cavity capped by two flexible flap regions. The dimer presents closed or open conformations, which are involved in the substrate binding and release. Here the results of the analysis of a HIV-1 protease data set containing 552 dimer structures are reported. Different dimensionality reduction methods have been used in order to get information from this multidimensional database. Most of the structures in the data set belong to two conformational clusters. An interesting observation that comes from the analysis of these data is that some protease sequences are localized preferentially in specific areas of the conformational landscape of this protein. Copyright © 2017 Elsevier B.V. All rights reserved.

Simultaneous Aerodynamic and Structural Design Optimization (SASDO) for a 3-D Wing

NASA Technical Reports Server (NTRS)

Gumbert, Clyde R.; Hou, Gene J.-W.; Newman, Perry A.

2001-01-01

The formulation and implementation of an optimization method called Simultaneous Aerodynamic and Structural Design Optimization (SASDO) is shown as an extension of the Simultaneous Aerodynamic Analysis and Design Optimization (SAADO) method. It is extended by the inclusion of structure element sizing parameters as design variables and Finite Element Method (FEM) analysis responses as constraints. The method aims to reduce the computational expense. incurred in performing shape and sizing optimization using state-of-the-art Computational Fluid Dynamics (CFD) flow analysis, FEM structural analysis and sensitivity analysis tools. SASDO is applied to a simple. isolated, 3-D wing in inviscid flow. Results show that the method finds the saine local optimum as a conventional optimization method with some reduction in the computational cost and without significant modifications; to the analysis tools.

Drawing simulation by static implicit analysis with the artificial damping method

NASA Astrophysics Data System (ADS)

Oide, K.; Mihara, Y.; Kobayashi, T.; Takizawa, H.; Amaishi, T.; Umezu, Y.

2016-08-01

Wrinkling during draw is typically a local instability problem. When the structural instability is localized, there will be a local transfer of strain energy from one part of the structure to neighboring parts, and global solution methods, which is typically represented by the arc length method, may not work. So, this type of problems has to be solved either dynamically or with the artificial damping. On the other hand, the essential nature of the buckling behavior can be regarded as a static problem, even though it may be possible to raise some side issues due to the inertia effect. In this study, we traced the local buckling behavior of anisotropic elasto-plastic thin shells in Numisheet2014 BM4 using the artificial damping method.

The McMillan and Newton polygons of a feedback system and the construction of root loci

NASA Technical Reports Server (NTRS)

Byrnes, C. I.; Stevens, P. K.

1982-01-01

The local behaviour of root loci around zeros and poles is investigated. This is done by relating the Newton diagrams which arise in the local analysis to the McMillan structure of the open-loop system, by means of what we shall call the McMillan polygon. This geometric construct serves to clarify the precise relationship between the McMillan structure, the principal structure, and the branching patterns of the root loci. In addition, several rules are obtained which are useful in the construction of the root loci of multivariable control systems.

Structural changes in the nano-oxide layer with annealing in specular spin valves

NASA Astrophysics Data System (ADS)

Jang, S. H.; Kim, Y. W.; Kang, T.; Kim, H. J.; Kim, K. Y.

2003-05-01

We investigated microstructural changes in a nano-oxide layer (NOL) with annealing in specular spin valves (SVs) by cross-sectional transmission electron microscopy and x-ray photoelectron spectroscopy analysis. In the SV annealed at high temperature of 400 °C, an increase in thickness and a local breakdown of the NOL were observed. This local coarsening of the NOL is closely related to the formation of Mn oxides in the oxide-rich part of the NOL through Mn diffusion. Thus, the chemical structure of the NOL changes to the structure with Mn oxide-rich content after annealing.

Towards Structural Analysis of Audio Recordings in the Presence of Musical Variations

NASA Astrophysics Data System (ADS)

Müller, Meinard; Kurth, Frank

2006-12-01

One major goal of structural analysis of an audio recording is to automatically extract the repetitive structure or, more generally, the musical form of the underlying piece of music. Recent approaches to this problem work well for music, where the repetitions largely agree with respect to instrumentation and tempo, as is typically the case for popular music. For other classes of music such as Western classical music, however, musically similar audio segments may exhibit significant variations in parameters such as dynamics, timbre, execution of note groups, modulation, articulation, and tempo progression. In this paper, we propose a robust and efficient algorithm for audio structure analysis, which allows to identify musically similar segments even in the presence of large variations in these parameters. To account for such variations, our main idea is to incorporate invariance at various levels simultaneously: we design a new type of statistical features to absorb microvariations, introduce an enhanced local distance measure to account for local variations, and describe a new strategy for structure extraction that can cope with the global variations. Our experimental results with classical and popular music show that our algorithm performs successfully even in the presence of significant musical variations.

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.

Introducing Anisotropic Minkowski Functionals and Quantitative Anisotropy Measures for Local Structure Analysis in Biomedical Imaging

PubMed Central

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

2017-01-01

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. PMID:29170580

Local atomic and magnetic structure of dilute magnetic semiconductor (Ba ,K ) (Zn,Mn ) 2As2

NASA Astrophysics Data System (ADS)

Frandsen, Benjamin A.; Gong, Zizhou; Terban, Maxwell W.; Banerjee, Soham; Chen, Bijuan; Jin, Changqing; Feygenson, Mikhail; Uemura, Yasutomo J.; Billinge, Simon J. L.

2016-09-01

We have studied the atomic and magnetic structure of the dilute ferromagnetic semiconductor system (Ba ,K )(Zn ,Mn )2As2 through atomic and magnetic pair distribution function analysis of temperature-dependent x-ray and neutron total scattering data. We detected a change in curvature of the temperature-dependent unit cell volume of the average tetragonal crystallographic structure at a temperature coinciding with the onset of ferromagnetic order. We also observed the existence of a well-defined local orthorhombic structure on a short length scale of ≲5 Å , resulting in a rather asymmetrical local environment of the Mn and As ions. Finally, the magnetic PDF revealed ferromagnetic alignment of Mn spins along the crystallographic c axis, with robust nearest-neighbor ferromagnetic correlations that exist even above the ferromagnetic ordering temperature. We discuss these results in the context of other experiments and theoretical studies on this system.

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

PubMed Central

Yoo, Jejoong; Aksimentiev, Aleksei

2013-01-01

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

Super-resolution binding activated localization microscopy through reversible change of DNA conformation.

PubMed

Szczurek, Aleksander; Birk, Udo; Knecht, Hans; Dobrucki, Jurek; Mai, Sabine; Cremer, Christoph

2018-01-01

Methods of super-resolving light microscopy (SRM) have found an exponentially growing range of applications in cell biology, including nuclear structure analyses. Recent developments have proven that Single Molecule Localization Microscopy (SMLM), a type of SRM, is particularly useful for enhanced spatial analysis of the cell nucleus due to its highest resolving capability combined with very specific fluorescent labeling. In this commentary we offer a brief review of the latest methodological development in the field of SMLM of chromatin designated DNA Structure Fluctuation Assisted Binding Activated Localization Microscopy (abbreviated as fBALM) as well as its potential future applications in biology and medicine.

Super-resolution binding activated localization microscopy through reversible change of DNA conformation

PubMed Central

Knecht, Hans; Dobrucki, Jurek; Mai, Sabine

2018-01-01

ABSTRACT Methods of super-resolving light microscopy (SRM) have found an exponentially growing range of applications in cell biology, including nuclear structure analyses. Recent developments have proven that Single Molecule Localization Microscopy (SMLM), a type of SRM, is particularly useful for enhanced spatial analysis of the cell nucleus due to its highest resolving capability combined with very specific fluorescent labeling. In this commentary we offer a brief review of the latest methodological development in the field of SMLM of chromatin designated DNA Structure Fluctuation Assisted Binding Activated Localization Microscopy (abbreviated as fBALM) as well as its potential future applications in biology and medicine. PMID:29297245

Use and traditional management of Anadenanthera colubrina (Vell.) Brenan in the semi-arid region of northeastern Brazil

PubMed Central

Monteiro, Júlio Marcelino; de Almeida, Cecília de Fátima CB Rangel; de Albuquerque, Ulysses Paulino; de Lucena, Reinaldo Farias Paiva; Florentino, Alissandra Trajano N; de Oliveira, Rodrigo Leonardo C

2006-01-01

The use and management of "angico" (Anadenanthera colubrina (Vell.) Brenan) by a rural community in northeastern Brazil was examined. By employing different techniques of data collection and population structure analysis, it was determined that this species had multiple uses within the local community (especially as timber and for other wood products), and that local management of this species is based on simple maintenance and harvesting of individuals in agroforest homegardens. The study of the population structure of this tree species indicated that management and conservation strategies must include the participation of the local community. PMID:16420708

Localized multi-scale energy and vorticity analysis. II. Finite-amplitude instability theory and validation

NASA Astrophysics Data System (ADS)

San Liang, X.; Robinson, Allan R.

2007-12-01

A novel localized finite-amplitude hydrodynamic stability analysis is established in a unified treatment for the study of real oceanic and atmospheric processes, which are in general highly nonlinear, and intermittent in space and time. We first re-state the classical definition using the multi-scale energy and vorticity analysis (MS-EVA) developed in Liang and Robinson [Liang, X.S., Robinson, A.R., 2005. Localized multiscale energy and vorticity analysis. I. Fundamentals. Dyn. Atmos. Oceans 38, 195-230], and then manipulate certain global operators to achieve the temporal and spatial localization. The key of the spatial localization is transfer-transport separation, which is made precise with the concept of perfect transfer, while relaxation of marginalization leads to the localization of time. In doing so the information of transfer lost in the averages is retrieved and an easy-to-use instability metric is obtained. The resulting metric is field-like (Eulerian), conceptually generalizing the classical formalism, a bulk notion over the whole system. In this framework, an instability has a structure, which is of particular use for open flow processes. We check the structure of baroclinic instability with the benchmark Eady model solution, and the Iceland-Faeroe Frontal (IFF) intrusion, a highly localized and nonlinear process occurring frequently in the region between Iceland and Faeroe Islands. A clear isolated baroclinic instability is identified around the intrusion, which is further found to be characterized by the transition from a spatially growing mode to a temporally growing mode. We also check the consistency of the MS-EVA dynamics with the barotropic Kuo model. An observation is that a local perturbation burst does not necessarily imply an instability: the perturbation energy could be transported from other processes occurring elsewhere. We find that our analysis yields a Kuo theorem-consistent mean-eddy interaction, which is not seen in a conventional Reynolds stress framework. Using the techniques of marginalization and localization, this work sets up an example for the generalization of certain geophysical fluid dynamics theories for more generic purposes.

Akhmediev Breather dynamics and the nonlinear modulation instability spectrum

NASA Astrophysics Data System (ADS)

Genty, Go"ry; Dias, Frederic; Kibler, Bertrand; Akhmediev, Nail; Dudley, John M.

2010-06-01

We consider various aspects of supercontinuum generation in the quasi-CW regime through analysis, numerical simulations and experiments. A new interpretation of certain features of the developing spectrum in terms of localized periodic structures known as "Akhmediev Breathers" is proposed. We also briefly consider the role of breather collisions and turbulence in the presence of higher order dispersion and show that they lead to the formation of very large amplitude localized structures that may be analogous to the infamous oceanic rogue waves.

Structural Design and Analysis of the Upper Pressure Shell Section of a Composite Crew Module

NASA Technical Reports Server (NTRS)

Sleight, David W.; Paddock, David; Jeans, Jim W.; Hudeck, John D.

2008-01-01

This paper presents the results of the structural design and analysis of the upper pressure shell section of a carbon composite demonstration structure for the Composite Crew Module (CCM) Project. The project is managed by the NASA Engineering and Safety Center with participants from eight NASA Centers, the Air Force Research Laboratory, and multiple aerospace contractors including ATK/Swales, Northrop Grumman, Lockheed Martin, Collier Research Corporation, Genesis Engineering, and Janicki Industries. The paper discusses details of the upper pressure shell section design of the CCM and presents the structural analysis results using the HyperSizer structural sizing software and the MSC Nastran finite element analysis software. The HyperSizer results showed that the controlling load case driving most of the sizing in the upper pressure shell section was the internal pressure load case. The regions around the cutouts were controlled by internal pressure and the main parachute load cases. The global finite element analysis results showed that the majority of the elements of the CCM had a positive margin of safety with the exception of a few hot spots around the cutouts. These hot spots are currently being investigated with a more detailed analysis. Local finite element models of the Low Impact Docking System (LIDS) interface ring and the forward bay gussets with greater mesh fidelity were created for local sizing and analysis. The sizing of the LIDS interface ring was driven by the drogue parachute loads, Trans-Lunar Insertion (TLI) loads, and internal pressure. The drogue parachute loads controlled the sizing of the gusset cap on the drogue gusset and TLI loads controlled the sizing of the other five gusset caps. The main parachute loads controlled the sizing of the lower ends of the gusset caps on the main parachute fittings. The results showed that the gusset web/pressure shell and gusset web/gusset cap interfaces bonded using Pi-preform joints had local hot spots in the Pi-preform termination regions. These regions require a detailed three-dimensional analysis, which is currently being performed, to accurately address the load distribution near the Pi-preform termination in the upper and lower gusset caps.

The structure of geopolymers - Theoretical studies

NASA Astrophysics Data System (ADS)

Koleżyński, Andrzej; Król, Magdalena; Żychowicz, Mikołaj

2018-07-01

This work presents the results of DFT and classical mechanics' calculations and theoretical analysis of geopolymer structure. The calculations were carried out using a bottom-up approach (from small oligomers to clusters with increasing size) for various Si:Al ratio. For all model structures after geometry optimization, respective IR spectra were simulated and compared with the experimental ones. The obtained results show that the concordance of simulated spectra with the experiment, for a given Si:Al ratio, increases with the size of the cluster and increasing local order. Moreover, the increase of the level of local disorder (structure "openness") results in significant band splitting, not observable in real geopolymers. This suggest that, in the case of real geopolymeric structures one can expect the presence of reasonably big, ordered structural fragments, analogous to zeolites.

Local structure analysis of diluted magnetic semiconductor Co and Al co-doped ZnO nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hyodo, K.; Morimoto, S.; Yamazaki, T.

2016-02-01

In this study, Co and Al ions co-doped ZnO nanoparticles (Zn(Al, Co)O NPs) were prepared by our original chemical preparation method. The obtained samples prepared by this method, were encapsulated in amorphous SiO{sub 2}. X-ray diffraction (XRD) results showed Zn(Al, Co)O NPs had a single-phase nature with hexagonal wurtzite structure. These particle sizes could be controlled to be approximately 30 nm. We investigate the effect that the increase in the carrier has on the magnetization by doping Al to Co-doped ZnO NPs. The local structures were qualitatively analyzed using X-ray absorption fine structure (XAFS) measurements.

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.

PDBFlex: exploring flexibility in protein structures

PubMed Central

Hrabe, Thomas; Li, Zhanwen; Sedova, Mayya; Rotkiewicz, Piotr; Jaroszewski, Lukasz; Godzik, Adam

2016-01-01

The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software. PMID:26615193

Microsatellite variation in Donax trunculus from the Iberian Peninsula, with particular attention to Galician estuaries (NW Spain)

NASA Astrophysics Data System (ADS)

Nantón, A.; Arias-Pérez, A.; Freire, R.; Fernández-Pérez, J.; Nóvoa, S.; Méndez, J.

2017-10-01

Genetic variation and population structure information is essential for conservation and stock management policies. The wedge clam Donax trunculus is an important fishing resource in the Iberian Peninsula and in some areas, such as the northwestern Spain, wild stocks have decreased greatly. Despite this, information is mainly from the southwestern Atlantic to the northwestern Mediterranean of the Iberian Peninsula. In this study, fifteen microsatellite loci were examined at 17 localities along the Iberian Peninsula to characterize its genetic diversity and population structure. Particular attention was paid to the northwestern Atlantic area, and to test if the pattern previously described for this species is confirmed when localities distributed across the Atlantic coast are included and different microsatellite markers are used. All localities displayed similar allelic richness values and heterozygosity levels but when genetic diversity levels were compared among groups of localities, tests were significant and samples from the northwestern area (Galicia) showed the lowest values. The analysis of population structure indicated that localities from the Atlantic coast are genetically homogeneous although some samples showed significant pairwise Fst values. These values were low and Bayesian analysis of genetic differentiation did not show a consistent structure along the Atlantic coast of the Iberian Peninsula. However, Atlantic samples were genetically different from those located in Mediterranean coast, which may be explained by the existence of the Almeria-Oran front. Moreover, Fuengirola, locality situated in the Alboran Sea between the Strait of Gibraltar and Mediterranean Sea, showed significant differences from all remaining localities included in the study. Overall, the data showed the existence of genetic homogeneity along the Atlantic coast of the Iberian Peninsula and support the three management units (Atlantic Ocean, the Alboran Sea and the northwestern Mediterranean) previously described in this species. Reduced diversity in the northwestern Spain samples could be related to the exploitation of this resource.

Inferring coarse-grain histone-DNA interaction potentials from high-resolution structures of the nucleosome

NASA Astrophysics Data System (ADS)

Meyer, Sam; Everaers, Ralf

2015-02-01

The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unknown despite increasing structural knowledge of the complex. In this paper, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We applied the procedure to a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at histone-DNA contact sites, the DNA base-pairs are shifted outwards locally, consistent with locally repulsive forces exerted by the histones. The second step shows that the various force profiles of the structures under analysis derive locally from a unique, sequence-independent, quadratic repulsive force-field, while the sequence preferences are entirely due to internal DNA mechanics. We have thus obtained the first knowledge-derived nanoscale interaction potential for histone-DNA in the nucleosome. The conformations obtained by relaxation of nucleosomal DNA with high-affinity sequences in this potential accurately reproduce the experimental values of binding preferences. Finally we address the more generic binding mechanisms relevant to the 80% genomic sequences incorporated in nucleosomes, by computing the conformation of nucleosomal DNA with sequence-averaged properties. This conformation differs from those found in crystals, and the analysis suggests that repulsive histone forces are related to local stretch tension in nucleosomal DNA, mostly between adjacent contact points. This tension could play a role in the stability of the complex.

New insight into the properties of proton conducting oxides from neutron total scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Proffen, Thomas E; Kim, Hyunjeong; Malavasi, Lorenzo

In recent years there has been a growing interest in searching for new proton conducting materials that could be successfully used in medium temperature solid oxide fuel cells (SOFC). In particular, proton conducting oxides have been the subject of a massive research activity. Among the most promising oxide the acceptor doped cerates appears to be those most appealing in view of practical applications. A relevant aspect of these materials is the investigation of the local distortion of the structure arising from water incorporation. This kind of study is of great help in defining how the structure changes in order tomore » accommodate the proton which is usually thought to enter the structure in form of hydroxyl group where the oxygen vacancy results from the acceptor doping on the Ce site. Atomistic simulation work confirmed that the preferential location of dopant ions is on the Ce site. To the best of our knowledge the only experimental work addressing the role of dopant and water incorporation on the local structure of V-doped cerates is a X-ray absorption spectroscopy (XAS) work carried out by Longo and coworkers at the Y K-edge. The main conclusion of that work was the observation that Y-doping induces a distortion of the parent BaCe0{sub 3} structure resulting in a significantly distorted Y local environment. However, local structure information derived from XAS study does not provide a direct structural information and depends strongly upon the model used to calcualte theoretical {chi}(k) which is not unique. Moreover, the XAS analysis usually provide significant information only up to the second shell. As a consequence, a more reliable and useful technique to investigate the local arrangement in these proton conducting oxides appears to be the Pair Distribution Function (PDF) analysis derived from total neutron scattering measurements. In the present work we investigated the pure BaCeO{sub 3} and the acceptor doped BaCe{sub 0.90}Y{sub 0.10}O{sub 2.85} compounds. In both cases the samples have been measured at room temperature and after being exposed to dry and wet air (humidification attained through bubbling air in D{sub 2}O). Aim of this work is to look at the effect of Y-doping and water doping on the local structure of the above mentioned samples.« less

Best Manufacturing Practices Survey Conducted at Litton Data Systems Division, Van Nuys, California

DTIC Science & Technology

1988-10-01

Hardware and Software ................................ 10 DESIGN RELEASE Engineering Change Order Processing and Analysis...structured using bridges to isolate local traffic. Long term plans call for a wide-band network. ENGINEERING CHANGE ORDER PROCESSING AND ANALYSIS

Characterizing structural transitions using localized free energy landscape analysis.

PubMed

Banavali, Nilesh K; Mackerell, Alexander D

2009-01-01

Structural changes in molecules are frequently observed during biological processes like replication, transcription and translation. These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes. Molecular dynamics simulations combined with a variation of the Weighted Histogram Analysis Method for potential of mean force determination are applied to characterize localized structural changes for the test case of cytosine (underlined) base flipping in a GTCAGCGCATGG DNA duplex. Free energy landscapes for backbone torsion and sugar pucker degrees of freedom in the DNA are used to understand their behavior in response to the base flipping perturbation. By simplifying the base flipping structural change into a two-state model, a free energy difference of upto 14 kcal/mol can be attributed to the flipped state relative to the stacked Watson-Crick base paired state. This two-state classification allows precise evaluation of the effect of base flipping on local backbone degrees of freedom. The calculated free energy landscapes of individual backbone and sugar degrees of freedom expectedly show the greatest change in the vicinity of the flipping base itself, but specific delocalized effects can be discerned upto four nucleotide positions away in both 5' and 3' directions. Free energy landscape analysis thus provides a quantitative method to pinpoint the determinants of structural change on the atomic scale and also delineate the extent of propagation of the perturbation along the molecule. In addition to nucleic acids, this methodology is anticipated to be useful for studying conformational changes in all macromolecules, including carbohydrates, lipids, and proteins.

Analyzing the Magnetopause Internal Structure: New Possibilities Offered by MMS Tested in a Case Study

NASA Astrophysics Data System (ADS)

Rezeau, L.; Belmont, G.; Manuzzo, R.; Aunai, N.; Dargent, J.

2018-01-01

We explore the structure of the magnetopause using a crossing observed by the Magnetospheric Multiscale (MMS) spacecraft on 16 October 2015. Several methods (minimum variance analysis, BV method, and constant velocity analysis) are first applied to compute the normal to the magnetopause considered as a whole. The different results obtained are not identical, and we show that the whole boundary is not stationary and not planar, so that basic assumptions of these methods are not well satisfied. We then analyze more finely the internal structure for investigating the departures from planarity. Using the basic mathematical definition of what is a one-dimensional physical problem, we introduce a new single spacecraft method, called LNA (local normal analysis) for determining the varying normal, and we compare the results so obtained with those coming from the multispacecraft minimum directional derivative (MDD) tool developed by Shi et al. (2005). This last method gives the dimensionality of the magnetic variations from multipoint measurements and also allows estimating the direction of the local normal when the variations are locally 1-D. This study shows that the magnetopause does include approximate one-dimensional substructures but also two- and three-dimensional structures. It also shows that the dimensionality of the magnetic variations can differ from the variations of other fields so that, at some places, the magnetic field can have a 1-D structure although all the plasma variations do not verify the properties of a global one-dimensional problem. A generalization of the MDD tool is proposed.

Numerical Characterization of a Composite Bonded Wing-Box

NASA Technical Reports Server (NTRS)

Smeltzer, Stanley S., III; Lovejoy, Andrew E.; Satyanarayana, Arunkumar

2008-01-01

The development of composite wing structures has focused on the use of mechanical fasteners to join heavily-loaded areas, while bonded joints have been used only for select locations. The focus of this paper is the examination of the adhesive layer in a generic bonded wing box that represents a "fastenerless" or unitized structure in order to characterize the general behavior and failure mechanisms. A global/local approach was applied to study the response of the adhesive layer using a global shell model and a local shell/solid model. The wing box was analyzed under load to represent a high-g up-bending condition such that the strains in the composite sandwich face sheets are comparable to an expected design allowable. The global/local analysis indicates that at these wing load levels the strains in the adhesive layer are well within the adhesive's elastic region, such that yielding would not be expected in the adhesive layer. The global/local methodology appears to be a promising approach to evaluate the structural integrity of the adhesively bonded structures.

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

PubMed Central

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

2012-01-01

The constant increase in the number of solved protein structures is of great help in understanding the basic principles behind protein folding and evolution. 3-D structural knowledge is valuable in designing and developing methods for comparison, modelling and prediction of protein structures. These approaches for structure analysis can be directly implicated in studying protein function and for drug design. The backbone of a protein structure favours certain local conformations which include α-helices, β-strands and turns. Libraries of limited number of local conformations (Structural Alphabets) were developed in the past to obtain a useful categorization of backbone conformation. Protein Block (PB) is one such Structural Alphabet that gave a reasonable structure approximation of 0.42 Å. In this study, we use PB description of local structures to analyse conformations that are preferred sites for structural variations and insertions, among group of related folds. This knowledge can be utilized in improving tools for structure comparison that work by analysing local structure similarities. Conformational differences between homologous proteins are known to occur often in the regions comprising turns and loops. Interestingly, these differences are found to have specific preferences depending upon the structural classes of proteins. Such class-specific preferences are mainly seen in the all-β class with changes involving short helical conformations and hairpin turns. A test carried out on a benchmark dataset also indicates that the use of knowledge on the class specific variations can improve the performance of a PB based structure comparison approach. The preference for the indel sites also seem to be confined to a few backbone conformations involving β-turns and helix C-caps. These are mainly associated with short loops joining the regular secondary structures that mediate a reversal in the chain direction. Rare β-turns of type I’ and II’ are also identified as preferred sites for insertions. PMID:22745680

The devil is in the detail: brain dynamics in preparation for a global-local task.

PubMed

Leaver, Echo E; Low, Kathy A; DiVacri, Assunta; Merla, Arcangelo; Fabiani, Monica; Gratton, Gabriele

2015-08-01

When analyzing visual scenes, it is sometimes important to determine the relevant "grain" size. Attention control mechanisms may help direct our processing to the intended grain size. Here we used the event-related optical signal, a method possessing high temporal and spatial resolution, to examine the involvement of brain structures within the dorsal attention network (DAN) and the visual processing network (VPN) in preparation for the appropriate level of analysis. Behavioral data indicate that the small features of a hierarchical stimulus (local condition) are more difficult to process than the large features (global condition). Consistent with this finding, cues predicting a local trial were associated with greater DAN activation. This activity was bilateral but more pronounced in the left hemisphere, where it showed a frontal-to-parietal progression over time. Furthermore, the amount of DAN activation, especially in the left hemisphere and in parietal regions, was predictive of subsequent performance. Although local cues elicited left-lateralized DAN activity, no preponderantly right activity was observed for global cues; however, the data indicated an interaction between level of analysis (local vs. global) and hemisphere in VPN. They further showed that local processing involves structures in the ventral VPN, whereas global processing involves structures in the dorsal VPN. These results indicate that in our study preparation for analyzing different size features is an asymmetric process, in which greater preparation is required to focus on small rather than large features, perhaps because of their lesser salience. This preparation involves the same DAN used for other attention control operations.

Improving Distributed Diagnosis Through Structural Model Decomposition

NASA Technical Reports Server (NTRS)

Bregon, Anibal; Daigle, Matthew John; Roychoudhury, Indranil; Biswas, Gautam; Koutsoukos, Xenofon; Pulido, Belarmino

2011-01-01

Complex engineering systems require efficient fault diagnosis methodologies, but centralized approaches do not scale well, and this motivates the development of distributed solutions. This work presents an event-based approach for distributed diagnosis of abrupt parametric faults in continuous systems, by using the structural model decomposition capabilities provided by Possible Conflicts. We develop a distributed diagnosis algorithm that uses residuals computed by extending Possible Conflicts to build local event-based diagnosers based on global diagnosability analysis. The proposed approach is applied to a multitank system, and results demonstrate an improvement in the design of local diagnosers. Since local diagnosers use only a subset of the residuals, and use subsystem models to compute residuals (instead of the global system model), the local diagnosers are more efficient than previously developed distributed approaches.

46 CFR 54.30-15 - Requirement for analysis and computation.

Code of Federal Regulations, 2010 CFR

2010-10-01

... PRESSURE VESSELS Mechanical Stress Relief § 54.30-15 Requirement for analysis and computation. (a) A stress... mechanical stress relief process. This analysis should include consideration of the local stresses in way of saddles or other supporting structure and additional bending stresses due to the weight of the...

46 CFR 54.30-15 - Requirement for analysis and computation.

Code of Federal Regulations, 2012 CFR

2012-10-01

... PRESSURE VESSELS Mechanical Stress Relief § 54.30-15 Requirement for analysis and computation. (a) A stress... mechanical stress relief process. This analysis should include consideration of the local stresses in way of saddles or other supporting structure and additional bending stresses due to the weight of the...

46 CFR 54.30-15 - Requirement for analysis and computation.

Code of Federal Regulations, 2014 CFR

2014-10-01

... PRESSURE VESSELS Mechanical Stress Relief § 54.30-15 Requirement for analysis and computation. (a) A stress... mechanical stress relief process. This analysis should include consideration of the local stresses in way of saddles or other supporting structure and additional bending stresses due to the weight of the...

46 CFR 54.30-15 - Requirement for analysis and computation.

Code of Federal Regulations, 2013 CFR

2013-10-01

... PRESSURE VESSELS Mechanical Stress Relief § 54.30-15 Requirement for analysis and computation. (a) A stress... mechanical stress relief process. This analysis should include consideration of the local stresses in way of saddles or other supporting structure and additional bending stresses due to the weight of the...

46 CFR 54.30-15 - Requirement for analysis and computation.

Code of Federal Regulations, 2011 CFR

2011-10-01

... PRESSURE VESSELS Mechanical Stress Relief § 54.30-15 Requirement for analysis and computation. (a) A stress... mechanical stress relief process. This analysis should include consideration of the local stresses in way of saddles or other supporting structure and additional bending stresses due to the weight of the...

Development of pair distribution function analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vondreele, R.; Billinge, S.; Kwei, G.

1996-09-01

This is the final report of a 3-year LDRD project at LANL. It has become more and more evident that structural coherence in the CuO{sub 2} planes of high-{Tc} superconducting materials over some intermediate length scale (nm range) is important to superconductivity. In recent years, the pair distribution function (PDF) analysis of powder diffraction data has been developed for extracting structural information on these length scales. This project sought to expand and develop this technique, use it to analyze neutron powder diffraction data, and apply it to problems. In particular, interest is in the area of high-{Tc} superconductors, although wemore » planned to extend the study to the closely related perovskite ferroelectric materials andother materials where the local structure affects the properties where detailed knowledge of the local and intermediate range structure is important. In addition, we planned to carry out single crystal experiments to look for diffuse scattering. This information augments the information from the PDF.« less

Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation.

PubMed

Shinada, Hiroshi; Yamamoto, Toshio; Yamamoto, Eiji; Hori, Kiyosumi; Yonemaru, Junichi; Matsuba, Shuichi; Fujino, Kenji

2014-04-01

The rice local population was clearly differentiated into six groups over the 100-year history of rice breeding programs in the northern limit of rice cultivation over the world. Genetic improvements in plant breeding programs in local regions have led to the development of new cultivars with specific agronomic traits under environmental conditions and generated the unique genetic structures of local populations. Understanding historical changes in genome structures and phenotypic characteristics within local populations may be useful for identifying profitable genes and/or genetic resources and the creation of new gene combinations in plant breeding programs. In the present study, historical changes were elucidated in genome structures and phenotypic characteristics during 100-year rice breeding programs in Hokkaido, the northern limit of rice cultivation in the world. We selected 63 rice cultivars to represent the historical diversity of this local population from landraces to the current breeding lines. The results of the phylogenetic analysis demonstrated that these cultivars clearly differentiated into six groups over the history of rice breeding programs. Significant differences among these groups were detected in five of the seven traits, indicating that the differentiation of the Hokkaido rice population into these groups was correlated with these phenotypic changes. These results demonstrated that breeding practices in Hokkaido have created new genetic structures for adaptability to specific environmental conditions and breeding objectives. They also provide a new strategy for rice breeding programs in which such unique genes in local populations in the world can explore the genetic potentials of the local populations.

Synthesis and Characterization of LaTiO2N

NASA Astrophysics Data System (ADS)

Rugen, Evan E.

Photocatalysts offer an excellent opportunity to shift the global energy landscape from a fossil fuel-dependent paradigm to sustainable and carbon-neutral solar fuels. Oxynitride materials such as LaTiO2N are potential photocatalysts for the water splitting reaction due to their high oxidative stability and their narrow band gaps, which are suitable for visible light absorption. However, facile synthetic routes to metal oxynitrides with controlled morphologies are rare, and the local structures of these materials are under-characterized. Ultrasonic spray synthesis (USS) offers a facile method toward complex metal oxides which can potentially be converted to oxynitrides with preservation of the microsphere structures that typify the products from such aerosol routes. Here, La-Ti-O microspheres were facilely produced by USS and converted by ammonolysis to LaTiO2N microspheres with porous shells and hollow interiors. This particle architecture is accounted for by coupling suitable combustion chemistry with the aerosol technique, producing precursor particles where the La3+ and Ti4+ are well-mixed at small length scales; this feature enables preservation of the microsphere morphology during nitridation despite the crystallographic changes that occur. The LaTiO2N microspheres are comparable oxygen evolving photocatalysts to samples produced by conventional solid state methods. Pair distribution function (PDF) analysis is a local probe designed to examine the structure of disordered crystalline materials, and is an ideal technique for characterizing the ordering of anions in oxynitrides. Preliminary studies using PDF analysis to determine the presence of anion ordering and local structure in LaTiO2N produced by solid state methods are presented here. Future experiments are proposed that will grant detailed insight into the factors driving the degree of anion ordering in these types of materials. These results demonstrate the utility of USS as a facile, potentially scalable route to complex photocatalytic materials and their precursors, and the feasibility of PDF analysis for the determination of local structures in complex oxynitrides.

Microscopic structural descriptor of liquid water

NASA Astrophysics Data System (ADS)

Shi, Rui; Tanaka, Hajime

2018-03-01

The microscopic structure of liquid water has been believed to be the key to the understanding of the unique properties of this extremely important substance. Many structural descriptors have been developed for revealing local structural order in water, but their properties are still not well understood. The essential difficulty comes from structural fluctuations due to thermal noise, which are intrinsic to the liquid state. The most popular and widely used descriptors are the local structure index (LSI) and d5. Recently, Russo and Tanaka [Nat. Commun. 3, 3556 (2014)] introduced a new descriptor ζ which measures the translational order between the first and second shells considering hydrogen bonding (H-bonding) in the first shell. In this work, we compare the performance of these three structural descriptors for a popular water model known as TIP5P water. We show that local structural ordering can be properly captured only by the structural descriptor ζ, but not by the other two descriptors particularly at a high temperature, where thermal noise effects are severe. The key difference of ζ from LSI and d5 is that only ζ considers H-bonding which is crucial to detect high translational and tetrahedral order of not only oxygen but also hydrogen atoms. The importance of H-bonding is very natural, considering the fact that the locally favored structures are stabilized by energy gain due to the formation of four hydrogen bonds between the central water molecule and its neighboring ones in the first shell. Our analysis of the water structure by using ζ strongly supports the two-state model of water: water is a dynamic mixture of locally favored (ordered) and normal-liquid (disordered) structures. This work demonstrates the importance of H-bonding in the characterization of water's structures and provides a useful structural descriptor for water-type tetrahedral liquids to study their structure and dynamics.

The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.

PubMed

Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

2015-11-01

The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ψ and/or φ. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(α) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations. © 2015 Wiley Periodicals, Inc.

Identification of Germ Plasm-Associated Transcripts by Microarray Analysis of Xenopus Vegetal Cortex RNA

PubMed Central

Cuykendall, Tawny N.; Houston, Douglas W.

2011-01-01

RNA localization is a common mechanism for regulating cell structure and function. Localized RNAs in Xenopus oocytes are critical for early development, including germline specification by the germ plasm. Despite the importance of these localized RNAs, only approximately 25 have been identified and fewer are functionally characterized. Using microarrays, we identified a large set of localized RNAs from the vegetal cortex. Overall, our results indicate a minimum of 275 localized RNAs in oocytes, or 2–3% of maternal transcripts, which are in general agreement with previous findings. We further validated vegetal localization for 24 candidates and further characterized three genes expressed in the germ plasm. We identified novel germ plasm expression for reticulon 3.1, exd2 (a novel exonuclease-domain encoding gene), and a putative noncoding RNA. Further analysis of these and other localized RNAs will likely identify new functions of germ plasm and facilitate the identification of cis-acting RNA localization elements. PMID:20503379

Order-disorder effects in structure and color relation of photonic-crystal-type nanostructures in butterfly wing scales.

PubMed

Márk, Géza I; Vértesy, Zofia; Kertész, Krisztián; Bálint, Zsolt; Biró, László P

2009-11-01

In order to study local and global order in butterfly wing scales possessing structural colors, we have developed a direct space algorithm, based on averaging the local environment of the repetitive units building up the structure. The method provides the statistical distribution of the local environments, including the histogram of the nearest-neighbor distance and the number of nearest neighbors. We have analyzed how the different kinds of randomness present in the direct space structure influence the reciprocal space structure. It was found that the Fourier method is useful in the case of a structure randomly deviating from an ordered lattice. The direct space averaging method remains applicable even for structures lacking long-range order. Based on the first Born approximation, a link is established between the reciprocal space image and the optical reflectance spectrum. Results calculated within this framework agree well with measured reflectance spectra because of the small width and moderate refractive index contrast of butterfly scales. By the analysis of the wing scales of Cyanophrys remus and Albulina metallica butterflies, we tested the methods for structures having long-range order, medium-range order, and short-range order.

Order-disorder effects in structure and color relation of photonic-crystal-type nanostructures in butterfly wing scales

NASA Astrophysics Data System (ADS)

Márk, Géza I.; Vértesy, Zofia; Kertész, Krisztián; Bálint, Zsolt; Biró, László P.

2009-11-01

In order to study local and global order in butterfly wing scales possessing structural colors, we have developed a direct space algorithm, based on averaging the local environment of the repetitive units building up the structure. The method provides the statistical distribution of the local environments, including the histogram of the nearest-neighbor distance and the number of nearest neighbors. We have analyzed how the different kinds of randomness present in the direct space structure influence the reciprocal space structure. It was found that the Fourier method is useful in the case of a structure randomly deviating from an ordered lattice. The direct space averaging method remains applicable even for structures lacking long-range order. Based on the first Born approximation, a link is established between the reciprocal space image and the optical reflectance spectrum. Results calculated within this framework agree well with measured reflectance spectra because of the small width and moderate refractive index contrast of butterfly scales. By the analysis of the wing scales of Cyanophrys remus and Albulina metallica butterflies, we tested the methods for structures having long-range order, medium-range order, and short-range order.

Computation material science of structural-phase transformation in casting aluminium alloys

NASA Astrophysics Data System (ADS)

Golod, V. M.; Dobosh, L. Yu

2017-04-01

Successive stages of computer simulation the formation of the casting microstructure under non-equilibrium conditions of crystallization of multicomponent aluminum alloys are presented. On the basis of computer thermodynamics and heat transfer during solidification of macroscale shaped castings are specified the boundary conditions of local heat exchange at mesoscale modeling of non-equilibrium formation the solid phase and of the component redistribution between phases during coalescence of secondary dendrite branches. Computer analysis of structural - phase transitions based on the principle of additive physico-chemical effect of the alloy components in the process of diffusional - capillary morphological evolution of the dendrite structure and the o of local dendrite heterogeneity which stochastic nature and extent are revealed under metallographic study and modeling by the Monte Carlo method. The integrated computational materials science tools at researches of alloys are focused and implemented on analysis the multiple-factor system of casting processes and prediction of casting microstructure.

Numerical simulation of actuation behavior of active fiber composites in helicopter rotor blade application

NASA Astrophysics Data System (ADS)

Paik, Seung Hoon; Kim, Ji Yeon; Shin, Sang Joon; Kim, Seung Jo

2004-07-01

Smart structures incorporating active materials have been designed and analyzed to improve aerospace vehicle performance and its vibration/noise characteristics. Helicopter integral blade actuation is one example of those efforts using embedded anisotropic piezoelectric actuators. To design and analyze such integrally-actuated blades, beam approach based on homogenization methodology has been traditionally used. Using this approach, the global behavior of the structures is predicted in an averaged sense. However, this approach has intrinsic limitations in describing the local behaviors in the level of the constituents. For example, the failure analysis of the individual active fibers requires the knowledge of the local behaviors. Microscopic approach for the analysis of integrally-actuated structures is established in this paper. Piezoelectric fibers and matrices are modeled individually and finite element method using three-dimensional solid elements is adopted. Due to huge size of the resulting finite element meshes, high performance computing technology is required in its solution process. The present methodology is quoted as Direct Numerical Simulation (DNS) of the smart structure. As an initial validation effort, present analytical results are correlated with the experiments from a small-scaled integrally-actuated blade, Active Twist Rotor (ATR). Through DNS, local stress distribution around the interface of fiber and matrix can be analyzed.

Understanding the Formation of Kinetically Stable Compounds and the Development of Thin Film Pair Distribution Function Analysis

NASA Astrophysics Data System (ADS)

Wood, Suzannah Rebecca

Navigating the synthesis landscape poses many challenges when developing novel solid state materials. Advancements in both synthesis and characterization are necessary to facilitate the targeting of specific materials. This dissertation discusses the formation of chalcogenide heterostructures and their properties in the first part and the development of thin film pair distribution function analysis (tfPDF) in the second part. The heterostructures were formed by the self-assembly of designed precursors deposited by physical vapor deposition in a modulated elemental reactants approach, which provides the control and predictability to synthesis. Specifically, a series of (BiSe)1+delta(TiSe2) n, where n = 2,3,&4, were synthesized to explore the extent of charge transfer from the BiSe to TiSe2 layers. To further explore the role Bi plays in charge donation, a family of structurally similar compounds, (Bix Sn1-xSe)1+deltaTiSe2, where 0≥x≥1, were synthesized and characterized. Electrical measurements show doping efficiency decreases as x increases, correlated with the structural distortion and the formation of periodic antiphase boundaries containing Bi-Bi pairs. The first heterostructures composed of three unique structural types were synthesized and Bi2Se3 layer thickness was used to tune electrical properties and further explore charge transfer. To better understand the potential energy landscape on which these kinetically stable compounds exist, two investigations were undertaken. The first was a study of the formation and subsequent decomposition of [(BiSe)1+delta]n(TiSe2)n compounds, where n= 2&3, the second an investigation of precursor structure for thermodynamically stable FeSb2 and kinetically stable FeSb3. The second section describes the development of thin film pair distribution function analysis, a technique in which total scattering data for pair distribution function (PDF) analysis is obtained from thin films, suitable for local structure analysis. This study illustrates how analysis of the local structure in amorphous precursor films can help to understand the crystallization processes of metastable phases and enables a range of new local structure studies of thin films. tfPDF was then demonstrated on In-Ga-O film materials and compared to traditional powder PDF analysis. This highlights differences between the products, and the utility of tfPDF to determined structural features of amorphous materials. This dissertation includes previously published and unpublished co-authored materials.

Blind identification of full-field vibration modes of output-only structures from uniformly-sampled, possibly temporally-aliased (sub-Nyquist), video measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Yongchao; Dorn, Charles; Mancini, Tyler

Enhancing the spatial and temporal resolution of vibration measurements and modal analysis could significantly benefit dynamic modelling, analysis, and health monitoring of structures. For example, spatially high-density mode shapes are critical for accurate vibration-based damage localization. In experimental or operational modal analysis, higher (frequency) modes, which may be outside the frequency range of the measurement, contain local structural features that can improve damage localization as well as the construction and updating of the modal-based dynamic model of the structure. In general, the resolution of vibration measurements can be increased by enhanced hardware. Traditional vibration measurement sensors such as accelerometers havemore » high-frequency sampling capacity; however, they are discrete point-wise sensors only providing sparse, low spatial sensing resolution measurements, while dense deployment to achieve high spatial resolution is expensive and results in the mass-loading effect and modification of structure's surface. Non-contact measurement methods such as scanning laser vibrometers provide high spatial and temporal resolution sensing capacity; however, they make measurements sequentially that requires considerable acquisition time. As an alternative non-contact method, digital video cameras are relatively low-cost, agile, and provide high spatial resolution, simultaneous, measurements. Combined with vision based algorithms (e.g., image correlation or template matching, optical flow, etc.), video camera based measurements have been successfully used for experimental and operational vibration measurement and subsequent modal analysis. However, the sampling frequency of most affordable digital cameras is limited to 30–60 Hz, while high-speed cameras for higher frequency vibration measurements are extremely costly. This work develops a computational algorithm capable of performing vibration measurement at a uniform sampling frequency lower than what is required by the Shannon-Nyquist sampling theorem for output-only modal analysis. In particular, the spatio-temporal uncoupling property of the modal expansion of structural vibration responses enables a direct modal decoupling of the temporally-aliased vibration measurements by existing output-only modal analysis methods, yielding (full-field) mode shapes estimation directly. Then the signal aliasing properties in modal analysis is exploited to estimate the modal frequencies and damping ratios. Furthermore, the proposed method is validated by laboratory experiments where output-only modal identification is conducted on temporally-aliased acceleration responses and particularly the temporally-aliased video measurements of bench-scale structures, including a three-story building structure and a cantilever beam.« less

Blind identification of full-field vibration modes of output-only structures from uniformly-sampled, possibly temporally-aliased (sub-Nyquist), video measurements

DOE PAGES

Yang, Yongchao; Dorn, Charles; Mancini, Tyler; ...

2016-12-05

Enhancing the spatial and temporal resolution of vibration measurements and modal analysis could significantly benefit dynamic modelling, analysis, and health monitoring of structures. For example, spatially high-density mode shapes are critical for accurate vibration-based damage localization. In experimental or operational modal analysis, higher (frequency) modes, which may be outside the frequency range of the measurement, contain local structural features that can improve damage localization as well as the construction and updating of the modal-based dynamic model of the structure. In general, the resolution of vibration measurements can be increased by enhanced hardware. Traditional vibration measurement sensors such as accelerometers havemore » high-frequency sampling capacity; however, they are discrete point-wise sensors only providing sparse, low spatial sensing resolution measurements, while dense deployment to achieve high spatial resolution is expensive and results in the mass-loading effect and modification of structure's surface. Non-contact measurement methods such as scanning laser vibrometers provide high spatial and temporal resolution sensing capacity; however, they make measurements sequentially that requires considerable acquisition time. As an alternative non-contact method, digital video cameras are relatively low-cost, agile, and provide high spatial resolution, simultaneous, measurements. Combined with vision based algorithms (e.g., image correlation or template matching, optical flow, etc.), video camera based measurements have been successfully used for experimental and operational vibration measurement and subsequent modal analysis. However, the sampling frequency of most affordable digital cameras is limited to 30–60 Hz, while high-speed cameras for higher frequency vibration measurements are extremely costly. This work develops a computational algorithm capable of performing vibration measurement at a uniform sampling frequency lower than what is required by the Shannon-Nyquist sampling theorem for output-only modal analysis. In particular, the spatio-temporal uncoupling property of the modal expansion of structural vibration responses enables a direct modal decoupling of the temporally-aliased vibration measurements by existing output-only modal analysis methods, yielding (full-field) mode shapes estimation directly. Then the signal aliasing properties in modal analysis is exploited to estimate the modal frequencies and damping ratios. Furthermore, the proposed method is validated by laboratory experiments where output-only modal identification is conducted on temporally-aliased acceleration responses and particularly the temporally-aliased video measurements of bench-scale structures, including a three-story building structure and a cantilever beam.« less

Structural characterization of vanadium oxide catalysts supported on nanostructured silica SBA-15 using X-ray absorption spectroscopy

PubMed Central

2010-01-01

The local structure of vanadium oxide supported on nanostructured SiO2 (VxOy/SBA-15) was investigated by in situ X-ray absorption spectroscopy (XAS). Because the number of potential parameters in XAS data analysis often exceeds the number of "independent" parameters, evaluating the reliability and significance of a particular fitting procedure is mandatory. The number of independent parameters (Nyquist) may not be sufficient. Hence, in addition to the number of independent parameters, a novel approach to evaluate the significance of structural fitting parameters in XAS data analysis is introduced. Three samples with different V loadings (i.e. 2.7 wt %, 5.4 wt %, and 10.8 wt %) were employed. Thermal treatment in air at 623 K resulted in characteristic structural changes of the V oxide species. Independent of the V loading, the local structure around V centers in dehydrated VxOy/SBA-15 corresponded to an ordered arrangement of adjacent V2O7 units. Moreover, the V2O7 units were found to persist under selective oxidation reaction conditions. PMID:20181222

Structural characterization of vanadium oxide catalysts supported on nanostructured silica SBA-15 using X-ray absorption spectroscopy.

PubMed

Walter, Anke; Herbert, Rita; Hess, Christian; Ressler, Thorsten

2010-02-11

The local structure of vanadium oxide supported on nanostructured SiO2 (VxOy/SBA-15) was investigated by in situ X-ray absorption spectroscopy (XAS). Because the number of potential parameters in XAS data analysis often exceeds the number of "independent" parameters, evaluating the reliability and significance of a particular fitting procedure is mandatory. The number of independent parameters (Nyquist) may not be sufficient. Hence, in addition to the number of independent parameters, a novel approach to evaluate the significance of structural fitting parameters in XAS data analysis is introduced. Three samples with different V loadings (i.e. 2.7 wt %, 5.4 wt %, and 10.8 wt %) were employed. Thermal treatment in air at 623 K resulted in characteristic structural changes of the V oxide species. Independent of the V loading, the local structure around V centers in dehydrated VxOy/SBA-15 corresponded to an ordered arrangement of adjacent V2O7 units. Moreover, the V2O7 units were found to persist under selective oxidation reaction conditions.

An intrinsic representation of atomic structure: From clusters to periodic systems

NASA Astrophysics Data System (ADS)

Li, Xiao-Tian; Xu, Shao-Gang; Yang, Xiao-Bao; Zhao, Yu-Jun

2017-10-01

We have improved our distance matrix and eigen-subspace projection function (EPF) [X.-T. Li et al., J. Chem. Phys. 146, 154108 (2017)] to describe the atomic structure for periodic systems. Depicting the local structure of an atom, the EPF turns out to be invariant with respect to the choices of the unit cell and coordinate frame, leading to an intrinsic representation of the crystal with a set of EPFs of the nontrivial atoms. The difference of EPFs reveals the difference of atoms in local structure, while the accumulated difference between two sets of EPFs can be taken as the distance between configurations. Exemplified with the cases of carbon allotropes and boron sheets, our EPF approach shows exceptional rationality and efficiency to distinguish the atomic structures, which is crucial in structure recognition, comparison, and analysis.

An intrinsic representation of atomic structure: From clusters to periodic systems.

PubMed

Li, Xiao-Tian; Xu, Shao-Gang; Yang, Xiao-Bao; Zhao, Yu-Jun

2017-10-14

We have improved our distance matrix and eigen-subspace projection function (EPF) [X.-T. Li et al., J. Chem. Phys. 146, 154108 (2017)] to describe the atomic structure for periodic systems. Depicting the local structure of an atom, the EPF turns out to be invariant with respect to the choices of the unit cell and coordinate frame, leading to an intrinsic representation of the crystal with a set of EPFs of the nontrivial atoms. The difference of EPFs reveals the difference of atoms in local structure, while the accumulated difference between two sets of EPFs can be taken as the distance between configurations. Exemplified with the cases of carbon allotropes and boron sheets, our EPF approach shows exceptional rationality and efficiency to distinguish the atomic structures, which is crucial in structure recognition, comparison, and analysis.

Automatic quantification of morphological features for hepatic trabeculae analysis in stained liver specimens

PubMed Central

Ishikawa, Masahiro; Murakami, Yuri; Ahi, Sercan Taha; Yamaguchi, Masahiro; Kobayashi, Naoki; Kiyuna, Tomoharu; Yamashita, Yoshiko; Saito, Akira; Abe, Tokiya; Hashiguchi, Akinori; Sakamoto, Michiie

2016-01-01

Abstract. This paper proposes a digital image analysis method to support quantitative pathology by automatically segmenting the hepatocyte structure and quantifying its morphological features. To structurally analyze histopathological hepatic images, we isolate the trabeculae by extracting the sinusoids, fat droplets, and stromata. We then measure the morphological features of the extracted trabeculae, divide the image into cords, and calculate the feature values of the local cords. We propose a method of calculating the nuclear–cytoplasmic ratio, nuclear density, and number of layers using the local cords. Furthermore, we evaluate the effectiveness of the proposed method using surgical specimens. The proposed method was found to be an effective method for the quantification of the Edmondson grade. PMID:27335894

Granular metamaterials for vibration mitigation

NASA Astrophysics Data System (ADS)

Gantzounis, G.; Serra-Garcia, M.; Homma, K.; Mendoza, J. M.; Daraio, C.

2013-09-01

Acoustic metamaterials that allow low-frequency band gaps are interesting for many practical engineering applications, where vibration control and sound insulation are necessary. In most prior studies, the mechanical response of these structures has been described using linear continuum approximations. In this work, we experimentally and theoretically address the formation of low-frequency band gaps in locally resonant granular crystals, where the dynamics of the system is governed by discrete equations. We investigate the quasi-linear behavior of such structures. The analysis shows that a stopband can be introduced at about one octave lower frequency than in materials without local resonances. Broadband and multi-frequency stopband characteristics can also be achieved by strategically tailoring the non-uniform local resonance parameters.

Characterization of technical surfaces by structure function analysis

NASA Astrophysics Data System (ADS)

Kalms, Michael; Kreis, Thomas; Bergmann, Ralf B.

2018-03-01

The structure function is a tool for characterizing technical surfaces that exhibits a number of advantages over Fourierbased analysis methods. So it is optimally suited for analyzing the height distributions of surfaces measured by full-field non-contacting methods. The structure function is thus a useful method to extract global or local criteria like e. g. periodicities, waviness, lay, or roughness to analyze and evaluate technical surfaces. After the definition of line- and area-structure function and offering effective procedures for their calculation this paper presents examples using simulated and measured data of technical surfaces including aircraft parts.

Structural design of composite rotor blades with consideration of manufacturability, durability, and manufacturing uncertainties

NASA Astrophysics Data System (ADS)

Li, Leihong

A modular structural design methodology for composite blades is developed. This design method can be used to design composite rotor blades with sophisticate geometric cross-sections. This design method hierarchically decomposed the highly-coupled interdisciplinary rotor analysis into global and local levels. In the global level, aeroelastic response analysis and rotor trim are conduced based on multi-body dynamic models. In the local level, variational asymptotic beam sectional analysis methods are used for the equivalent one-dimensional beam properties. Compared with traditional design methodology, the proposed method is more efficient and accurate. Then, the proposed method is used to study three different design problems that have not been investigated before. The first is to add manufacturing constraints into design optimization. The introduction of manufacturing constraints complicates the optimization process. However, the design with manufacturing constraints benefits the manufacturing process and reduces the risk of violating major performance constraints. Next, a new design procedure for structural design against fatigue failure is proposed. This procedure combines the fatigue analysis with the optimization process. The durability or fatigue analysis employs a strength-based model. The design is subject to stiffness, frequency, and durability constraints. Finally, the manufacturing uncertainty impacts on rotor blade aeroelastic behavior are investigated, and a probabilistic design method is proposed to control the impacts of uncertainty on blade structural performance. The uncertainty factors include dimensions, shapes, material properties, and service loads.

Drying-induced atomic structural rearrangements in sodium-based calcium-alumino-silicate-hydrate gel and the mitigating effects of ZrO 2 nanoparticles

DOE PAGES

Yang, Kengran; Özçelik, V. Ongun; Garg, Nishant; ...

2018-01-01

Drying-induced nanoscopic alterations to the local atomic structure of silicate-activated slag and the mitigated effects of nano-ZrO2 are elucidated using in situ X-ray pair distribution function analysis.

Drying-induced atomic structural rearrangements in sodium-based calcium-alumino-silicate-hydrate gel and the mitigating effects of ZrO 2 nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Kengran; Özçelik, V. Ongun; Garg, Nishant

Drying-induced nanoscopic alterations to the local atomic structure of silicate-activated slag and the mitigated effects of nano-ZrO2 are elucidated using in situ X-ray pair distribution function analysis.

A new method to detect transitory signatures and local time/space variability structures in the climate system: the scale-dependent correlation analysis

NASA Astrophysics Data System (ADS)

Rodó, Xavier; Rodríguez-Arias, Miquel-Àngel

2006-10-01

The study of transitory signals and local variability structures in both/either time and space and their role as sources of climatic memory, is an important but often neglected topic in climate research despite its obvious importance and extensive coverage in the literature. Transitory signals arise either from non-linearities, in the climate system, transitory atmosphere-ocean couplings, and other processes in the climate system evolving after a critical threshold is crossed. These temporary interactions that, though intense, may not last long, can be responsible for a large amount of unexplained variability but are normally considered of limited relevance and often, discarded. With most of the current techniques at hand these typology of signatures are difficult to isolate because the low signal-to-noise ratio in midlatitudes, the limited recurrence of the transitory signals during a customary interval of data considered. Also, there is often a serious problem arising from the smoothing of local or transitory processes if statistical techniques are applied, that consider all the length of data available, rather than taking into account the size of the specific variability structure under investigation. Scale-dependent correlation (SDC) analysis is a new statistical method capable of highlighting the presence of transitory processes, these former being understood as temporary significant lag-dependent autocovariance in a single series, or covariance structures between two series. This approach, therefore, complements other approaches such as those resulting from the families of wavelet analysis, singular-spectrum analysis and recurrence plots. A main feature of SDC is its high-performance for short time series, its ability to characterize phase-relationships and thresholds in the bivariate domain. Ultimately, SDC helps tracking short-lagged relationships among processes that locally or temporarily couple and uncouple. The use of SDC is illustrated in the present paper by means of some synthetic time-series examples of increasing complexity, and it is compared with wavelet analysis in order to provide a well-known reference of its capabilities. A comparison between SDC and companion techniques is also addressed and results are exemplified for the specific case of some relevant El Niño-Southern Oscillation teleconnections.

Optimization of composite box-beam structures including effects of subcomponent interactions

NASA Technical Reports Server (NTRS)

Ragon, Scott A.; Guerdal, Zafer; Starnes, James H., Jr.

1995-01-01

Minimum mass designs are obtained for a simple box beam structure subject to bending, torque and combined bending/torque load cases. These designs are obtained subject to point strain and linear buckling constraints. The present work differs from previous efforts in that special attention is payed to including the effects of subcomponent panel interaction in the optimal design process. Two different approaches are used to impose the buckling constraints. When the global approach is used, buckling constraints are imposed on the global structure via a linear eigenvalue analysis. This approach allows the subcomponent panels to interact in a realistic manner. The results obtained using this approach are compared to results obtained using a traditional, less expensive approach, called the local approach. When the local approach is used, in-plane loads are extracted from the global model and used to impose buckling constraints on each subcomponent panel individually. In the global cases, it is found that there can be significant interaction between skin, spar, and rib design variables. This coupling is weak or nonexistent in the local designs. It is determined that weight savings of up to 7% may be obtained by using the global approach instead of the local approach to design these structures. Several of the designs obtained using the linear buckling analysis are subjected to a geometrically nonlinear analysis. For the designs which were subjected to bending loads, the innermost rib panel begins to collapse at less than half the intended design load and in a mode different from that predicted by linear analysis. The discrepancy between the predicted linear and nonlinear responses is attributed to the effects of the nonlinear rib crushing load, and the parameter which controls this rib collapse failure mode is shown to be the rib thickness. The rib collapse failure mode may be avoided by increasing the rib thickness above the value obtained from the (linear analysis based) optimizer. It is concluded that it would be necessary to include geometric nonlinearities in the design optimization process if the true optimum in this case were to be found.

Strain-Dependent Edge Structures in MoS2 Layers.

PubMed

Tinoco, Miguel; Maduro, Luigi; Masaki, Mukai; Okunishi, Eiji; Conesa-Boj, Sonia

2017-11-08

Edge structures are low-dimensional defects unavoidable in layered materials of the transition metal dichalcogenides (TMD) family. Among the various types of such structures, the armchair (AC) and zigzag (ZZ) edge types are the most common. It has been predicted that the presence of intrinsic strain localized along these edges structures can have direct implications for the customization of their electronic properties. However, pinning down the relation between local structure and electronic properties at these edges is challenging. Here, we quantify the local strain field that arises at the edges of MoS 2 flakes by combining aberration-corrected transmission electron microscopy (TEM) with the geometrical-phase analysis (GPA) method. We also provide further insight on the possible effects of such edge strain on the resulting electronic behavior by means of electron energy loss spectroscopy (EELS) measurements. Our results reveal that the two-dominant edge structures, ZZ and AC, induce the formation of different amounts of localized strain fields. We also show that by varying the free edge curvature from concave to convex, compressive strain turns into tensile strain. These results pave the way toward the customization of edge structures in MoS 2 , which can be used to engineer the properties of layered materials and thus contribute to the optimization of the next generation of atomic-scale electronic devices built upon them.

Comment on {open_quotes}Local frequency analysis and the structure of classical phase space of the LiNC/LiCN molecular system{close_quotes} [J. Chem. Phys. {bold 108}, 63 (1998)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martens, C.C.; Davis, M.J.; Ezra, G.S.

In this Comment, we correct a misunderstanding in the title paper concerning the accuracy of the fast Fourier transform method of local frequency analysis of Martens, Davis, and Ezra. We also discuss the application of the Martens{endash}Davis{endash}Ezra method to a two degree of freedom model of OSC. {copyright} {ital 1998 American Institute of Physics.}

Development of automated extraction method of biliary tract from abdominal CT volumes based on local intensity structure analysis

NASA Astrophysics Data System (ADS)

Koga, Kusuto; Hayashi, Yuichiro; Hirose, Tomoaki; Oda, Masahiro; Kitasaka, Takayuki; Igami, Tsuyoshi; Nagino, Masato; Mori, Kensaku

2014-03-01

In this paper, we propose an automated biliary tract extraction method from abdominal CT volumes. The biliary tract is the path by which bile is transported from liver to the duodenum. No extraction method have been reported for the automated extraction of the biliary tract from common contrast CT volumes. Our method consists of three steps including: (1) extraction of extrahepatic bile duct (EHBD) candidate regions, (2) extraction of intrahepatic bile duct (IHBD) candidate regions, and (3) combination of these candidate regions. The IHBD has linear structures and intensities of the IHBD are low in CT volumes. We use a dark linear structure enhancement (DLSE) filter based on a local intensity structure analysis method using the eigenvalues of the Hessian matrix for the IHBD candidate region extraction. The EHBD region is extracted using a thresholding process and a connected component analysis. In the combination process, we connect the IHBD candidate regions to each EHBD candidate region and select a bile duct region from the connected candidate regions. We applied the proposed method to 22 cases of CT volumes. An average Dice coefficient of extraction result was 66.7%.

Heterogeneous structure and surface tension effects on mechanical response in pulmonary acinus: A finite element analysis.

PubMed

Koshiyama, Kenichiro; Nishimoto, Keisuke; Ii, Satoshi; Sera, Toshihiro; Wada, Shigeo

2018-01-20

The pulmonary acinus is a dead-end microstructure that consists of ducts and alveoli. High-resolution micro-CT imaging has recently provided detailed anatomical information of a complete in vivo acinus, but relating its mechanical response with its detailed acinar structure remains challenging. This study aimed to investigate the mechanical response of acinar tissue in a whole acinus for static inflation using computational approaches. We performed finite element analysis of a whole acinus for static inflation. The acinar structure model was generated based on micro-CT images of an intact acinus. A continuum mechanics model of the lung parenchyma was used for acinar tissue material model, and surface tension effects were explicitly included. An anisotropic mechanical field analysis based on a stretch tensor was combined with a curvature-based local structure analysis. The airspace of the acinus exhibited nonspherical deformation as a result of the anisotropic deformation of acinar tissue. A strain hotspot occurred at the ridge-shaped region caused by a rod-like deformation of acinar tissue on the ridge. The local structure becomes bowl-shaped for inflation and, without surface tension effects, the surface of the bowl-shaped region primarily experiences isotropic deformation. Surface tension effects suppressed the increase in airspace volume and inner surface area, while facilitating anisotropic deformation on the alveolar surface. In the lungs, the heterogeneous acinar structure and surface tension induce anisotropic deformation at the acinar and alveolar scales. Further research is needed on structural variation of acini, inter-acini connectivity, or dynamic behavior to understand multiscale lung mechanics. Copyright © 2018 Elsevier Ltd. All rights reserved.

Emergence of scale-free close-knit friendship structure in online social networks.

PubMed

Cui, Ai-Xiang; Zhang, Zi-Ke; Tang, Ming; Hui, Pak Ming; Fu, Yan

2012-01-01

Although the structural properties of online social networks have attracted much attention, the properties of the close-knit friendship structures remain an important question. Here, we mainly focus on how these mesoscale structures are affected by the local and global structural properties. Analyzing the data of four large-scale online social networks reveals several common structural properties. It is found that not only the local structures given by the indegree, outdegree, and reciprocal degree distributions follow a similar scaling behavior, the mesoscale structures represented by the distributions of close-knit friendship structures also exhibit a similar scaling law. The degree correlation is very weak over a wide range of the degrees. We propose a simple directed network model that captures the observed properties. The model incorporates two mechanisms: reciprocation and preferential attachment. Through rate equation analysis of our model, the local-scale and mesoscale structural properties are derived. In the local-scale, the same scaling behavior of indegree and outdegree distributions stems from indegree and outdegree of nodes both growing as the same function of the introduction time, and the reciprocal degree distribution also shows the same power-law due to the linear relationship between the reciprocal degree and in/outdegree of nodes. In the mesoscale, the distributions of four closed triples representing close-knit friendship structures are found to exhibit identical power-laws, a behavior attributed to the negligible degree correlations. Intriguingly, all the power-law exponents of the distributions in the local-scale and mesoscale depend only on one global parameter, the mean in/outdegree, while both the mean in/outdegree and the reciprocity together determine the ratio of the reciprocal degree of a node to its in/outdegree. Structural properties of numerical simulated networks are analyzed and compared with each of the four real networks. This work helps understand the interplay between structures on different scales in online social networks.

Emergence of Scale-Free Close-Knit Friendship Structure in Online Social Networks

PubMed Central

Cui, Ai-Xiang; Zhang, Zi-Ke; Tang, Ming; Hui, Pak Ming; Fu, Yan

2012-01-01

Although the structural properties of online social networks have attracted much attention, the properties of the close-knit friendship structures remain an important question. Here, we mainly focus on how these mesoscale structures are affected by the local and global structural properties. Analyzing the data of four large-scale online social networks reveals several common structural properties. It is found that not only the local structures given by the indegree, outdegree, and reciprocal degree distributions follow a similar scaling behavior, the mesoscale structures represented by the distributions of close-knit friendship structures also exhibit a similar scaling law. The degree correlation is very weak over a wide range of the degrees. We propose a simple directed network model that captures the observed properties. The model incorporates two mechanisms: reciprocation and preferential attachment. Through rate equation analysis of our model, the local-scale and mesoscale structural properties are derived. In the local-scale, the same scaling behavior of indegree and outdegree distributions stems from indegree and outdegree of nodes both growing as the same function of the introduction time, and the reciprocal degree distribution also shows the same power-law due to the linear relationship between the reciprocal degree and in/outdegree of nodes. In the mesoscale, the distributions of four closed triples representing close-knit friendship structures are found to exhibit identical power-laws, a behavior attributed to the negligible degree correlations. Intriguingly, all the power-law exponents of the distributions in the local-scale and mesoscale depend only on one global parameter, the mean in/outdegree, while both the mean in/outdegree and the reciprocity together determine the ratio of the reciprocal degree of a node to its in/outdegree. Structural properties of numerical simulated networks are analyzed and compared with each of the four real networks. This work helps understand the interplay between structures on different scales in online social networks. PMID:23272067

WONKA: objective novel complex analysis for ensembles of protein-ligand structures.

PubMed

Bradley, A R; Wall, I D; von Delft, F; Green, D V S; Deane, C M; Marsden, B D

2015-10-01

WONKA is a tool for the systematic analysis of an ensemble of protein-ligand structures. It makes the identification of conserved and unusual features within such an ensemble straightforward. WONKA uses an intuitive workflow to process structural co-ordinates. Ligand and protein features are summarised and then presented within an interactive web application. WONKA's power in consolidating and summarising large amounts of data is described through the analysis of three bromodomain datasets. Furthermore, and in contrast to many current methods, WONKA relates analysis to individual ligands, from which we find unusual and erroneous binding modes. Finally the use of WONKA as an annotation tool to share observations about structures is demonstrated. WONKA is freely available to download and install locally or can be used online at http://wonka.sgc.ox.ac.uk.

Local x-ray structure analysis of optically manipulated biological micro-objects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cojoc, Dan; Ferrari, Enrico; Santucci, Silvia C.

2010-12-13

X-ray diffraction using micro- and nanofocused beams is well suited for nanostructure analysis at different sites of a biological micro-object. To conduct in vitro studies without mechanical contact, we developed object manipulation by optical tweezers in a microfluidic cell. Here we report x-ray microdiffraction analysis of a micro-object optically trapped in three dimensions. We revealed the nanostructure of a single starch granule at different points and investigated local radiation damage induced by repeated x-ray exposures at the same position, demonstrating high stability and full control of the granule orientation by multiple optical traps.

Structural deformation upon protein-protein interaction: A structural alphabet approach

PubMed Central

Martin, Juliette; Regad, Leslie; Lecornet, Hélène; Camproux, Anne-Claude

2008-01-01

Background In a number of protein-protein complexes, the 3D structures of bound and unbound partners significantly differ, supporting the induced fit hypothesis for protein-protein binding. Results In this study, we explore the induced fit modifications on a set of 124 proteins available in both bound and unbound forms, in terms of local structure. The local structure is described thanks to a structural alphabet of 27 structural letters that allows a detailed description of the backbone. Using a control set to distinguish induced fit from experimental error and natural protein flexibility, we show that the fraction of structural letters modified upon binding is significantly greater than in the control set (36% versus 28%). This proportion is even greater in the interface regions (41%). Interface regions preferentially involve coils. Our analysis further reveals that some structural letters in coil are not favored in the interface. We show that certain structural letters in coil are particularly subject to modifications at the interface, and that the severity of structural change also varies. These information are used to derive a structural letter substitution matrix that summarizes the local structural changes observed in our data set. We also illustrate the usefulness of our approach to identify common binding motifs in unrelated proteins. Conclusion Our study provides qualitative information about induced fit. These results could be of help for flexible docking. PMID:18307769

Structural deformation upon protein-protein interaction: a structural alphabet approach.

PubMed

Martin, Juliette; Regad, Leslie; Lecornet, Hélène; Camproux, Anne-Claude

2008-02-28

In a number of protein-protein complexes, the 3D structures of bound and unbound partners significantly differ, supporting the induced fit hypothesis for protein-protein binding. In this study, we explore the induced fit modifications on a set of 124 proteins available in both bound and unbound forms, in terms of local structure. The local structure is described thanks to a structural alphabet of 27 structural letters that allows a detailed description of the backbone. Using a control set to distinguish induced fit from experimental error and natural protein flexibility, we show that the fraction of structural letters modified upon binding is significantly greater than in the control set (36% versus 28%). This proportion is even greater in the interface regions (41%). Interface regions preferentially involve coils. Our analysis further reveals that some structural letters in coil are not favored in the interface. We show that certain structural letters in coil are particularly subject to modifications at the interface, and that the severity of structural change also varies. These information are used to derive a structural letter substitution matrix that summarizes the local structural changes observed in our data set. We also illustrate the usefulness of our approach to identify common binding motifs in unrelated proteins. Our study provides qualitative information about induced fit. These results could be of help for flexible docking.

Analysis of high speed flow, thermal and structural interactions

NASA Technical Reports Server (NTRS)

Thornton, Earl A.

1994-01-01

Research for this grant focused on the following tasks: (1) the prediction of severe, localized aerodynamic heating for complex, high speed flows; (2) finite element adaptive refinement methodology for multi-disciplinary analyses; (3) the prediction of thermoviscoplastic structural response with rate-dependent effects and large deformations; (4) thermoviscoplastic constitutive models for metals; and (5) coolant flow/structural heat transfer analyses.

The virtues of localism and arctic wilderness politics

Treesearch

James N. Gladden

2007-01-01

An analysis of co-managing structures and land use issues in three case studies of arctic wilderness politics shows that more formal and informal power sharing by government officials with local people results in less conflict. Greater input and control by nearby communities may also help to protect wilderness ecosystems and traditional values of northern cultures....

Structural analysis of a Petri net model of oxidative stress in atherosclerosis.

PubMed

Kozak, Adam; Formanowicz, Dorota; Formanowicz, Piotr

2018-06-01

Atherosclerosis is a complex process of gathering sub-endothelial plaques decreasing lumen of the blood vessels. This disorder affects people of all ages, but its progression is asymptomatic for many years. It is regulated by many typical and atypical factors including the immune system response, a chronic kidney disease, a diet rich in lipids, a local inflammatory process and a local oxidative stress that is here one of the key factors. In this study, a Petri net model of atherosclerosis regulation is presented. This model includes also some information about stoichiometric relationships between its components and covers all mentioned factors. For the model, a structural analysis based on invariants was made and biological conclusions are presented. Since the model contains inhibitor arcs, a heuristic method for analysis of such cases is presented. This method can be used to extend the concept of feasible t -invariants.

Music Structure Analysis from Acoustic Signals

NASA Astrophysics Data System (ADS)

Dannenberg, Roger B.; Goto, Masataka

Music is full of structure, including sections, sequences of distinct musical textures, and the repetition of phrases or entire sections. The analysis of music audio relies upon feature vectors that convey information about music texture or pitch content. Texture generally refers to the average spectral shape and statistical fluctuation, often reflecting the set of sounding instruments, e.g., strings, vocal, or drums. Pitch content reflects melody and harmony, which is often independent of texture. Structure is found in several ways. Segment boundaries can be detected by observing marked changes in locally averaged texture.

From average to local structure: a Rietveld and an atomic pair distribution function (PDF) study of selenium clusters in zeolite-NdY.

PubMed

Abeykoon, A M Milinda; Donner, Wolfgang; Brunelli, Michela; Castro-Colin, Miguel; Jacobson, Allan J; Moss, Simon C

2009-09-23

The structure of Se particles in the approximately 13 A diameter alpha-cages of zeolite NdY has been determined by Rietveld refinement and pair distribution function (PDF) analysis of X-ray data. With the diffuse scattering subtracted an average structure comprised of an undistorted framework containing nanoclusters of 20 Se atoms is observed. The intracluster correlations and the cluster-framework correlations which give rise to diffuse scattering were modeled by using PDF analysis.

Numerical analysis of strain localization for transversely isotropic model with non-coaxial flow rule

NASA Astrophysics Data System (ADS)

Wei, Ding; Cong-cong, Yu; Chen-hui, Wu; Zheng-yi, Shu

2018-03-01

To analyse the strain localization behavior of geomaterials, the forward Euler schemes and the tangent modulus matrix are formulated based on the transversely isotropic yield criterion with non-coaxial flow rule developed by Lade, the program code is implemented based on the user subroutine (UMAT) of ABAQUS. The influence of the material principal direction on the strain localization and the bearing capacity of the structure are investigated and analyzed. Numerical results show the validity and performance of the proposed model in simulating the strain localization behavior of geostructures.

Local atomic and magnetic structure of dilute magnetic semiconductor ( Ba , K ) ( Zn , Mn ) 2 As 2

DOE PAGES

Frandsen, Benjamin A.; Gong, Zizhou; Terban, Maxwell W.; ...

2016-09-06

We studied the atomic and magnetic structure of the dilute ferromagnetic semiconductor system (Ba,K)(Zn,Mn) 2As 2 through atomic and magnetic pair distribution function analysis of temperature-dependent x-ray and neutron total scattering data. Furthermore, we detected a change in curvature of the temperature-dependent unit cell volume of the average tetragonal crystallographic structure at a temperature coinciding with the onset of ferromagnetic order. We also observed the existence of a well-defined local orthorhombic structure on a short length scale of ≲5Å, resulting in a rather asymmetrical local environment of the Mn and As ions. Finally, the magnetic PDF revealed ferromagnetic alignment ofmore » Mn spins along the crystallographic c axis, with robust nearest-neighbor ferromagnetic correlations that exist even above the ferromagnetic ordering temperature. Finally, we discuss these results in the context of other experiments and theoretical studies on this system.« less

Evidence of sharp and diffuse domain walls in BiFeO3 by means of unit-cell-wise strain and polarization maps obtained with high resolution scanning transmission electron microscopy.

PubMed

Lubk, A; Rossell, M D; Seidel, J; He, Q; Yang, S Y; Chu, Y H; Ramesh, R; Hÿtch, M J; Snoeck, E

2012-07-27

Domain walls (DWs) substantially influence a large number of applications involving ferroelectric materials due to their limited mobility when shifted during polarization switching. The discovery of greatly enhanced conduction at BiFeO(3) DWs has highlighted yet another role of DWs as a local material state with unique properties. However, the lack of precise information on the local atomic structure is still hampering microscopical understanding of DW properties. Here, we examine the atomic structure of BiFeO(3) 109° DWs with pm precision by a combination of high-angle annular dark-field scanning transmission electron microscopy and a dedicated structural analysis. By measuring simultaneously local polarization and strain, we provide direct experimental proof for the straight DW structure predicted by ab initio calculations as well as the recently proposed theory of diffuse DWs, thus resolving a long-standing discrepancy between experimentally measured and theoretically predicted DW mobilities.

Micronucleus-specific histone H1 is required for micronuclear chromosome integrity in Tetrahymena thermophila

PubMed Central

Qiao, Juxia; Xu, Jing; Bo, Tao

2017-01-01

Histone H1 molecules play a key role in establishing and maintaining higher order chromatin structures. They can bind to linker DNA entering and exiting the nucleosome and regulate transcriptional activity. Tetrahymena thermophila has two histone H1, namely, macronuclear histone H1 and micronuclear histone H1 (Mlh1). Mlh1 is specifically localized at micronuclei during growth and starvation stages. Moreover, Mlh1 is localized around micronuclei and forms a specific structure during the conjugation stage. It co-localizes partially with spindle apparatus during micronuclear meiosis. Analysis of MLH1 knock-out revealed that Mlh1 was required for the micronuclear integrity and development during conjugation stage. Overexpression of Mlh1 led to abnormal conjugation progression. RT-PCR analysis indicated that the expression level of HMGB3 increased in ΔMLH1 strains, while the expression level of MLH1 increased in ΔHMGB3 cells during conjugation. These results indicate that micronuclear integrity and sexual development require normal expression level of Mlh1 and that HmgB3 and Mlh1 may functionally compensate each other in regulating micronuclear structure in T. thermophila. PMID:29095884

A Parametric Study of Nonlinear Seismic Response Analysis of Transmission Line Structures

PubMed Central

Wang, Yanming; Yi, Zhenhua

2014-01-01

A parametric study of nonlinear seismic response analysis of transmission line structures subjected to earthquake loading is studied in this paper. The transmission lines are modeled by cable element which accounts for the nonlinearity of the cable based on a real project. Nonuniform ground motions are generated using a stochastic approach based on random vibration analysis. The effects of multicomponent ground motions, correlations among multicomponent ground motions, wave travel, coherency loss, and local site on the responses of the cables are investigated using nonlinear time history analysis method, respectively. The results show the multicomponent seismic excitations should be considered, but the correlations among multicomponent ground motions could be neglected. The wave passage effect has a significant influence on the responses of the cables. The change of the degree of coherency loss has little influence on the response of the cables, but the responses of the cables are affected significantly by the effect of coherency loss. The responses of the cables change little with the degree of the difference of site condition changing. The effect of multicomponent ground motions, wave passage, coherency loss, and local site should be considered for the seismic design of the transmission line structures. PMID:25133215

Multidisciplinary Optimization and Damage Tolerance of Stiffened Structures

NASA Astrophysics Data System (ADS)

Jrad, Mohamed

THE structural optimization of a cantilever aircraft wing with curvilinear spars and ribs and stiffeners is described. For the optimization of a complex wing, a common strategy is to divide the optimization procedure into two subsystems: the global wing optimization which optimizes the geometry of spars, ribs and wing skins; and the local panel optimization which optimizes the design variables of local panels bordered by spars and ribs. The stiffeners are placed on the local panels to increase the stiffness and buckling resistance. During the local panel optimization, the stress information is taken from the global model as a displacement boundary condition on the panel edges using the so-called "Global-Local Approach". Particle swarm optimization is used in the integration of global/local optimization to optimize the SpaRibs. Parallel computing approach has been developed in the Python programming language to reduce the CPU time. The license cycle-check method and memory self-adjustment method are two approaches that have been applied in the parallel framework in order to optimize the use of the resources by reducing the license and memory limitations and making the code robust. The integrated global-local optimization approach has been applied to subsonic NASA common research model (CRM) wing, which proves the methodology's application scaling with medium fidelity FEM analysis. The structural weight of the wing has been reduced by 42% and the parallel implementation allowed a reduction in the CPU time by 89%. The aforementioned Global-Local Approach is investigated and applied to a composite panel with crack at its center. Because of composite laminates' heterogeneity, an accurate analysis of these requires very high time and storage space. A possible alternative to reduce the computational complexity is the global-local analysis which involves an approximate analysis of the whole structure followed by a detailed analysis of a significantly smaller region of interest. Buckling analysis of a composite panel with attached longitudinal stiffeners under compressive loads is performed using Ritz method with trigonometric functions. Results are then compared to those from Abaqus FEA for different shell elements. The case of composite panel with one, two, and three stiffeners is investigated. The effect of the distance between the stiffeners on the buckling load is also studied. The variation of the buckling load and buckling modes with the stiffeners' height is investigated. It is shown that there is an optimum value of stiffeners' height beyond which the structural response of the stiffened panel is not improved and the buckling load does not increase. Furthermore, there exist different critical values of stiffener's height at which the buckling mode of the structure changes. Next, buckling analysis of a composite panel with two straight stiffeners and a crack at the center is performed. Finally, buckling analysis of a composite panel with curvilinear stiffeners and a crack at the center is also conducted. Results show that panels with a larger crack have a reduced buckling load and that the buckling load decreases slightly when using higher order 2D shell FEM elements. A damage tolerance framework, EBF3PanelOpt, has been developed to design and analyze curvilinearly stiffened panels. The framework is written with the scripting language Python and it interacts with the commercial software MSC. Patran (for geometry and mesh creation), MSC. Nastran (for finite element analysis), and MSC. Marc (for damage tolerance analysis). The crack location is set to the location of the maximum value of the major principal stress while its orientation is set normal to the major principal axis direction. The effective stress intensity factor is calculated using the Virtual Crack Closure Technique and compared to the fracture toughness of the material in order to decide whether the crack will expand or not. The ratio of these two quantities is used as a constraint, along with the buckling factor, Kreisselmeier and Steinhauser criteria, and crippling factor. The EBF3PanelOpt framework is integrated within a two-step Particle Swarm Optimization in order to minimize the weight of the panel while satisfying the aforementioned constraints and using all the shape and thickness parameters as design variables. The result of the PSO is used then as an initial guess for the Gradient Based Optimization using only the thickness parameters as design variables and employing VisualDOC. Stiffened panel with two curvilinear stiffeners is optimized for two load cases. In both cases, significant reduction has been made for the panel's weight.

Development and verification of local/global analysis techniques for laminated composites

NASA Technical Reports Server (NTRS)

Griffin, O. Hayden, Jr.

1989-01-01

Analysis and design methods for laminated composite materials have been the subject of considerable research over the past 20 years, and are currently well developed. In performing the detailed three-dimensional analyses which are often required in proximity to discontinuities, however, analysts often encounter difficulties due to large models. Even with the current availability of powerful computers, models which are too large to run, either from a resource or time standpoint, are often required. There are several approaches which can permit such analyses, including substructuring, use of superelements or transition elements, and the global/local approach. This effort is based on the so-called zoom technique to global/local analysis, where a global analysis is run, with the results of that analysis applied to a smaller region as boundary conditions, in as many iterations as is required to attain an analysis of the desired region. Before beginning the global/local analyses, it was necessary to evaluate the accuracy of the three-dimensional elements currently implemented in the Computational Structural Mechanics (CSM) Testbed. It was also desired to install, using the Experimental Element Capability, a number of displacement formulation elements which have well known behavior when used for analysis of laminated composites.

Magnetorotational instability: nonmodal growth and the relationship of global modes to the shearing box

DOE Office of Scientific and Technical Information (OSTI.GOV)

Squire, J.; Bhattacharjee, A.

2014-12-10

We study magnetorotational instability (MRI) using nonmodal stability techniques. Despite the spectral instability of many forms of MRI, this proves to be a natural method of analysis that is well-suited to deal with the non-self-adjoint nature of the linear MRI equations. We find that the fastest growing linear MRI structures on both local and global domains can look very different from the eigenmodes, invariably resembling waves shearing with the background flow (shear waves). In addition, such structures can grow many times faster than the least stable eigenmode over long time periods, and be localized in a completely different region ofmore » space. These ideas lead—for both axisymmetric and non-axisymmetric modes—to a natural connection between the global MRI and the local shearing box approximation. By illustrating that the fastest growing global structure is well described by the ordinary differential equations (ODEs) governing a single shear wave, we find that the shearing box is a very sensible approximation for the linear MRI, contrary to many previous claims. Since the shear wave ODEs are most naturally understood using nonmodal analysis techniques, we conclude by analyzing local MRI growth over finite timescales using these methods. The strong growth over a wide range of wave-numbers suggests that nonmodal linear physics could be of fundamental importance in MRI turbulence.« less

Electric field dependent local structure of (KxNa1-x) 0.5B i0.5Ti O3

NASA Astrophysics Data System (ADS)

Goetzee-Barral, A. J.; Usher, T.-M.; Stevenson, T. J.; Jones, J. L.; Levin, I.; Brown, A. P.; Bell, A. J.

2017-07-01

The in situ x-ray pair-distribution function (PDF) characterization technique has been used to study the behavior of (KxNa1-x) 0.5B i0.5Ti O3 , as a function of electric field. As opposed to conventional x-ray Bragg diffraction techniques, PDF is sensitive to local atomic displacements, detecting local structural changes at the angstrom to nanometer scale. Several field-dependent ordering mechanisms can be observed in x =0.15 , 0.18 and at the morphotropic phase boundary composition x =0.20 . X-ray total scattering shows suppression of diffuse scattering with increasing electric-field amplitude, indicative of an increase in structural ordering. Analysis of PDF peaks in the 3-4-Å range shows ordering of Bi-Ti distances parallel to the applied electric field, illustrated by peak amplitude redistribution parallel and perpendicular to the electric-field vector. A transition from <110 > to <112 > -type off-center displacements of Bi relative to the neighboring Ti atoms is observable with increasing x . Analysis of PDF peak shift with electric field shows the effects of Bi-Ti redistribution and onset of piezoelectric lattice strain. The combination of these field-induced ordering mechanisms is consistent with local redistribution of Bi-Ti distances associated with domain reorientation and an overall increase in order of atomic displacements.

Electric field dependent local structure of ( K x N a 1 - x ) 0.5 B i 0.5 Ti O 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goetzee-Barral, A. J.; Usher, T. -M.; Stevenson, T. J.

The in situ x-ray pair-distribution function (PDF) characterization technique has been used to study the behavior of (K xNa 1–x) 0.5Bi 0.5TiO 3, as a function of electric field. As opposed to conventional x-ray Bragg diffraction techniques, PDF is sensitive to local atomic displacements, detecting local structural changes at the angstrom to nanometer scale. Several field-dependent ordering mechanisms can be observed in x = 0.15, 0.18 and at the morphotropic phase boundary composition x = 0.20. X-ray total scattering shows suppression of diffuse scattering with increasing electric-field amplitude, indicative of an increase in structural ordering. Analysis of PDF peaks inmore » the 3–4-Å range shows ordering of Bi-Ti distances parallel to the applied electric field, illustrated by peak amplitude redistribution parallel and perpendicular to the electric-field vector. A transition from < 110 > to < 112 >-type off-center displacements of Bi relative to the neighboring Ti atoms is observable with increasing x. Analysis of PDF peak shift with electric field shows the effects of Bi-Ti redistribution and onset of piezoelectric lattice strain. Furthermore, the combination of these field-induced ordering mechanisms is consistent with local redistribution of Bi-Ti distances associated with domain reorientation and an overall increase in order of atomic displacements.« less

Electric field dependent local structure of ( K x N a 1 - x ) 0.5 B i 0.5 Ti O 3

DOE PAGES

Goetzee-Barral, A. J.; Usher, T. -M.; Stevenson, T. J.; ...

2017-07-31

The in situ x-ray pair-distribution function (PDF) characterization technique has been used to study the behavior of (K xNa 1–x) 0.5Bi 0.5TiO 3, as a function of electric field. As opposed to conventional x-ray Bragg diffraction techniques, PDF is sensitive to local atomic displacements, detecting local structural changes at the angstrom to nanometer scale. Several field-dependent ordering mechanisms can be observed in x = 0.15, 0.18 and at the morphotropic phase boundary composition x = 0.20. X-ray total scattering shows suppression of diffuse scattering with increasing electric-field amplitude, indicative of an increase in structural ordering. Analysis of PDF peaks inmore » the 3–4-Å range shows ordering of Bi-Ti distances parallel to the applied electric field, illustrated by peak amplitude redistribution parallel and perpendicular to the electric-field vector. A transition from < 110 > to < 112 >-type off-center displacements of Bi relative to the neighboring Ti atoms is observable with increasing x. Analysis of PDF peak shift with electric field shows the effects of Bi-Ti redistribution and onset of piezoelectric lattice strain. Furthermore, the combination of these field-induced ordering mechanisms is consistent with local redistribution of Bi-Ti distances associated with domain reorientation and an overall increase in order of atomic displacements.« less

Structural phase transition and 5f-electrons localization of PuSe explored by ab initio calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cui Shouxin, E-mail: shouxincui@yahoo.co; Feng Wenxia; Hu Haiquan

2010-04-15

An investigation into the structural phase transformation, electronic and optical properties of PuSe under high pressure was conducted by using the full potential linearized augmented plane wave plus local orbitals (FP-LAPW+lo) method, in the presence and in the absence of spin-orbit coupling (SOC). Our results demonstrate that there exists a structural phase transition from rocksalt (B 1) structure to CsCl-type (B 2) structure at the transition pressure of 36.3 GPa (without SOC) and 51.3 GPa (with SOC). The electronic density of states (DOS) for PuSe show that the f-electrons of Pu are more localized and concentrated in a narrow peakmore » near the Fermi level, which is consistent with the experimental studies. The band structure shows that B 1-PuSe is metallic. A pseudogap appears around the Fermi level of the total density of states of B 1 phase PuSe, which may contribute to its stability. The calculated reflectivity R(omega) shows agreement with the available experimental results. Furthermore, the absorption spectrum, refractive index, extinction coefficient, energy-loss spectrum and dielectric function were calculated. The origin of the spectral peaks was interpreted based on the electronic structures. - Abstract: Graphical Abstract Legend (TOC Figure): 5f-electrons are more localized by the analysis of the density of states (SOC). The origin spectra peaks was interpreted based on electronic structures.« less

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

NASA Technical Reports Server (NTRS)

Yahil, Amos

1994-01-01

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

Understanding the organization of public health delivery systems: an empirical typology.

PubMed

Mays, Glen P; Scutchfield, F Douglas; Bhandari, Michelyn W; Smith, Sharla A

2010-03-01

Policy discussions about improving the U.S. health care system increasingly recognize the need to strengthen its capacities for delivering public health services. A better understanding of how public health delivery systems are organized across the United States is critical to improvement. To facilitate the development of such evidence, this article presents an empirical method of classifying and comparing public health delivery systems based on key elements of their organizational structure. This analysis uses data collected through a national longitudinal survey of local public health agencies serving communities with at least 100,000 residents. The survey measured the availability of twenty core public health activities in local communities and the types of organizations contributing to each activity. Cluster analysis differentiated local delivery systems based on the scope of activities delivered, the range of organizations contributing, and the distribution of effort within the system. Public health delivery systems varied widely in organizational structure, but the observed patterns of variation suggested that systems adhere to one of seven distinct configurations. Systems frequently migrated from one configuration to another over time, with an overall trend toward offering a broader scope of services and engaging a wider range of organizations. Public health delivery systems exhibit important structural differences that may influence their operations and outcomes. The typology developed through this analysis can facilitate comparative studies to identify which delivery system configurations perform best in which contexts.

Critical ratios for structural analysis of triacylglycerols using mass spectrometry

USDA-ARS?s Scientific Manuscript database

Recent developments have finally allowed fragment behaviors using APCI-MS to be elucidated after twenty years of literature reports. Critical Ratios have been defined that correspond to various aspects of triacylglycerol (TAG) analysis, from overall degree of unsaturation to localization of fatty ac...

Function Invariant and Parameter Scale-Free Transformation Methods

ERIC Educational Resources Information Center

Bentler, P. M.; Wingard, Joseph A.

1977-01-01

A scale-invariant simple structure function of previously studied function components for principal component analysis and factor analysis is defined. First and second partial derivatives are obtained, and Newton-Raphson iterations are utilized. The resulting solutions are locally optimal and subjectively pleasing. (Author/JKS)

ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Richard A.; Brown, Joseph M.; Colby, Sean M.

ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multiomics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS provides robust taxonomy based onmore » majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.« less

Plasmodium knowlesi Skeleton-Binding Protein 1 Localizes to the 'Sinton and Mulligan' Stipplings in the Cytoplasm of Monkey and Human Erythrocytes.

PubMed

Lucky, Amuza Byaruhanga; Sakaguchi, Miako; Katakai, Yuko; Kawai, Satoru; Yahata, Kazuhide; Templeton, Thomas J; Kaneko, Osamu

2016-01-01

The malaria parasite, Plasmodium, exports protein products to the infected erythrocyte to introduce modifications necessary for the establishment of nutrient acquisition and surface display of host interaction ligands. Erythrocyte remodeling impacts parasite virulence and disease pathology and is well documented for the human malaria parasite Plasmodium falciparum, but has been less described for other Plasmodium species. For P. falciparum, the exported protein skeleton-binding protein 1 (PfSBP1) is involved in the trafficking of erythrocyte surface ligands and localized to membranous structures within the infected erythrocyte, termed Maurer's clefts. In this study, we analyzed SBP1 orthologs across the Plasmodium genus by BLAST analysis and conserved gene synteny, which were also recently described by de Niz et al. (2016). To evaluate the localization of an SBP1 ortholog, we utilized the zoonotic malaria parasite, Plasmodium knowlesi. Immunofluorescence assay of transgenic P. knowlesi parasites expressing epitope-tagged recombinant PkSBP1 revealed a punctate staining pattern reminiscent of Maurer's clefts, following infection of either monkey or human erythrocytes. The recombinant PkSBP1-positive puncta co-localized with Giemsa-stained structures, known as 'Sinton and Mulligan' stipplings. Immunoelectron microscopy also showed that recombinant PkSBP1 localizes within or on the membranous structures akin to the Maurer's clefts. The recombinant PkSBP1 expressed in P. falciparum-infected erythrocytes co-localized with PfSBP1 at the Maurer's clefts, indicating an analogous trafficking pattern. A member of the P. knowlesi 2TM protein family was also expressed and localized to membranous structures in infected monkey erythrocytes. These results suggest that the trafficking machinery and induced erythrocyte cellular structures of P. knowlesi are similar following infection of both monkey and human erythrocytes, and are conserved with P. falciparum.

Investigating homology between proteins using energetic profiles.

PubMed

Wrabl, James O; Hilser, Vincent J

2010-03-26

Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding) and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved local stability, may provide guidance for a future thermodynamically informed classification of protein homology.

Electronic structure and magnetic properties of dilute U impurities in metals

NASA Astrophysics Data System (ADS)

Mohanta, S. K.; Cottenier, S.; Mishra, S. N.

2016-05-01

The electronic structure and magnetic moment of dilute U impurity in metallic hosts have been calculated from first principles. The calculations have been performed within local density approximation of the density functional theory using Augmented plane wave+local orbital (APW+lo) technique, taking account of spin-orbit coupling and Coulomb correlation through LDA+U approach. We present here our results for the local density of states, magnetic moment and hyperfine field calculated for an isolated U impurity embedded in hosts with sp-, d- and f-type conduction electrons. The results of our systematic study provide a comprehensive insight on the pressure dependence of 5f local magnetism in metallic systems. The unpolarized local density of states (LDOS), analyzed within the frame work of Stoner model suggest the occurrence of local moment for U in sp-elements, noble metals and f-block hosts like La, Ce, Lu and Th. In contrast, U is predicted to be nonmagnetic in most transition metal hosts except in Sc, Ti, Y, Zr, and Hf consistent with the results obtained from spin polarized calculation. The spin and orbital magnetic moments of U computed within the frame of LDA+U formalism show a scaling behavior with lattice compression. We have also computed the spin and orbital hyperfine fields and a detail analysis has been carried out. The host dependent trends for the magnetic moment, hyperfine field and 5f occupation reflect pressure induced change of electronic structure with U valency changing from 3+ to 4+ under lattice compression. In addition, we have made a detailed analysis of the impurity induced host spin polarization suggesting qualitatively different roles of f-band electrons on moment stability. The results presented in this work would be helpful towards understanding magnetism and spin fluctuation in U based alloys.

Local structural aspects of metal-metal transition in IrTe2 from x-ray PDF

NASA Astrophysics Data System (ADS)

Yu, Runze; Abeykoon, Milinda; Zhou, Haidong; Yin, Weiguo; Bozin, Emil S.

Evolution of local atomic structure across the metal-metal transition in IrTe2 is explored by pair distribution function (PDF) analysis of x-ray total scattering data over 80 K

Mapping local anisotropy axis for scattering media using backscattering Mueller matrix imaging

NASA Astrophysics Data System (ADS)

He, Honghui; Sun, Minghao; Zeng, Nan; Du, E.; Guo, Yihong; He, Yonghong; Ma, Hui

2014-03-01

Mueller matrix imaging techniques can be used to detect the micro-structure variations of superficial biological tissues, including the sizes and shapes of cells, the structures in cells, and the densities of the organelles. Many tissues contain anisotropic fibrous micro-structures, such as collagen fibers, elastin fibers, and muscle fibers. Changes of these fibrous structures are potentially good indicators for some pathological variations. In this paper, we propose a quantitative analysis technique based on Mueller matrix for mapping local anisotropy axis of scattering media. By conducting both experiments on silk sample and Monte Carlo simulation based on the sphere-cylinder scattering model (SCSM), we extract anisotropy axis parameters from different backscattering Mueller matrix elements. Moreover, we testify the possible applications of these parameters for biological tissues. The preliminary experimental results of human cancerous samples show that, these parameters are capable to map the local axis of fibers. Since many pathological changes including early stage cancers affect the well aligned structures for tissues, the experimental results indicate that these parameters can be used as potential tools in clinical applications for biomedical diagnosis purposes.

How to Define the Mean Square Amplitude of Solar Wind Fluctuations With Respect to the Local Mean Magnetic Field

NASA Astrophysics Data System (ADS)

Podesta, John J.

2017-12-01

Over the last decade it has become popular to analyze turbulent solar wind fluctuations with respect to a coordinate system aligned with the local mean magnetic field. This useful analysis technique has provided new information and new insights about the nature of solar wind fluctuations and provided some support for phenomenological theories of MHD turbulence based on the ideas of Goldreich and Sridhar. At the same time it has drawn criticism suggesting that the use of a scale-dependent local mean field is somehow inconsistent or irreconcilable with traditional analysis techniques based on second-order structure functions and power spectra that, for stationary time series, are defined with respect to the constant (scale-independent) ensemble average magnetic field. Here it is shown that for fluctuations with power law spectra, such as those observed in solar wind turbulence, it is possible to define the local mean magnetic field in a special way such that the total mean square amplitude (trace amplitude) of turbulent fluctuations is approximately the same, scale by scale, as that obtained using traditional second-order structure functions or power spectra. This fact should dispel criticism concerning the physical validity or practical usefulness of the local mean magnetic field in these applications.

A financial network perspective of financial institutions' systemic risk contributions

NASA Astrophysics Data System (ADS)

Huang, Wei-Qiang; Zhuang, Xin-Tian; Yao, Shuang; Uryasev, Stan

2016-08-01

This study considers the effects of the financial institutions' local topology structure in the financial network on their systemic risk contribution using data from the Chinese stock market. We first measure the systemic risk contribution with the Conditional Value-at-Risk (CoVaR) which is estimated by applying dynamic conditional correlation multivariate GARCH model (DCC-MVGARCH). Financial networks are constructed from dynamic conditional correlations (DCC) with graph filtering method of minimum spanning trees (MSTs). Then we investigate dynamics of systemic risk contributions of financial institution. Also we study dynamics of financial institution's local topology structure in the financial network. Finally, we analyze the quantitative relationships between the local topology structure and systemic risk contribution with panel data regression analysis. We find that financial institutions with greater node strength, larger node betweenness centrality, larger node closeness centrality and larger node clustering coefficient tend to be associated with larger systemic risk contributions.

Generalized non-Local Resistance Expression and its Application in F/N/F Spintronic Structure with Graphene Channel

NASA Astrophysics Data System (ADS)

Wei, Huazhou; Fu, Shiwei

We report our work on the spin transport properties in the F/N/F(ferromagnets/normal metal/ferromagnets) spintronic structure from a new theoretical perspective. A significant problem in the field is to explain the inferior measured order of magnitude for spin lifetime. Based on the known non-local resistance formula and the mechanism analysis of spin-flipping within the interfaces between F and N, we analytically derive a broadly applicable new non-local resistance expression and a generalized Hanle curve formula. After employing them in the F/N/F structure under different limits, especially in the case of graphene channel, we find that the fitting from experimental data would yield a longer spin lifetime, which approaches its theoretical predicted value in graphene. The authors acknowledge the financial support by China University of Petroleum-Beijing and the Key Laboratory of Optical Detection Technology for Oil and Gas in this institution.

The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation.

PubMed

Suzuki, K; Kirisako, T; Kamada, Y; Mizushima, N; Noda, T; Ohsumi, Y

2001-11-01

Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Several key reactions performed by these proteins have been described, but a comprehensive understanding of the overall network is still lacking. Based on Apg protein localization, we have identified a novel structure that functions in autophagosome formation. This pre-autophagosomal structure, containing at least five Apg proteins, i.e. Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p, is localized in the vicinity of the vacuole. Analysis of apg mutants revealed that the formation of both a phosphatidylethanolamine-conjugated Aut7p and an Apg12p- Apg5p conjugate is essential for the localization of Aut7p to the pre-autophagosomal structure. Vps30p/Apg6p and Apg14p, components of an autophagy- specific phosphatidylinositol 3-kinase complex, Apg9p and Apg16p are all required for the localization of Apg5p and Aut7p to the structure. The Apg1p protein kinase complex functions in the late stage of autophagosome formation. Here, we present the classification of Apg proteins into three groups that reflect each step of autophagosome formation.

The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation

PubMed Central

Suzuki, Kuninori; Kirisako, Takayoshi; Kamada, Yoshiaki; Mizushima, Noboru; Noda, Takeshi; Ohsumi, Yoshinori

2001-01-01

Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Several key reactions performed by these proteins have been described, but a comprehensive understanding of the overall network is still lacking. Based on Apg protein localization, we have identified a novel structure that functions in autophagosome formation. This pre-autophagosomal structure, containing at least five Apg proteins, i.e. Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p, is localized in the vicinity of the vacuole. Analysis of apg mutants revealed that the formation of both a phosphatidylethanolamine-conjugated Aut7p and an Apg12p– Apg5p conjugate is essential for the localization of Aut7p to the pre-autophagosomal structure. Vps30p/Apg6p and Apg14p, components of an autophagy- specific phosphatidylinositol 3-kinase complex, Apg9p and Apg16p are all required for the localization of Apg5p and Aut7p to the structure. The Apg1p protein kinase complex functions in the late stage of autophagosome formation. Here, we present the classification of Apg proteins into three groups that reflect each step of autophagosome formation. PMID:11689437

Exploring new topography-based subgrid spatial structures for improving land surface modeling

DOE PAGES

Tesfa, Teklu K.; Leung, Lai-Yung Ruby

2017-02-22

Topography plays an important role in land surface processes through its influence on atmospheric forcing, soil and vegetation properties, and river network topology and drainage area. Land surface models with a spatial structure that captures spatial heterogeneity, which is directly affected by topography, may improve the representation of land surface processes. Previous studies found that land surface modeling, using subbasins instead of structured grids as computational units, improves the scalability of simulated runoff and streamflow processes. In this study, new land surface spatial structures are explored by further dividing subbasins into subgrid structures based on topographic properties, including surface elevation,more » slope and aspect. Two methods (local and global) of watershed discretization are applied to derive two types of subgrid structures (geo-located and non-geo-located) over the topographically diverse Columbia River basin in the northwestern United States. In the global method, a fixed elevation classification scheme is used to discretize subbasins. The local method utilizes concepts of hypsometric analysis to discretize each subbasin, using different elevation ranges that also naturally account for slope variations. The relative merits of the two methods and subgrid structures are investigated for their ability to capture topographic heterogeneity and the implications of this on representations of atmospheric forcing and land cover spatial patterns. Results showed that the local method reduces the standard deviation (SD) of subgrid surface elevation in the study domain by 17 to 19 % compared to the global method, highlighting the relative advantages of the local method for capturing subgrid topographic variations. The comparison between the two types of subgrid structures showed that the non-geo-located subgrid structures are more consistent across different area threshold values than the geo-located subgrid structures. Altogether the local method and non-geo-located subgrid structures effectively and robustly capture topographic, climatic and vegetation variability, which is important for land surface modeling.« less

Exploring new topography-based subgrid spatial structures for improving land surface modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tesfa, Teklu K.; Leung, Lai-Yung Ruby

Topography plays an important role in land surface processes through its influence on atmospheric forcing, soil and vegetation properties, and river network topology and drainage area. Land surface models with a spatial structure that captures spatial heterogeneity, which is directly affected by topography, may improve the representation of land surface processes. Previous studies found that land surface modeling, using subbasins instead of structured grids as computational units, improves the scalability of simulated runoff and streamflow processes. In this study, new land surface spatial structures are explored by further dividing subbasins into subgrid structures based on topographic properties, including surface elevation,more » slope and aspect. Two methods (local and global) of watershed discretization are applied to derive two types of subgrid structures (geo-located and non-geo-located) over the topographically diverse Columbia River basin in the northwestern United States. In the global method, a fixed elevation classification scheme is used to discretize subbasins. The local method utilizes concepts of hypsometric analysis to discretize each subbasin, using different elevation ranges that also naturally account for slope variations. The relative merits of the two methods and subgrid structures are investigated for their ability to capture topographic heterogeneity and the implications of this on representations of atmospheric forcing and land cover spatial patterns. Results showed that the local method reduces the standard deviation (SD) of subgrid surface elevation in the study domain by 17 to 19 % compared to the global method, highlighting the relative advantages of the local method for capturing subgrid topographic variations. The comparison between the two types of subgrid structures showed that the non-geo-located subgrid structures are more consistent across different area threshold values than the geo-located subgrid structures. Altogether the local method and non-geo-located subgrid structures effectively and robustly capture topographic, climatic and vegetation variability, which is important for land surface modeling.« less

Parallel and competitive processes in hierarchical analysis: perceptual grouping and encoding of closure.

PubMed

Han, S; Humphreys, G W; Chen, L

1999-10-01

The role of perceptual grouping and the encoding of closure of local elements in the processing of hierarchical patterns was studied. Experiments 1 and 2 showed a global advantage over the local level for 2 tasks involving the discrimination of orientation and closure, but there was a local advantage for the closure discrimination task relative to the orientation discrimination task. Experiment 3 showed a local precedence effect for the closure discrimination task when local element grouping was weakened by embedding the stimuli from Experiment 1 in a background made up of cross patterns. Experiments 4A and 4B found that dissimilarity of closure between the local elements of hierarchical stimuli and the background figures could facilitate the grouping of closed local elements and enhanced the perception of global structure. Experiment 5 showed that the advantage for detecting the closure of local elements in hierarchical analysis also held under divided- and selective-attention conditions. Results are consistent with the idea that grouping between local elements takes place in parallel and competes with the computation of closure of local elements in determining the selection between global and local levels of hierarchical patterns for response.

Spatial localization of the first and last enzymes effectively connects active metabolic pathways in bacteria.

PubMed

Meyer, Pablo; Cecchi, Guillermo; Stolovitzky, Gustavo

2014-12-14

Although much is understood about the enzymatic cascades that underlie cellular biosynthesis, comparatively little is known about the rules that determine their cellular organization. We performed a detailed analysis of the localization of E.coli GFP-tagged enzymes for cells growing exponentially. We found that out of 857 globular enzymes, at least 219 have a discrete punctuate localization in the cytoplasm and catalyze the first or the last reaction in 60% of biosynthetic pathways. A graph-theoretic analysis of E.coli's metabolic network shows that localized enzymes, in contrast to non-localized ones, form a tree-like hierarchical structure, have a higher within-group connectivity, and are traversed by a higher number of feed-forward and feedback loops than their non-localized counterparts. A Gene Ontology analysis of these enzymes reveals an enrichment of terms related to essential metabolic functions in growing cells. Given that these findings suggest a distinct metabolic role for localization, we studied the dynamics of cellular localization of the cell wall synthesizing enzymes in B. subtilis and found that enzymes localize during exponential growth but not during stationary growth. We conclude that active biochemical pathways inside the cytoplasm are organized spatially following a rule where their first or their last enzymes localize to effectively connect the different active pathways and thus could reflect the activity state of the cell's metabolic network.

Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER.

PubMed

Han, Xusi; Wei, Qing; Kihara, Daisuke

2017-12-08

With the rapid growth in the number of solved protein structures stored in the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB), it is essential to develop tools to perform real-time structure similarity searches against the entire structure database. Since conventional structure alignment methods need to sample different orientations of proteins in the three-dimensional space, they are time consuming and unsuitable for rapid, real-time database searches. To this end, we have developed 3D-SURFER and EM-SURFER, which utilize 3D Zernike descriptors (3DZD) to conduct high-throughput protein structure comparison, visualization, and analysis. Taking an atomic structure or an electron microscopy map of a protein or a protein complex as input, the 3DZD of a query protein is computed and compared with the 3DZD of all other proteins in PDB or EMDB. In addition, local geometrical characteristics of a query protein can be analyzed using VisGrid and LIGSITE CSC in 3D-SURFER. This article describes how to use 3D-SURFER and EM-SURFER to carry out protein surface shape similarity searches, local geometric feature analysis, and interpretation of the search results. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

An ecological genetic delineation of local seed-source provenance for ecological restoration

PubMed Central

Krauss, Siegfried L; Sinclair, Elizabeth A; Bussell, John D; Hobbs, Richard J

2013-01-01

An increasingly important practical application of the analysis of spatial genetic structure within plant species is to help define the extent of local provenance seed collection zones that minimize negative impacts in ecological restoration programs. Here, we derive seed sourcing guidelines from a novel range-wide assessment of spatial genetic structure of 24 populations of Banksia menziesii (Proteaceae), a widely distributed Western Australian tree of significance in local ecological restoration programs. An analysis of molecular variance (AMOVA) of 100 amplified fragment length polymorphism (AFLP) markers revealed significant genetic differentiation among populations (ΦPT = 0.18). Pairwise population genetic dissimilarity was correlated with geographic distance, but not environmental distance derived from 15 climate variables, suggesting overall neutrality of these markers with regard to these climate variables. Nevertheless, Bayesian outlier analysis identified four markers potentially under selection, although these were not correlated with the climate variables. We calculated a global R-statistic using analysis of similarities (ANOSIM) to test the statistical significance of population differentiation and to infer a threshold seed collection zone distance of ∼60 km (all markers) and 100 km (outlier markers) when genetic distance was regressed against geographic distance. Population pairs separated by >60 km were, on average, twice as likely to be significantly genetically differentiated than population pairs separated by <60 km, suggesting that habitat-matched sites within a 30-km radius around a restoration site genetically defines a local provenance seed collection zone for B. menziesii. Our approach is a novel probability-based practical solution for the delineation of a local seed collection zone to minimize negative genetic impacts in ecological restoration. PMID:23919158

Mapping local deformation behavior in single cell metal lattice structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carlton, Holly D.; Lind, Jonathan; Messner, Mark C.

The deformation behavior of metal lattice structures is extremely complex and challenging to predict, especially since strain is not uniformly distributed throughout the structure. Understanding and predicting the failure behavior for these types of light-weighting structures is of great interest due to the excellent scaling of stiffness- and strength-to weight ratios they display. Therefore, there is a need to perform simplified experiments that probe unit cell mechanisms. This study reports on high resolution mapping of the heterogeneous structural response of single unit cells to the macro-scale loading condition. Two types of structures, known to show different stress-strain responses, were evaluatedmore » using synchrotron radiation micro-tomography while performing in-situ uniaxial compression tests to capture the local micro-strain deformation. These structures included the octet-truss, a stretch-dominated lattice, and the rhombic-dodecahedron, a bend-dominated lattice. The tomographic analysis showed that the stretch- and bend-dominated lattices exhibit different failure mechanisms and that the defects built into the structure cause a heterogeneous localized deformation response. Also shown here is a change in failure mode for stretch-dominated lattices, where there appears to be a transition from buckling to plastic yielding for samples with a relative density between 10 and 20%. In conclusion, the experimental results were also used to inform computational studies designed to predict the mesoscale deformation behavior of lattice structures. Here an equivalent continuum model and a finite element model were used to predict both local strain fields and mechanical behavior of lattices with different topologies.« less

Mapping local deformation behavior in single cell metal lattice structures

DOE PAGES

Carlton, Holly D.; Lind, Jonathan; Messner, Mark C.; ...

2017-02-08

The deformation behavior of metal lattice structures is extremely complex and challenging to predict, especially since strain is not uniformly distributed throughout the structure. Understanding and predicting the failure behavior for these types of light-weighting structures is of great interest due to the excellent scaling of stiffness- and strength-to weight ratios they display. Therefore, there is a need to perform simplified experiments that probe unit cell mechanisms. This study reports on high resolution mapping of the heterogeneous structural response of single unit cells to the macro-scale loading condition. Two types of structures, known to show different stress-strain responses, were evaluatedmore » using synchrotron radiation micro-tomography while performing in-situ uniaxial compression tests to capture the local micro-strain deformation. These structures included the octet-truss, a stretch-dominated lattice, and the rhombic-dodecahedron, a bend-dominated lattice. The tomographic analysis showed that the stretch- and bend-dominated lattices exhibit different failure mechanisms and that the defects built into the structure cause a heterogeneous localized deformation response. Also shown here is a change in failure mode for stretch-dominated lattices, where there appears to be a transition from buckling to plastic yielding for samples with a relative density between 10 and 20%. In conclusion, the experimental results were also used to inform computational studies designed to predict the mesoscale deformation behavior of lattice structures. Here an equivalent continuum model and a finite element model were used to predict both local strain fields and mechanical behavior of lattices with different topologies.« less

Analysis and prediction of calcium-binding pockets from apo-protein structures exhibiting calcium-induced localized conformational changes

PubMed Central

Wang, Xue; Zhao, Kun; Kirberger, Michael; Wong, Hing; Chen, Guantao; Yang, Jenny J

2010-01-01

Calcium binding in proteins exhibits a wide range of polygonal geometries that relate directly to an equally diverse set of biological functions. The binding process stabilizes protein structures and typically results in local conformational change and/or global restructuring of the backbone. Previously, we established the MUG program, which utilized multiple geometries in the Ca2+-binding pockets of holoproteins to identify such pockets, ignoring possible Ca2+-induced conformational change. In this article, we first report our progress in the analysis of Ca2+-induced conformational changes followed by improved prediction of Ca2+-binding sites in the large group of Ca2+-binding proteins that exhibit only localized conformational changes. The MUGSR algorithm was devised to incorporate side chain torsional rotation as a predictor. The output from MUGSR presents groups of residues where each group, typically containing two to five residues, is a potential binding pocket. MUGSR was applied to both X-ray apo structures and NMR holo structures, which did not use calcium distance constraints in structure calculations. Predicted pockets were validated by comparison with homologous holo structures. Defining a “correct hit” as a group of residues containing at least two true ligand residues, the sensitivity was at least 90%; whereas for a “correct hit” defined as a group of residues containing at least three true ligand residues, the sensitivity was at least 78%. These data suggest that Ca2+-binding pockets are at least partially prepositioned to chelate the ion in the apo form of the protein. PMID:20512971

Phenomenology and energetics of diffusion across cell phase states.

PubMed

Ashrafuzzaman, Md

2015-11-01

Cell based transport properties have been mathematically addressed. Cell contained cross boundary diffusion of materials has been explained using valid formalisms and related analytical expressions have been developed. Various distinguishable physical structures and their properties raise different general structure specific diffusion mechanisms and controlled transport related parameters. Some of these parameters play phenomenological roles and some cause regulatory effects. The cell based compartments may be divided into three major physical phase states namely liquid, plasma and solid phase states. Transport of ions, nutrients, small molecules like proteins, etc. across inter phase states and intraphase states follows general transport related formalisms. Creation of some localized permanent and/or temporary structures e.g., ion channels, clustering of constituents, etc. and the transitions between such structures appear as regulators of the transport mechanisms. In this article, I have developed mainly a theoretical analysis of the commonly observed cell transport phenomena. I have attempted to develop formalisms on general cell based diffusion followed by a few numerical computations to address the analytical expression phenomenologically. I have then extended the analysis to adopting with the local structure originated energetics. Independent or correlated molecular transport naturally relies on some general parameters that define the nature of local cell environment as well as on some occasionally raised or transiently active stochastic resonance due to localized interactions. Short and long range interaction energies play crucial roles in this regard. Physical classification of cellular compartments has led us developing analytical expressions on both biologically observed diffusion mechanisms and the diffusions's occasional stochasticity causing energetics. These analytical expressions help us address the diffusion phenomena generally considering the physical properties of the biostructures across the diffusion pathways. A specific example case of single molecule transport and localized interaction energetics in a specific cell phase has been utilized to address the diffusion quite clearly. This article helps to address the mechanisms of cell based diffusion and nutrient movements and thus helps develop strategic templates to manipulate the diffusion mechanisms. Application of the theoretical knowledge into designing or discovering drugs or small molecule inhibitors targeting cell based structures may open up new avenues in biomedical sciences.

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication

PubMed Central

Stetz, Gabrielle; Verkhivker, Gennady M.

2017-01-01

Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of allostery, we introduced a community-hopping model of allosteric communication. Atomistic reconstruction of signaling pathways in the DnaK structures captured a direction-specific mechanism and molecular details of signal transmission that are fully consistent with the mutagenesis experiments. The results of our study reconciled structural and functional experiments from a network-centric perspective by showing that global properties of the residue interaction networks and coevolutionary signatures may be linked with specificity and diversity of allosteric regulation mechanisms. PMID:28095400

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.

PubMed

Stetz, Gabrielle; Verkhivker, Gennady M

2017-01-01

Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of allostery, we introduced a community-hopping model of allosteric communication. Atomistic reconstruction of signaling pathways in the DnaK structures captured a direction-specific mechanism and molecular details of signal transmission that are fully consistent with the mutagenesis experiments. The results of our study reconciled structural and functional experiments from a network-centric perspective by showing that global properties of the residue interaction networks and coevolutionary signatures may be linked with specificity and diversity of allosteric regulation mechanisms.

Community investment in wind farms: funding structure effects in wind energy infrastructure development.

PubMed

Beery, Joshua A; Day, Jennifer E

2015-03-03

Wind energy development is an increasingly popular form of renewable energy infrastructure in rural areas. Communities generally perceive socioeconomic benefits accrue and that community funding structures are preferable to corporate structures, yet lack supporting quantitative data to inform energy policy. This study uses the Everpower wind development, to be located in Midwestern Ohio, as a hypothetical modeling environment to identify and examine socioeconomic impact trends arising from corporate, community and diversified funding structures. Analysis of five National Renewable Energy Laboratory Jobs and Economic Development Impact models incorporating local economic data and review of relevant literature were conducted. The findings suggest that community and diversified funding structures exhibit 40-100% higher socioeconomic impact levels than corporate structures. Prioritization of funding sources and retention of federal tax incentives were identified as key elements. The incorporation of local shares was found to mitigate the negative effects of foreign private equity, local debt financing increased economic output and opportunities for private equity investment were identified. The results provide the groundwork for energy policies focused to maximize socioeconomic impacts while creating opportunities for inclusive economic participation and improved social acceptance levels fundamental to the deployment of renewable energy technology.

A Solid-State NMR Experiment: Analysis of Local Structural Environments in Phosphate Glasses

ERIC Educational Resources Information Center

Anderson, Stanley E.; Saiki, David; Eckert, Hellmut; Meise-Gresch, Karin

2004-01-01

An experiment that can be used to directly study the local chemical environments of phosphorus in solid amorphous materials is demonstrated. The experiment aims at familiarizing the students of chemistry with the principles of solid-state NMR, by having them synthesize a simple phosphate glass, and making them observe the (super 31)P NMR spectrum,…

The role of a food policy coalition in influencing a local food environment: an Australian case study.

PubMed

McCartan, Julia; Palermo, Claire

2017-04-01

To explore how an Australian rural food policy coalition acts to influence a local food environment, focusing specifically on its composition, functions and processes as well as its food-related strategies and policy outputs. A qualitative case study approach was undertaken. Three sources were used to triangulate data: eleven semi-structured in-depth interviews with coalition members, analysis of thirty-seven documents relating to the coalition and observation at one coalition meeting. Data were analysed using a thematic and constant comparison approach. Community Coalition Action Theory provided a theoretical framework from which to interpret findings. Two rural local government areas on the south-eastern coast of Victoria, Australia. Eleven members of the food policy coalition. Five themes emerged from the data analysis. The themes described the coalition's leadership processes, membership structure, function to pool resources for food system advocacy, focus on collaborative cross-jurisdictional strategies and ability to influence policy change. This Australian case study demonstrates that with strong leadership, a small-sized core membership and focus on collaborative strategies, food policy coalitions may be a mechanism to positively influence local food environments.

Structural zooming research and development of an interactive computer graphical interface for stress analysis of cracks

NASA Technical Reports Server (NTRS)

Gerstle, Walter

1989-01-01

Engineering problems sometimes involve the numerical solution of boundary value problems over domains containing geometric feature with widely varying scales. Often, a detailed solution is required at one or more of these features. Small details in large structures may have profound effects upon global performance. Conversely, large-scale conditions may effect local performance. Many man-hours and CPU-hours are currently spent in modeling such problems. With the structural zooming technique, it is now possible to design an integrated program which allows the analyst to interactively focus upon a small region of interest, to modify the local geometry, and then to obtain highly accurate responses in that region which reflect both the properties of the overall structure and the local detail. A boundary integral equation analysis program, called BOAST, was recently developed for the stress analysis of cracks. This program can accurately analyze two-dimensional linear elastic fracture mechanics problems with far less computational effort than existing finite element codes. An interactive computer graphical interface to BOAST was written. The graphical interface would have several requirements: it would be menu-driven, with mouse input; all aspects of input would be entered graphically; the results of a BOAST analysis would be displayed pictorially but also the user would be able to probe interactively to get numerical values of displacement and stress at desired locations within the analysis domain; the entire procedure would be integrated into a single, easy to use package; and it would be written using calls to the graphic package called HOOPS. The program is nearing completion. All of the preprocessing features are working satisfactorily and were debugged. The postprocessing features are under development, and rudimentary postprocessing should be available by the end of the summer. The program was developed and run on a VAX workstation, and must be ported to the SUN workstation. This activity is currently underway.

Direct observation of strain localization along the differentially exhumed SEMP fault system, Austria

NASA Astrophysics Data System (ADS)

Frost, E.; Dolan, J. F.; Hacker, B. R.; Ratschbacher, L.; Sammis, C. G.; Seward, G.; Cole, J.

2009-12-01

Structural analysis of key outcrops from ~5 to ~25 km exhumation depth along the Salzach-Ennstal-Mariazell-Puchberg (SEMP) fault-zone in Austria reveal highly localized deformation in the seismogenic crust down through the brittle-ductile transition (BDT), widening into a 2-km-wide mylonite at mid-crustal levels. Specifically, grain-size distribution analysis of brittley-deformed dolomite exhumed from the seismogenic crust reveals that strain progressively localized into a 10-m-wide fault core. Microstructural analysis of marbles and greywackes exhumed from the BDT shows off-fault ductile deformation only accommodated a minor portion of the displacement along the SEMP, with most of the strain localized along the contact between these two units. Similar analysis of gneisses and amphibolite-facies metasediments exhumed from just below the BDT shows that at this depth, the majority of displacement is focused into a 100-m-wide ductile shear zone, with further evidence for strain localization along grain boundaries, creating throughgoing shear zones at the grain-scale. At deeper exhumation levels (Rosenberg and Schneider, 2008), the SEMP is a 1-2-km-wide mylonite zone that extends to depths of at least 25 km. Collectively, these data indicate that slip along the SEMP was highly localized from throughout the seismogenic crust downward into at least the mid-crust.

Imaging and reconstruction of cell cortex structures near the cell surface

NASA Astrophysics Data System (ADS)

Jin, Luhong; Zhou, Xiaoxu; Xiu, Peng; Luo, Wei; Huang, Yujia; Yu, Feng; Kuang, Cuifang; Sun, Yonghong; Liu, Xu; Xu, Yingke

2017-11-01

Total internal reflection fluorescence microscopy (TIRFM) provides high optical sectioning capability and superb signal-to-noise ratio for imaging of cell cortex structures. The development of multi-angle (MA)-TIRFM permits high axial resolution imaging and reconstruction of cellular structures near the cell surface. Cytoskeleton is composed of a network of filaments, which are important for maintenance of cell function. The high-resolution imaging and quantitative analysis of filament organization would contribute to our understanding of cytoskeleton regulation in cell. Here, we used a custom-developed MA-TIRFM setup, together with stochastic photobleaching and single molecule localization method, to enhance the lateral resolution of TIRFM imaging to about 100 nm. In addition, we proposed novel methods to perform filament segmentation and 3D reconstruction from MA-TIRFM images. Furthermore, we applied these methods to study the 3D localization of cortical actin and microtubule structures in U373 cancer cells. Our results showed that cortical actins localize ∼ 27 nm closer to the plasma membrane when compared with microtubules. We found that treatment of cells with chemotherapy drugs nocodazole and cytochalasin B disassembles cytoskeletal network and induces the reorganization of filaments towards the cell periphery. In summary, this study provides feasible approaches for 3D imaging and analyzing cell surface distribution of cytoskeletal network. Our established microscopy platform and image analysis toolkits would facilitate the study of cytoskeletal network in cells.

Non-traditional Infrasound Deployment

NASA Astrophysics Data System (ADS)

McKenna, M. H.; McComas, S.; Simpson, C. P.; Diaz-Alvarez, H.; Costley, R. D.; Hayward, C.; Golden, P.; Endress, A.

2017-12-01

Historically, infrasound arrays have been deployed in rural environments where anthropological noise sources are limited. As interest in monitoring low energy sources at local distances grows in the infrasound community, it will be vital to understand how to monitor infrasound sources in an urban environment. Arrays deployed in urban centers have to overcome the decreased signal-to-noise ratio and reduced amount of real estate available to deploy an array. To advance the understanding of monitoring infrasound sources in urban environments, local and regional infrasound arrays were deployed on building rooftops on the campus at Southern Methodist University (SMU), and data were collected for one seasonal cycle. The data were evaluated for structural source signals (continuous-wave packets), and when a signal was identified, the back azimuth to the source was determined through frequency-wavenumber analysis. This information was used to identify hypothesized structural sources; these sources were verified through direct measurement and dynamic structural analysis modeling. In addition to the rooftop arrays, a camouflaged infrasound sensor was installed on the SMU campus and evaluated to determine its effectiveness for wind noise reduction. Permission to publish was granted by Director, Geotechnical and Structures Laboratory.

Average and local crystal structures of (Ga 1–xZn x)(N 1–xO x) solid solution nanoparticles

DOE PAGES

Feygenson, Mikhail; Neuefeind, Joerg C.; Tyson, Trevor A.; ...

2015-11-06

We report the comprehensive study of the crystal structure of (Ga 1–xZn x)(N 1–xO x) solid solution nanoparticles by means of neutron and synchrotron x-ray scattering. In our study we used four different types of (Ga 1–xZn x)(N 1–xO x) nanoparticles, with diameters of 10–27 nm and x = 0.075–0.51, which show the narrow energy-band gaps from 2.21 to 2.61 eV. The Rietveld analysis of the neutron diffraction data revealed that the average crystal structure is the hexagonal wurtzite (space group P6 3mc), in agreement with previous reports on similar bulk materials. The pair-distribution function (PDF) analysis of the samemore » data found that the local structure is more disordered than the average one. It is best described by the model with a lower symmetry space group P1, where atoms are quasirandomly distorted from their nominal positions in the hexagonal wurtzite lattice.« less

Stress Analysis of Bolted, Segmented Cylindrical Shells Exhibiting Flange Mating-Surface Waviness

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.; Phillips, Dawn R.; Raju, Ivatury S.

2009-01-01

Bolted, segmented cylindrical shells are a common structural component in many engineering systems especially for aerospace launch vehicles. Segmented shells are often needed due to limitations of manufacturing capabilities or transportation issues related to very long, large-diameter cylindrical shells. These cylindrical shells typically have a flange or ring welded to opposite ends so that shell segments can be mated together and bolted to form a larger structural system. As the diameter of these shells increases, maintaining strict fabrication tolerances for the flanges to be flat and parallel on a welded structure is an extreme challenge. Local fit-up stresses develop in the structure due to flange mating-surface mismatch (flange waviness). These local stresses need to be considered when predicting a critical initial flaw size. Flange waviness is one contributor to the fit-up stress state. The present paper describes the modeling and analysis effort to simulate fit-up stresses due to flange waviness in a typical bolted, segmented cylindrical shell. Results from parametric studies are presented for various flange mating-surface waviness distributions and amplitudes.

Analysis and modeling of localized invariant solutions in pipe flow

NASA Astrophysics Data System (ADS)

Ritter, Paul; Zammert, Stefan; Song, Baofang; Eckhardt, Bruno; Avila, Marc

2018-01-01

Turbulent spots surrounded by laminar flow are a landmark of transitional shear flows, but the dependence of their kinematic properties on spatial structure is poorly understood. We here investigate this dependence in pipe flow for Reynolds numbers between 1500 and 5000. We compute spatially localized relative periodic orbits in long pipes and show that their upstream and downstream fronts decay exponentially towards the laminar profile. This allows us to model the fronts by employing the linearized Navier-Stokes equations, and the resulting model yields the spatial decay rate and the front velocity profiles of the periodic orbits as a function of Reynolds number, azimuthal wave number, and propagation speed. In addition, when applied to a localized turbulent puff, the model is shown to accurately approximate the spatial decay rate of its upstream and downstream tails. Our study provides insight into the relationship between the kinematics and spatial structure of localized turbulence and more generally into the physics of localization.

Discrete crack growth analysis methodology for through cracks in pressurized fuselage structures

NASA Technical Reports Server (NTRS)

Potyondy, David O.; Wawrzynek, Paul A.; Ingraffea, Anthony R.

1994-01-01

A methodology for simulating the growth of long through cracks in the skin of pressurized aircraft fuselage structures is described. Crack trajectories are allowed to be arbitrary and are computed as part of the simulation. The interaction between the mechanical loads acting on the superstructure and the local structural response near the crack tips is accounted for by employing a hierarchical modeling strategy. The structural response for each cracked configuration is obtained using a geometrically nonlinear shell finite element analysis procedure. Four stress intensity factors, two for membrane behavior and two for bending using Kirchhoff plate theory, are computed using an extension of the modified crack closure integral method. Crack trajectories are determined by applying the maximum tangential stress criterion. Crack growth results in localized mesh deletion, and the deletion regions are remeshed automatically using a newly developed all-quadrilateral meshing algorithm. The effectiveness of the methodology and its applicability to performing practical analyses of realistic structures is demonstrated by simulating curvilinear crack growth in a fuselage panel that is representative of a typical narrow-body aircraft. The predicted crack trajectory and fatigue life compare well with measurements of these same quantities from a full-scale pressurized panel test.

Hydrogen positions in single nanocrystals revealed by electron diffraction

NASA Astrophysics Data System (ADS)

Palatinus, L.; Brázda, P.; Boullay, P.; Perez, O.; Klementová, M.; Petit, S.; Eigner, V.; Zaarour, M.; Mintova, S.

2017-01-01

The localization of hydrogen atoms is an essential part of crystal structure analysis, but it is difficult because of their small scattering power. We report the direct localization of hydrogen atoms in nanocrystalline materials, achieved using the recently developed approach of dynamical refinement of precession electron diffraction tomography data. We used this method to locate hydrogen atoms in both an organic (paracetamol) and an inorganic (framework cobalt aluminophosphate) material. The results demonstrate that the technique can reliably reveal fine structural details, including the positions of hydrogen atoms in single crystals with micro- to nanosized dimensions.

The transformation of amorphous calcium carbonate, ACC, to crystalline phases as function of time and temperature.

NASA Astrophysics Data System (ADS)

Gies, Hermann; Happel, Marian; Niedermayr, Andrea; Immenhauser, Adrian

2017-04-01

We present results from a structural study of the transformation of freeze dried amorphous calcium carbonate, ACC, in crystalline material using pair distribution function analysis, PDF analysis, of X-ray powder diffraction data, XPD data. PDF analysis allows for the analysis of local order of structural subunit in the range between molecular unit (1. and 2. coordination sphere) and long range periodicity as in crystalline materials. ACC was precipitated from aqueous solutions at 298 K and 278 K using different amounts of Mg cations as stabilizer. The samples were immediately separated from the solution and freeze dried. For the transformation study, the samples were heated and analysed using XPD until they were crystallized. The radial distribution obtained from the XPD data were compared to simulated radial distributions of the calcium carbonate polymorphs and their hydrated phases. An ACC precipitated from a solution with Ca:Mg:CO3 = 1:5:4 at 298 K (ration in mmol, pH = 8.2) and freeze dried right after isolation from the solution revealed a close resemblance with ikaite in its local order. Another ACC with Ca:Mg:CO3 = 1:10:1.4 (T = 298, pH = 8.7) showed distinctly different local order resembling monohydrocalcite. Both ACC, however, still had considerable amounts of water dominating the Ca-coordination sphere. During the transformation to calcite, the structural changes in the sample concerned the hydrate water coordinating Ca which was removed and replaced by the carbonate oxygens. The study shows that ACC obtained from different starting solutions show specific local order. Freeze drying leads to solid ACC powder which still contain considerable amounts of hydrate water. Structural subunits are distinct in ACC and different from the crystalline phase. The study supplements recent reports presented by Konrad et al., Purgstaller et al., and Tobler et al.. F. Konrad et al., Cryst. Growth Des. 16, 6310-6317(2016) B. Purgstaller et al., Geochimica et Cosmochimica Acta 174, 180-195(2016) DJ. Tobler et al., Cryst. Growth Des. 16, 4500-4508(2016)

Scaling analysis of Anderson localizing optical fibers

NASA Astrophysics Data System (ADS)

Abaie, Behnam; Mafi, Arash

2017-02-01

Anderson localizing optical fibers (ALOF) enable a novel optical waveguiding mechanism; if a narrow beam is scanned across the input facet of the disordered fiber, the output beam follows the transverse position of the incoming wave. Strong transverse disorder induces several localized modes uniformly spread across the transverse structure of the fiber. Each localized mode acts like a transmission channel which carries a narrow input beam along the fiber without transverse expansion. Here, we investigate scaling of transverse size of the localized modes of ALOF with respect to transverse dimensions of the fiber. Probability density function (PDF) of the mode-area is applied and it is shown that PDF converges to a terminal shape at transverse dimensions considerably smaller than the previous experimental implementations. Our analysis turns the formidable numerical task of ALOF simulations into a much simpler problem, because the convergence of mode-area PDF to a terminal shape indicates that a much smaller disordered fiber, compared to previous numerical and experimental implementations, provides all the statistical information required for the precise analysis of the fiber.

Morphometry Based on Effective and Accurate Correspondences of Localized Patterns (MEACOLP)

PubMed Central

Wang, Hu; Ren, Yanshuang; Bai, Lijun; Zhang, Wensheng; Tian, Jie

2012-01-01

Local features in volumetric images have been used to identify correspondences of localized anatomical structures for brain morphometry. However, the correspondences are often sparse thus ineffective in reflecting the underlying structures, making it unreliable to evaluate specific morphological differences. This paper presents a morphometry method (MEACOLP) based on correspondences with improved effectiveness and accuracy. A novel two-level scale-invariant feature transform is used to enhance the detection repeatability of local features and to recall the correspondences that might be missed in previous studies. Template patterns whose correspondences could be commonly identified in each group are constructed to serve as the basis for morphometric analysis. A matching algorithm is developed to reduce the identification errors by comparing neighboring local features and rejecting unreliable matches. The two-sample t-test is finally adopted to analyze specific properties of the template patterns. Experiments are performed on the public OASIS database to clinically analyze brain images of Alzheimer's disease (AD) and normal controls (NC). MEACOLP automatically identifies known morphological differences between AD and NC brains, and characterizes the differences well as the scaling and translation of underlying structures. Most of the significant differences are identified in only a single hemisphere, indicating that AD-related structures are characterized by strong anatomical asymmetry. In addition, classification trials to differentiate AD subjects from NC confirm that the morphological differences are reliably related to the groups of interest. PMID:22540000

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

PubMed

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

2008-04-01

The detection of Outer Membrane Proteins (OMP) in whole genomes is an actual question, their sequence characteristics have thus been intensively studied. This class of protein displays a common beta-barrel architecture, formed by adjacent antiparallel strands. However, due to the lack of available structures, few structural studies have been made on this class of proteins. Here we propose a novel OMP local structure investigation, based on a structural alphabet approach, i.e., the decomposition of 3D structures using a library of four-residue protein fragments. The optimal decomposition of structures using hidden Markov model results in a specific structural alphabet of 20 fragments, six of them dedicated to the decomposition of beta-strands. This optimal alphabet, called SA20-OMP, is analyzed in details, in terms of local structures and transitions between fragments. It highlights a particular and strong organization of beta-strands as series of regular canonical structural fragments. The comparison with alphabets learned on globular structures indicates that the internal organization of OMP structures is more constrained than in globular structures. The analysis of OMP structures using SA20-OMP reveals some recurrent structural patterns. The preferred location of fragments in the distinct regions of the membrane is investigated. The study of pairwise specificity of fragments reveals that some contacts between structural fragments in beta-sheets are clearly favored whereas others are avoided. This contact specificity is stronger in OMP than in globular structures. Moreover, SA20-OMP also captured sequential information. This can be integrated in a scoring function for structural model ranking with very promising results. (c) 2007 Wiley-Liss, Inc.

Special Features of Strain Localization and Nanodipoles of Partial Disclinations in the Region of Elastic Distortions

NASA Astrophysics Data System (ADS)

Tyumentsev, A. N.; Ditenberg, I. A.; Sukhanov, I. I.

2018-02-01

In the zones of strain localization in the region of elastic distortions and nanodipoles of partial disclinations representing the defects of elastically deformed medium, a theoretical analysis of the elastically stressed state and the energy of these defects, including the cases of their transformation into more complex ensembles of interrelated disclinations, is performed. Using the analytical results, the mechanisms of strain localization are discussed in the stages of nucleation and propagation of the bands of elastic and plastic strain localization formed in these zones (including the cases of nanocrystalline structure formation).

In-situ chemical analyses of trans-polyisoprene by histochemical staining and Fourier transform infrared microspectroscopy in a rubber-producing plant, Eucommia ulmoides Oliver.

PubMed

Bamba, Takeshi; Fukusaki, Ei-Ichiro; Nakazawa, Yoshihisa; Kobayashi, Akio

2002-10-01

The localization of polyisoprene in young stem tissues of Eucommia ulmoides Oliver was investigated by histochemical staining and Fourier transform infrared (FT-IR) microspectroscopy. The fibrous structures were stained with Oil Red O. FT-IR microspectroscopic analysis proved that the fibrous structures were trans-polyisoprene. Granular structures stained with the dye, and characteristic absorptions at 2,960 cm(-1) and 1,430 cm(-1) in FT-IR suggested that trans-polyisoprene accumulated in the vicinity of the cambium layer. We have thus successfully shown for the first time the localization of trans-polyisoprene in plant tissues, and our histological investigation allowed us to presume the main sites of biosynthesis and accumulation of trans-rubber. Furthermore, a new technical approach, the preparation of sections using an electronic freezing unit and the in situ analysis of polyisoprene using FT-IR microspectroscopy, is demonstrated to be a promising method for determining the accumulation of polyisoprene as well as other metabolites.

Synthesis, crystal structure analysis, molecular docking studies and density functional theory predictions of the local reactive properties and degradation properties of a novel halochalcone

NASA Astrophysics Data System (ADS)

Arshad, Suhana; Pillai, Renjith Raveendran; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.

2017-09-01

In the present study, single crystals of E)-3-(3,5-dichlorophenyl)-1-(4-fluorophenyl)prop-2-en-1-one, were prepared and structurally characterized by single crystal X-ray diffraction analysis. The molecular structure crystallized in monoclinic crystal system with P21/c space group. Sensitivity of the title molecule towards electrophilic attacks has been examined by calculations of average localized ionization energies (ALIE) and their mapping to electron density surface. Further determination of atoms that could be important reactive centres has been performed by calculations of Fukui functions. Sensitivity of title molecule towards autoxidation and hydrolysis mechanisms has been assessed by calculations of bond dissociation energies and radial distribution functions (RDF), respectively. Also, in order to explore possible binding mode of the title compound towards Dihydrofolate reductase enzyme, we have utilized in silico molecular docking to explore possible binding modes of the title compound with the DHFR enzyme.

Automatic abdominal lymph node detection method based on local intensity structure analysis from 3D x-ray CT images

NASA Astrophysics Data System (ADS)

Nakamura, Yoshihiko; Nimura, Yukitaka; Kitasaka, Takayuki; Mizuno, Shinji; Furukawa, Kazuhiro; Goto, Hidemi; Fujiwara, Michitaka; Misawa, Kazunari; Ito, Masaaki; Nawano, Shigeru; Mori, Kensaku

2013-03-01

This paper presents an automated method of abdominal lymph node detection to aid the preoperative diagnosis of abdominal cancer surgery. In abdominal cancer surgery, surgeons must resect not only tumors and metastases but also lymph nodes that might have a metastasis. This procedure is called lymphadenectomy or lymph node dissection. Insufficient lymphadenectomy carries a high risk for relapse. However, excessive resection decreases a patient's quality of life. Therefore, it is important to identify the location and the structure of lymph nodes to make a suitable surgical plan. The proposed method consists of candidate lymph node detection and false positive reduction. Candidate lymph nodes are detected using a multi-scale blob-like enhancement filter based on local intensity structure analysis. To reduce false positives, the proposed method uses a classifier based on support vector machine with the texture and shape information. The experimental results reveal that it detects 70.5% of the lymph nodes with 13.0 false positives per case.

Scope of inextensible frame hypothesis in local action analysis of spherical reservoirs

NASA Astrophysics Data System (ADS)

Vinogradov, Yu. I.

2017-05-01

Spherical reservoirs, as objects perfect with respect to their weight, are used in spacecrafts, where thin-walled elements are joined by frames into multifunction structures. The junctions are local, which results in origination of stress concentration regions and the corresponding rigidity problems. The thin-walled elements are reinforced by frame to decrease the stresses in them. To simplify the analysis of the mathematical model of common deformation of the shell (which is a mathematical idealization of the reservoir) and the frame, the assumption that the frame axial line is inextensible is used widely (in particular, in the manual literature). The unjustified use of this assumption significantly distorts the concept of the stress-strain state. In this paper, an example of a lens-shaped structure formed as two spherical shell segments connected by a frame of square profile is used to carry out a numerical comparative analysis of the solutions with and without the inextensible frame hypothesis taken into account. The scope of the hypothesis is shown depending on the structure geometric parameters and the load location degree. The obtained results can be used to determine the stress-strain state of the thin-walled structure with an a priori prescribed error, for example, in research and experimental design of aerospace systems.

Printed strain sensors for early damage detection in engineering structures

NASA Astrophysics Data System (ADS)

Zymelka, Daniel; Yamashita, Takahiro; Takamatsu, Seiichi; Itoh, Toshihiro; Kobayashi, Takeshi

2018-05-01

In this paper, we demonstrate the analysis of strain measurements recorded using a screen-printed sensors array bonded to a metal plate and subjected to high strains. The analysis was intended to evaluate the capabilities of the printed strain sensors to detect abnormal strain distribution before actual defects (cracks) in the analyzed structures appear. The results demonstrate that the developed device can accurately localize the enhanced strains at the very early stage of crack formation. The promising performance and low fabrication cost confirm the potential suitability of the printed strain sensors for applications within the framework of structural health monitoring (SHM).

Geometrical analysis of woven fabric microstructure based on micron-resolution computed tomography data

NASA Astrophysics Data System (ADS)

Krieger, Helga; Seide, Gunnar; Gries, Thomas; Stapleton, Scott E.

2018-04-01

The global mechanical properties of textiles such as elasticity and strength, as well as transport properties such as permeability depend strongly on the microstructure of the textile. Textiles are heterogeneous structures with highly anisotropic material properties, including local fiber orientation and local fiber volume fraction. In this paper, an algorithm is presented to generate a virtual 3D-model of a woven fabric architecture with information about the local fiber orientation and the local fiber volume fraction. The geometric data of the woven fabric impregnated with resin was obtained by micron-resolution computed tomography (μCT). The volumetric μCT-scan was discretized into cells and the microstructure of each cell was analyzed and homogenized. Furthermore, the discretized data was used to calculate the local permeability tensors of each cell. An example application of the analyzed data is the simulation of the resin flow through a woven fabric based on the determined local permeability tensors and on Darcy's law. The presented algorithm is an automated and robust method of going from μCT-scans to structural or flow models.

Localized Symmetry Breaking for Tuning Thermal Expansion in ScF 3 Nanoscale Frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Lei; Qin, Feiyu; Sanson, Andrea

The local symmetry, beyond the averaged crystallographic structure, tends to bring unu-sual performances. Negative thermal expansion is a peculiar physical property of solids. Here, we report the delicate design of the localized symmetry breaking to achieve the controllable thermal expansion in ScF3 nano-scale frameworks. Intriguingly, an isotropic zero thermal expansion is concurrently engi-neered by localized symmetry breaking, with a remarkably low coefficient of thermal expansion of about +4.0×10-8/K up to 675K. This mechanism is investigated by the joint analysis of atomic pair dis-tribution function of synchrotron X-ray total scattering and extended X-ray absorption fine structure spectra. A localized rhombohedral distortionmore » presumably plays a critical role in stiffening ScF3 nano-scale frameworks and concomitantly suppressing transverse thermal vibrations of fluorine atoms. This physical scenario is also theoretically corroborated by the extinction of phonon modes with negative Grüneisen parameters in the rhombohedral ScF3. The present work opens an untraditional chemical modification to achieve controllable thermal expansion by breaking local symmetries of materials.« less

Scaling of membrane-type locally resonant acoustic metamaterial arrays.

PubMed

Naify, Christina J; Chang, Chia-Ming; McKnight, Geoffrey; Nutt, Steven R

2012-10-01

Metamaterials have emerged as promising solutions for manipulation of sound waves in a variety of applications. Locally resonant acoustic materials (LRAM) decrease sound transmission by 500% over acoustic mass law predictions at peak transmission loss (TL) frequencies with minimal added mass, making them appealing for weight-critical applications such as aerospace structures. In this study, potential issues associated with scale-up of the structure are addressed. TL of single-celled and multi-celled LRAM was measured using an impedance tube setup with systematic variation in geometric parameters to understand the effects of each parameter on acoustic response. Finite element analysis was performed to predict TL as a function of frequency for structures with varying complexity, including stacked structures and multi-celled arrays. Dynamic response of the array structures under discrete frequency excitation was investigated using laser vibrometry to verify negative dynamic mass behavior.

Query3d: a new method for high-throughput analysis of functional residues in protein structures.

PubMed

Ausiello, Gabriele; Via, Allegra; Helmer-Citterich, Manuela

2005-12-01

The identification of local similarities between two protein structures can provide clues of a common function. Many different methods exist for searching for similar subsets of residues in proteins of known structure. However, the lack of functional and structural information on single residues, together with the low level of integration of this information in comparison methods, is a limitation that prevents these methods from being fully exploited in high-throughput analyses. Here we describe Query3d, a program that is both a structural DBMS (Database Management System) and a local comparison method. The method conserves a copy of all the residues of the Protein Data Bank annotated with a variety of functional and structural information. New annotations can be easily added from a variety of methods and known databases. The algorithm makes it possible to create complex queries based on the residues' function and then to compare only subsets of the selected residues. Functional information is also essential to speed up the comparison and the analysis of the results. With Query3d, users can easily obtain statistics on how many and which residues share certain properties in all proteins of known structure. At the same time, the method also finds their structural neighbours in the whole PDB. Programs and data can be accessed through the PdbFun web interface.

Query3d: a new method for high-throughput analysis of functional residues in protein structures

PubMed Central

Ausiello, Gabriele; Via, Allegra; Helmer-Citterich, Manuela

2005-01-01

Background The identification of local similarities between two protein structures can provide clues of a common function. Many different methods exist for searching for similar subsets of residues in proteins of known structure. However, the lack of functional and structural information on single residues, together with the low level of integration of this information in comparison methods, is a limitation that prevents these methods from being fully exploited in high-throughput analyses. Results Here we describe Query3d, a program that is both a structural DBMS (Database Management System) and a local comparison method. The method conserves a copy of all the residues of the Protein Data Bank annotated with a variety of functional and structural information. New annotations can be easily added from a variety of methods and known databases. The algorithm makes it possible to create complex queries based on the residues' function and then to compare only subsets of the selected residues. Functional information is also essential to speed up the comparison and the analysis of the results. Conclusion With Query3d, users can easily obtain statistics on how many and which residues share certain properties in all proteins of known structure. At the same time, the method also finds their structural neighbours in the whole PDB. Programs and data can be accessed through the PdbFun web interface. PMID:16351754

Local linear regression for function learning: an analysis based on sample discrepancy.

PubMed

Cervellera, Cristiano; Macciò, Danilo

2014-11-01

Local linear regression models, a kind of nonparametric structures that locally perform a linear estimation of the target function, are analyzed in the context of empirical risk minimization (ERM) for function learning. The analysis is carried out with emphasis on geometric properties of the available data. In particular, the discrepancy of the observation points used both to build the local regression models and compute the empirical risk is considered. This allows to treat indifferently the case in which the samples come from a random external source and the one in which the input space can be freely explored. Both consistency of the ERM procedure and approximating capabilities of the estimator are analyzed, proving conditions to ensure convergence. Since the theoretical analysis shows that the estimation improves as the discrepancy of the observation points becomes smaller, low-discrepancy sequences, a family of sampling methods commonly employed for efficient numerical integration, are also analyzed. Simulation results involving two different examples of function learning are provided.

Two-generation analysis of pollen flow across a landscape. V. A stepwise approach for extracting factors contributing to pollen structure.

Treesearch

R. J. Dyer; R. D. Westfall; V. L. Sork; P. E. Smouse

2004-01-01

Patterns of pollen dispersal are central to both the ecology and evolution of plant populations. However, the mechanisms controlling either the dispersal process itself or our estimation of that process may be influenced by site-specific factors such as local forest structure and nonuniform adult genetic structure. Here, we present an extension of the AMOVA model...

Social disorganization and the profile of child welfare: Explaining child welfare activity by the community-level factors.

PubMed

Harrikari, Timo

2014-10-01

This article addresses the question of the structure of local child welfare activities in light of community-level factors. It poses the following research questions: how are different community-level factors related to child welfare client structures in communities and what is the extent to which these factors explain structural differences? The applied theoretical framework is based on social disorganization and strain theories as well as human developmental approach. The data has been collected from two Finnish national databases and it consists of variables containing 257 Finnish municipalities. The method of analysis is multinomial logistic regression. The results suggest that the local child welfare structures are tied to social disorganization, policing and culture as well as to the intensity of control in the communities. In general, the more fragile the communal structures, the more last-resort child welfare there is in the community. Combining fragile communal structures with weak dependency ratio and high proportion of social workers, the more intense the level of child welfare statistics indicated. The results indicate that the theoretical framework for the application of child welfare activity analysis is justified, but they also suggest that it requires further development through both context-bound reflection and application. Copyright © 2014 Elsevier Ltd. All rights reserved.

Development of a composite repair and the associated inspection intervals for the F-111C stiffener runout region

NASA Technical Reports Server (NTRS)

Jones, R.; Molent, L.; Paul, J.; Saunders, T.; Chiu, W. K.

1994-01-01

This paper presents an overview of the structural aspects of the design and development of a local reinforcement designed to lower the stresses in a region of the F-111C wing fitting which is prone to cracking. The stress analysis, with particular emphasis on the use of a unified constitutive model for the cyclic inelastic response of the structure, representative specimen testing, thermal analysis and full scale static testing of this design are summarized.

Processing Cones: A Computational Structure for Image Analysis.

DTIC Science & Technology

1981-12-01

image analysis applications, referred to as a processing cone, is described and sample algorithms are presented. A fundamental characteristic of the structure is its hierarchical organization into two-dimensional arrays of decreasing resolution. In this architecture, a protypical function is defined on a local window of data and applied uniformly to all windows in a parallel manner. Three basic modes of processing are supported in the cone: reduction operations (upward processing), horizontal operations (processing at a single level) and projection operations (downward

Bridging Zirconia Nodes within a Metal–Organic Framework via Catalytic Ni-Hydroxo Clusters to Form Heterobimetallic Nanowires

DOE Office of Scientific and Technical Information (OSTI.GOV)

Platero-Prats, Ana E.; League, Aaron B.; Bernales, Varinia

2017-07-24

Metal-organic frameworks (MOFs), with their well-ordered pore networks and tunable surface chemistries, offer a versatile platform for preparing well-defined nanostructures wherein functionality such as catalysis can be incorporated. We resolved the atomic structure of Ni-oxo species deposited in the MOF NU-1000 through atomic layer deposition using local and long-range structure probes, including X-ray absorption spectroscopy, pair distribution function analysis and difference envelope density analysis, with electron microscopy imaging and computational modeling.

Residue-level global and local ensemble-ensemble comparisons of protein domains.

PubMed

Clark, Sarah A; Tronrud, Dale E; Karplus, P Andrew

2015-09-01

Many methods of protein structure generation such as NMR-based solution structure determination and template-based modeling do not produce a single model, but an ensemble of models consistent with the available information. Current strategies for comparing ensembles lose information because they use only a single representative structure. Here, we describe the ENSEMBLATOR and its novel strategy to directly compare two ensembles containing the same atoms to identify significant global and local backbone differences between them on per-atom and per-residue levels, respectively. The ENSEMBLATOR has four components: eePREP (ee for ensemble-ensemble), which selects atoms common to all models; eeCORE, which identifies atoms belonging to a cutoff-distance dependent common core; eeGLOBAL, which globally superimposes all models using the defined core atoms and calculates for each atom the two intraensemble variations, the interensemble variation, and the closest approach of members of the two ensembles; and eeLOCAL, which performs a local overlay of each dipeptide and, using a novel measure of local backbone similarity, reports the same four variations as eeGLOBAL. The combination of eeGLOBAL and eeLOCAL analyses identifies the most significant differences between ensembles. We illustrate the ENSEMBLATOR's capabilities by showing how using it to analyze NMR ensembles and to compare NMR ensembles with crystal structures provides novel insights compared to published studies. One of these studies leads us to suggest that a "consistency check" of NMR-derived ensembles may be a useful analysis step for NMR-based structure determinations in general. The ENSEMBLATOR 1.0 is available as a first generation tool to carry out ensemble-ensemble comparisons. © 2015 The Protein Society.

Residue-level global and local ensemble-ensemble comparisons of protein domains

PubMed Central

Clark, Sarah A; Tronrud, Dale E; Andrew Karplus, P

2015-01-01

Many methods of protein structure generation such as NMR-based solution structure determination and template-based modeling do not produce a single model, but an ensemble of models consistent with the available information. Current strategies for comparing ensembles lose information because they use only a single representative structure. Here, we describe the ENSEMBLATOR and its novel strategy to directly compare two ensembles containing the same atoms to identify significant global and local backbone differences between them on per-atom and per-residue levels, respectively. The ENSEMBLATOR has four components: eePREP (ee for ensemble-ensemble), which selects atoms common to all models; eeCORE, which identifies atoms belonging to a cutoff-distance dependent common core; eeGLOBAL, which globally superimposes all models using the defined core atoms and calculates for each atom the two intraensemble variations, the interensemble variation, and the closest approach of members of the two ensembles; and eeLOCAL, which performs a local overlay of each dipeptide and, using a novel measure of local backbone similarity, reports the same four variations as eeGLOBAL. The combination of eeGLOBAL and eeLOCAL analyses identifies the most significant differences between ensembles. We illustrate the ENSEMBLATOR's capabilities by showing how using it to analyze NMR ensembles and to compare NMR ensembles with crystal structures provides novel insights compared to published studies. One of these studies leads us to suggest that a “consistency check” of NMR-derived ensembles may be a useful analysis step for NMR-based structure determinations in general. The ENSEMBLATOR 1.0 is available as a first generation tool to carry out ensemble-ensemble comparisons. PMID:26032515

Conductivity and structure of ErAs nanoparticles embedded in GaAs pn junctions analyzed via conductive atomic force microscopy

NASA Astrophysics Data System (ADS)

Park, K. W.; Dasika, V. D.; Nair, H. P.; Crook, A. M.; Bank, S. R.; Yu, E. T.

2012-06-01

We have used conductive atomic force microscopy to investigate the influence of growth temperature on local current flow in GaAs pn junctions with embedded ErAs nanoparticles grown by molecular beam epitaxy. Three sets of samples, one with 1 ML ErAs deposited at different growth temperatures and two grown at 530 °C and 575 °C with varying ErAs depositions, were characterized. Statistical analysis of local current images suggests that the structures grown at 575 °C have about 3 times thicker ErAs nanoparticles than structures grown at 530 °C, resulting in degradation of conductivity due to reduced ErAs coverage. These findings explain previous studies of macroscopic tunnel junctions.

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.

Hierarchical mechanism of development of wealth and structure for a premodern local society

NASA Astrophysics Data System (ADS)

Matsuo, Miki Y.

2011-06-01

We propose a hierarchical model of social development composed of two associated hierarchies, each of which describes economic and noneconomic activities in society, respectively. The model is designed to explain the development of wealth distribution and social structure over 50 years in a premodern Japanese local society. Data analysis shows that the wealth distribution has a well-known universal power-law tail throughout the observed period, while the Pareto index gradually decreases with time. We further show that the noneconomic social properties, such as the household number, average family size, and number of collaterals in a household, of the local society, also have decreasing or increasing trends throughout the observed period. We show that the hierarchical model consistently demonstrates the correlations of these economic and noneconomic properties.

Recognition of Simple 3D Geometrical Objects under Partial Occlusion

NASA Astrophysics Data System (ADS)

Barchunova, Alexandra; Sommer, Gerald

In this paper we present a novel procedure for contour-based recognition of partially occluded three-dimensional objects. In our approach we use images of real and rendered objects whose contours have been deformed by a restricted change of the viewpoint. The preparatory part consists of contour extraction, preprocessing, local structure analysis and feature extraction. The main part deals with an extended construction and functionality of the classifier ensemble Adaptive Occlusion Classifier (AOC). It relies on a hierarchical fragmenting algorithm to perform a local structure analysis which is essential when dealing with occlusions. In the experimental part of this paper we present classification results for five classes of simple geometrical figures: prism, cylinder, half cylinder, a cube, and a bridge. We compare classification results for three classical feature extractors: Fourier descriptors, pseudo Zernike and Zernike moments.

Analysing taxonomic structures and local ecological processes in temperate forests in North Eastern China.

PubMed

Fan, Chunyu; Tan, Lingzhao; Zhang, Chunyu; Zhao, Xiuhai; von Gadow, Klaus

2017-10-30

One of the core issues of forest community ecology is the exploration of how ecological processes affect community structure. The relative importance of different processes is still under debate. This study addresses four questions: (1) how is the taxonomic structure of a forest community affected by spatial scale? (2) does the taxonomic structure reveal effects of local processes such as environmental filtering, dispersal limitation or interspecific competition at a local scale? (3) does the effect of local processes on the taxonomic structure vary with the spatial scale? (4) does the analysis based on taxonomic structures provide similar insights when compared with the use of phylogenetic information? Based on the data collected in two large forest observational field studies, the taxonomic structures of the plant communities were analyzed at different sampling scales using taxonomic ratios (number of genera/number of species, number of families/number of species), and the relationship between the number of higher taxa and the number of species. Two random null models were used and the "standardized effect size" (SES) of taxonomic ratios was calculated, to assess possible differences between the observed and simulated taxonomic structures, which may be caused by specific ecological processes. We further applied a phylogeny-based method to compare results with those of the taxonomic approach. As expected, the taxonomic ratios decline with increasing grain size. The quantitative relationship between genera/families and species, described by a linearized power function, showed a good fit. With the exception of the family-species relationship in the Jiaohe study area, the exponents of the genus/family-species relationships did not show any scale dependent effects. The taxonomic ratios of the observed communities had significantly lower values than those of the simulated random community under the test of two null models at almost all scales. Null Model 2 which considered the spatial dispersion of species generated a taxonomic structure which proved to be more consistent with that in the observed community. As sampling sizes increased from 20 m × 20 m to 50 m × 50 m, the magnitudes of SESs of taxonomic ratios increased. Based on the phylogenetic analysis, we found that the Jiaohe plot was phylogenetically clustered at almost all scales. We detected significant phylogenetically overdispersion at the 20 m × 20 m and 30 m × 30 m scales in the Liangshui plot. The results suggest that the effect of abiotic filtering is greater than the effects of interspecific competition in shaping the local community at almost all scales. Local processes influence the taxonomic structures, but their combined effects vary with the spatial scale. The taxonomic approach provides similar insights as the phylogenetic approach, especially when we applied a more conservative null model. Analysing taxonomic structure may be a useful tool for communities where well-resolved phylogenetic data are not available.

Cortical and subcortical atrophy in Alzheimer disease: parallel atrophy of thalamus and hippocampus.

PubMed

Štěpán-Buksakowska, Irena; Szabó, Nikoletta; Hořínek, Daniel; Tóth, Eszter; Hort, Jakub; Warner, Joshua; Charvát, František; Vécsei, László; Roček, Miloslav; Kincses, Zsigmond T

2014-01-01

Brain atrophy is a key imaging hallmark of Alzheimer disease (AD). In this study, we carried out an integrative evaluation of AD-related atrophy. Twelve patients with AD and 13 healthy controls were enrolled. We conducted a cross-sectional analysis of total brain tissue volumes with SIENAX. Localized gray matter atrophy was identified with optimized voxel-wise morphometry (FSL-VBM), and subcortical atrophy was evaluated by active shape model implemented in FMRIB's Integrated Registration Segmentation Toolkit. SIENAX analysis demonstrated total brain atrophy in AD patients; voxel-based morphometry analysis showed atrophy in the bilateral mediotemporal regions and in the posterior brain regions. In addition, regarding the diminished volumes of thalami and hippocampi in AD patients, subsequent vertex analysis of the segmented structures indicated shrinkage of the bilateral anterior thalami and the left medial hippocampus. Interestingly, the volume of the thalami and hippocampi were highly correlated with the volume of the thalami and amygdalae on both sides in AD patients, but not in healthy controls. This complex structural information proved useful in the detailed interpretation of AD-related neurodegenerative process, as the multilevel approach showed both global and local atrophy on cortical and subcortical levels. Most importantly, our results raise the possibility that subcortical structure atrophy is not independent in AD patients.

A framework of analysis for field experiments with alternative materials in road construction.

PubMed

François, D; Jullien, A

2009-01-01

In France, a wide variety of alternative materials is produced or exists in the form of stockpiles built up over time. Such materials are distributed over various regions of the territory depending on local industrial development and urbanisation trends. The use of alternative materials at a national scale implies sharing local knowledge and experience. Building a national database on alternative materials for road construction is useful in gathering and sharing information. An analysis of feedback from onsite experiences (back analysis) is essential to improve knowledge on alternative material use in road construction. Back analysis of field studies has to be conducted in accordance with a single common framework. This could enable drawing comparisons between alternative materials and between road applications. A framework for the identification and classification of data used in back analyses is proposed. Since the road structure is an open system, this framework has been based on a stress-response approach at both the material and structural levels and includes a description of external factors applying during the road service life. The proposal has been shaped from a review of the essential characteristics of road materials and structures, as well as from the state of knowledge specific to alternative material characterisation.

Using structured decision making to manage disease risk for Montana wildlife

USGS Publications Warehouse

Mitchell, Michael S.; Gude, Justin A.; Anderson, Neil J.; Ramsey, Jennifer M.; Thompson, Michael J.; Sullivan, Mark G.; Edwards, Victoria L.; Gower, Claire N.; Cochrane, Jean Fitts; Irwin, Elise R.; Walshe, Terry

2013-01-01

We used structured decision-making to develop a 2-part framework to assist managers in the proactive management of disease outbreaks in Montana, USA. The first part of the framework is a model to estimate the probability of disease outbreak given field observations available to managers. The second part of the framework is decision analysis that evaluates likely outcomes of management alternatives based on the estimated probability of disease outbreak, and applies managers' values for different objectives to indicate a preferred management strategy. We used pneumonia in bighorn sheep (Ovis canadensis) as a case study for our approach, applying it to 2 populations in Montana that differed in their likelihood of a pneumonia outbreak. The framework provided credible predictions of both probability of disease outbreaks, as well as biological and monetary consequences of management actions. The structured decision-making approach to this problem was valuable for defining the challenges of disease management in a decentralized agency where decisions are generally made at the local level in cooperation with stakeholders. Our approach provides local managers with the ability to tailor management planning for disease outbreaks to local conditions. Further work is needed to refine our disease risk models and decision analysis, including robust prediction of disease outbreaks and improved assessment of management alternatives.

Mental health network governance: comparative analysis across Canadian regions.

PubMed

Wiktorowicz, Mary E; Fleury, Marie-Josée; Adair, Carol E; Lesage, Alain; Goldner, Elliot; Peters, Suzanne

2010-10-26

Modes of governance were compared in ten local mental health networks in diverse contexts (rural/urban and regionalized/non-regionalized) to clarify the governance processes that foster inter-organizational collaboration and the conditions that support them. Case studies of ten local mental health networks were developed using qualitative methods of document review, semi-structured interviews and focus groups that incorporated provincial policy, network and organizational levels of analysis. Mental health networks adopted either a corporate structure, mutual adjustment or an alliance governance model. A corporate structure supported by regionalization offered the most direct means for local governance to attain inter-organizational collaboration. The likelihood that networks with an alliance model developed coordination processes depended on the presence of the following conditions: a moderate number of organizations, goal consensus and trust among the organizations, and network-level competencies. In the small and mid-sized urban networks where these conditions were met their alliance realized the inter-organizational collaboration sought. In the large urban and rural networks where these conditions were not met, externally brokered forms of network governance were required to support alliance based models. In metropolitan and rural networks with such shared forms of network governance as an alliance or voluntary mutual adjustment, external mediation by a regional or provincial authority was an important lever to foster inter-organizational collaboration.

Joint source based analysis of multiple brain structures in studying major depressive disorder

NASA Astrophysics Data System (ADS)

Ramezani, Mahdi; Rasoulian, Abtin; Hollenstein, Tom; Harkness, Kate; Johnsrude, Ingrid; Abolmaesumi, Purang

2014-03-01

We propose a joint Source-Based Analysis (jSBA) framework to identify brain structural variations in patients with Major Depressive Disorder (MDD). In this framework, features representing position, orientation and size (i.e. pose), shape, and local tissue composition are extracted. Subsequently, simultaneous analysis of these features within a joint analysis method is performed to generate the basis sources that show signi cant di erences between subjects with MDD and those in healthy control. Moreover, in a cross-validation leave- one-out experiment, we use a Fisher Linear Discriminant (FLD) classi er to identify individuals within the MDD group. Results show that we can classify the MDD subjects with an accuracy of 76% solely based on the information gathered from the joint analysis of pose, shape, and tissue composition in multiple brain structures.

Stability of mechanical joints in launching vehicles: Local and global stationary values of energy density

NASA Astrophysics Data System (ADS)

Chue, Ching-Hwei

A method was developed for predicting the behavior of mechanical joints in launch vehicles with particular emphasis placed on how the combined effects of loading, geometry, and materials could be optimized in terms of structure instability and/or integrity. What was considered to be essential is the fluctuation of the volume energy density with time in the structure. The peaks and valleys of the volume energy density function will be associated with failure by fracture and/or yielding while the distance between their local and global stationary values govern the structure instability. The Solid Rocket Booster (SRB) of the space shuttle was analyzed under axisymmetric and non-axisymmetric loadings. A semi-analytical finite element program was developed for solving the case of non-axisymmetric loading. Following a dynamic stress analysis, contours of the volume energy density in the structure were obtained as a function of time. The magnitudes and locations of these stationary values were then calculated locally and globally and related to possible failure by fracture. In the case of axisymmetric flight, the local and global instability behavior do not change appreciably. Fluctuations in the energy density and the dynamic stability length parameter become appreciable when the non-axisymmetric loads are considered. The magnitude of the energy in the shell structure is sensitive to alterations in the gas pressure induced by the solid propellant.

Activation of preexisting transverse structures in an evolving magmatic rift in East Africa

NASA Astrophysics Data System (ADS)

Muirhead, J. D.; Kattenhorn, S. A.

2018-01-01

Inherited crustal weaknesses have long been recognized as important factors in strain localization and basin development in the East African Rift System (EARS). However, the timing and kinematics (e.g., sense of slip) of transverse (rift-oblique) faults that exploit these weaknesses are debated, and thus the roles of inherited weaknesses at different stages of rift basin evolution are often overlooked. The mechanics of transverse faulting were addressed through an analysis of the Kordjya fault of the Magadi basin (Kenya Rift). Fault kinematics were investigated from field and remote-sensing data collected on fault and joint systems. Our analysis indicates that the Kordjya fault consists of a complex system of predominantly NNE-striking, rift-parallel fault segments that collectively form a NNW-trending array of en echelon faults. The transverse Kordjya fault therefore reactivated existing rift-parallel faults in ∼1 Ma lavas as oblique-normal faults with a component of sinistral shear. In all, these fault motions accommodate dip-slip on an underlying transverse structure that exploits the Aswa basement shear zone. This study shows that transverse faults may be activated through a complex interplay among magma-assisted strain localization, preexisting structures, and local stress rotations. Rather than forming during rift initiation, transverse structures can develop after the establishment of pervasive rift-parallel fault systems, and may exhibit dip-slip kinematics when activated from local stress rotations. The Kordjya fault is shown here to form a kinematic linkage that transfers strain to a newly developing center of concentrated magmatism and normal faulting. It is concluded that recently activated transverse faults not only reveal the effects of inherited basement weaknesses on fault development, but also provide important clues regarding developing magmatic and tectonic systems as young continental rift basins evolve.

An Analysis of the Effects of Program Structure and Content on Outcomes of Community Leadership Education Programs

ERIC Educational Resources Information Center

Apaliyah, Godwin Tayese

2011-01-01

This study examined community leadership education programs employed in rural communities and organizations of several states to empower both local leaders and residents. In particular, the study investigated the relationships between community leadership education program design and structure (contact hours and content) and six outcome indices of…

Fundamental Studies of Strength Physics--Methodology of Longevity Prediction of Materials under Arbitrary Thermally and Forced Effects

ERIC Educational Resources Information Center

Petrov, Mark G.

2016-01-01

Thermally activated analysis of experimental data allows considering about the structure features of each material. By modelling the structural heterogeneity of materials by means of rheological models, general and local plastic flows in metals and alloys can be described over. Based on physical fundamentals of failure and deformation of materials…

Time-localized frequency analysis of ultrasonic guided waves for nondestructive testing

NASA Astrophysics Data System (ADS)

Shin, Hyeon Jae; Song, Sung-Jin

2000-05-01

A time-localized frequency (TLF) analysis is employed for the guided wave mode identification and improved guided wave applications. For the analysis of time-localized frequency contents of digitized ultrasonic signals, TLF analysis consists of splitting the time domain signal into overlapping segments, weighting each with the hanning window, and forming the columns of discrete Fourier transforms. The result is presented by a frequency versus time domain diagram showing frequency variation along the signal arrival time. For the demonstration of the utility of TLF analysis, an experimental group velocity dispersion pattern obtained by TLF analysis is compared with the dispersion diagram obtained by theory of elasticity. Sample piping is carbon steel piping that is used for the transportation of natural gas underground. Guided wave propagation characteristic on the piping is considered with TLF analysis and wave structure concepts. TLF analysis is used for the detection of simulated corrosion defects and the assessment of weld joint using ultrasonic guided waves. TLF analysis has revealed that the difficulty of mode identification in multi-mode propagation could be overcome. Group velocity dispersion pattern obtained by TLF analysis agrees well with theoretical results.

Fluorescence X-ray absorption spectroscopy using a Ge pixel array detector: application to high-temperature superconducting thin-film single crystals.

PubMed

Oyanagi, H; Tsukada, A; Naito, M; Saini, N L; Lampert, M O; Gutknecht, D; Dressler, P; Ogawa, S; Kasai, K; Mohamed, S; Fukano, A

2006-07-01

A Ge pixel array detector with 100 segments was applied to fluorescence X-ray absorption spectroscopy, probing the local structure of high-temperature superconducting thin-film single crystals (100 nm in thickness). Independent monitoring of pixel signals allows real-time inspection of artifacts owing to substrate diffractions. By optimizing the grazing-incidence angle theta and adjusting the azimuthal angle phi, smooth extended X-ray absorption fine structure (EXAFS) oscillations were obtained for strained (La,Sr)2CuO4 thin-film single crystals grown by molecular beam epitaxy. The results of EXAFS data analysis show that the local structure (CuO6 octahedron) in (La,Sr)2CuO4 thin films grown on LaSrAlO4 and SrTiO3 substrates is uniaxially distorted changing the tetragonality by approximately 5 x 10(-3) in accordance with the crystallographic lattice mismatch. It is demonstrated that the local structure of thin-film single crystals can be probed with high accuracy at low temperature without interference from substrates.

Local Chemical Ordering and Negative Thermal Expansion in PtNi Alloy Nanoparticles.

PubMed

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

2017-12-13

An atomic insight into the local chemical ordering and lattice strain is particular interesting to recent emerging bimetallic nanocatalysts such as PtNi alloys. Here, we reported the atomic distribution, chemical environment, and lattice thermal evolution in full-scale structural description of PtNi alloy nanoparticles (NPs). The different segregation of elements in the well-faceted PtNi nanoparticles is convinced by extended X-ray absorption fine structure (EXAFS). Atomic pair distribution function (PDF) study evidences the coexistence of the face-centered cubic and tetragonal ordering parts in the local environment of PtNi nanoparticles. Further reverse Monte Carlo (RMC) simulation with PDF data obviously exposed the segregation as Ni and Pt in the centers of {111} and {001} facets, respectively. Layer-by-layer statistical analysis up to 6 nm for the local atomic pairs revealed the distribution of local tetragonal ordering on the surface. This local coordination environment facilitates the distribution of heteroatomic Pt-Ni pairs, which plays an important role in the negative thermal expansion of Pt 41 Ni 59 NPs. The present study on PtNi alloy NPs from local short-range coordination to long-range average lattice provides a new perspective on tailoring physical properties in nanomaterials.

Genetic diversity and relationships among six local cattle populations in semi-arid areas assessed by a bovine medium-density single nucleotide polymorphism data.

PubMed

Boushaba, N; Boujenane, I; Moazami-Goudarzi, K; Flori, L; Saïdi-Mehtar, N; Tabet-Aoul, N; Laloë, D

2018-06-18

The local cattle populations belonging to the 'Brune de l'Atlas' cattle in Algeria and Morocco are potential resources in terms of genetic diversity and socioeconomic prevalence and their characterization is an essential step in any program designed to conserve genetic diversity. Our objectives were to assess the genetic diversity, the population structure and relationships among four Algerian cattle breeds, the Biskra, Cheurfa, Chelifienne and Guelmoise and of two Moroccan, the Oulmès-Zaër and Tidili by genotyping 50 309 single nucleotide polymorphism in 203 unrelated animals. A low population structure was observed across breeds with pairwise F ST values ranging from 0.008 to 0.043, suggesting a high level of gene flow. These data were combined with the available data on cattle populations representative of Europe (EUT), West African taurine (WAT) and zebu (ZEB). Principle Components Analysis was carried out which revealed that the Maghrebin populations are closer to the EUT/ZEB population than to the WAT. Structure analysis confirmed this mixed origin of the Maghrebin cattle populations. We also detected the influence of zebu breeds in Cheurfa and Guelmoise populations. This study provides the first information about genetic diversity within and between Algerian and Moroccan cattle populations and gives a detailed description of their genetic structure and relationships according to their historical origins. This study revealed that several combined effects contributed to shape the genetic diversity of the six Maghrebin populations studied: (i) gene flow among local breeds, (ii) the recent introgression of European breeds in local Algerian breeds and (iii) the traditional management systems. The results of this study will primarily assist policy makers and livestock keepers to make useful decisions for improvement of genetic resources while ensuring the preservation and conservation of local breeds in Algeria and Morocco.

Mixture models for protein structure ensembles.

PubMed

Hirsch, Michael; Habeck, Michael

2008-10-01

Protein structure ensembles provide important insight into the dynamics and function of a protein and contain information that is not captured with a single static structure. However, it is not clear a priori to what extent the variability within an ensemble is caused by internal structural changes. Additional variability results from overall translations and rotations of the molecule. And most experimental data do not provide information to relate the structures to a common reference frame. To report meaningful values of intrinsic dynamics, structural precision, conformational entropy, etc., it is therefore important to disentangle local from global conformational heterogeneity. We consider the task of disentangling local from global heterogeneity as an inference problem. We use probabilistic methods to infer from the protein ensemble missing information on reference frames and stable conformational sub-states. To this end, we model a protein ensemble as a mixture of Gaussian probability distributions of either entire conformations or structural segments. We learn these models from a protein ensemble using the expectation-maximization algorithm. Our first model can be used to find multiple conformers in a structure ensemble. The second model partitions the protein chain into locally stable structural segments or core elements and less structured regions typically found in loops. Both models are simple to implement and contain only a single free parameter: the number of conformers or structural segments. Our models can be used to analyse experimental ensembles, molecular dynamics trajectories and conformational change in proteins. The Python source code for protein ensemble analysis is available from the authors upon request.

Structural optimization: Status and promise

NASA Astrophysics Data System (ADS)

Kamat, Manohar P.

Chapters contained in this book include fundamental concepts of optimum design, mathematical programming methods for constrained optimization, function approximations, approximate reanalysis methods, dual mathematical programming methods for constrained optimization, a generalized optimality criteria method, and a tutorial and survey of multicriteria optimization in engineering. Also included are chapters on the compromise decision support problem and the adaptive linear programming algorithm, sensitivity analyses of discrete and distributed systems, the design sensitivity analysis of nonlinear structures, optimization by decomposition, mixed elements in shape sensitivity analysis of structures based on local criteria, and optimization of stiffened cylindrical shells subjected to destabilizing loads. Other chapters are on applications to fixed-wing aircraft and spacecraft, integrated optimum structural and control design, modeling concurrency in the design of composite structures, and tools for structural optimization. (No individual items are abstracted in this volume)

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

PubMed

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

2014-02-12

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

An Efficient Analysis Methodology for Fluted-Core Composite Structures

NASA Technical Reports Server (NTRS)

Oremont, Leonard; Schultz, Marc R.

2012-01-01

The primary loading condition in launch-vehicle barrel sections is axial compression, and it is therefore important to understand the compression behavior of any structures, structural concepts, and materials considered in launch-vehicle designs. This understanding will necessarily come from a combination of test and analysis. However, certain potentially beneficial structures and structural concepts do not lend themselves to commonly used simplified analysis methods, and therefore innovative analysis methodologies must be developed if these structures and structural concepts are to be considered. This paper discusses such an analysis technique for the fluted-core sandwich composite structural concept. The presented technique is based on commercially available finite-element codes, and uses shell elements to capture behavior that would normally require solid elements to capture the detailed mechanical response of the structure. The shell thicknesses and offsets using this analysis technique are parameterized, and the parameters are adjusted through a heuristic procedure until this model matches the mechanical behavior of a more detailed shell-and-solid model. Additionally, the detailed shell-and-solid model can be strategically placed in a larger, global shell-only model to capture important local behavior. Comparisons between shell-only models, experiments, and more detailed shell-and-solid models show excellent agreement. The discussed analysis methodology, though only discussed in the context of fluted-core composites, is widely applicable to other concepts.

On-Line Monitoring and Diagnostics of the Integrity of Nuclear Plant Steam Generators and Heat Exchangers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belle R. Upadhyaya; J. Wesley Hines

2004-09-27

Integrity monitoring and flaw diagnostics of flat beams and tubular structures was investigated in this research task using guided acoustic signals. A piezo-sensor suite was deployed to activate and collect Lamb wave signals that propagate along metallic specimens. The dispersion curves of Lamb waves along plate and tubular structures are generated through numerical analysis. Several advanced techniques were explored to extract representative features from acoustic time series. Among them, the Hilbert-Huang transform (HHT) is a recently developed technique for the analysis of non-linear and transient signals. A moving window method was introduced to generate the local peak characters from acousticmore » time series, and a zooming window technique was developed to localize the structural flaws. The time-frequency analysis and pattern recognition techniques were combined for classifying structural defects in brass tubes. Several types of flaws in brass tubes were tested, both in the air and in water. The techniques also proved to be effective under background/process noise. A detailed theoretical analysis of Lamb wave propagation was performed and simulations were carried out using the finite element software system ABAQUS. This analytical study confirmed the behavior of the acoustic signals acquired from the experimental studies. The report presents the background the analysis of acoustic signals acquired from piezo-electric transducers for structural defect monitoring. A comparison of the use of time-frequency techniques, including the Hilbert-Huang transform, is presented. The report presents the theoretical study of Lamb wave propagation in flat beams and tubular structures, and the need for mode separation in order to effectively perform defect diagnosis. The results of an extensive experimental study of detection, location, and isolation of structural defects in flat aluminum beams and brass tubes are presented. The results of this research show the feasibility of on-line monitoring of small structural flaws by the use of transient and nonlinear acoustic signal analysis, and its implementation by the proper design of a piezo-electric transducer suite.« less

Structural domains and main-chain flexibility in prion proteins.

PubMed

Blinov, N; Berjanskii, M; Wishart, D S; Stepanova, M

2009-02-24

In this study we describe a novel approach to define structural domains and to characterize the local flexibility in both human and chicken prion proteins. The approach we use is based on a comprehensive theory of collective dynamics in proteins that was recently developed. This method determines the essential collective coordinates, which can be found from molecular dynamics trajectories via principal component analysis. Under this particular framework, we are able to identify the domains where atoms move coherently while at the same time to determine the local main-chain flexibility for each residue. We have verified this approach by comparing our results for the predicted dynamic domain systems with the computed main-chain flexibility profiles and the NMR-derived random coil indexes for human and chicken prion proteins. The three sets of data show excellent agreement. Additionally, we demonstrate that the dynamic domains calculated in this fashion provide a highly sensitive measure of protein collective structure and dynamics. Furthermore, such an analysis is capable of revealing structural and dynamic properties of proteins that are inaccessible to the conventional assessment of secondary structure. Using the collective dynamic simulation approach described here along with a high-temperature simulations of unfolding of human prion protein, we have explored whether locations of relatively low stability could be identified where the unfolding process could potentially be facilitated. According to our analysis, the locations of relatively low stability may be associated with the beta-sheet formed by strands S1 and S2 and the adjacent loops, whereas helix HC appears to be a relatively stable part of the protein. We suggest that this kind of structural analysis may provide a useful background for a more quantitative assessment of potential routes of spontaneous misfolding in prion proteins.

Efficacy of a numerical value of a fixed-effect estimator in stochastic frontier analysis as an indicator of hospital production structure.

PubMed

Kawaguchi, Hiroyuki; Hashimoto, Hideki; Matsuda, Shinya

2012-09-22

The casemix-based payment system has been adopted in many countries, although it often needs complementary adjustment taking account of each hospital's unique production structure such as teaching and research duties, and non-profit motives. It has been challenging to numerically evaluate the impact of such structural heterogeneity on production, separately of production inefficiency. The current study adopted stochastic frontier analysis and proposed a method to assess unique components of hospital production structures using a fixed-effect variable. There were two stages of analyses in this study. In the first stage, we estimated the efficiency score from the hospital production function using a true fixed-effect model (TFEM) in stochastic frontier analysis. The use of a TFEM allowed us to differentiate the unobserved heterogeneity of individual hospitals as hospital-specific fixed effects. In the second stage, we regressed the obtained fixed-effect variable for structural components of hospitals to test whether the variable was explicitly related to the characteristics and local disadvantages of the hospitals. In the first analysis, the estimated efficiency score was approximately 0.6. The mean value of the fixed-effect estimator was 0.784, the standard deviation was 0.137, the range was between 0.437 and 1.212. The second-stage regression confirmed that the value of the fixed effect was significantly correlated with advanced technology and local conditions of the sample hospitals. The obtained fixed-effect estimator may reflect hospitals' unique structures of production, considering production inefficiency. The values of fixed-effect estimators can be used as evaluation tools to improve fairness in the reimbursement system for various functions of hospitals based on casemix classification.

Cooling rate dependence and local structure in aluminum monatomic metallic glass

NASA Astrophysics Data System (ADS)

Kbirou, M.; Trady, S.; Hasnaoui, A.; Mazroui, M.

2017-10-01

The local atomic structure in aluminium monatomic metallic glass is studied using molecular dynamics simulations combined with the embedded atom method (EAM). We have used a variety of analytical methods to characterise the atomic configurations of our system: the Pair Distribution Function (PDF), the Common Neighbour Analysis (CNA) and the Voronoi Tessellation Analysis. CNA was used to investigate the order change from liquid to amorphous phases, recognising that the amount of icosahedral clusters increases with the decrease of temperature. The Voronoi analysis revealed that the icosahedral-like polyhedral are the predominant ones. It has been observed that the PDF function shows a splitting in the second peak, which cannot be attributed to the only ideal icosahedral polyhedron 〈0, 0, 12, 0〉, but also to the formation of other Voronoi polyhedra 〈0, 1, 10, 2〉 . Further, the PDFs were then integrated giving the cumulative coordination number in order to compute the fractal dimension (df).

Local Structure Evolution and Modes of Charge Storage in Secondary Li–FeS 2 Cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Butala, Megan M.; Mayo, Martin; Doan-Nguyen, Vicky V. T.

2017-03-27

In the pursuit of high-capacity electrochemical energy storage, a promising domain of research involves conversion reaction schemes, wherein electrode materials are fully transformed during charge and discharge. There are, however, numerous difficulties in realizing theoretical capacity and high rate capability in many conversion schemes. Here we employ operando studies to understand the conversion material FeS2, focusing on the local structure evolution of this relatively reversible material. X-ray absorption spectroscopy, pair distribution function analysis, and first-principles calculations of intermediate structures shed light on the mechanism of charge storage in the Li-FeS2 system, with some general principles emerging for charge storage inmore » chalcogenide materials. Focusing on second and later charge/discharge cycles, we find small, disordered domains that locally resemble Fe and Li2S at the end of the first discharge. Upon charge, this is converted to a Li-Fe-S composition whose local structure reveals tetrahedrally coordinated Fe. With continued charge, this ternary composition displays insertion extraction behavior at higher potentials and lower Li content. The finding of hybrid modes of charge storage, rather than simple conversion, points to the important role of intermediates that appear to store charge by mechanisms that more closely resemble intercalation.« less

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.

Temperature dependence of local structural changes around transition metal centers Cr3+ and Mn2+ in RAl3(BO3)4 crystals studied by EMR

NASA Astrophysics Data System (ADS)

Açıkgöz, Muhammed; Rudowicz, Czesław; Gnutek, Paweł

2017-11-01

Theoretical investigations are carried out to determine the temperature dependence of the local structural parameters of Cr3+ and Mn2+ ions doped into RAl3(BO3)4 (RAB, R = Y, Eu, Tm) crystals. The zero-field splitting (ZFS) parameters (ZFSPs) obtained from the spin Hamiltonian (SH) analysis of EMR (EPR) spectra serve for fine-tuning the theoretically predicted ZFSPs obtained using the semi-empirical superposition model (SPM). The SPM analysis enables to determine the local structure changes around Cr3+ and Mn2+ centers in RAB crystals and explain the observed temperature dependence of the ZFSPs. The local monoclinic C2 site symmetry of all Al sites in YAB necessitates consideration of one non-zero monoclinic ZFSP (in the Stevens notation, b21) for Cr3+ ions. However, the experimental second-rank ZFSPs (D =b20 , E = 1 / 3b22) were expressed in a nominal principal axis system. To provide additional insight into low symmetry aspects, the distortions (ligand's distances ΔRi and angular distortions Δθi) have been varied while preserving monoclinic site symmetry, in such way as to obtain the calculated values (D, E) close to the experimental ones, while keeping b21 close to zero. This procedure yields good matching of the calculated ZFSPs and the experimental ones, and enables determination of the corresponding local distortions. The present results may be useful in future studies aimed at technological applications of the Huntite-type borates with the formula RM3(BO3)4. The model parameters determined here may be utilized for ZFSP calculations for Cr3+ and Mn2+ ions at octahedral sites in single-molecule magnets and single-chain magnets.

Structure of the 5' region of the Hst70 gene transcription unit: presence of an intron and multiple transcription initiation sites.

PubMed Central

Scieglinska, D; Widłak, W; Konopka, W; Poutanen, M; Rahman, N; Huhtaniemi, I; Krawczyk, Z

2001-01-01

The rat Hst70 gene and its mouse counterpart Hsp70.2 belong to the family of Hsp70 heat shock genes and are specifically expressed in male germ cells. Previous studies regarding the structure of the 5' region of the transcription unit of these genes as well as localization of the 'cis' elements conferring their testis-specific expression gave contradictory results [Widlak, Markkula, Krawczyk, Kananen and Huhtaniemi (1995) Biochim. Biophys. Acta 1264, 191-200; Dix, Rosario-Herrle, Gotoh, Mori, Goulding, Barret and Eddy (1996) Dev. Biol. 174, 310-321]. In the present paper we solve these controversies and show that the 5' untranslated region (UTR) of the Hst70 gene contains an intron which is localized similar to that of the mouse Hsp70.2 gene. Reverse transcriptase-mediated PCR, Northern blotting and RNase protection analysis revealed that the transcription initiation of both genes starts at two main distant sites, and one of them is localized within the intron. As a result two populations of Hst70 gene transcripts with similar sizes but different 5' UTR structures can be detected in total testicular RNA. Functional analysis of the Hst70 gene promoter in transgenic mice and transient transfection assays proved that the DNA fragment of approx. 360 bp localized upstream of the ATG transcription start codon is the minimal promoter required for testis-specific expression of the HST70/chloramphenicol acetyltransferase transgene. These experiments also suggest that the expression of the gene may depend on 'cis' regulatory elements localized within exon 1 and the intron sequences. PMID:11563976

Chromosomal localization and partial genomic structure of the human peroxisome proliferator activated receptor-gamma (hPPAR gamma) gene.

PubMed

Beamer, B A; Negri, C; Yen, C J; Gavrilova, O; Rumberger, J M; Durcan, M J; Yarnall, D P; Hawkins, A L; Griffin, C A; Burns, D K; Roth, J; Reitman, M; Shuldiner, A R

1997-04-28

We determined the chromosomal localization and partial genomic structure of the coding region of the human PPAR gamma gene (hPPAR gamma), a nuclear receptor important for adipocyte differentiation and function. Sequence analysis and long PCR of human genomic DNA with primers that span putative introns revealed that intron positions and sizes of hPPAR gamma are similar to those previously determined for the mouse PPAR gamma gene[13]. Fluorescent in situ hybridization localized hPPAR gamma to chromosome 3, band 3p25. Radiation hybrid mapping with two independent primer pairs was consistent with hPPAR gamma being within 1.5 Mb of marker D3S1263 on 3p25-p24.2. These sequences of the intron/exon junctions of the 6 coding exons shared by hPPAR gamma 1 and hPPAR gamma 2 will facilitate screening for possible mutations. Furthermore, D3S1263 is a suitable polymorphic marker for linkage analysis to evaluate PPAR gamma's potential contribution to genetic susceptibility to obesity, lipoatrophy, insulin resistance, and diabetes.

Sexual Violence in the Backlands: Toward a Macro-Level Understanding of Rural Sex Crimes.

PubMed

Braithwaite, Jeremy

2015-10-01

This research focuses on structural covariates of sex crimes in rural communities (using urban and urbanizing communities as comparison groups), with particular analysis on exploring how the magnitude and direction of such covariates differ with respect to type of sex crime. Using 2000 sex crime data from the National Incident-Based Reporting System (NIBRS) for the population of reporting U.S. cities, negative binomial and logistic regression procedures were used to explore the relationship between resource disadvantage, local investment, and economic inequality and sex crime subtypes. For sex crimes that occurred almost exclusively in the home, urban and urbanizing community rates were largely influenced by resource disadvantage and local investment, while these measures did not reach significance for explaining rural rates. Conversely, local investment was a significant predictor of sex crimes that occurred outside the home in rural communities. This research indicates that a structural analysis of sexual victimization (widely absent from the scientific literature) does yield significant findings and that disaggregation of crime into subtypes allows for a more detailed differentiation between urban and rural communities. © The Author(s) 2014.

Nested Neural Networks

NASA Technical Reports Server (NTRS)

Baram, Yoram

1992-01-01

Report presents analysis of nested neural networks, consisting of interconnected subnetworks. Analysis based on simplified mathematical models more appropriate for artificial electronic neural networks, partly applicable to biological neural networks. Nested structure allows for retrieval of individual subpatterns. Requires fewer wires and connection devices than fully connected networks, and allows for local reconstruction of damaged subnetworks without rewiring entire network.

"I'm Just Kind of Winging It": Preparing and Supporting Educators of Adult Refugee Learners

ERIC Educational Resources Information Center

Perry, Kristen H.; Hart, Susan J.

2012-01-01

In this qualitative case study, we explore local adult educators' preparation to teach refugees, along with their professional development needs. This analysis focuses on 10 tutors and instructors in a midsize Southeastern city. Data collection involved an open-ended questionnaire, semi-structured interviews, and observations; analysis involved…

Bearing-Load Modeling and Analysis Study for Mechanically Connected Structures

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.

2006-01-01

Bearing-load response for a pin-loaded hole is studied within the context of two-dimensional finite element analyses. Pin-loaded-hole configurations are representative of mechanically connected structures, such as a stiffener fastened to a rib of an isogrid panel, that are idealized as part of a larger structural component. Within this context, the larger structural component may be idealized as a two-dimensional shell finite element model to identify load paths and high stress regions. Finite element modeling and analysis aspects of a pin-loaded hole are considered in the present paper including the use of linear and nonlinear springs to simulate the pin-bearing contact condition. Simulating pin-connected structures within a two-dimensional finite element analysis model using nonlinear spring or gap elements provides an effective way for accurate prediction of the local effective stress state and peak forces.

Nonlinear analysis for high-temperature multilayered fiber composite structures. M.S. Thesis; [turbine blades

NASA Technical Reports Server (NTRS)

Hopkins, D. A.

1984-01-01

A unique upward-integrated top-down-structured approach is presented for nonlinear analysis of high-temperature multilayered fiber composite structures. Based on this approach, a special purpose computer code was developed (nonlinear COBSTRAN) which is specifically tailored for the nonlinear analysis of tungsten-fiber-reinforced superalloy (TFRS) composite turbine blade/vane components of gas turbine engines. Special features of this computational capability include accounting of; micro- and macro-heterogeneity, nonlinear (stess-temperature-time dependent) and anisotropic material behavior, and fiber degradation. A demonstration problem is presented to mainfest the utility of the upward-integrated top-down-structured approach, in general, and to illustrate the present capability represented by the nonlinear COBSTRAN code. Preliminary results indicate that nonlinear COBSTRAN provides the means for relating the local nonlinear and anisotropic material behavior of the composite constituents to the global response of the turbine blade/vane structure.

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

PubMed Central

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

2014-01-01

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

Structural and contextual dimensions of Iranian primary health care system at local level.

PubMed

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

2015-01-01

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

Near-edge X-ray absorption spectra for metallic Cu and Mn

NASA Astrophysics Data System (ADS)

Greaves, G. N.; Durham, P. J.; Diakun, G.; Quinn, P.

1981-11-01

The measurement of X-ray absorption fine structure of metals- both in the extended region (EXAFS) as well as in the near edge region (XANES)-has been widely discussed (see refs 1-6 for Cu and refs 7-9 for Mn). The recent availability of intense X-ray fluxes from storage rings has usually been exploited for EXAFS leaving the XANES often with poorer resolution than earlier work performed on conventional sources (for example, compare the near edge structure for copper in ref. 1 with refs 3 or 6). In addition, whilst the theory and analysis of EXAFS is relatively well-established2,10, a theory for the strong scattering regime near to the absorption edge has only recently been developed11. We report here the first high resolution XANES spectra for Cu and Mn which were performed at the SRS storage ring at Daresbury. Although both metals have close-packed structures consisting of atoms of similar size their local atomic structure is different in detail. Significant differences are found in their respective XANES reflecting the senstivity of this region of the X-ray absorption fine structure to the local atomic structure. Spectra for the two metals have been analysed using the new multiple scattering formalism. This is a real space calculation and unlike a conventional band structure approach it does not require structural periodicity but works from the local arrangement of atoms.

Population structure of the large Japanese field mouse, Apodemus speciosus (Rodentia: Muridae), in suburban landscape, based on mitochondrial D-loop sequences.

PubMed

Hirota, Tadao; Hirohata, Tetsuo; Mashima, Hiroshi; Satoh, Toshiyuki; Obara, Yoshiaki

2004-11-01

Genetic structure of the large Japanese field mouse populations in suburban landscape of West Tokyo, Japan was determined using mitochondrial DNA control region sequence. Samples were collected from six habitats linked by forests and green tract along the Tama River, and from two forests segregated by urban areas from those continuous habitats. Thirty-five haplotypes were detected in 221 animals. Four to eight haplotypes were found within each local population belonging to the continuous landscape. Some haplotypes were shared by two or three adjacent local populations. On the other hand, two isolated habitats were occupied by one or two indigenous haplotypes. Significant genetic differentiation between all pairs of local populations, except for one pair in the continuous habitats, was found by analysis of molecular variance (amova). The geographical distance between habitats did not explain the large variance of pairwise F(ST)-values among local populations. F(ST)-values between local populations segregated by urban areas were higher than those between local populations in the continuous habitat, regardless of geographical distance. The results of this study demonstrated quantitatively that urban areas inhibit the migration of Apodemus speciosus, whereas a linear green tract along a river functions as a corridor. Moreover, it preserves the metapopulation structure of A. speciosus as well as the corridors in suburban landscape.

Reason for high strength and good ductility in dual phase steels composed of soft ferrite and hard martensite

NASA Astrophysics Data System (ADS)

Terada, Daisuke; Ikeda, Gosuke; Park, Myeong-heom; Shibata, Akinobu; Tsuji, Nobuhiro

2017-07-01

Dual phase (DP) steels in which the microstructures are composed of a soft ferrite phase and a hard martensite phase are known to show good strain-hardening, high strength and large elongation, but reasons for their superior mechanical properties are still unclear. In the present study, two types of DP structures, having either networked martensite or isolated martensite were fabricated in a low-carbon steel by different heat treatment routes, and their tensile deformation behavior was analyzed using the digital image correlation (DIC) technique. It was revealed that the DP specimens having networked martensite microstructures showed a better strength-ductility balance than the DP specimens with isolated martensite structures. The microscopic DIC analysis of identical areas showed that the strain distribution within the DP microstructures was not uniform and the plastic strain was localized in soft ferrite grains. The strain localized regions tended to detour around hard martensite but eventually propagated across the martensite. It was found also from the DIC analysis that the degree of strain partitioning between ferrite and martensite in the networked DP structure was lower than that in the isolated DP structure. The deformation became more homogeneous when the hard phase (martensite) was connected to form a network structure, which could be one of the reasons for the better strength-ductility balance in the networked DP structure compared to that in the isolated DP structure.

The effect of local atomic structure on the optical properties of GeSi self-assembled islands buried in silicon matrix

NASA Astrophysics Data System (ADS)

Demchenko, I. N.; Lawniczak-Jablonska, K.; Kret, S.; Novikov, A. V.; Laval, J.-Y.; Zak, M.; Szczepanska, A.; Yablonskiy, A. N.; Krasilnik, Z. F.

2007-03-01

The local atomic structure of GeSi self-assembled islands buried in a silicon matrix strongly influences the optical properties of such systems. In the present paper this structure was determined by x-ray absorption fine-structure (XAFS) spectroscopy and high resolution transmission electron microscopy (HRTEM) and used to build a schematic description of the band structure model. Quantitative analysis of the extended XAFS (EXAFS) spectrum was performed for three coordination shells around the Ge absorbing atom with multiple scattering taken into account. It was proved that the coordination number of elements in an alloy resulting from EXAFS analysis for all three coordination spheres (i.e. 'mixing degree' parameters) cannot be taken as the concentration of alloy but can be used together with a proper model of the alloy unit cell to calculate a realistic concentration. The fraction of Ge calculated in this way is consistent with HRTEM results. The found model of the unit cell was used to generate a x-ray absorption near edge structure spectrum by ab initio calculations. This approach yielded a spectrum in good agreement with the experimental one. The information gained from XAFS and HRTEM was then used for calculation of the band structure diagram. Results of the calculation are discussed and compared with the experimental photoluminescence spectrum.

Metacommunity ecology meets biogeography: effects of geographical region, spatial dynamics and environmental filtering on community structure in aquatic organisms.

PubMed

Heino, Jani; Soininen, Janne; Alahuhta, Janne; Lappalainen, Jyrki; Virtanen, Risto

2017-01-01

Metacommunity patterns and underlying processes in aquatic organisms have typically been studied within a drainage basin. We examined variation in the composition of six freshwater organismal groups across various drainage basins in Finland. We first modelled spatial structures within each drainage basin using Moran eigenvector maps. Second, we partitioned variation in community structure among three groups of predictors using constrained ordination: (1) local environmental variables, (2) spatial variables, and (3) dummy variable drainage basin identity. Third, we examined turnover and nestedness components of multiple-site beta diversity, and tested the best fit patterns of our datasets using the "elements of metacommunity structure" analysis. Our results showed that basin identity and local environmental variables were significant predictors of community structure, whereas within-basin spatial effects were typically negligible. In half of the organismal groups (diatoms, bryophytes, zooplankton), basin identity was a slightly better predictor of community structure than local environmental variables, whereas the opposite was true for the remaining three organismal groups (insects, macrophytes, fish). Both pure basin and local environmental fractions were, however, significant after accounting for the effects of the other predictor variable sets. All organismal groups exhibited high levels of beta diversity, which was mostly attributable to the turnover component. Our results showed consistent Clementsian-type metacommunity structures, suggesting that subgroups of species responded similarly to environmental factors or drainage basin limits. We conclude that aquatic communities across large scales are mostly determined by environmental and basin effects, which leads to high beta diversity and prevalence of Clementsian community types.

Insight into the local environment of magnesium and calcium in low-coordination-number organo-complexes using 25Mg and 43Ca solid-state NMR: a DFT study.

PubMed

Gervais, Christel; Jones, Cameron; Bonhomme, Christian; Laurencin, Danielle

2017-03-01

With the increasing number of organocalcium and organomagnesium complexes under development, there is a real need to be able to characterize in detail their local environment in order to fully rationalize their reactivity. For crystalline structures, in cases when diffraction techniques are insufficient, additional local spectroscopies like 25 Mg and 43 Ca solid-state NMR may provide valuable information to help fully establish the local environment of the metal ions. In this current work, a prospective DFT investigation on crystalline magnesium and calcium complexes involving low-coordination numbers and N-bearing organic ligands was carried out, in which the 25 Mg and 43 Ca NMR parameters [isotropic chemical shift, chemical shift anisotropy (CSA) and quadrupolar parameters] were calculated for each structure. The analysis of the calculated parameters in relation to the local environment of the metal ions revealed that they are highly sensitive to very small changes in geometry/distances, and hence that they could be used to assist in the refinement of crystal structures. Moreover, such calculations provide a guideline as to how the NMR measurements will need to be performed, revealing that these will be very challenging.

Graded Interface Models for more accurate Determination of van der Waals-London Dispersion Interactions across Grain Boundaries

DOE Office of Scientific and Technical Information (OSTI.GOV)

van Benthem, Klaus; Tan, Guolong; French, Roger H

2006-01-01

Attractive van der Waals V London dispersion interactions between two half crystals arise from local physical property gradients within the interface layer separating the crystals. Hamaker coefficients and London dispersion energies were quantitatively determined for 5 and near- 13 grain boundaries in SrTiO3 by analysis of spatially resolved valence electron energy-loss spectroscopy (VEELS) data. From the experimental data, local complex dielectric functions were determined, from which optical properties can be locally analysed. Both local electronic structures and optical properties revealed gradients within the grain boundary cores of both investigated interfaces. The obtained results show that even in the presence ofmore » atomically structured grain boundary cores with widths of less than 1 nm, optical properties have to be represented with gradual changes across the grain boundary structures to quantitatively reproduce accurate van der Waals V London dispersion interactions. London dispersion energies of the order of 10% of the apparent interface energies of SrTiO3 were observed, demonstrating their significance in the grain boundary formation process. The application of different models to represent optical property gradients shows that long-range van der Waals V London dispersion interactions scale significantly with local, i.e atomic length scale property variations.« less

Equilibrium structure of δ-Bi(2)O(3) from first principles.

PubMed

Music, Denis; Konstantinidis, Stephanos; Schneider, Jochen M

2009-04-29

Using ab initio calculations, we have systematically studied the structure of δ-Bi(2)O(3) (fluorite prototype, 25% oxygen vacancies) probing [Formula: see text] and combined [Formula: see text] and [Formula: see text] oxygen vacancy ordering, random distribution of oxygen vacancies with two different statistical descriptions as well as local relaxations. We observe that the combined [Formula: see text] and [Formula: see text] oxygen vacancy ordering is the most stable configuration. Radial distribution functions for these configurations can be classified as discrete (ordered configurations) and continuous (random configurations). This classification can be understood on the basis of local structural relaxations. Up to 28.6% local relaxation of the oxygen sublattice is present in the random configurations, giving rise to continuous distribution functions. The phase stability obtained may be explained with the bonding analysis. Electron lone-pair charges in the predominantly ionic Bi-O matrix may stabilize the combined [Formula: see text] and [Formula: see text] oxygen vacancy ordering.

Study of diffusion and local structure of sodium-silicate liquid: the molecular dynamic simulation

NASA Astrophysics Data System (ADS)

Hung, Pham Khac; Noritake, Fumiya; San, Luyen Thi; Van, To Ba; Vinh, Le The

2017-10-01

A systematic analysis on sodium-silicate melt with various silica contents was carried out. The simulation revealed two diffusion mechanisms occurred in the melt: the bond-breaking and hopping between sites. The local structure was analyzed through T-simplexes. It was revealed that T-clusters have a non-spherical shape and represent the diffusion channel, in which Na atoms are dominant, but no any O atoms are located. The SiO2-poor melt acquires a long channel. In contrast, the SiO2-rich melt consists of unconnected short channels. The simulation also revealed the immobile and mobile regions which differ in local structure and constituent composition. We propose a new CL-function to characterizing the spatial distribution of different atom component. The spatial distribution of mobile and immobile atoms is found quite different. In particular, the immobile atoms are concentrated in high-density regions possessing very large density of immobile atoms. The spatial distribution of mobile atoms in contrast is more homogeneous.

Robust membrane detection based on tensor voting for electron tomography.

PubMed

Martinez-Sanchez, Antonio; Garcia, Inmaculada; Asano, Shoh; Lucic, Vladan; Fernandez, Jose-Jesus

2014-04-01

Electron tomography enables three-dimensional (3D) visualization and analysis of the subcellular architecture at a resolution of a few nanometers. Segmentation of structural components present in 3D images (tomograms) is often necessary for their interpretation. However, it is severely hampered by a number of factors that are inherent to electron tomography (e.g. noise, low contrast, distortion). Thus, there is a need for new and improved computational methods to facilitate this challenging task. In this work, we present a new method for membrane segmentation that is based on anisotropic propagation of the local structural information using the tensor voting algorithm. The local structure at each voxel is then refined according to the information received from other voxels. Because voxels belonging to the same membrane have coherent structural information, the underlying global structure is strengthened. In this way, local information is easily integrated at a global scale to yield segmented structures. This method performs well under low signal-to-noise ratio typically found in tomograms of vitrified samples under cryo-tomography conditions and can bridge gaps present on membranes. The performance of the method is demonstrated by applications to tomograms of different biological samples and by quantitative comparison with standard template matching procedure. Copyright © 2014 Elsevier Inc. All rights reserved.

Investigation of local tunneling current noise spectra on the silicon crystal surfaces by means of STM/STS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mantsevich, V. N., E-mail: vmantsev@spmlab.phys.msu.su; Maslova, N. S.; Cao, G. Y.

We report on a careful analysis of the local tunneling conductivity by means of ultra-high vacuum scanning tunneling microscopy/spectroscopy (STM/STS) technique in the vicinity of low-dimensional structures on the Si(111)–(7 × 7) and Si(110)–(16 × 2) surfaces. The power-law exponent α of low-frequency tunneling current noise spectra is investigated for different values of the tunneling contact parameters: relaxation rates, the localized state coupling, and the tunneling barrier width and height.

Investigation of local tunneling current noise spectra on the silicon crystal surfaces by means of STM/STS

NASA Astrophysics Data System (ADS)

Mantsevich, V. N.; Maslova, N. S.; Cao, G. Y.

2015-08-01

We report on a careful analysis of the local tunneling conductivity by means of ultra-high vacuum scanning tunneling microscopy/spectroscopy (STM/STS) technique in the vicinity of low-dimensional structures on the Si(111)-(7 × 7) and Si(110)-(16 × 2) surfaces. The power-law exponent α of low-frequency tunneling current noise spectra is investigated for different values of the tunneling contact parameters: relaxation rates, the localized state coupling, and the tunneling barrier width and height.

Self-similar pyramidal structures and signal reconstruction

NASA Astrophysics Data System (ADS)

Benedetto, John J.; Leon, Manuel; Saliani, Sandra

1998-03-01

Pyramidal structures are defined which are locally a combination of low and highpass filtering. The structures are analogous to but different from wavelet packet structures. In particular, new frequency decompositions are obtained; and these decompositions can be parameterized to establish a correspondence with a large class of Cantor sets. Further correspondences are then established to relate such frequency decompositions with more general self- similarities. The role of the filters in defining these pyramidal structures gives rise to signal reconstruction algorithms, and these, in turn, are used in the analysis of speech data.

Multichannel biomedical time series clustering via hierarchical probabilistic latent semantic analysis.

PubMed

Wang, Jin; Sun, Xiangping; Nahavandi, Saeid; Kouzani, Abbas; Wu, Yuchuan; She, Mary

2014-11-01

Biomedical time series clustering that automatically groups a collection of time series according to their internal similarity is of importance for medical record management and inspection such as bio-signals archiving and retrieval. In this paper, a novel framework that automatically groups a set of unlabelled multichannel biomedical time series according to their internal structural similarity is proposed. Specifically, we treat a multichannel biomedical time series as a document and extract local segments from the time series as words. We extend a topic model, i.e., the Hierarchical probabilistic Latent Semantic Analysis (H-pLSA), which was originally developed for visual motion analysis to cluster a set of unlabelled multichannel time series. The H-pLSA models each channel of the multichannel time series using a local pLSA in the first layer. The topics learned in the local pLSA are then fed to a global pLSA in the second layer to discover the categories of multichannel time series. Experiments on a dataset extracted from multichannel Electrocardiography (ECG) signals demonstrate that the proposed method performs better than previous state-of-the-art approaches and is relatively robust to the variations of parameters including length of local segments and dictionary size. Although the experimental evaluation used the multichannel ECG signals in a biometric scenario, the proposed algorithm is a universal framework for multichannel biomedical time series clustering according to their structural similarity, which has many applications in biomedical time series management. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Fatigue Analysis of the Piston Rod in a Kaplan Turbine Based on Crack Propagation under Unsteady Hydraulic Loads

NASA Astrophysics Data System (ADS)

Liu, X.; Y Luo, Y.; Wang, Z. W.

2014-03-01

As an important component of the blade-control system in Kaplan turbines, piston rods are subjected to fluctuating forces transferred by the turbines blades from hydraulic pressure oscillations. Damage due to unsteady hydraulic loads might generate unexpected down time and high repair cost. In one running hydropower plant, the fracture failure of the piston rod was found twice at the same location. With the transient dynamic analysis, the retainer ring structure of the piston rod existed a relative high stress concentration. This predicted position of the stress concentration agreed well with the actual fracture position in the plant. However, the local strain approach was not able to explain why this position broke frequently. Since traditional structural fatigue analyses use a local stress strain approach to assess structural integrity, do not consider the effect of flaws which can significantly degrade structural life. Using linear elastic fracture mechanism (LEFM) approaches that include the effect of flaws is becoming common practice in many industries. In this research, a case involving a small semi-ellipse crack was taken into account at the stress concentration area, crack growth progress was calculated by FEM. The relationship between crack length and remaining life was obtained. The crack propagation path approximately agreed with the actual fracture section. The results showed that presence of the crack had significantly changed the local stress and strain distributions of the piston rod compared with non-flaw assumption.

Local election: does bureaucracy become one of main political power?

NASA Astrophysics Data System (ADS)

Amin, Muryanto; Musthafa Sembiring, Walid

2018-03-01

This writing aims to analyze the emergence of bureaucracy as one of political power in local level after the local election is held in Indonesia. Due to information authorization, media network, and stable structure, the bureaucracy soon transforms into political power which can compete with the other political power at the local level. In Medan local election in 2010 and 2015 has evidently proven the power of bureaucracy network in winning the bureaucrat-background candidates. As methods of the research, the researcher held a Focus-Group Discussion (FGD) and had an in-depth interview with ten bureaucracy elites in Medan and local political elites. The observation and Focus-Group Discussion (FGD) are analyzed using qualitative analysis technique typology. The result states that the bureaucracy network in Medan has been used in a massive way as the political power of winning. The structure of bureaucracy – from the top to the low – is involved in the winning. The most governmental programs were applied to attract the mass’ sympathy toward the candidates. The bureaucratic proximity to media network is also used to do a campaign in a massive way. The conclusion of the research is that bureaucracy emerges as a new, massive, effective local political power in the local election.

Plasmodium knowlesi Skeleton-Binding Protein 1 Localizes to the ‘Sinton and Mulligan’ Stipplings in the Cytoplasm of Monkey and Human Erythrocytes

PubMed Central

Lucky, Amuza Byaruhanga; Sakaguchi, Miako; Katakai, Yuko; Kawai, Satoru; Yahata, Kazuhide; Templeton, Thomas J.

2016-01-01

The malaria parasite, Plasmodium, exports protein products to the infected erythrocyte to introduce modifications necessary for the establishment of nutrient acquisition and surface display of host interaction ligands. Erythrocyte remodeling impacts parasite virulence and disease pathology and is well documented for the human malaria parasite Plasmodium falciparum, but has been less described for other Plasmodium species. For P. falciparum, the exported protein skeleton-binding protein 1 (PfSBP1) is involved in the trafficking of erythrocyte surface ligands and localized to membranous structures within the infected erythrocyte, termed Maurer's clefts. In this study, we analyzed SBP1 orthologs across the Plasmodium genus by BLAST analysis and conserved gene synteny, which were also recently described by de Niz et al. (2016). To evaluate the localization of an SBP1 ortholog, we utilized the zoonotic malaria parasite, Plasmodium knowlesi. Immunofluorescence assay of transgenic P. knowlesi parasites expressing epitope-tagged recombinant PkSBP1 revealed a punctate staining pattern reminiscent of Maurer's clefts, following infection of either monkey or human erythrocytes. The recombinant PkSBP1-positive puncta co-localized with Giemsa-stained structures, known as ‘Sinton and Mulligan’ stipplings. Immunoelectron microscopy also showed that recombinant PkSBP1 localizes within or on the membranous structures akin to the Maurer's clefts. The recombinant PkSBP1 expressed in P. falciparum-infected erythrocytes co-localized with PfSBP1 at the Maurer's clefts, indicating an analogous trafficking pattern. A member of the P. knowlesi 2TM protein family was also expressed and localized to membranous structures in infected monkey erythrocytes. These results suggest that the trafficking machinery and induced erythrocyte cellular structures of P. knowlesi are similar following infection of both monkey and human erythrocytes, and are conserved with P. falciparum. PMID:27732628

A mRNA and cognate microRNAs localize in the nucleolus.

PubMed

Reyes-Gutierrez, Pablo; Ritland Politz, Joan C; Pederson, Thoru

2014-01-01

We previously discovered that a set of 5 microRNAs are concentrated in the nucleolus of rat myoblasts. We now report that several mRNAs are also localized in the nucleoli of these cells as determined by microarray analysis of RNA from purified nucleoli. Among the most abundant of these nucleolus-localized mRNAs is that encoding insulin-like growth factor 2 (IGF2), a regulator of myoblast proliferation and differentiation. The presence of IGF2 mRNA in nucleoli was confirmed by fluorescence in situ hybridization, and RT-PCR experiments demonstrated that these nucleolar transcripts are spliced, thus arriving from the nucleoplasm. Bioinformatics analysis predicted canonically structured, highly thermodynamically stable interactions between IGF2 mRNA and all 5 of the nucleolus-localized microRNAs. These results raise the possibility that the nucleolus is a staging site for setting up particular mRNA-microRNA interactions prior to export to the cytoplasm.

Management of local economic and ecological system of coal processing company

NASA Astrophysics Data System (ADS)

Kiseleva, T. V.; Mikhailov, V. G.; Karasev, V. A.

2016-10-01

The management issues of local ecological and economic system of coal processing company - coal processing plant - are considered in the article. The objectives of the research are the identification and the analysis of local ecological and economic system (coal processing company) performance and the proposals for improving the mechanism to support the management decision aimed at improving its environmental safety. The data on the structure of run-of-mine coal processing products are shown. The analysis of main ecological and economic indicators of coal processing enterprises, characterizing the state of its environmental safety, is done. The main result of the study is the development of proposals to improve the efficiency of local enterprise ecological and economic system management, including technical, technological and business measures. The results of the study can be recommended to industrial enterprises to improve their ecological and economic efficiency.

Fine-scale natal homing and localized movement as shaped by sex and spawning habitat in Chinook salmon: Insights from spatial autocorrelation analysis of individual genotypes

Treesearch

H. M. Neville; D. J. Isaak; J. B. Dunham; R. F. Thurow; B. E. Rieman

2006-01-01

Natal homing is a hallmark of the life history of salmonid fishes, but the spatial scale of homing within local, naturally reproducing salmon populations is still poorly understood. Accurate homing (paired with restricted movement) should lead to the existence of finescale genetic structuring due to the spatial clustering of related individuals on spawning grounds....

High Temperature Composite Analyzer (HITCAN) demonstration manual, version 1.0

NASA Technical Reports Server (NTRS)

Singhal, S. N; Lackney, J. J.; Murthy, P. L. N.

1993-01-01

This manual comprises a variety of demonstration cases for the HITCAN (HIgh Temperature Composite ANalyzer) code. HITCAN is a general purpose computer program for predicting nonlinear global structural and local stress-strain response of arbitrarily oriented, multilayered high temperature metal matrix composite structures. HITCAN is written in FORTRAN 77 computer language and has been configured and executed on the NASA Lewis Research Center CRAY XMP and YMP computers. Detailed description of all program variables and terms used in this manual may be found in the User's Manual. The demonstration includes various cases to illustrate the features and analysis capabilities of the HITCAN computer code. These cases include: (1) static analysis, (2) nonlinear quasi-static (incremental) analysis, (3) modal analysis, (4) buckling analysis, (5) fiber degradation effects, (6) fabrication-induced stresses for a variety of structures; namely, beam, plate, ring, shell, and built-up structures. A brief discussion of each demonstration case with the associated input data file is provided. Sample results taken from the actual computer output are also included.

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes.

PubMed

Pervouchine, Dmitri D

2018-06-15

The ability to form an intramolecular structure plays a fundamental role in eukaryotic RNA biogenesis. Proximate regions in the primary transcripts fold into a local secondary structure, which is then hierarchically assembled into a tertiary structure that is stabilized by RNA-binding proteins and long-range intramolecular base pairings. While the local RNA structure can be predicted reasonably well for short sequences, long-range structure at the scale of eukaryotic genes remains problematic from the computational standpoint. The aim of this review is to list functional examples of long-range RNA structures, to summarize current comparative methods of structure prediction, and to highlight their advances and limitations in the context of long-range RNA structures. Most comparative methods implement the “first-align-then-fold” principle, i.e., they operate on multiple sequence alignments, while functional RNA structures often reside in non-conserved parts of the primary transcripts. The opposite “first-fold-then-align” approach is currently explored to a much lesser extent. Developing novel methods in both directions will improve the performance of comparative RNA structure analysis and help discover novel long-range structures, their higher-order organization, and RNA⁻RNA interactions across the transcriptome.

Local Structure Analysis and Interface Layer Effect of Phase-Change Recording Material Using Actual Media

NASA Astrophysics Data System (ADS)

Nakai, Tsukasa; Yoshiki, Masahiko; Satoh, Yasuhiro; Ashida, Sumio

2008-07-01

The influences of the interface layer on crystal structure, the local atomic arrangement, and the electronic and chemical structure of a GeBiTe (GBT) phase-change recording material have been investigated using X-ray diffraction (XRD), X-ray absorption fine structure (XAFS), and hard X-ray photoelectron spectroscopy (HX-PES) methods using actual rewritable high-speed HD DVD media without special sample processing. XRD results showed that the crystal structure of laser-crystallized GBT alloy in the actual HD DVD media is the same as that of GeSbTe (GST) alloy, which has a NaCl-type structure. No differences between samples with and without interface layers were found. The lattice constant of GBT is larger than that of GST. Bi increases the lattice constant of GST with respect to the Bi substitution ratio of Sb. According to HX-PES, the DOS of in the recording film amorphous state with an interface layer is closer to that of the crystalline state than the recording film without an interface layer. From XAFS results, clear differences between amorphous (Amo.) and crystalline states (Cry.) were observed. The interatomic distance of amorphous recording material is independent of the existence of an interface layer. On the other hand, the coordination number varied slightly due to the presence of the interface layer. Therefore, the electronic state of the recording layer changes because of the interface layer, although the local structure changes only slightly except for the coordination number. Combining these results, we conclude that the interface layer changes the electronic state of the recording layer and promotes crystallization, but only affects the local structure of the atomic arrangement slightly.

Simulation of Weld Mechanical Behavior to Include Welding-Induced Residual Stress and Distortion: Coupling of SYSWELD and Abaqus Codes

DTIC Science & Technology

2015-11-01

induced residual stresses and distortions from weld simulations in the SYSWELD software code in structural Finite Element Analysis ( FEA ) simulations...performed in the Abaqus FEA code is presented. The translation of these results is accomplished using a newly developed Python script. Full details of...Local Weld Model in Structural FEA ....................................................15 CONCLUSIONS

Holism and structuralism in U(1) gauge theory

NASA Astrophysics Data System (ADS)

Lyre, Holger

After decades of neglect philosophers of physics have discovered gauge theories-arguably the paradigm of modern field physics-as a genuine topic for foundational and philosophical research. Incidentally, in the last couple of years interest from the philosophy of physics in structural realism-in the eyes of its proponents the best suited realist position towards modern physics-has also raised. This paper tries to connect both topics and aims to show that structural realism gains further credence from an ontological analysis of gauge theories-in particular U (1) gauge theory. In the first part of the paper the framework of fiber bundle gauge theories is briefly presented and the interpretation of local gauge symmetry will be examined. In the second part, an ontological underdetermination of gauge theories is carved out by considering the various kinds of non-locality involved in such typical effects as the Aharonov-Bohm effect. The analysis shows that the peculiar form of non-separability figuring in gauge theories is a variant of spatiotemporal holism and can be distinguished from quantum theoretic holism. In the last part of the paper the arguments for a gauge theoretic support of structural realism are laid out and discussed.

Structural Connectivity Networks of Transgender People

PubMed Central

Hahn, Andreas; Kranz, Georg S.; Küblböck, Martin; Kaufmann, Ulrike; Ganger, Sebastian; Hummer, Allan; Seiger, Rene; Spies, Marie; Winkler, Dietmar; Kasper, Siegfried; Windischberger, Christian; Swaab, Dick F.; Lanzenberger, Rupert

2015-01-01

Although previous investigations of transsexual people have focused on regional brain alterations, evaluations on a network level, especially those structural in nature, are largely missing. Therefore, we investigated the structural connectome of 23 female-to-male (FtM) and 21 male-to-female (MtF) transgender patients before hormone therapy as compared with 25 female and 25 male healthy controls. Graph theoretical analysis of whole-brain probabilistic tractography networks (adjusted for differences in intracranial volume) showed decreased hemispheric connectivity ratios of subcortical/limbic areas for both transgender groups. Subsequent analysis revealed that this finding was driven by increased interhemispheric lobar connectivity weights (LCWs) in MtF transsexuals and decreased intrahemispheric LCWs in FtM patients. This was further reflected on a regional level, where the MtF group showed mostly increased local efficiencies and FtM patients decreased values. Importantly, these parameters separated each patient group from the remaining subjects for the majority of significant findings. This work complements previously established regional alterations with important findings of structural connectivity. Specifically, our data suggest that network parameters may reflect unique characteristics of transgender patients, whereas local physiological aspects have been shown to represent the transition from the biological sex to the actual gender identity. PMID:25217469

Dynamical, structural and chemical heterogeneities in a binary metallic glass-forming liquid

NASA Astrophysics Data System (ADS)

Puosi, F.; Jakse, N.; Pasturel, A.

2018-04-01

As it approaches the glass transition, particle motion in liquids becomes highly heterogeneous and regions with virtually no mobility coexist with liquid-like domains. This complex dynamic is believed to be responsible for different phenomena including non-exponential relaxation and the breakdown of the Stokes-Einstein relation. Understanding the relationships between dynamical heterogeneities and local structure in metallic liquids and glasses is a major scientific challenge. Here we use classical molecular dynamics simulations to study the atomic dynamics and microscopic structure of Cu50Zr50 alloy in the supercooling regime. Dynamical heterogeneities are identified via an isoconfigurational analysis. We demonstrate the transition from isolated to clustering low mobility with decreasing temperature. These slow clusters, whose sizes grow upon cooling, are also associated with concentration fluctuations, characterized by a Zr-enriched phase, with a composition CuZr2 . In addition, a structural analysis of slow clusters based on Voronoi tessellation evidences an increase with respect of the bulk system of the fraction of Cu atoms having a local icosahedral order. These results are in agreement with the consolidated scenario of the relevant role played by icosahedral order in the dynamic slowing-down in supercooled metal alloys.

Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest

PubMed Central

2013-01-01

Background In stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence. Methods Here we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana. Results Sampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales. Conclusions The abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and geographically restricted groups. Local samples for the cosmopolitan C. briggsae mirror its pan-tropical patterns of intraspecific polymorphism. It remains an important challenge to decipher what drives Caenorhabditis distributions and diversity within and between species. PMID:23311925

Local spin density functional investigations of a manganite with perovskite-type derived structures

NASA Astrophysics Data System (ADS)

Matar, S. F.; Studer, F.; Siberchicot, B.; Subramanian, M. A.; Demazeau, G.; Etourneau, J.

1998-11-01

The electronic and magnetic structures of the perovskite CaMnO3 are self-consistently calculated assuming two crystal structures at the same formula unit volume within the local spin density functional theory and the augmented spherical wave (ASW) method. From the comparisons of energy differences between the different magnetic states the ground state configuration is an insulator with G-type ordering. This result together with the magnitudes of the magnetic moments are in agreement with experiment. The influence of mixing between Mn and O is found spin dependent from the analysis of the crystal orbital overlap population (COOP) which enable to describe the chemical bond. The calculations underline a feature of a half metallic ferromagnet which could be connected with the colossal magnetoresistance (CMR) property of related compounds.

The impact of structural uncertainty on cost-effectiveness models for adjuvant endocrine breast cancer treatments: the need for disease-specific model standardization and improved guidance.

PubMed

Frederix, Gerardus W J; van Hasselt, Johan G C; Schellens, Jan H M; Hövels, Anke M; Raaijmakers, Jan A M; Huitema, Alwin D R; Severens, Johan L

2014-01-01

Structural uncertainty relates to differences in model structure and parameterization. For many published health economic analyses in oncology, substantial differences in model structure exist, leading to differences in analysis outcomes and potentially impacting decision-making processes. The objectives of this analysis were (1) to identify differences in model structure and parameterization for cost-effectiveness analyses (CEAs) comparing tamoxifen and anastrazole for adjuvant breast cancer (ABC) treatment; and (2) to quantify the impact of these differences on analysis outcome metrics. The analysis consisted of four steps: (1) review of the literature for identification of eligible CEAs; (2) definition and implementation of a base model structure, which included the core structural components for all identified CEAs; (3) definition and implementation of changes or additions in the base model structure or parameterization; and (4) quantification of the impact of changes in model structure or parameterizations on the analysis outcome metrics life-years gained (LYG), incremental costs (IC) and the incremental cost-effectiveness ratio (ICER). Eleven CEA analyses comparing anastrazole and tamoxifen as ABC treatment were identified. The base model consisted of the following health states: (1) on treatment; (2) off treatment; (3) local recurrence; (4) metastatic disease; (5) death due to breast cancer; and (6) death due to other causes. The base model estimates of anastrazole versus tamoxifen for the LYG, IC and ICER were 0.263 years, €3,647 and €13,868/LYG, respectively. In the published models that were evaluated, differences in model structure included the addition of different recurrence health states, and associated transition rates were identified. Differences in parameterization were related to the incidences of recurrence, local recurrence to metastatic disease, and metastatic disease to death. The separate impact of these model components on the LYG ranged from 0.207 to 0.356 years, while incremental costs ranged from €3,490 to €3,714 and ICERs ranged from €9,804/LYG to €17,966/LYG. When we re-analyzed the published CEAs in our framework by including their respective model properties, the LYG ranged from 0.207 to 0.383 years, IC ranged from €3,556 to €3,731 and ICERs ranged from €9,683/LYG to €17,570/LYG. Differences in model structure and parameterization lead to substantial differences in analysis outcome metrics. This analysis supports the need for more guidance regarding structural uncertainty and the use of standardized disease-specific models for health economic analyses of adjuvant endocrine breast cancer therapies. The developed approach in the current analysis could potentially serve as a template for further evaluations of structural uncertainty and development of disease-specific models.

Random vectors and spatial analysis by geostatistics for geotechnical applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young, D.S.

1987-08-01

Geostatistics is extended to the spatial analysis of vector variables by defining the estimation variance and vector variogram in terms of the magnitude of difference vectors. Many random variables in geotechnology are in vectorial terms rather than scalars, and its structural analysis requires those sample variable interpolations to construct and characterize structural models. A better local estimator will result in greater quality of input models; geostatistics can provide such estimators; kriging estimators. The efficiency of geostatistics for vector variables is demonstrated in a case study of rock joint orientations in geological formations. The positive cross-validation encourages application of geostatistics tomore » spatial analysis of random vectors in geoscience as well as various geotechnical fields including optimum site characterization, rock mechanics for mining and civil structures, cavability analysis of block cavings, petroleum engineering, and hydrologic and hydraulic modelings.« less

Ellipsoidal analysis of coordination polyhedra

PubMed Central

Cumby, James; Attfield, J. Paul

2017-01-01

The idea of the coordination polyhedron is essential to understanding chemical structure. Simple polyhedra in crystalline compounds are often deformed due to structural complexity or electronic instabilities so distortion analysis methods are useful. Here we demonstrate that analysis of the minimum bounding ellipsoid of a coordination polyhedron provides a general method for studying distortion, yielding parameters that are sensitive to various orders in metal oxide examples. Ellipsoidal analysis leads to discovery of a general switching of polyhedral distortions at symmetry-disallowed transitions in perovskites that may evidence underlying coordination bistability, and reveals a weak off-centre ‘d5 effect' for Fe3+ ions that could be exploited in multiferroics. Separating electronic distortions from intrinsic deformations within the low temperature superstructure of magnetite provides new insights into the charge and trimeron orders. Ellipsoidal analysis can be useful for exploring local structure in many materials such as coordination complexes and frameworks, organometallics and organic molecules. PMID:28146146

Factors Influencing Progressive Failure Analysis Predictions for Laminated Composite Structure

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.

2008-01-01

Progressive failure material modeling methods used for structural analysis including failure initiation and material degradation are presented. Different failure initiation criteria and material degradation models are described that define progressive failure formulations. These progressive failure formulations are implemented in a user-defined material model for use with a nonlinear finite element analysis tool. The failure initiation criteria include the maximum stress criteria, maximum strain criteria, the Tsai-Wu failure polynomial, and the Hashin criteria. The material degradation model is based on the ply-discounting approach where the local material constitutive coefficients are degraded. Applications and extensions of the progressive failure analysis material model address two-dimensional plate and shell finite elements and three-dimensional solid finite elements. Implementation details are described in the present paper. Parametric studies for laminated composite structures are discussed to illustrate the features of the progressive failure modeling methods that have been implemented and to demonstrate their influence on progressive failure analysis predictions.

The problem and promise of scale dependency in community phylogenetics.

PubMed

Swenson, Nathan G; Enquist, Brian J; Pither, Jason; Thompson, Jill; Zimmerman, Jess K

2006-10-01

The problem of scale dependency is widespread in investigations of ecological communities. Null model investigations of community assembly exemplify the challenges involved because they typically include subjectively defined "regional species pools." The burgeoning field of community phylogenetics appears poised to face similar challenges. Our objective is to quantify the scope of the problem of scale dependency by comparing the phylogenetic structure of assemblages across contrasting geographic and taxonomic scales. We conduct phylogenetic analyses on communities within three tropical forests, and perform a sensitivity analysis with respect to two scaleable inputs: taxonomy and species pool size. We show that (1) estimates of phylogenetic overdispersion within local assemblages depend strongly on the taxonomic makeup of the local assemblage and (2) comparing the phylogenetic structure of a local assemblage to a species pool drawn from increasingly larger geographic scales results in an increased signal of phylogenetic clustering. We argue that, rather than posing a problem, "scale sensitivities" are likely to reveal general patterns of diversity that could help identify critical scales at which local or regional influences gain primacy for the structuring of communities. In this way, community phylogenetics promises to fill an important gap in community ecology and biogeography research.

Influence of Aromatic Molecules on the Structure and Spectroscopy of Water Clusters

NASA Astrophysics Data System (ADS)

Tabor, Daniel P.; Sibert, Edwin; Walsh, Patrick S.; Zwier, Timothy S.

2016-06-01

Isomer-specific resonant ion-dip infrared spectra are presented for benzene-(water)_n, 1-2-diphenoxyethane-(water)_n, and tricyclophane-(water)_n clusters. The IR spectra are modeled with a local mode Hamiltonian that was originally formulated for the analysis of benzene-(water)_n clusters with up to seven waters. The model accounts for stretch-bend Fermi coupling, which can complicate the IR spectra in the 3150-3300 cm-1 region. When the water clusters interact with each of the solutes, the hydrogen bond lengths between the water molecules change in a characteristic way, reflecting the strength of the solute-water interaction. These structural effects are also reflected spectroscopically in the shifts of the local mode OH stretch frequencies. When diphenoxyethane is the solute, the water clusters distort more significantly than when bound to benzene. Tricyclophane's structure provides an aromatic-rich binding pocket for the water clusters. The local mode model is used to extract Hamiltonians for individual water molecules. These monomer Hamiltonians divide into groups based on their local H-bonding architecture, allowing for further classification of the wide variety of water environments encountered in this study.

Changes in Phosphatidylcholine Headgroup Tilt and Water Order Induced by Monovalent Salts: Molecular Dynamics Simulations

PubMed Central

Sachs, Jonathan N.; Nanda, Hirsh; Petrache, Horia I.; Woolf, Thomas B.

2004-01-01

The association between monovalent salts and neutral lipid bilayers is known to influence global bilayer structural properties such as headgroup conformational fluctuations and the dipole potential. The local influence of the ions, however, has been unknown due to limited structural resolution of experimental methods. Molecular dynamics simulations are used here to elucidate local structural rearrangements upon association of a series of monovalent Na+ salts to a palmitoyl-oleoyl-phosphatidylcholine bilayer. We observe association of all ion types in the interfacial region. Larger anions, which are meant to rationalize data regarding a Hofmeister series of anions, bind more deeply within the bilayer than either Cl− or Na+. Although the simulations are able to reproduce experimentally measured quantities, the analysis is focused on local properties currently invisible to experiments, which may be critical to biological systems. As such, for all ion types, including Cl−, we show local ion-induced perturbations to headgroup tilt, the extent and direction of which is sensitive to ion charge and size. Additionally, we report salt-induced ordering of the water well beyond the interfacial region, which may be significant in terms of hydration repulsion between stacked bilayers. PMID:15189873

How the Electronic Structure in URu2Si2 Changes with Temperature: A High-Resolution Compton Scattering Study

NASA Astrophysics Data System (ADS)

Koizumi, Akihisa; Kubo, Yasunori; Motoyama, Gaku; Yamamura, Tomoo; Sakurai, Yoshiharu

2018-06-01

We have measured directional Compton profiles on the (001) plane in URu2Si2 single crystal at several temperatures. Two-dimensional electron occupation number densities (2D-EONDs) were obtained from the profiles through electron momentum reconstruction and Lock-Crisp-West folding analyses. We have also performed band calculations based on 5f-electron itinerant and localized models and derived theoretical 2D-EONDs for comparison. The experimental 2D-EOND at 300 K is well described by the localized model, and the 2D-EOND at 10 K is consistent with the theoretical one based on the itinerant model. The difference between 2D-EONDs at 30 and 100 K reflects a gradual change in the electronic structure, which reveals some of the crossover phenomena from localized to itinerant states. The change from localized to itinerant states is also reflected in a B(r) function, which is obtained in the reconstruction analysis and is an autocorrelation function of the wave function in the position space. The process by which the electronic structure in URu2Si2 changes is demonstrated through a series of experimental results.

Director Field Analysis (DFA): Exploring Local White Matter Geometric Structure in Diffusion MRI.

PubMed

Cheng, Jian; Basser, Peter J

2018-01-01

In Diffusion Tensor Imaging (DTI) or High Angular Resolution Diffusion Imaging (HARDI), a tensor field or a spherical function field (e.g., an orientation distribution function field), can be estimated from measured diffusion weighted images. In this paper, inspired by the microscopic theoretical treatment of phases in liquid crystals, we introduce a novel mathematical framework, called Director Field Analysis (DFA), to study local geometric structural information of white matter based on the reconstructed tensor field or spherical function field: (1) We propose a set of mathematical tools to process general director data, which consists of dyadic tensors that have orientations but no direction. (2) We propose Orientational Order (OO) and Orientational Dispersion (OD) indices to describe the degree of alignment and dispersion of a spherical function in a single voxel or in a region, respectively; (3) We also show how to construct a local orthogonal coordinate frame in each voxel exhibiting anisotropic diffusion; (4) Finally, we define three indices to describe three types of orientational distortion (splay, bend, and twist) in a local spatial neighborhood, and a total distortion index to describe distortions of all three types. To our knowledge, this is the first work to quantitatively describe orientational distortion (splay, bend, and twist) in general spherical function fields from DTI or HARDI data. The proposed DFA and its related mathematical tools can be used to process not only diffusion MRI data but also general director field data, and the proposed scalar indices are useful for detecting local geometric changes of white matter for voxel-based or tract-based analysis in both DTI and HARDI acquisitions. The related codes and a tutorial for DFA will be released in DMRITool. Copyright © 2017 Elsevier B.V. All rights reserved.

A comparative study of theoretical graph models for characterizing structural networks of human brain.

PubMed

Li, Xiaojin; Hu, Xintao; Jin, Changfeng; Han, Junwei; Liu, Tianming; Guo, Lei; Hao, Wei; Li, Lingjiang

2013-01-01

Previous studies have investigated both structural and functional brain networks via graph-theoretical methods. However, there is an important issue that has not been adequately discussed before: what is the optimal theoretical graph model for describing the structural networks of human brain? In this paper, we perform a comparative study to address this problem. Firstly, large-scale cortical regions of interest (ROIs) are localized by recently developed and validated brain reference system named Dense Individualized Common Connectivity-based Cortical Landmarks (DICCCOL) to address the limitations in the identification of the brain network ROIs in previous studies. Then, we construct structural brain networks based on diffusion tensor imaging (DTI) data. Afterwards, the global and local graph properties of the constructed structural brain networks are measured using the state-of-the-art graph analysis algorithms and tools and are further compared with seven popular theoretical graph models. In addition, we compare the topological properties between two graph models, namely, stickiness-index-based model (STICKY) and scale-free gene duplication model (SF-GD), that have higher similarity with the real structural brain networks in terms of global and local graph properties. Our experimental results suggest that among the seven theoretical graph models compared in this study, STICKY and SF-GD models have better performances in characterizing the structural human brain network.

STRUCTURE IN THE ROTATION MEASURE SKY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stil, J. M.; Taylor, A. R.; Sunstrum, C.

2011-01-01

An analysis of structure in rotation measure (RM) across the sky based on the RM catalog of Taylor et al. is presented. Several resolved RM structures are identified with structure in the local interstellar medium, including radio loops I, II, and III, the Gum nebula, and the Orion-Eridanus superbubble. Structure functions (SFs) of RM are presented for selected areas, and maps of SF amplitude and slope across the sky are compared with H{alpha} intensity and diffuse polarized intensity. RM variance on an angular scale of 1{sup 0} is correlated with length of the line of sight through the Galaxy, withmore » a contribution from local structures. The slope of the SFs is less concentrated to the Galactic plane and less correlated with length of the line of sight through the Galaxy, suggesting a more local origin for RM structure on angular scales {approx}10{sup 0}. The RM variance is a factor of {approx}2 higher toward the South Galactic Pole than toward the North Galactic Pole, reflecting a more wide-spread asymmetry between the northern and southern Galactic hemispheres. Depolarization of diffuse Galactic synchrotron emission at latitudes <30{sup 0} can be explained largely by Faraday dispersion related to small-scale variance in RM, but the errors allow a significant contribution from differential Faraday rotation along the line of sight.« less

Analysis of the HIV-2 protease's adaptation to various ligands: characterization of backbone asymmetry using a structural alphabet.

PubMed

Triki, Dhoha; Cano Contreras, Mario Enrique; Flatters, Delphine; Visseaux, Benoit; Descamps, Diane; Camproux, Anne-Claude; Regad, Leslie

2018-01-15

The HIV-2 protease (PR2) is a homodimer of 99 residues with asymmetric assembly and binding various ligands. We propose an exhaustive study of the local structural asymmetry between the two monomers of all available PR2 structures complexed with various inhibitors using a structural alphabet approach. On average, PR2 exhibits asymmetry in 31% of its positions-i.e., exhibiting different backbone local conformations in the two monomers. This asymmetry was observed all along its structure, particularly in the elbow and flap regions. We first differentiated structural asymmetry conserved in most PR2 structures from the one specific to some PR2. Then, we explored the origin of the detected asymmetry in PR2. We localized asymmetry that could be induced by PR2's flexibility, allowing transition from the semi-open to closed conformations and the asymmetry potentially induced by ligand binding. This latter could be important for the PR2's adaptation to diverse ligands. Our results highlighted some differences between asymmetry of PR2 bound to darunavir and amprenavir that could explain their differences of affinity. This knowledge is critical for a better description of PR2's recognition and adaptation to various ligands and for a better understanding of the resistance of PR2 to most PR2 inhibitors, a major antiretroviral class.

Progressive Fracture of Composite Structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Minnetyan, Levon

2008-01-01

A new approach is described for evaluating fracture in composite structures. This approach is independent of classical fracture mechanics parameters like fracture toughness. It relies on computational simulation and is programmed in a stand-alone integrated computer code. It is multiscale, multifunctional because it includes composite mechanics for the composite behavior and finite element analysis for predicting the structural response. It contains seven modules; layered composite mechanics (micro, macro, laminate), finite element, updating scheme, local fracture, global fracture, stress based failure modes, and fracture progression. The computer code is called CODSTRAN (Composite Durability Structural ANalysis). It is used in the present paper to evaluate the global fracture of four composite shell problems and one composite built-up structure. Results show that the composite shells and the built-up composite structure global fracture are enhanced when internal pressure is combined with shear loads.

Thermostability of In Vitro Evolved Bacillus subtilis Lipase A: A Network and Dynamics Perspective

PubMed Central

Srivastava, Ashutosh; Sinha, Somdatta

2014-01-01

Proteins in thermophilic organisms remain stable and function optimally at high temperatures. Owing to their important applicability in many industrial processes, such thermostable proteins have been studied extensively, and several structural factors attributed to their enhanced stability. How these factors render the emergent property of thermostability to proteins, even in situations where no significant changes occur in their three-dimensional structures in comparison to their mesophilic counter-parts, has remained an intriguing question. In this study we treat Lipase A from Bacillus subtilis and its six thermostable mutants in a unified manner and address the problem with a combined complex network-based analysis and molecular dynamic studies to find commonality in their properties. The Protein Contact Networks (PCN) of the wild-type and six mutant Lipase A structures developed at a mesoscopic scale were analyzed at global network and local node (residue) level using network parameters and community structure analysis. The comparative PCN analysis of all proteins pointed towards important role of specific residues in the enhanced thermostability. Network analysis results were corroborated with finer-scale molecular dynamics simulations at both room and high temperatures. Our results show that this combined approach at two scales can uncover small but important changes in the local conformations that add up to stabilize the protein structure in thermostable mutants, even when overall conformation differences among them are negligible. Our analysis not only supports the experimentally determined stabilizing factors, but also unveils the important role of contacts, distributed throughout the protein, that lead to thermostability. We propose that this combined mesoscopic-network and fine-grained molecular dynamics approach is a convenient and useful scheme not only to study allosteric changes leading to protein stability in the face of negligible over-all conformational changes due to mutations, but also in other molecular networks where change in function does not accompany significant change in the network structure. PMID:25122499

Developing Information Skills Test for Malaysian Youth Students Using Rasch Analysis

ERIC Educational Resources Information Center

Karim, Aidah Abdul; Shah, Parilah M.; Din, Rosseni; Ahmad, Mazalah; Lubis, Maimun Aqhsa

2014-01-01

This study explored the psychometric properties of a locally developed information skills test for youth students in Malaysia using Rasch analysis. The test was a combination of 24 structured and multiple choice items with a 4-point grading scale. The test was administered to 72 technical college students and 139 secondary school students. The…

Acoustic emission analysis as a non-destructive test procedure for fiber compound structures

NASA Technical Reports Server (NTRS)

Block, J.

1983-01-01

The concept of acoustic emission analysis is explained in scientific terms. The detection of acoustic events, their localization, damage discrimination, and event summation curves are discussed. A block diagram of the concept of damage-free testing of fiber-reinforced synthetic materials is depicted. Prospects for application of the concept are assessed.

Local Atomic Structure of Ca-Mg-Zn Metallic Glasses (Postprint)

DTIC Science & Technology

2010-09-16

218 2010. 23 A. C. Hannon, Nucl. Instrum. Methods Phys. Res. A 551, 88 2005. 24 A. K. Soper private communication; GUDRUN software, http...analysis/xrd-data-analysis9203 html 26 A. C. Hannon, W. S. Howells, and A. K. Soper , Inst. Phys. Conf. Ser. 107, 193 1990. 27 D. A. Keen, J. Appl

Structural health monitoring of localized internal corrosion in high temperature piping for oil industry

NASA Astrophysics Data System (ADS)

Eason, Thomas J.; Bond, Leonard J.; Lozev, Mark G.

2015-03-01

Crude oil is becoming more corrosive with higher sulfur concentration, chloride concentration, and acidity. The increasing presence of naphthenic acids in oils with various environmental conditions at temperatures between 150°C and 400°C can lead to different internal degradation morphologies in refineries that are uniform, non-uniform, or localized pitting. Improved corrosion measurement technology is needed to better quantify the integrity risk associated with refining crude oils of higher acid concentration. This paper first reports a consolidated review of corrosion inspection technology to establish the foundation for structural health monitoring of localized internal corrosion in high temperature piping. An approach under investigation is to employ flexible ultrasonic thin-film piezoelectric transducer arrays fabricated by the sol-gel manufacturing process for monitoring localized internal corrosion at temperatures up to 400°C. A statistical analysis of sol-gel transducer measurement accuracy using various time of flight thickness calculation algorithms on a flat calibration block is demonstrated.

Extended electron energy loss fine structure simulation of the local boron environment in sodium aluminoborosilicate glasses containing gadolinium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qian, Morris; Li, Hong; Li, Liyu

Gadolinium can be dissolved in sodium-alumino-borosilicate glasses up to 47 wt% in a baseline borosilicate glass (mol%) 20 B2O3, 5 Al2O3, 60 SiO2,and 20 Na2O. Understanding of Gd dissolution in borosilicate melts is important in glass formulation optimization. Electron energy loss fine structure (ELFS) spectroscopy is chosen, which provides well resolved local atomic structure information for both amorphous and crystalline materials with high sensitivity to low Z elements such as Al, B, Na, O, and Si where the x-ray absorption fine structure (XAFS) technique faces experimental difficulty. In this study, we report our results of boron K-edge ELFS study. Twomore » borosilicate glass samples with 30 and 47 mass% Gd2O3, B20Gd30 and B20Gd47were chosen for B K-edge ELFS study. EEL spectra were acquired on a Philips 430 TEM equipped with Gatan PEELS system 666 and EL/P 2.1 software with Custom function AcqLong. The ELFS data analysis was performed using UWELFS, UWXAFS and FEFF software. From our Gd solubility study, the local structure of Gd in the borate environment possibly resembles double chain structure found in crystalline Gd(BO2)3 as proposed by Chakraborty et al. The B/Gd ratio's in both glasses are smaller then 3, which means the excess Gd atoms in the Si-sites would be 17 and 60 mol% of the total Gd atoms, respectively according to the model, yet the local environment of borate sites saturated with Gd should be remained. To verity above hypothesis, the double chain structure model was applied to fit boron K-edge. The model was shown to well fit experimental boron K-edge EELS spectra for both glasses with some degree of distance distortion which is understandable in amorphous structure. Therefore, it is very likely that Gd stabilized in borate sites has a local structure resembling the double chain Gd(BO2)3 structure as proposed by our solubility study and literature.« less

Localization of optic disc and fovea in retinal images using intensity based line scanning analysis.

PubMed

Kamble, Ravi; Kokare, Manesh; Deshmukh, Girish; Hussin, Fawnizu Azmadi; Mériaudeau, Fabrice

2017-08-01

Accurate detection of diabetic retinopathy (DR) mainly depends on identification of retinal landmarks such as optic disc and fovea. Present methods suffer from challenges like less accuracy and high computational complexity. To address this issue, this paper presents a novel approach for fast and accurate localization of optic disc (OD) and fovea using one-dimensional scanned intensity profile analysis. The proposed method utilizes both time and frequency domain information effectively for localization of OD. The final OD center is located using signal peak-valley detection in time domain and discontinuity detection in frequency domain analysis. However, with the help of detected OD location, the fovea center is located using signal valley analysis. Experiments were conducted on MESSIDOR dataset, where OD was successfully located in 1197 out of 1200 images (99.75%) and fovea in 1196 out of 1200 images (99.66%) with an average computation time of 0.52s. The large scale evaluation has been carried out extensively on nine publicly available databases. The proposed method is highly efficient in terms of quickly and accurately localizing OD and fovea structure together compared with the other state-of-the-art methods. Copyright © 2017 Elsevier Ltd. All rights reserved.

Analysis of biomolecular solvation sites by 3D-RISM theory.

PubMed

Sindhikara, Daniel J; Hirata, Fumio

2013-06-06

We derive, implement, and apply equilibrium solvation site analysis for biomolecules. Our method utilizes 3D-RISM calculations to quickly obtain equilibrium solvent distributions without either necessity of simulation or limits of solvent sampling. Our analysis of these distributions extracts highest likelihood poses of solvent as well as localized entropies, enthalpies, and solvation free energies. We demonstrate our method on a structure of HIV-1 protease where excellent structural and thermodynamic data are available for comparison. Our results, obtained within minutes, show systematic agreement with available experimental data. Further, our results are in good agreement with established simulation-based solvent analysis methods. This method can be used not only for visual analysis of active site solvation but also for virtual screening methods and experimental refinement.

Correlation Function Analysis of Fiber Networks: Implications for Thermal Conductivity

NASA Technical Reports Server (NTRS)

Martinez-Garcia, Jorge; Braginsky, Leonid; Shklover, Valery; Lawson, John W.

2011-01-01

The heat transport in highly porous fiber structures is investigated. The fibers are supposed to be thin, but long, so that the number of the inter-fiber connections along each fiber is large. We show that the effective conductivity of such structures can be found from the correlation length of the two-point correlation function of the local conductivities. Estimation of the parameters, determining the conductivity, from the 2D images of the structures is analyzed.

Comparative study on fast classification of brick samples by combination of principal component analysis and linear discriminant analysis using stand-off and table-top laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Vítková, Gabriela; Prokeš, Lubomír; Novotný, Karel; Pořízka, Pavel; Novotný, Jan; Všianský, Dalibor; Čelko, Ladislav; Kaiser, Jozef

2014-11-01

Focusing on historical aspect, during archeological excavation or restoration works of buildings or different structures built from bricks it is important to determine, preferably in-situ and in real-time, the locality of bricks origin. Fast classification of bricks on the base of Laser-Induced Breakdown Spectroscopy (LIBS) spectra is possible using multivariate statistical methods. Combination of principal component analysis (PCA) and linear discriminant analysis (LDA) was applied in this case. LIBS was used to classify altogether the 29 brick samples from 7 different localities. Realizing comparative study using two different LIBS setups - stand-off and table-top it is shown that stand-off LIBS has a big potential for archeological in-field measurements.

High-speed all-optical DNA local sequence alignment based on a three-dimensional artificial neural network.

PubMed

Maleki, Ehsan; Babashah, Hossein; Koohi, Somayyeh; Kavehvash, Zahra

2017-07-01

This paper presents an optical processing approach for exploring a large number of genome sequences. Specifically, we propose an optical correlator for global alignment and an extended moiré matching technique for local analysis of spatially coded DNA, whose output is fed to a novel three-dimensional artificial neural network for local DNA alignment. All-optical implementation of the proposed 3D artificial neural network is developed and its accuracy is verified in Zemax. Thanks to its parallel processing capability, the proposed structure performs local alignment of 4 million sequences of 150 base pairs in a few seconds, which is much faster than its electrical counterparts, such as the basic local alignment search tool.

Local Guided Wavefield Analysis for Characterization of Delaminations in Composites

NASA Technical Reports Server (NTRS)

Rogge, Matthew D.; Campbell Leckey, Cara A.

2012-01-01

Delaminations in composite laminates resulting from impact events may be accompanied by minimal indication of damage at the surface. As such, inspection techniques are required to ensure defects are within allowable limits. Conventional ultrasonic scanning techniques have been shown to effectively characterize the size and depth of delaminations but require physical contact with the structure. Alternatively, a noncontact scanning laser vibrometer may be used to measure guided wave propagation in the laminate structure. A local Fourier domain analysis method is presented for processing guided wavefield data to estimate spatially-dependent wavenumber values, which can be used to determine delamination depth. The technique is applied to simulated wavefields and results are analyzed to determine limitations of the technique with regards to determining defect size and depth. Finally, experimental wavefield data obtained in quasi-isotropic carbon fiber reinforced polymer (CFRP) laminates with impact damage is analyzed and wavenumber is measured to an accuracy of 8.5% in the region of shallow delaminations. Keywords: Ultrasonic wavefield imaging, Windowed Fourier transforms, Guided waves, Structural health monitoring, Nondestructive evaluation

Structure and evolution of a European Parliament via a network and correlation analysis

NASA Astrophysics Data System (ADS)

Puccio, Elena; Pajala, Antti; Piilo, Jyrki; Tumminello, Michele

2016-11-01

We present a study of the network of relationships among elected members of the Finnish parliament, based on a quantitative analysis of initiative co-signatures, and its evolution over 16 years. To understand the structure of the parliament, we constructed a statistically validated network of members, based on the similarity between the patterns of initiatives they signed. We looked for communities within the network and characterized them in terms of members' attributes, such as electoral district and party. To gain insight on the nested structure of communities, we constructed a hierarchical tree of members from the correlation matrix. Afterwards, we studied parliament dynamics yearly, with a focus on correlations within and between parties, by also distinguishing between government and opposition. Finally, we investigated the role played by specific individuals, at a local level. In particular, whether they act as proponents who gather consensus, or as signers. Our results provide a quantitative background to current theories in political science. From a methodological point of view, our network approach has proven able to highlight both local and global features of a complex social system.

Size effects on rhodium nanoparticles related to hydrogen-storage capability.

PubMed

Song, Chulho; Yang, Anli; Sakata, Osami; Kumara, L S R; Hiroi, Satoshi; Cui, Yi-Tao; Kusada, Kohei; Kobayashi, Hirokazu; Kitagawa, Hiroshi

2018-06-06

To unveil the origin of the hydrogen-storage properties of rhodium nanoparticles (Rh NPs), we investigated the electronic and crystal structures of the Rh NPs using various synchrotron based X-ray techniques. Electronic structure studies revealed that the hydrogen-storage capability of Rh NPs could be attributed to their more unoccupied d-DOSs than that of the bulk near the Fermi level. Crystal structure studies indicated that lattice distortion and mean-square displacement increase while coordination number decreases with decreasing particle size and the hydrogen-absorption capability of Rh NPs improves to a greater extent with increased structural disorder in the local structure than with that in the mean structure. The smallest Rh NPs, having the largest structural disorder/increased vacancy spaces and the smallest coordination number, exhibited excellent hydrogen-storage capacity. Finally, from the bond-orientational order analysis, we confirmed that the localized disordering is distributed more over the surface part than the core part and hydrogen can be trapped on the surface part of Rh NPs which increases with a decrease in NP diameter.

Combining density functional theory (DFT) and pair distribution function (PDF) analysis to solve the structure of metastable materials: the case of metakaolin.

PubMed

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

2010-04-07

Understanding the atomic structure of complex metastable (including glassy) materials is of great importance in research and industry, however, such materials resist solution by most standard techniques. Here, a novel technique combining thermodynamics and local structure is presented to solve the structure of the metastable aluminosilicate material metakaolin (calcined kaolinite) without the use of chemical constraints. The structure is elucidated by iterating between least-squares real-space refinement using neutron pair distribution function data, and geometry optimisation using density functional modelling. The resulting structural representation is both energetically feasible and in excellent agreement with experimental data. This accurate structural representation of metakaolin provides new insight into the local environment of the aluminium atoms, with evidence of the existence of tri-coordinated aluminium. By the availability of this detailed chemically feasible atomic description, without the need to artificially impose constraints during the refinement process, there exists the opportunity to tailor chemical and mechanical processes involving metakaolin and other complex metastable materials at the atomic level to obtain optimal performance at the macro-scale.

Accelerating atomic structure search with cluster regularization

NASA Astrophysics Data System (ADS)

Sørensen, K. H.; Jørgensen, M. S.; Bruix, A.; Hammer, B.

2018-06-01

We present a method for accelerating the global structure optimization of atomic compounds. The method is demonstrated to speed up the finding of the anatase TiO2(001)-(1 × 4) surface reconstruction within a density functional tight-binding theory framework using an evolutionary algorithm. As a key element of the method, we use unsupervised machine learning techniques to categorize atoms present in a diverse set of partially disordered surface structures into clusters of atoms having similar local atomic environments. Analysis of more than 1000 different structures shows that the total energy of the structures correlates with the summed distances of the atomic environments to their respective cluster centers in feature space, where the sum runs over all atoms in each structure. Our method is formulated as a gradient based minimization of this summed cluster distance for a given structure and alternates with a standard gradient based energy minimization. While the latter minimization ensures local relaxation within a given energy basin, the former enables escapes from meta-stable basins and hence increases the overall performance of the global optimization.

Large-scale distribution patterns of mangrove nematodes: A global meta-analysis.

PubMed

Brustolin, Marco C; Nagelkerken, Ivan; Fonseca, Gustavo

2018-05-01

Mangroves harbor diverse invertebrate communities, suggesting that macroecological distribution patterns of habitat-forming foundation species drive the associated faunal distribution. Whether these are driven by mangrove biogeography is still ambiguous. For small-bodied taxa, local factors and landscape metrics might be as important as macroecology. We performed a meta-analysis to address the following questions: (1) can richness of mangrove trees explain macroecological patterns of nematode richness? and (2) do local landscape attributes have equal or higher importance than biogeography in structuring nematode richness? Mangrove areas of Caribbean-Southwest Atlantic, Western Indian, Central Indo-Pacific, and Southwest Pacific biogeographic regions. We used random-effects meta-analyses based on natural logarithm of the response ratio (lnRR) to assess the importance of macroecology (i.e., biogeographic regions, latitude, longitude), local factors (i.e., aboveground mangrove biomass and tree richness), and landscape metrics (forest area and shape) in structuring nematode richness from 34 mangroves sites around the world. Latitude, mangrove forest area, and forest shape index explained 19% of the heterogeneity across studies. Richness was higher at low latitudes, closer to the equator. At local scales, richness increased slightly with landscape complexity and decreased with forest shape index. Our results contrast with biogeographic diversity patterns of mangrove-associated taxa. Global-scale nematode diversity may have evolved independently of mangrove tree richness, and diversity of small-bodied metazoans is probably more closely driven by latitude and associated climates, rather than local, landscape, or global biogeographic patterns.

Application of Interface Technology in Nonlinear Analysis of a Stitched/RFI Composite Wing Stub Box

NASA Technical Reports Server (NTRS)

Wang, John T.; Ransom, Jonathan B.

1997-01-01

A recently developed interface technology was successfully employed in the geometrically nonlinear analysis of a full-scale stitched/RFI composite wing box loaded in bending. The technology allows mismatched finite element models to be joined in a variationally consistent manner and reduces the modeling complexity by eliminating transition meshing. In the analysis, local finite element models of nonlinearly deformed wide bays of the wing box are refined without the need for transition meshing to the surrounding coarse mesh. The COMET-AR finite element code, which has the interface technology capability, was used to perform the analyses. The COMET-AR analysis is compared to both a NASTRAN analysis and to experimental data. The interface technology solution is shown to be in good agreement with both. The viability of interface technology for coupled global/local analysis of large scale aircraft structures is demonstrated.

Stripe-PZT Sensor-Based Baseline-Free Crack Diagnosis in a Structure with a Welded Stiffener.

PubMed

An, Yun-Kyu; Shen, Zhiqi; Wu, Zhishen

2016-09-16

This paper proposes a stripe-PZT sensor-based baseline-free crack diagnosis technique in the heat affected zone (HAZ) of a structure with a welded stiffener. The proposed technique enables one to identify and localize a crack in the HAZ using only current data measured using a stripe-PZT sensor. The use of the stripe-PZT sensor makes it possible to significantly improve the applicability to real structures and minimize man-made errors associated with the installation process by embedding multiple piezoelectric sensors onto a printed circuit board. Moreover, a new frequency-wavenumber analysis-based baseline-free crack diagnosis algorithm minimizes false alarms caused by environmental variations by avoiding simple comparison with the baseline data accumulated from the pristine condition of a target structure. The proposed technique is numerically as well as experimentally validated using a plate-like structure with a welded stiffener, reveling that it successfully identifies and localizes a crack in HAZ.

Stripe-PZT Sensor-Based Baseline-Free Crack Diagnosis in a Structure with a Welded Stiffener

PubMed Central

An, Yun-Kyu; Shen, Zhiqi; Wu, Zhishen

2016-01-01

This paper proposes a stripe-PZT sensor-based baseline-free crack diagnosis technique in the heat affected zone (HAZ) of a structure with a welded stiffener. The proposed technique enables one to identify and localize a crack in the HAZ using only current data measured using a stripe-PZT sensor. The use of the stripe-PZT sensor makes it possible to significantly improve the applicability to real structures and minimize man-made errors associated with the installation process by embedding multiple piezoelectric sensors onto a printed circuit board. Moreover, a new frequency-wavenumber analysis-based baseline-free crack diagnosis algorithm minimizes false alarms caused by environmental variations by avoiding simple comparison with the baseline data accumulated from the pristine condition of a target structure. The proposed technique is numerically as well as experimentally validated using a plate-like structure with a welded stiffener, reveling that it successfully identifies and localizes a crack in HAZ. PMID:27649200

Experimental characterization and numerical simulation of riveted lap-shear joints using Rivet Element

NASA Astrophysics Data System (ADS)

Vivio, Francesco; Fanelli, Pierluigi; Ferracci, Michele

2018-03-01

In aeronautical and automotive industries the use of rivets for applications requiring several joining points is now very common. In spite of a very simple shape, a riveted junction has many contact surfaces and stress concentrations that make the local stiffness very difficult to be calculated. To overcome this difficulty, commonly finite element models with very dense meshes are performed for single joint analysis because the accuracy is crucial for a correct structural analysis. Anyhow, when several riveted joints are present, the simulation becomes computationally too heavy and usually significant restrictions to joint modelling are introduced, sacrificing the accuracy of local stiffness evaluation. In this paper, we tested the accuracy of a rivet finite element presented in previous works by the authors. The structural behaviour of a lap joint specimen with a rivet joining is simulated numerically and compared to experimental measurements. The Rivet Element, based on a closed-form solution of a reference theoretical model of the rivet joint, simulates local and overall stiffness of the junction combining high accuracy with low degrees of freedom contribution. In this paper the Rivet Element performances are compared to that of a FE non-linear model of the rivet, built with solid elements and dense mesh, and to experimental data. The promising results reported allow to consider the Rivet Element able to simulate, with a great accuracy, actual structures with several rivet connections.

Embrittlement and Flow Localization in Reactor Structural Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 neckingmore » 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.« less

Mental health network governance: comparative analysis across Canadian regions

PubMed Central

Wiktorowicz, Mary E; Fleury, Marie-Josée; Adair, Carol E; Lesage, Alain; Goldner, Elliot; Peters, Suzanne

2010-01-01

Objective Modes of governance were compared in ten local mental health networks in diverse contexts (rural/urban and regionalized/non-regionalized) to clarify the governance processes that foster inter-organizational collaboration and the conditions that support them. Methods Case studies of ten local mental health networks were developed using qualitative methods of document review, semi-structured interviews and focus groups that incorporated provincial policy, network and organizational levels of analysis. Results Mental health networks adopted either a corporate structure, mutual adjustment or an alliance governance model. A corporate structure supported by regionalization offered the most direct means for local governance to attain inter-organizational collaboration. The likelihood that networks with an alliance model developed coordination processes depended on the presence of the following conditions: a moderate number of organizations, goal consensus and trust among the organizations, and network-level competencies. In the small and mid-sized urban networks where these conditions were met their alliance realized the inter-organizational collaboration sought. In the large urban and rural networks where these conditions were not met, externally brokered forms of network governance were required to support alliance based models. Discussion In metropolitan and rural networks with such shared forms of network governance as an alliance or voluntary mutual adjustment, external mediation by a regional or provincial authority was an important lever to foster inter-organizational collaboration. PMID:21289999

S-wave attenuation of the shallow sediments in the North China basin based on borehole seismograms of local earthquakes

NASA Astrophysics Data System (ADS)

Wang, Sheng; Li, Zhiwei

2018-06-01

S-wave velocity and attenuation structures of shallow sediments play important roles in accurate prediction of strong ground motion. However, it is more difficult to investigate the attenuation than velocity structures. In this study, we developed a new approach for estimating frequency-dependent S-wave attenuation (Q_S^{ - 1}) structures of shallow sediments based on multiple time window analysis of borehole seismograms from local earthquakes. Multiple time windows for separating direct and surface-reflected S-waves in local earthquake waveforms at borehole stations are selected with a global optimization scheme. With respect to different time windows, the transfer functions between direct and surface-reflected S-waves are achieved with a weighted averaging scheme, based on which frequency dependent Q_S^{ - 1} values are obtained. Synthetic tests suggest that the proposed method can restore robust and reliableQ_S^{ - 1} values, especially when the dataset of local earthquakes is not abundant. We utilize this method for local earthquake waveforms at 14 borehole seismic stations in the North China basin, and obtain Q_S^{ - 1} values in 2 ˜ 10 Hz frequency band, as well as average {V_P}, {V_S} and {V_P}/{{}}{V_S} ratio for shallow sediments deep to a few hundred meters. Results suggest that Q_S^{ - 1} values are to 0.01˜0.06, and generally decrease with frequency. The average attenuation structure of shallow sediments within the depth of a few hundred meters beneath 14 borehole stations in the North China basin can be modeled as Q_S^{ - 1} = 0.056{f^{ - 0.61}}. It is generally consistent with the attenuation structure of sedimentary basins in other areas, such as Mississippi Embayment sediments in the United States and Sendai basin in Japan.

Correlations between Transition Metal Chemistry, Local Structure and Global Structure in Li 2Ru 0.5Mn 0.5O 3 Investigated in a Wide Voltage Window

DOE PAGES

Lyu, Yingchun; Hu, Enyuan; Xiao, Dongdong; ...

2017-10-20

Li 2Ru 0.5Mn 0.5O 3, a high capacity lithium rich layered cathode material for lithium-ion batteries, was subject to comprehen-sive diagnostic studies including in situ/ex situ X-ray diffraction (XRD), X-ray absorption spectroscopy (XAS), pair distribu-tion function (PDF) and high resolution scanning transmission electron microscopy (STEM) analysis, to understand the cor-relations between transition metal chemistry, structure and lithium storage electrochemical behavior. Ru-Ru dimers have been identified in the as-prepared sample and found to be preserved upon prolonged cycling. Presence of these dimers, which are likely caused by the delocalized nature of 4d electrons, is found to favor the stabilization of themore » structure in a lay-ered phase. The in situ XAS results confirm the participation of oxygen redox into the charge compensation at high charge voltage, and the great flexibility of the covalent bond between Ru and O may provide great reversibility of the global struc-ture despite of the significant local distortion around Ru. In contrast, the local distortion around Mn occurs at low discharge voltage and is accompanied by a “layered to 1T” phase transformation, which is found to be detrimental to the cycle per-formances. It is clear that the changes of local structure around individual transition metal cations respond separately and differently to lithium intercalation/deintercalation. Here, cations with the capability to tolerate the lattice distortion will benefit for maintaining the integrality of the crystal structure and therefore is able to enhance the long-term cycling performance of the electrode materials.« less

Correlations between Transition Metal Chemistry, Local Structure and Global Structure in Li 2Ru 0.5Mn 0.5O 3 Investigated in a Wide Voltage Window

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lyu, Yingchun; Hu, Enyuan; Xiao, Dongdong

Li 2Ru 0.5Mn 0.5O 3, a high capacity lithium rich layered cathode material for lithium-ion batteries, was subject to comprehen-sive diagnostic studies including in situ/ex situ X-ray diffraction (XRD), X-ray absorption spectroscopy (XAS), pair distribu-tion function (PDF) and high resolution scanning transmission electron microscopy (STEM) analysis, to understand the cor-relations between transition metal chemistry, structure and lithium storage electrochemical behavior. Ru-Ru dimers have been identified in the as-prepared sample and found to be preserved upon prolonged cycling. Presence of these dimers, which are likely caused by the delocalized nature of 4d electrons, is found to favor the stabilization of themore » structure in a lay-ered phase. The in situ XAS results confirm the participation of oxygen redox into the charge compensation at high charge voltage, and the great flexibility of the covalent bond between Ru and O may provide great reversibility of the global struc-ture despite of the significant local distortion around Ru. In contrast, the local distortion around Mn occurs at low discharge voltage and is accompanied by a “layered to 1T” phase transformation, which is found to be detrimental to the cycle per-formances. It is clear that the changes of local structure around individual transition metal cations respond separately and differently to lithium intercalation/deintercalation. Here, cations with the capability to tolerate the lattice distortion will benefit for maintaining the integrality of the crystal structure and therefore is able to enhance the long-term cycling performance of the electrode materials.« less

A versatile phenomenological model for the S-shaped temperature dependence of photoluminescence energy for an accurate determination of the exciton localization energy in bulk and quantum well structures

NASA Astrophysics Data System (ADS)

Dixit, V. K.; Porwal, S.; Singh, S. D.; Sharma, T. K.; Ghosh, Sandip; Oak, S. M.

2014-02-01

Temperature dependence of the photoluminescence (PL) peak energy of bulk and quantum well (QW) structures is studied by using a new phenomenological model for including the effect of localized states. In general an anomalous S-shaped temperature dependence of the PL peak energy is observed for many materials which is usually associated with the localization of excitons in band-tail states that are formed due to potential fluctuations. Under such conditions, the conventional models of Varshni, Viña and Passler fail to replicate the S-shaped temperature dependence of the PL peak energy and provide inconsistent and unrealistic values of the fitting parameters. The proposed formalism persuasively reproduces the S-shaped temperature dependence of the PL peak energy and provides an accurate determination of the exciton localization energy in bulk and QW structures along with the appropriate values of material parameters. An example of a strained InAs0.38P0.62/InP QW is presented by performing detailed temperature and excitation intensity dependent PL measurements and subsequent in-depth analysis using the proposed model. Versatility of the new formalism is tested on a few other semiconductor materials, e.g. GaN, nanotextured GaN, AlGaN and InGaN, which are known to have a significant contribution from the localized states. A quantitative evaluation of the fractional contribution of the localized states is essential for understanding the temperature dependence of the PL peak energy of bulk and QW well structures having a large contribution of the band-tail states.

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.

Intracellular Localization and Trafficking of Serine Proteinase AhSub and Cysteine Proteinase AhCP of Acanthamoeba healyi

PubMed Central

Moon, E.-K.; Lee, S.-T.; Chung, D.-I.; Kong, H.-H.

2006-01-01

Proteinases have been proposed to play important roles in pathogenesis and various biologic actions in Acanthamoeba. Although genetic characteristics of several proteases of Acanthamoeba have been reported, the intracellular localization and trafficking of these enzymes has yet to be studied. In the present study, we analyzed the intracellular localization and trafficking of two proteinases, AhSub and AhCP, of Acanthamoeba healyi by transient transfection. Full-length AhSub-enhanced green fluorescent protein (EGFP) fusion protein was found in intracellular vesicle-like structures of transfected amoebae. Time-lapse photographs confirmed the secretion of the fluorescent material of the vesicle toward the extracellular space. The mutated AhSub, of which the pre or prepro region was deleted, was found to localize diffusely throughout the cytoplasm of the amoeba rather than concentrated in the secretory vesicle. Transfection of the construct containing the pre region only showed the same localization and trafficking of the full-length AhSub. A cysteine proteinase AhCP-EGFP fusion protein showed similar localization in the vesicle-like structure in the amoeba. However, using Lyso Tracker analysis, these vesicular structures of AhCP were confirmed to be lysosomes rather than secretory vesicles. The AhCP construct with a deletion of the prepro region showed a dispersed distribution of fluorescence in the cytoplasm of the cells. These results indicated that AhSub and AhCP would play different roles in Acanthameoba biology and that the pre region of AhSub and pro region of AhCP are important for proper intracellular localization and trafficking of each proteinase. PMID:16400174

Testing thin-skinned inversion of a prerift salt-bearing passive margin (Eastern Prebetic Zone, SE Iberia)

NASA Astrophysics Data System (ADS)

Escosa, Frederic O.; Roca, Eduard; Ferrer, Oriol

2018-04-01

Detailed geologic mapping combined with well and seismic data from the Eastern Prebetic Zone (SE Iberia) reveal extensional and contractional structures that permit characterization of passive margin development and its incorporation into a thin-skinned fold-and-thrust belt. The study area is represented by NW-directed, ENE-trending folds and thrusts faults locally disrupted by the NW-trending Matamoros Basin and the active Jumilla and La Rosa diapirs. These structures resulted from the thin-skinned inversion of the proximal part of the Eastern South Iberian passive margin containing prerift salt. Here, Upper Jurassic to Santonian thick-skinned extension controlled the accumulation of sediment over mobile prerift salt. This in turn defined the style of salt tectonics characterized by monoclinal drape folds, suprasalt extensional faults and diapirs. The structural and sedimentological analysis suggests that during extension, salt localizes strain thus decoupling sub- and suprasalt deformation. Thick-skinned extension controls suprasalt deformation as well as its location and distribution which changes over time. Salt also localizes strain during inversion. The preexisting salt structures, weaker than adjacent areas, preferentially absorb the contractional deformation. In addition, the stepped subsalt geometry that results from thick-skinned extension also controls the shortening propagation. Therefore, the degree of strain localization depends on the thickness of the suprasalt cover and on the dip of subsalt faults relative to the thin-skinned transport direction.

Tertiary structural propensities reveal fundamental sequence/structure relationships.

PubMed

Zheng, Fan; Zhang, Jian; Grigoryan, Gevorg

2015-05-05

Extracting useful generalizations from the continually growing Protein Data Bank (PDB) is of central importance. We hypothesize that the PDB contains valuable quantitative information on the level of local tertiary structural motifs (TERMs). We show that by breaking a protein structure into its constituent TERMs, and querying the PDB to characterize the natural ensemble matching each, we can estimate the compatibility of the structure with a given amino acid sequence through a metric we term "structure score." Considering submissions from recent Critical Assessment of Structure Prediction (CASP) experiments, we found a strong correlation (R = 0.69) between structure score and model accuracy, with poorly predicted regions readily identifiable. This performance exceeds that of leading atomistic statistical energy functions. Furthermore, TERM-based analysis of two prototypical multi-state proteins rapidly produced structural insights fully consistent with prior extensive experimental studies. We thus find that TERM-based analysis should have considerable utility for protein structural biology. Copyright © 2015 Elsevier Ltd. All rights reserved.

Documentation for a Structural Optimization Procedure Developed Using the Engineering Analysis Language (EAL)

NASA Technical Reports Server (NTRS)

Martin, Carl J., Jr.

1996-01-01

This report describes a structural optimization procedure developed for use with the Engineering Analysis Language (EAL) finite element analysis system. The procedure is written primarily in the EAL command language. Three external processors which are written in FORTRAN generate equivalent stiffnesses and evaluate stress and local buckling constraints for the sections. Several built-up structural sections were coded into the design procedures. These structural sections were selected for use in aircraft design, but are suitable for other applications. Sensitivity calculations use the semi-analytic method, and an extensive effort has been made to increase the execution speed and reduce the storage requirements. There is also an approximate sensitivity update method included which can significantly reduce computational time. The optimization is performed by an implementation of the MINOS V5.4 linear programming routine in a sequential liner programming procedure.

Unmasking the masked Universe: the 2M++ catalogue through Bayesian eyes

NASA Astrophysics Data System (ADS)

Lavaux, Guilhem; Jasche, Jens

2016-01-01

This work describes a full Bayesian analysis of the Nearby Universe as traced by galaxies of the 2M++ survey. The analysis is run in two sequential steps. The first step self-consistently derives the luminosity-dependent galaxy biases, the power spectrum of matter fluctuations and matter density fields within a Gaussian statistic approximation. The second step makes a detailed analysis of the three-dimensional large-scale structures, assuming a fixed bias model and a fixed cosmology. This second step allows for the reconstruction of both the final density field and the initial conditions at z = 1000 assuming a fixed bias model. From these, we derive fields that self-consistently extrapolate the observed large-scale structures. We give two examples of these extrapolation and their utility for the detection of structures: the visibility of the Sloan Great Wall, and the detection and characterization of the Local Void using DIVA, a Lagrangian based technique to classify structures.

Maturation of Structural Health Management Systems for Solid Rocket Motors

NASA Technical Reports Server (NTRS)

Quing, Xinlin; Beard, Shawn; Zhang, Chang

2011-01-01

Concepts of an autonomous and automated space-compliant diagnostic system were developed for conditioned-based maintenance (CBM) of rocket motors for space exploration vehicles. The diagnostic system will provide real-time information on the integrity of critical structures on launch vehicles, improve their performance, and greatly increase crew safety while decreasing inspection costs. Using the SMART Layer technology as a basis, detailed procedures and calibration techniques for implementation of the diagnostic system were developed. The diagnostic system is a distributed system, which consists of a sensor network, local data loggers, and a host central processor. The system detects external impact to the structure. The major functions of the system include an estimate of impact location, estimate of impact force at impacted location, and estimate of the structure damage at impacted location. This system consists of a large-area sensor network, dedicated multiple local data loggers with signal processing and data analysis software to allow for real-time, in situ monitoring, and longterm tracking of structural integrity of solid rocket motors. Specifically, the system could provide easy installation of large sensor networks, onboard operation under harsh environments and loading, inspection of inaccessible areas without disassembly, detection of impact events and impact damage in real-time, and monitoring of a large area with local data processing to reduce wiring.

Single particle maximum likelihood reconstruction from superresolution microscopy images

PubMed Central

Verdier, Timothée; Gunzenhauser, Julia; Manley, Suliana; Castelnovo, Martin

2017-01-01

Point localization superresolution microscopy enables fluorescently tagged molecules to be imaged beyond the optical diffraction limit, reaching single molecule localization precisions down to a few nanometers. For small objects whose sizes are few times this precision, localization uncertainty prevents the straightforward extraction of a structural model from the reconstructed images. We demonstrate in the present work that this limitation can be overcome at the single particle level, requiring no particle averaging, by using a maximum likelihood reconstruction (MLR) method perfectly suited to the stochastic nature of such superresolution imaging. We validate this method by extracting structural information from both simulated and experimental PALM data of immature virus-like particles of the Human Immunodeficiency Virus (HIV-1). MLR allows us to measure the radii of individual viruses with precision of a few nanometers and confirms the incomplete closure of the viral protein lattice. The quantitative results of our analysis are consistent with previous cryoelectron microscopy characterizations. Our study establishes the framework for a method that can be broadly applied to PALM data to determine the structural parameters for an existing structural model, and is particularly well suited to heterogeneous features due to its single particle implementation. PMID:28253349

The effects of local blowing perturbations on thermal turbulent structures

NASA Astrophysics Data System (ADS)

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

2013-11-01

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

Structure and similarity of helminth communities of six species of Australian turtles.

PubMed

Zelmer, Derek A; Platt, Thomas R

2008-08-01

Patterns of infracommunity structure and infra- and component community similarity were examined for helminths of 6 species of turtles, each collected from a single locality in Australia in 1993 and 1994. Elseya latisternum (N = 11) and Emydura kreffti (N = 16) were collected from northern Queensland, Emydura macquarii macquarii (N = 11) from southern Queensland, Emydura macquarii dhara (N = 11) and Chelodina longicollis (N = 11) from northern New South Wales, and Chelodina oblonga (N = 5) from Western Australia. Local parasite species richness was not correlated with host geographical range. Differences in parasite diversity among host species were related primarily to differences in evenness, a pattern attributed to local habitat characteristics, rather than species-specific differences in colonization potential. Ordination and analysis of similarity demonstrated the patterns of infracommunity structure of Chelodina spp. to be distinct from those of the other host species sampled, which showed considerable overlap among patterns of infracommunity structure. Despite overlap with the component communities of Em. kreffti and El. latisternum, the component communities of Em. m. dhara and Em. m. macquarii were more distinct from one another than either was to the component communities of Em. kreffti or El. latisternum.

Centripetal myosin redistribution in thrombin-stimulated platelets. Relationship to platelet Factor 4 secretion.

PubMed

Painter, R G; Ginsberg, M H

1984-11-01

We have examined the F-actin and myosin distribution in resting and thrombin-activated platelets by double label immunofluorescence microscopy. In resting, discoid platelets, F-actin and myosin staining was distributed in a diffuse pattern throughout the interior of the cell with slight accentuation at the cell periphery. In contrast, platelet factor 4 antigen (PF4) was more centrally localized in a fine punctate distribution which is consistent with its localization in alpha-granules. Within 5 sec after thrombin stimulation both F-actin and myosin staining were increased at the periphery of the now spherical platelets. Subsequently, a myosin-containing spherical structure decreased in diameter closely surrounding a phase-dense central zone. In contrast, F-actin staining continued to be accentuated at the cell periphery and was prominent in filopodia and blebs. As previously shown, PF4 staining was localized after 30 sec within large intracellular masses that corresponded to closed vacuolar structures at the ultrastructural level. Morphometric analysis of electron micrographs showed that formation of these vacuolar structures kinetically paralleled alpha-granule disappearance and preceded PF4 release. These PF4-containing structures translocated to the cell periphery after 1-3 min, where they appeared to fuse with the plasma membrane. Ultrastructural analysis of thin sections showed that the myosin-rich spherical structure spatially and temporally correlated with a band of microfilaments that closely surrounded the organelle-rich central zone of the cell. Morphometric analysis of these micrographs showed that the absolute volume of this central zone decreased with time after thrombin addition, showing a significant change after 15 sec and reaching a maximum value after 3-5 min. Changes in the volume of this compartment kinetically preceded PF4 release. On the basis of these data, we propose that an actomyosin contractile force is generated which centripetally redistributes the myosinrich structure and organelle zone. Conceivably this inward force may not only accelerate granule-granule fusion to form intracellular secretory vacuoles, but may also provide aid in their extrusion toward the platelet plasma membrane.

Improving the durability of the optical fiber sensor based on strain transfer analysis

NASA Astrophysics Data System (ADS)

Wang, Huaping; Jiang, Lizhong; Xiang, Ping

2018-05-01

To realize the reliable and long-term strain detection, the durability of optical fiber sensors has attracted more and more attention. The packaging technique has been considered as an effective method, which can enhance the survival ratios of optical fiber sensors to resist the harsh construction and service environment in civil engineering. To monitor the internal strain of structures, the embedded installation is adopted. Due to the different material properties between host material and the protective layer, the monitored structure embedded with sensors can be regarded as a typical model containing inclusions. Interfacial characteristic between the sensor and host material exists obviously, and the contacted interface is prone to debonding failure induced by the large interfacial shear stress. To recognize the local interfacial debonding damage and extend the effective life cycle of the embedded sensor, strain transfer analysis of a general three-layered sensing model is conducted to investigate the failure mechanism. The perturbation of the embedded sensor on the local strain field of host material is discussed. Based on the theoretical analysis, the distribution of the interfacial shear stress along the sensing length is characterized and adopted for the diagnosis of local interfacial debonding, and the sensitive parameters influencing the interfacial shear stress are also investigated. The research in this paper explores the interfacial debonding failure mechanism of embedded sensors based on the strain transfer analysis and provides theoretical basis for enhancing the interfacial bonding properties and improving the durability of embedded optical fiber sensors.

The importance of building construction materials relative to other factors affecting structure survival during wildfire

USGS Publications Warehouse

Syphard, Alexandra D.; Brennan, Teresa J.; Keeley, Jon E.

2017-01-01

Structure loss to wildfire is a serious problem in wildland-urban interface areas across the world. Laboratory experiments suggest that fire-resistant building construction and design could be important for reducing structure destruction, but these need to be evaluated under real wildfire conditions, especially relative to other factors. Using empirical data from destroyed and surviving structures from large wildfires in southern California, we evaluated the relative importance of building construction and structure age compared to other local and landscape-scale variables associated with structure survival. The local-scale analysis showed that window preparation was especially important but, in general, creating defensible space adjacent to the home was as important as building construction. At the landscape scale, structure density and structure age were the two most important factors affecting structure survival, but there was a significant interaction between them. That is, young structure age was most important in higher-density areas where structure survival overall was more likely. On the other hand, newer-construction structures were less likely to survive wildfires at lower density. Here, appropriate defensible space near the structure and accessibility to major roads were important factors. In conclusion, community safety is a multivariate problem that will require a comprehensive solution involving land use planning, fire-safe construction, and property maintenance.

Estimating 3D positions and velocities of projectiles from monocular views.

PubMed

Ribnick, Evan; Atev, Stefan; Papanikolopoulos, Nikolaos P

2009-05-01

In this paper, we consider the problem of localizing a projectile in 3D based on its apparent motion in a stationary monocular view. A thorough theoretical analysis is developed, from which we establish the minimum conditions for the existence of a unique solution. The theoretical results obtained have important implications for applications involving projectile motion. A robust, nonlinear optimization-based formulation is proposed, and the use of a local optimization method is justified by detailed examination of the local convexity structure of the cost function. The potential of this approach is validated by experimental results.

Dynamics of bulk versus nanoscale W S2 : Local strain and charging effects

NASA Astrophysics Data System (ADS)

Luttrell, R. D.; Brown, S.; Cao, J.; Musfeldt, J. L.; Rosentsveig, R.; Tenne, R.

2006-01-01

We measured the infrared vibrational properties of bulk and nanoparticle WS2 in order to investigate the structure-property relations in these materials. In addition to the symmetry-breaking effects of local strain, nanoparticle curvature modifies the local charging environment of the bulk material. Performing a charge analysis on the xy -polarized E1u vibrational mode, we find an approximate 1.5:1 intralayer charge difference between the layered 2H material and inorganic fullerene-like (IF) nanoparticles. This effective charge difference may impact the solid-state lubrication properties of nanoscale metal dichalcogenides.

Dynamics of Bulk vs. Nanoscale WS2: Local Strain and Charging Effects

NASA Astrophysics Data System (ADS)

Musfeldt, J. L.; Brown, S.; Luttrell, R. D.; Cao, J.; Rosentsveig, R.; Tenne, R.

2006-03-01

We measured the infrared vibrational properties of bulk and nanoparticle WS2 in order to investigate the structure- property relations in these novel materials. In addition to the symmetry-breaking effects of local strain, nanoparticle curvature modifies the local charging environment of the bulk material. Performing a charge analysis on the xy-polarized E1u vibrational mode, we find an approximate 1.5:1 intralayer charge difference between the layered 2H material and inorganic fullerene-like (IF) nanoparticles. This effective charge difference may impact the solid-state lubrication properties of nanoscale metal dichalcogenides.

Electro-mechanical analysis of composite and sandwich multilayered structures by shell elements with node-dependent kinematics

NASA Astrophysics Data System (ADS)

Carrera; Valvano; Kulikov

2018-01-01

In this work, a new class of finite elements for the analysis of composite and sandwich shells embedding piezoelectric skins and patches is proposed. The main idea of models coupling is developed by presenting the concept of nodal dependent kinematics where the same finite element can present at each node a different approximation of the main unknowns by setting a node-wise through-the-thickness approximation base. In a global/local approach scenario, the computational costs can be reduced drastically by assuming refined theories only in those zones/nodes of the structural domain where the resulting strain and stress states, and their electro-mechanical coupling present a complex distribution. Several numerical investigations are carried out to validate the accuracy and efficiency of the present shell element. An accurate representation of mechanical stresses and electric displacements in localized zones is possible with reduction of the computational costs if an accurate distribution of the higher-order kinematic capabilities is performed. On the contrary, the accuracy of the solution in terms of mechanical displacements and electric potential values depends on the global approximation over the whole structure. The efficacy of the present node-dependent variable kinematic models, thus, depends on the characteristics of the problem under consideration as well as on the required analysis type.

Integrated Risk Research. Case of Study: Motozintla, Chiapas, Mexico

NASA Astrophysics Data System (ADS)

Novelo-Casanova, D. A.; Jaimes, M.

2015-12-01

This integrated risk research include the analysis of all components of individual constituents of risk such hazard identification, hazard exposure, and vulnerability. We determined risk to natural hazards in the community of Motozintla located in southern Mexico in the state of Chiapas (15.37ºN, 92.25ºW. Due to its geographical and geological location, this community is continuously exposed mainly to earthquakes, landslides and floods. We developed integrated studies and analysis of seismic zonation, landslides and flood susceptibility using standard methodologies. Vulnerability was quantified from data collected from local families interviews considering five social variables: characteristics of housing construction, availability of basic public services, family economic conditions, existing community plans for disaster preparedness, and risk perception. Local families surveyed were randomly selected considering a sample statistically significant. Our results were spatially represented using a Geographical Information System (GIS). Structural vulnerability curves were generated for typical housing constructions. Our integrated risk analysis demonstrates that the community of Motozintla has a high level of structural and socio-economical risk to floods and earthquakes. More than half of the population does not know any existing Civil Protection Plan and perceive that they are in high risk to landslides and floods. Although the community is located in a high seismic risk zone, most of the local people believe that cannot be impacted by a large earthquake. These natural and social conditions indicate that the community of Motozintla has a very high level of risk to natural hazards. This research will support local decision makers in developing an integrated comprehensive natural hazards mitigation and prevention program.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liakh, Dmitry I

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

Investigation of the local environment of Eu3+ in a silicophosphate glass using site-selective spectroscopy and Molecular Dynamics simulations

NASA Astrophysics Data System (ADS)

Ben Slimen, F.; Haouari, M.; Ben Ouada, H.; Guichaoua, D.; Raso, P.; Bidault, X.; Turlier, J.; Gaumer, N.; Chaussedent, S.

2017-02-01

Silicophosphate glasses (SiO2-P2O5) doped with Eu3+ ions were synthesized by the sol-gel process. Optical properties of these glasses were investigated by means of emission spectra and lifetime measurements. The Fluorescence Line Narrowing (FLN) technique was also used to explore the local structure around the Eu3+ ions in this host and to understand the role of phosphate as a codopant. As it is the case for aluminum, the ability of phosphate to avoid the rare earth clustering was investigated, and the role of this codopant in modifying the local order around the rare earth ion was evidenced. The analysis of the FLN spectra and lifetime measurements is consistent with this interpretation. Molecular Dynamics simulations were performed to evaluate and confirm these structural features. Two classes of europium sites were distinguished in agreement with the experimental characterization.

Optimal atomic structure of amorphous silicon obtained from density functional theory calculations

NASA Astrophysics Data System (ADS)

Pedersen, Andreas; Pizzagalli, Laurent; Jónsson, Hannes

2017-06-01

Atomic structure of amorphous silicon consistent with several reported experimental measurements has been obtained from annealing simulations using electron density functional theory calculations and a systematic removal of weakly bound atoms. The excess energy and density with respect to the crystal are well reproduced in addition to radial distribution function, angular distribution functions, and vibrational density of states. No atom in the optimal configuration is locally in a crystalline environment as deduced by ring analysis and common neighbor analysis, but coordination defects are present at a level of 1%-2%. The simulated samples provide structural models of this archetypal disordered covalent material without preconceived notion of the atomic ordering or fitting to experimental data.

Local structure of In0.5Ga0.5As from joint high-resolution and differential pair distribution function analysis

NASA Astrophysics Data System (ADS)

Petkov, V.; Jeong, I.-K.; Mohiuddin-Jacobs, F.; Proffen, Th.; Billinge, S. J. L.; Dmowski, W.

2000-07-01

High resolution total and indium differential atomic pair distribution functions (PDFs) for In0.5Ga0.5As alloys have been obtained by high energy and anomalous x-ray diffraction experiments, respectively. The first peak in the total PDF is resolved as a doublet due to the presence of two distinct bond lengths, In-As and Ga-As. The In differential PDF, which involves only atomic pairs containing In, yields chemical specific information and helps ease the structure data interpretation. Both PDFs have been fit with structure models and the way in that the underlying cubic zinc-blende lattice of In0.5Ga0.5As semiconductor alloy distorts locally to accommodate the distinct In-As and Ga-As bond lengths present has been quantified.

Predictive simulation of guide-wave structural health monitoring

NASA Astrophysics Data System (ADS)

Giurgiutiu, Victor

2017-04-01

This paper presents an overview of recent developments on predictive simulation of guided wave structural health monitoring (SHM) with piezoelectric wafer active sensor (PWAS) transducers. The predictive simulation methodology is based on the hybrid global local (HGL) concept which allows fast analytical simulation in the undamaged global field and finite element method (FEM) simulation in the local field around and including the damage. The paper reviews the main results obtained in this area by researchers of the Laboratory for Active Materials and Smart Structures (LAMSS) at the University of South Carolina, USA. After thematic introduction and research motivation, the paper covers four main topics: (i) presentation of the HGL analysis; (ii) analytical simulation in 1D and 2D; (iii) scatter field generation; (iv) HGL examples. The paper ends with summary, discussion, and suggestions for future work.

Energy loss, range, and bremsstrahlung yield for 10-keV to 100-MeV electrons in various elements and chemical compounds

NASA Astrophysics Data System (ADS)

Pages, Lucien; Bertel, Evelyne; Joffre, Henri; Sklavenitis, Laodamas

2012-12-01

Even though the United States lacks a national climate policy, significant action has occurred at the local and regional levels. Some of the most aggressive climate change policies have occurred at the state and local levels and in interagency cooperation on specific management issues. While there is a long history of partnerships in dealing with a wide variety of policy issues, the uncertainty and the political debate surrounding climate change has generated new challenges to establishing effective policy networks. This paper investigates the formation of climate policy networks in the State of Nevada. It presents a methodology based on social network analysis for assessing the structure and function of local policy networks across a range of substantive climate impacted resources (water, landscape management, conservation, forestry and others). It draws from an emerging literature on federalism and climate policy, public sector innovation, and institutional analysis in socio-ecological systems. Comparisons across different policy issue networks in the state are used to highlight the influence of network structure, connectivity, bridging across vertical and horizontal organizational units, organizational diversity, and flows between organizational nodes.

Energy Based Multiscale Modeling with Non-Periodic Boundary Conditions

DTIC Science & Technology

2013-05-13

below in Figure 8. At each incremental step in the analysis , the user material defined subroutine (UMAT) was utilized to perform the communication...initiation and modeling using XFEM. Appropriate localization schemes will be developed to allow for deformations conducive for crack opening...REFERENCES 1. Talreja R., 2006, “Damage analysis for structural integrity and durability of composite materials ,” Fatigue & Fracture of

From the 2008 to the 2014 Crisis: Response of the Labor Market of Russia's Largest Cities

ERIC Educational Resources Information Center

Khmeleva, Galina A.; Bulavko, Olga A.

2016-01-01

The model of shift share analysis was improved to show that the foundation of economy's transition to industrially innovational type of development is created at the local level in case of developing countries. Analysis of structural shifts in 28 large cities in 2008-2014 showed that the perspective of industrially innovational development is yet…

An Assessment of the State-of-the-Art in Multidisciplinary Aeromechanical Analyses

DTIC Science & Technology

2008-01-01

monolithic formulations. In summary, for aerospace structures, partitioned formulations provide fundamental advantages over fully coupled ones, in addition...important frequencies of local analysis directly to global analysis using detailed modeling. Performed ju- diciously, based on a fundamental understanding of...in 2000 has com- prehensively described the problem, and reviewed the status of fundamental understanding, experimental data, and analytical

Method of center localization for objects containing concentric arcs

NASA Astrophysics Data System (ADS)

Kuznetsova, Elena G.; Shvets, Evgeny A.; Nikolaev, Dmitry P.

2015-02-01

This paper proposes a method for automatic center location of objects containing concentric arcs. The method utilizes structure tensor analysis and voting scheme optimized with Fast Hough Transform. Two applications of the proposed method are considered: (i) wheel tracking in video-based system for automatic vehicle classification and (ii) tree growth rings analysis on a tree cross cut image.

Population structure of the Korean gizzard shad, Konosirus punctatus (Clupeiformes, Clupeidae) using multivariate morphometric analysis

NASA Astrophysics Data System (ADS)

Myoung, Se Hun; Kim, Jin-Koo

2016-03-01

The gizzard shad, Konosirus punctatus, is one of the most important fish species in Korea, China, Japan and Taiwan, and therefore the implementation of an appropriate population structure analysis is both necessary and fitting. In order to clarify the current distribution range for the two lineages of the Korean gizzard shad (Myoung and Kim 2014), we conducted a multivariate morphometric analysis by locality and lineage. We analyzed 17 morphometric and 5 meristic characters of 173 individuals, which were sampled from eight localities in the East Sea, the Yellow Sea and the Korean Strait. Unlike population genetics studies, the canonical discriminant analysis (CDA) results showed that the two morphotypes were clearly segregated by the center value "0" of CAN1, of which morphotype A occurred from the Yellow Sea to the western Korean Strait with negative values, and morphotype B occurred from the East Sea to the eastern Korean Strait with positive values even though there exists an admixture zone in the eastern Korean Strait. Further studies using more sensitive markers such as microsatellite DNA are required in order to define the true relationship between the two lineages.

Probing the pH sensitivity of R-phycoerythrin: investigations of active conformational and functional variation.

PubMed

Liu, Lu-Ning; Su, Hai-Nan; Yan, Shi-Gan; Shao, Si-Mi; Xie, Bin-Bin; Chen, Xiu-Lan; Zhang, Xi-Ying; Zhou, Bai-Cheng; Zhang, Yu-Zhong

2009-07-01

Crystal structures of phycobiliproteins have provided valuable information regarding the conformations and amino acid organizations of peptides and chromophores, and enable us to investigate their structural and functional relationships with respect to environmental variations. In this work, we explored the pH-induced conformational and functional dynamics of R-phycoerythrin (R-PE) by means of absorption, fluorescence and circular dichroism spectra, together with analysis of its crystal structure. R-PE presents stronger functional stability in the pH range of 3.5-10 compared to the structural stability. Beyond this range, pronounced functional and structural changes occur. Crystal structure analysis shows that the tertiary structure of R-PE is fixed by several key anchoring points of the protein. With this specific association, the fundamental structure of R-PE is stabilized to present physiological spectroscopic properties, while local variations in protein peptides are also allowed in response to environmental disturbances. The functional stability and relative structural sensitivity of R-PE allow environmental adaptation.

Alternative difference analysis scheme combining R -space EXAFS fit with global optimization XANES fit for X-ray transient absorption spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhan, Fei; Tao, Ye; Zhao, Haifeng

Time-resolved X-ray absorption spectroscopy (TR-XAS), based on the laser-pump/X-ray-probe method, is powerful in capturing the change of the geometrical and electronic structure of the absorbing atom upon excitation. TR-XAS data analysis is generally performed on the laser-on minus laser-off difference spectrum. Here, a new analysis scheme is presented for the TR-XAS difference fitting in both the extended X-ray absorption fine-structure (EXAFS) and the X-ray absorption near-edge structure (XANES) regions.R-space EXAFS difference fitting could quickly provide the main quantitative structure change of the first shell. The XANES fitting part introduces a global non-derivative optimization algorithm and optimizes the local structure changemore » in a flexible way where both the core XAS calculation package and the search method in the fitting shell are changeable. The scheme was applied to the TR-XAS difference analysis of Fe(phen) 3spin crossover complex and yielded reliable distance change and excitation population.« less

Alternative difference analysis scheme combining R-space EXAFS fit with global optimization XANES fit for X-ray transient absorption spectroscopy.

PubMed

Zhan, Fei; Tao, Ye; Zhao, Haifeng

2017-07-01

Time-resolved X-ray absorption spectroscopy (TR-XAS), based on the laser-pump/X-ray-probe method, is powerful in capturing the change of the geometrical and electronic structure of the absorbing atom upon excitation. TR-XAS data analysis is generally performed on the laser-on minus laser-off difference spectrum. Here, a new analysis scheme is presented for the TR-XAS difference fitting in both the extended X-ray absorption fine-structure (EXAFS) and the X-ray absorption near-edge structure (XANES) regions. R-space EXAFS difference fitting could quickly provide the main quantitative structure change of the first shell. The XANES fitting part introduces a global non-derivative optimization algorithm and optimizes the local structure change in a flexible way where both the core XAS calculation package and the search method in the fitting shell are changeable. The scheme was applied to the TR-XAS difference analysis of Fe(phen) 3 spin crossover complex and yielded reliable distance change and excitation population.

Analytical Methodology for Predicting the Onset of Widespread Fatigue Damage in Fuselage Structure

NASA Technical Reports Server (NTRS)

Harris, Charles E.; Newman, James C., Jr.; Piascik, Robert S.; Starnes, James H., Jr.

1996-01-01

NASA has developed a comprehensive analytical methodology for predicting the onset of widespread fatigue damage in fuselage structure. The determination of the number of flights and operational hours of aircraft service life that are related to the onset of widespread fatigue damage includes analyses for crack initiation, fatigue crack growth, and residual strength. Therefore, the computational capability required to predict analytically the onset of widespread fatigue damage must be able to represent a wide range of crack sizes from the material (microscale) level to the global structural-scale level. NASA studies indicate that the fatigue crack behavior in aircraft structure can be represented conveniently by the following three analysis scales: small three-dimensional cracks at the microscale level, through-the-thickness two-dimensional cracks at the local structural level, and long cracks at the global structural level. The computational requirements for each of these three analysis scales are described in this paper.

Extended local similarity analysis (eLSA) reveals unique associations between bacterial community structure and odor emission during pig carcasses decomposition.

PubMed

Ki, Bo-Min; Ryu, Hee Wook; Cho, Kyung-Suk

2018-02-22

Soil burial and composting methods have been widely used for the disposal of pig carcasses. The relationship between bacterial community structure and odor emission was examined using extended local similarity analysis (eLSA) during the degradation of pig carcasses in soil and compost. In soil, Hyphomicrobium, Niastella, Rhodanobacter, Polaromonas, Dokdonella and Mesorhizobium were associated with the emission of sulfur-containing odors such as hydrogen sulfide, methyl mercaptan and dimethyl disulfide. Sphingomonas, Rhodanobacter, Mesorhizobium, Dokdonella, Leucobacter and Truepera were associated with the emission of nitrogen-containing odors including ammonia and trimetylamine. In compost, however, Carnobacteriaceae, Lachnospiaceae and Clostridiales were highly correlated with the emission of sulfur-containing odors, while Rumincoccaceae was associated with the emission of nitrogen-containing odors. The emission of organic acids was closely related to Massilia, Sphaerobacter and Bradyrhizobiaceae in soil, but to Actinobacteria, Sporacetigenium, Micromonosporaceae and Solirubrobacteriales in compost. This study suggests that network analysis using eLSA is a useful strategy for exploring the mechanisms of odor emission during biodegradation of pig carcasses.

Cluster and constraint analysis in tetrahedron packings

NASA Astrophysics Data System (ADS)

Jin, Weiwei; Lu, Peng; Liu, Lufeng; Li, Shuixiang

2015-04-01

The disordered packings of tetrahedra often show no obvious macroscopic orientational or positional order for a wide range of packing densities, and it has been found that the local order in particle clusters is the main order form of tetrahedron packings. Therefore, a cluster analysis is carried out to investigate the local structures and properties of tetrahedron packings in this work. We obtain a cluster distribution of differently sized clusters, and peaks are observed at two special clusters, i.e., dimer and wagon wheel. We then calculate the amounts of dimers and wagon wheels, which are observed to have linear or approximate linear correlations with packing density. Following our previous work, the amount of particles participating in dimers is used as an order metric to evaluate the order degree of the hierarchical packing structure of tetrahedra, and an order map is consequently depicted. Furthermore, a constraint analysis is performed to determine the isostatic or hyperstatic region in the order map. We employ a Monte Carlo algorithm to test jamming and then suggest a new maximally random jammed packing of hard tetrahedra from the order map with a packing density of 0.6337.

From bird's eye views to molecular communities: two-layered visualization of structure-activity relationships in large compound data sets

NASA Astrophysics Data System (ADS)

Kayastha, Shilva; Kunimoto, Ryo; Horvath, Dragos; Varnek, Alexandre; Bajorath, Jürgen

2017-11-01

The analysis of structure-activity relationships (SARs) becomes rather challenging when large and heterogeneous compound data sets are studied. In such cases, many different compounds and their activities need to be compared, which quickly goes beyond the capacity of subjective assessments. For a comprehensive large-scale exploration of SARs, computational analysis and visualization methods are required. Herein, we introduce a two-layered SAR visualization scheme specifically designed for increasingly large compound data sets. The approach combines a new compound pair-based variant of generative topographic mapping (GTM), a machine learning approach for nonlinear mapping, with chemical space networks (CSNs). The GTM component provides a global view of the activity landscapes of large compound data sets, in which informative local SAR environments are identified, augmented by a numerical SAR scoring scheme. Prioritized local SAR regions are then projected into CSNs that resolve these regions at the level of individual compounds and their relationships. Analysis of CSNs makes it possible to distinguish between regions having different SAR characteristics and select compound subsets that are rich in SAR information.

Theoretical study of the local structures and the EPR parameters for RLNKB glasses with VO2+ and Cu2+ dopants

NASA Astrophysics Data System (ADS)

Ding, Chang-Chun; Wu, Shao-Yi; Wu, Li-Na; Zhang, Li-Juan; Peng, Li; Wu, Ming-He; Teng, Bao-Hua

2018-02-01

The electron paramagnetic resonance (EPR) parameters and local structures for impurities VO2+ and Cu2+ in RO-Li2O-Na2O-K2O-B2O3 (RLNKB; R = Zn, Mg, Sr and Ba) glasses are theoretically investigated by using the perturbation formulas of the EPR parameters for tetragonally compressed octahedral 3d1 and tetragonally elongated octahedral 3d9 clusters, respectively. The VO2+ and Cu2+ dopants are found to undergo the tetragonal compression (characterized by the negative relative distortion ratios ρ ≈ -3%, -0.98%, -1% and -0.8% for R = Zn, Mg, Sr and Ba) and elongation (characterized by the positive relative distortion ratios ρ ≈ 29%, 17%, 16% and 28%), respectively, due to the Jahn-Teller effect. Both dopants show similar overall decreasing trends of cubic field parameter Dq and covalency factor N with decreasing electronegativity of alkali earth cation R. The conventional optical basicities Λth and local optical basicities Λloc are calculated for both systems, and the local Λloc are higher for Cu2+ than for VO2+ in the same RLNKB glass, despite the opposite relationship for the conventional Λth. This point is supported by the weaker covalency or stronger ionicity for Cu2+ than VO2+ in the same RLNKB system, characterized by the larger N in the former. The above comparative analysis on the spectral and local structural properties would be helpful to understand structures and spectroscopic properties for the similar oxide glasses with transition-metal dopants of complementary electronic configurations.

Deformation-induced spatiotemporal fluctuation, evolution and localization of strain fields in a bulk metallic glass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Yuan; Bei, Hongbin; Wang, Yanli

Deformation behavior and local strain evolutions upon loading and unloading of a bulk metallic glass (BMG) were systematically investigated by in situ digital image correlation (DIC). Distinct fluctuations and irreversible local strains were observed before the onset of macroscopic yielding. Statistical analysis shows that these fluctuations might be related to intrinsic structural heterogeneities, and that the evolution history and characteristics of local strain fields play an important role in the subsequent initiation of shear bands. Effects of sample size, pre-strain, and loading conditions were systematically analyzed in terms of the probability distributions of the resulting local strain fields. It ismore » found that a higher degree of local shear strain heterogeneity corresponds to a more ductile stressestrain curve. Implications of these findings are discussed for the design of new materials.« less

Deformation-induced spatiotemporal fluctuation, evolution and localization of strain fields in a bulk metallic glass

DOE PAGES

Wu, Yuan; Bei, Hongbin; Wang, Yanli; ...

2015-05-16

Deformation behavior and local strain evolutions upon loading and unloading of a bulk metallic glass (BMG) were systematically investigated by in situ digital image correlation (DIC). Distinct fluctuations and irreversible local strains were observed before the onset of macroscopic yielding. Statistical analysis shows that these fluctuations might be related to intrinsic structural heterogeneities, and that the evolution history and characteristics of local strain fields play an important role in the subsequent initiation of shear bands. Effects of sample size, pre-strain, and loading conditions were systematically analyzed in terms of the probability distributions of the resulting local strain fields. It ismore » found that a higher degree of local shear strain heterogeneity corresponds to a more ductile stressestrain curve. Implications of these findings are discussed for the design of new materials.« less

The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

PubMed

Olechnovič, Kliment; Venclovas, Ceslovas

2014-07-01

The Contact Area Difference score (CAD-score) web server provides a universal framework to compute and analyze discrepancies between different 3D structures of the same biological macromolecule or complex. The server accepts both single-subunit and multi-subunit structures and can handle all the major types of macromolecules (proteins, RNA, DNA and their complexes). It can perform numerical comparison of both structures and interfaces. In addition to entire structures and interfaces, the server can assess user-defined subsets. The CAD-score server performs both global and local numerical evaluations of structural differences between structures or interfaces. The results can be explored interactively using sortable tables of global scores, profiles of local errors, superimposed contact maps and 3D structure visualization. The web server could be used for tasks such as comparison of models with the native (reference) structure, comparison of X-ray structures of the same macromolecule obtained in different states (e.g. with and without a bound ligand), analysis of nuclear magnetic resonance (NMR) structural ensemble or structures obtained in the course of molecular dynamics simulation. The web server is freely accessible at: http://www.ibt.lt/bioinformatics/cad-score. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

Simultaneous Aerodynamic Analysis and Design Optimization (SAADO) for a 3-D Flexible Wing

NASA Technical Reports Server (NTRS)

Gumbert, Clyde R.; Hou, Gene J.-W.

2001-01-01

The formulation and implementation of an optimization method called Simultaneous Aerodynamic Analysis and Design Optimization (SAADO) are extended from single discipline analysis (aerodynamics only) to multidisciplinary analysis - in this case, static aero-structural analysis - and applied to a simple 3-D wing problem. The method aims to reduce the computational expense incurred in performing shape optimization using state-of-the-art Computational Fluid Dynamics (CFD) flow analysis, Finite Element Method (FEM) structural analysis and sensitivity analysis tools. Results for this small problem show that the method reaches the same local optimum as conventional optimization. However, unlike its application to the win,, (single discipline analysis), the method. as I implemented here, may not show significant reduction in the computational cost. Similar reductions were seen in the two-design-variable (DV) problem results but not in the 8-DV results given here.

Genetic Structure and Diversity of the Endangered Fir Tree of Lebanon (Abies cilicica Carr.): Implications for Conservation

PubMed Central

Awad, Lara; Fady, Bruno; Khater, Carla; Roig, Anne; Cheddadi, Rachid

2014-01-01

The threatened conifer Abies cilicica currently persists in Lebanon in geographically isolated forest patches. The impact of demographic and evolutionary processes on population genetic diversity and structure were assessed using 10 nuclear microsatellite loci. All remnant 15 local populations revealed a low genetic variation but a high recent effective population size. FST-based measures of population genetic differentiation revealed a low spatial genetic structure, but Bayesian analysis of population structure identified a significant Northeast-Southwest population structure. Populations showed significant but weak isolation-by-distance, indicating non-equilibrium conditions between dispersal and genetic drift. Bayesian assignment tests detected an asymmetric Northeast-Southwest migration involving some long-distance dispersal events. We suggest that the persistence and Northeast-Southwest geographic structure of Abies cilicica in Lebanon is the result of at least two demographic processes during its recent evolutionary history: (1) recent migration to currently marginal populations and (2) local persistence through altitudinal shifts along a mountainous topography. These results might help us better understand the mechanisms involved in the species response to expected climate change. PMID:24587219

On the mechanism of bandgap formation in locally resonant finite elastic metamaterials

NASA Astrophysics Data System (ADS)

Sugino, Christopher; Leadenham, Stephen; Ruzzene, Massimo; Erturk, Alper

2016-10-01

Elastic/acoustic metamaterials made from locally resonant arrays can exhibit bandgaps at wavelengths much longer than the lattice size for various applications spanning from low-frequency vibration/sound attenuation to wave guiding and filtering in mechanical and electromechanical devices. For an effective use of such locally resonant metamaterial concepts in finite structures, it is required to bridge the gap between the lattice dispersion characteristics and modal behavior of the host structure with its resonators. To this end, we develop a novel argument for bandgap formation in finite-length elastic metamaterial beams, relying on the modal analysis and the assumption of infinitely many resonators. We show that the dual problem to wave propagation through an infinite periodic beam is the modal analysis of a finite beam with an infinite number of resonators. A simple formula that depends only on the resonator natural frequency and total mass ratio is derived for placing the bandgap in a desired frequency range, yielding an analytical insight and a rule of thumb for design purposes. A method for understanding the importance of a resonator location and mass is discussed in the context of a Riemann sum approximation of an integral, and a method for determining the optimal number of resonators for a given set of boundary conditions and target frequency is introduced. The simulations of the theoretical framework are validated by experiments for bending vibrations of a locally resonant cantilever beam.

Diversity structure of culturable bacteria isolated from the Fildes Peninsula (King George Island, Antarctica): A phylogenetic analysis perspective

PubMed Central

González-Rocha, Gerardo; Muñoz-Cartes, Gabriel; Canales-Aguirre, Cristian B.; Lima, Celia A.; Domínguez-Yévenes, Mariana; Bello-Toledo, Helia

2017-01-01

It has been proposed that Antarctic environments select microorganisms with unique biochemical adaptations, based on the tenet ‘Everything is everywhere, but, the environment selects’ by Baas-Becking. However, this is a hypothesis that has not been extensively evaluated. This study evaluated the fundamental prediction contained in this hypothesis—in the sense that species are structured in the landscape according to their local habitats-, using as study model the phylogenetic diversity of the culturable bacteria of Fildes Peninsula (King George Island, Antarctica). Eighty bacterial strains isolated from 10 different locations in the area, were recovered. Based on phylogenetic analysis of 16S rRNA gene sequences, the isolates were grouped into twenty-six phylotypes distributed in three main clades, of which only six are exclusive to Antarctica. Results showed that phylotypes do not group significantly by habitat type; however, local habitat types had phylogenetic signal, which support the phylogenetic niche conservatism hypothesis and not a selective role of the environment like the Baas-Becking hypothesis suggests. We propose that, more than habitat selection resulting in new local adaptations and diversity, local historical colonization and species sorting (i.e. differences in speciation and extinction rates that arise by interaction of species level traits with the environment) play a fundamental role on the culturable bacterial diversity in Antarctica. PMID:28632790

Diversity structure of culturable bacteria isolated from the Fildes Peninsula (King George Island, Antarctica): A phylogenetic analysis perspective.

PubMed

González-Rocha, Gerardo; Muñoz-Cartes, Gabriel; Canales-Aguirre, Cristian B; Lima, Celia A; Domínguez-Yévenes, Mariana; Bello-Toledo, Helia; Hernández, Cristián E

2017-01-01

It has been proposed that Antarctic environments select microorganisms with unique biochemical adaptations, based on the tenet 'Everything is everywhere, but, the environment selects' by Baas-Becking. However, this is a hypothesis that has not been extensively evaluated. This study evaluated the fundamental prediction contained in this hypothesis-in the sense that species are structured in the landscape according to their local habitats-, using as study model the phylogenetic diversity of the culturable bacteria of Fildes Peninsula (King George Island, Antarctica). Eighty bacterial strains isolated from 10 different locations in the area, were recovered. Based on phylogenetic analysis of 16S rRNA gene sequences, the isolates were grouped into twenty-six phylotypes distributed in three main clades, of which only six are exclusive to Antarctica. Results showed that phylotypes do not group significantly by habitat type; however, local habitat types had phylogenetic signal, which support the phylogenetic niche conservatism hypothesis and not a selective role of the environment like the Baas-Becking hypothesis suggests. We propose that, more than habitat selection resulting in new local adaptations and diversity, local historical colonization and species sorting (i.e. differences in speciation and extinction rates that arise by interaction of species level traits with the environment) play a fundamental role on the culturable bacterial diversity in Antarctica.

Supervised orthogonal discriminant subspace projects learning for face recognition.

PubMed

Chen, Yu; Xu, Xiao-Hong

2014-02-01

In this paper, a new linear dimension reduction method called supervised orthogonal discriminant subspace projection (SODSP) is proposed, which addresses high-dimensionality of data and the small sample size problem. More specifically, given a set of data points in the ambient space, a novel weight matrix that describes the relationship between the data points is first built. And in order to model the manifold structure, the class information is incorporated into the weight matrix. Based on the novel weight matrix, the local scatter matrix as well as non-local scatter matrix is defined such that the neighborhood structure can be preserved. In order to enhance the recognition ability, we impose an orthogonal constraint into a graph-based maximum margin analysis, seeking to find a projection that maximizes the difference, rather than the ratio between the non-local scatter and the local scatter. In this way, SODSP naturally avoids the singularity problem. Further, we develop an efficient and stable algorithm for implementing SODSP, especially, on high-dimensional data set. Moreover, the theoretical analysis shows that LPP is a special instance of SODSP by imposing some constraints. Experiments on the ORL, Yale, Extended Yale face database B and FERET face database are performed to test and evaluate the proposed algorithm. The results demonstrate the effectiveness of SODSP. Copyright © 2013 Elsevier Ltd. All rights reserved.

Fine-scale genetic population structure in a mobile marine mammal: inshore bottlenose dolphins in Moreton Bay, Australia.

PubMed

Ansmann, Ina C; Parra, Guido J; Lanyon, Janet M; Seddon, Jennifer M

2012-09-01

Highly mobile marine species in areas with no obvious geographic barriers are expected to show low levels of genetic differentiation. However, small-scale variation in habitat may lead to resource polymorphisms and drive local differentiation by adaptive divergence. Using nuclear microsatellite genotyping at 20 loci, and mitochondrial control region sequencing, we investigated fine-scale population structuring of inshore bottlenose dolphins (Tursiops aduncus) inhabiting a range of habitats in and around Moreton Bay, Australia. Bayesian structure analysis identified two genetic clusters within Moreton Bay, with evidence of admixture between them (F(ST) = 0.05, P = 0.001). There was only weak isolation by distance but one cluster of dolphins was more likely to be found in shallow southern areas and the other in the deeper waters of the central northern bay. In further analysis removing admixed individuals, southern dolphins appeared genetically restricted with lower levels of variation (AR = 3.252, π = 0.003) and high mean relatedness (r = 0.239) between individuals. In contrast, northern dolphins were more diverse (AR = 4.850, π = 0.009) and were mixing with a group of dolphins outside the bay (microsatellite-based STRUCTURE analysis), which appears to have historically been distinct from the bay dolphins (mtDNA Φ(ST) = 0.272, P < 0.001). This study demonstrates the ability of genetic techniques to expose fine-scale patterns of population structure and explore their origins and mechanisms. A complex variety of inter-related factors including local habitat variation, differential resource use, social behaviour and learning, and anthropogenic disturbances are likely to have played a role in driving fine-scale population structure among bottlenose dolphins in Moreton Bay. © 2012 Blackwell Publishing Ltd.

Coronal electron stream and Langmuir wave detection inside a propagation channel at 4.3 AU

NASA Technical Reports Server (NTRS)

Buttighoffer, A.; Pick, M.; Roelof, E. C.; Hoang, S.; Mangeney, A.; Lanzerotti, L. J.; Forsyth, R. J.; Phillips, J. L.

1995-01-01

Observations of an energetic interplanetary electron event associated with the production of Langmuir waves, both of which are identified at 4.3 AU by instruments on the Ulysses spacecraft, are presented in this paper. This electron event propagates inside a well-defined magnetic structure. The existence of this structure is firmly established by joint particle and plasma observations made by Ulysses instruments. Its local estimated radial width is of the order of 2.3 x 10(exp 7) km (0.15 AU). The electron beam is associated with a type III burst observed from Earth at high frequencies and at low frequencies from Ulysses in association with Langmuir waves detected inside the structure. The consistency of local (Ulysses) and remote (Earth) observations in terms of temporal and geometrical considerations establishes that the structure is anchored in the solar corona near the solar active region responisble for the observed type III emission and gives an accurate determination of the injection time for the observed electron beam. Propagation analysis of the electron event is presented. In order to quantify the magnetic field properties, a variance analysis has been performed and is presented in this paper. The analysis establishes that inside the structure the amount of magnetic energy involved in the fluctuations is less than 4% of the total magnetic energy; the minimal variance direction is well defined and in coincidence with the direction of the mean magnetic field. This configuration may produce conditions favorable for scatter free streaming of energetic electrons and/or Langmuir wave production. The results presented show that the magnetic field might play a role in stabilizing the coronal-origin plasma structures and then preserving them to large, approximately 4 AU, distances in the heliosphere.

Combined structural analysis and dating of authigenic/synkinematic illite: A step towards unravelling brittle faulting processes in time and space

NASA Astrophysics Data System (ADS)

Viola, Giulio

2017-04-01

Faulting accommodates momentous deformation and its style reflects the complex interplay of often transient processes such as friction, fluid flow and rheological changes within generally dilatant systems. Brittle faults are thus unique archives of the stress state and the physical and chemical conditions at the time of both initial strain localization and subsequent slip(s) during structural reactivation. Opening those archives, however, may be challenging due to the commonly convoluted (if not even chaotic) nature of brittle fault architectures and fault rocks. This is because, once formed, faults are extremely sensitive to variations in stress field and environmental conditions and are prone to readily slip in a variety of conditions, also in regions affected by only weak, far-field stresses. The detailed, multi-scalar structural analysis of faults and of fault rocks has to be the starting point for any study aiming at reconstructing the complex framework of brittle deformation. However, considering that present-day exposures of faults only represent the end result of the faults' often protracted and heterogeneous histories, the obtained structural and mechanical results have to be integrated over the life span of the studied fault system. Dating of synkinematic illite/muscovite to constrain the time-integrated evolution of faults is therefore the natural addition to detailed structural studies. By means of selected examples it will be demonstrated how careful structural analysis integrated with illite characterization and K-Ar dating allows the high-resolution reconstruction of brittle deformation histories and, in turn, multiple constraints to be placed on strain localization, deformation mechanisms, fluid flow, mineral alteration and authigenesis within actively deforming brittle fault rocks. Complex and long brittle histories can thus be reconstructed and untangled in any tectonic setting.

One-step nanoimprinted hybrid micro-/nano-structure for in situ protein detection of isolated cell array via localized surface plasmon resonance

NASA Astrophysics Data System (ADS)

Ali, Riyaz Ahmad Mohamed; Villariza Espulgar, Wilfred; Aoki, Wataru; Jiang, Shu; Saito, Masato; Ueda, Mitsuyoshi; Tamiya, Eiichi

2018-03-01

Nanoplasmonic biosensors show high potentials as label-free devices for continuous monitoring in biomolecular analyses. However, most current sensors comprise multiple-dedicated layers with complicated fabrication procedures, which increases production time and manufacturing costs. In this work, we report the synergistic integration of cell-trapping microwell structures with plasmonic sensing nanopillar structures in a single-layered substrate by one-step thermal nanoimprinting. Here, microwell arrays are used for isolating cells, wherein gold-capped nanostructures sense changes in local refractive index via localized surface plasmon resonance (LSPR). Hence, proteins secreted from trapped cells can be label-freely detected as peak shifts in absorbance spectra. The fabricated device showed a detection limit of 10 ng/µL anti-IgA. In Pichia pastoris cells trial analysis, a red shift of 6.9 nm was observed over 12 h, which is likely due to the protein secretion from the cells. This approach provides an inexpensive, rapid, and reproducible alternative for mass production of biosensors for continuous biomolecular analyses.

Identification of spatially-localized initial conditions via sparse PCA

NASA Astrophysics Data System (ADS)

Dwivedi, Anubhav; Jovanovic, Mihailo

2017-11-01

Principal Component Analysis involves maximization of a quadratic form subject to a quadratic constraint on the initial flow perturbations and it is routinely used to identify the most energetic flow structures. For general flow configurations, principal components can be efficiently computed via power iteration of the forward and adjoint governing equations. However, the resulting flow structures typically have a large spatial support leading to a question of physical realizability. To obtain spatially-localized structures, we modify the quadratic constraint on the initial condition to include a convex combination with an additional regularization term which promotes sparsity in the physical domain. We formulate this constrained optimization problem as a nonlinear eigenvalue problem and employ an inverse power-iteration-based method to solve it. The resulting solution is guaranteed to converge to a nonlinear eigenvector which becomes increasingly localized as our emphasis on sparsity increases. We use several fluids examples to demonstrate that our method indeed identifies the most energetic initial perturbations that are spatially compact. This work was supported by Office of Naval Research through Grant Number N00014-15-1-2522.

Photo-Darkening Kinetics and Structural Anisotropic Modifications in the Chalcogenide Glass Arsenic Trisulfide: a Study of Kinetic X-Ray Absorption Spectroscopy

NASA Astrophysics Data System (ADS)

Lee, Jay Min

1990-08-01

The purpose of the study is to investigate the mechanisms involved with photo-induced atomic structural modifications in the chalcogenide glass As_2 S_3. This glass exhibits the reversible effects of photo-darkening followed by thermal bleaching. We observed the time behavior of photo-induced properties under the influence of linearly polarized band -gap light. In a macroscopic optical investigation, we monitor optical changes in the photo-darkening process, and in a local structural probe we study kinetic (or time -resolved dispersive) x-ray absorption spectroscopy. Our observations center on kinetic phenomena and structural modifications induced by polarized excitation of lone-pair orbitals in the chalcogenide glass. Experimental results include the following observations: (i) The polarity of the optically induced anisotropy is critically dependent on the intensity and the polarization of the band-gap irradiation beam. (ii) The near edge peak height in x-ray absorption spectra shows subtle but sensitive change during the photo-darkening process. (iii) Photon intensity dependent dichroic kinetics reflect a connection between the optically probed macroscopic property and the x-ray probed local anisotropic structure. Analysis of the x-ray absorption results includes a computer simulation of the polarized absorption spectra. These results suggest that specific structural units tend to orient themselves with respect to the photon polarization. A substantial part of the analysis involves a major effort in dealing with the x-ray kinetic data manipulation and the experimental difficulties caused by a synchrotron instability problem. Based on our observations, we propose a possible mechanism for the observed photo-structural modifications. Through a model of computer relaxed photo-darkening kinetics, we support the notion that a twisting of a specific intermediate range order structure is responsible for local directional variations and global network distortions. In the course of this study, we refine knowledge of intermediate range order structural configurations and the bistabilities related to these configurations. The importance of the lone-pair orbital interactions in the chalcogenide glassy network is underscored.

Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

PubMed Central

Lorenz, William A.; Clote, Peter

2011-01-01

An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in time and space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures – indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server and source code available at http://bioinformatics.bc.edu/clotelab/RNAlocopt/. PMID:21297972

Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces

PubMed Central

Haider, Kamran; Wickstrom, Lauren; Ramsey, Steven; Gilson, Michael K.; Kurtzman, Tom

2016-01-01

The principles underlying water reorganization around simple non-polar solutes are well understood and provide the framework for classical hydrophobic effect, whereby water molecules structure themselves around solutes so that they maintain favorable energetic contacts with both the solute and with other water molecules. However, for certain solute surface topographies, water molecules, due to their geometry and size, are unable to simultaneously maintain favorable energetic contacts with both the surface and neighboring water molecules. In this study, we analyze the solvation of ligand-binding sites for six structurally diverse proteins using hydration site analysis and measures of local water structure, in order to identify surfaces at which water molecules are unable to structure themselves in a way that maintains favorable enthalpy relative to bulk water. These surfaces are characterized by a high degree of enclosure, weak solute-water interactions, and surface constraints that induce unfavorable pair interactions between neighboring water molecules. Additionally, we find that the solvation of charged side-chains in an active site generally results in favorable enthalpy but can also lead to pair interactions between neighboring water molecules that are significantly unfavorable relative to bulk water. We find that frustrated local structure can occur not only in apolar and weakly polar pockets, where overall enthalpy tends to be unfavorable, but also in charged pockets, where overall water enthalpy tends to be favorable. The characterization of local water structure in these terms may prove useful for evaluating the displacement of water from diverse protein active-site environments. PMID:27169482

A statistical model to estimate the local vulnerability to severe weather

NASA Astrophysics Data System (ADS)

Pardowitz, Tobias

2018-06-01

We present a spatial analysis of weather-related fire brigade operations in Berlin. By comparing operation occurrences to insured losses for a set of severe weather events we demonstrate the representativeness and usefulness of such data in the analysis of weather impacts on local scales. We investigate factors influencing the local rate of operation occurrence. While depending on multiple factors - which are often not available - we focus on publicly available quantities. These include topographic features, land use information based on satellite data and information on urban structure based on data from the OpenStreetMap project. After identifying suitable predictors such as housing coverage or local density of the road network we set up a statistical model to be able to predict the average occurrence frequency of local fire brigade operations. Such model can be used to determine potential hotspots for weather impacts even in areas or cities where no systematic records are available and can thus serve as a basis for a broad range of tools or applications in emergency management and planning.

State funding for local public health: observations from six case studies.

PubMed

Potter, Margaret A; Fitzpatrick, Tiffany

2007-01-01

The purpose of this study is to describe state funding of local public health within the context of state public health system types. These types are based on administrative relationships, legal structures, and relative proportion of state funding in local public health budgets. We selected six states representing various types and geographic regions. A case study for each state summarized available information and was validated by state public health officials. An analysis of the case studies reveals that the variability of state public health systems--even within a given type--is matched by variability in approaches to funding local public health. Nevertheless, some meaningful associations appear. For example, higher proportions of state funding occur along with higher levels of state oversight and the existence of local service mandates in state law. These associations suggest topics for future research on public health financing in relation to local accountability, local input to state priority-setting, mandated local services, and the absence of state funds for public health services in some local jurisdictions.

Cleavage of bovine adenovirus type 3 non-structural 100K protein by protease is required for nuclear localization in infected cells but is not essential for virus replication.

PubMed

Makadiya, Nirajkumar; Gaba, Amit; Tikoo, Suresh K

2015-09-01

The L6 region of bovine adenovirus type 3 (BAdV-3) encodes a non-structural protein named 100K. Rabbit antiserum raised against BAdV-3 100K recognized a protein of 130 kDa at 12-24 h and proteins of 130, 100, 95 and 15 kDa at 36-48 h after BAdV-3 infection. The 100K species localized to the nucleus and the cytoplasm of BAdV-3-infected cells. In contrast, 100K localized predominantly to the cytoplasm of the transfected cells. However, BAdV-3 infection of cells transfected with 100K-enhanced yellow fluorescent protein-expressing plasmid detected fluorescent protein in the nucleus of the cells, suggesting that other viral proteins may be required for the nuclear localization of 100K. Interaction of BAdV-3 100K with BAdV-3 33K protein did not alter the cytoplasmic localization of 100K. However, co-expression of BAdV-3 100K and BAdV-3 protease localized 100K to the nucleolus of the transfected cells. Subsequent analysis suggested that BAdV-3 protease cleaves 100K at two identified potential protease cleavage sites (aa 740-745 and 781-786) in transfected or BAdV-3-infected cells. The cleaved C terminus (107 aa) was localized to the nucleolus of the transfected cells. Further analysis suggested that the cleaved C terminus contains a bipartite nuclear localization signal and utilizes import receptor importin-α3 of the classical importin-α/β transport pathway for nuclear transport. Successful isolation of recombinant BAdV-3 expressing mutant 100K (substitution of alanine for glycine in the potential protease cleavage site) suggested that cytoplasmic cleavage of BAdV-3 100K by adenoviral protease is not essential for virus replication.

Investigation of Local Ordering in Amorphous Materials.

NASA Astrophysics Data System (ADS)

Fan, Gary Guoyou

The intent of the research described in this dissertation, as indicated by the title, is to provide a better understanding of the structure of amorphous material. The possibility of using electron microscopy to study the amorphous structure is investigated. Chapter 1 gives a brief introduction to the understanding and modeling of the amorphous structure, electron microscopy and the image analysis in general. The difficulty of using 2-D images to infer 3-D structures information is illustrated in Chapter 2, where it is shown that some high resolution images are not qualitatively different from images of white -noises weak-phase objects or those of random atomic arrangements. The means of obtaining statistical information from these images is given in Chapters 3 and 5, where the quantitative differences between experimental images and simulated white-noise or simulated images corresponding to random arrangements are revealed. The use of image processing techniques in electron microscopy and the possible artifacts are presented in Chapter 4. The pattern recognition technique outlined in Chapter 6 demonstrates a feasible mode of scanning transition electron microscope operation. Statistical analysis can be effectively performed on a large number of nano-diffraction patterns from, for example, locally ordered samples. Some recent developments in physics as well as in electron microscopy are briefly reviewed, and their possible applications in the study of amorphous structures are discussed in Chapter 7.

Interference techniques in fluorescence microscopy

NASA Astrophysics Data System (ADS)

Dogan, Mehmet

We developed a set of interference-based optical microscopy techniques to study biological structures through nanometer-scale axial localization of fluorescent biomarkers. Spectral self-interference fluorescence microscopy (SSFM) utilizes interference of direct and reflected waves emitted from fluorescent molecules in the vicinity of planar reflectors to reveal the axial position of the molecules. A comprehensive calculation algorithm based on Green's function formalism is presented to verify the validity of approximations used in a far-field approach that describes the emission of fluorescent markers near interfaces. Using the validated model, theoretical limits of axial localization were determined with emphasis given to numerical aperture (NA) dependence of localization uncertainty. SSFM was experimentally demonstrated in conformational analysis of nucleoproteins. In particular, interaction between surface-tethered 75-mer double strand DNA and integration host factor (IHF) protein was probed on Si-SiO2 substrates by determining the axial position of fluorescent labels attached to the free ends of DNA molecules. Despite its sub-nanometer precision axial localization capability, SSFM lacks high lateral resolution due to the low-NA requirement for planar reflectors. We developed a second technique, 4Pi-SSFM, which improves the lateral resolution of a conventional SSFM system by an order of magnitude while achieving nanometer-scale axial localization precision. Using two opposing high-NA objectives, fluorescence signal is interferometrically collected and spectral interference pattern is recorded. Axial position of emitters is found from analysis of the spectra. The 4Pi-SSFM technique was experimentally demonstrated by determining the surface profiles of fabricated glass surfaces and outer membranes of Shigella, a type of Gram-negative bacteria. A further discussion is presented to localize surface O antigen, which is an important oligosaccharide structure in the virulence mechanism of the Gram-negative bacteria, including E. coli and Shigella.

Potencjał turystyczny regionu lubelskiego

NASA Astrophysics Data System (ADS)

Tucki, Andrzej

2009-01-01

The process of economic and political transformation held in the 90's contributed to the increase of significance of the local authorities (commune) in shaping of the economic processes and phenomena. The authorities of commune (administrative district, local authority) became the real owner of the area. Basing on the commune resources and the preferences of local society the authorities of commune may determine the directions of its development. The perception of the potential possibilities of the development of the tourism may have a crucial meaning for the improvement of the local society life standard, especially thanks to the economic usage of the natural resources, creation of new work places, as well as increasing the spending power of people. The merithorical range of this paper is devoted to the tourist potential, which is described as all elements of the geographical environment used directly for strict tourism reasons or organization of tourism. Taking into consideration the character of the factors of the tourism development, we can single out two major groups of the tourist potential elements: the structural and functional ones. The structural elements create the tourist values of the natural and cultural environment., the tourist land development and communications infrastructure. The external conditions of the tourism development such as political, administrative, technological, economic etc…ones can be included into the functional resources. The commune has been chosen the point of reference, as it is the base of gathering the information on socio-economic phenomena. The other point of reference is the area of regional and local activities of the local administration and authorities. The analysis of the tourist potential were conducted in 209 communes of the Lublin voivodship between 2004-2006, but the detailed analysis of the tourist potential relates only to the years:2005 and 2006.

Lateral ventricle morphology analysis via mean latitude axis.

PubMed

Paniagua, Beatriz; Lyall, Amanda; Berger, Jean-Baptiste; Vachet, Clement; Hamer, Robert M; Woolson, Sandra; Lin, Weili; Gilmore, John; Styner, Martin

2013-03-29

Statistical shape analysis has emerged as an insightful method for evaluating brain structures in neuroimaging studies, however most shape frameworks are surface based and thus directly depend on the quality of surface alignment. In contrast, medial descriptions employ thickness information as alignment-independent shape metric. We propose a joint framework that computes local medial thickness information via a mean latitude axis from the well-known spherical harmonic (SPHARM-PDM) shape framework. In this work, we applied SPHARM derived medial representations to the morphological analysis of lateral ventricles in neonates. Mild ventriculomegaly (MVM) subjects are compared to healthy controls to highlight the potential of the methodology. Lateral ventricles were obtained from MRI scans of neonates (9-144 days of age) from 30 MVM subjects as well as age- and sex-matched normal controls (60 total). SPHARM-PDM shape analysis was extended to compute a mean latitude axis directly from the spherical parameterization. Local thickness and area was straightforwardly determined. MVM and healthy controls were compared using local MANOVA and compared with the traditional SPHARM-PDM analysis. Both surface and mean latitude axis findings differentiate successfully MVM and healthy lateral ventricle morphology. Lateral ventricles in MVM neonates show enlarged shapes in tail and head. Mean latitude axis is able to find significant differences all along the lateral ventricle shape, demonstrating that local thickness analysis provides significant insight over traditional SPHARM-PDM. This study is the first to precisely quantify 3D lateral ventricle morphology in MVM neonates using shape analysis.

Big Data in Reciprocal Space: Sliding Fast Fourier Transforms for Determining Periodicity

DOE PAGES

Vasudevan, Rama K.; Belianinov, Alex; Gianfrancesco, Anthony G.; ...

2015-03-03

Significant advances in atomically resolved imaging of crystals and surfaces have occurred in the last decade allowing unprecedented insight into local crystal structures and periodicity. Yet, the analysis of the long-range periodicity from the local imaging data, critical to correlation of functional properties and chemistry to the local crystallography, remains a challenge. Here, we introduce a Sliding Fast Fourier Transform (FFT) filter to analyze atomically resolved images of in-situ grown La5/8Ca3/8MnO3 films. We demonstrate the ability of sliding FFT algorithm to differentiate two sub-lattices, resulting from a mixed-terminated surface. Principal Component Analysis (PCA) and Independent Component Analysis (ICA) of themore » Sliding FFT dataset reveal the distinct changes in crystallography, step edges and boundaries between the multiple sub-lattices. The method is universal for images with any periodicity, and is especially amenable to atomically resolved probe and electron-microscopy data for rapid identification of the sub-lattices present.« less

Big Data in Reciprocal Space: Sliding Fast Fourier Transforms for Determining Periodicity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vasudevan, Rama K.; Belianinov, Alex; Gianfrancesco, Anthony G.

Significant advances in atomically resolved imaging of crystals and surfaces have occurred in the last decade allowing unprecedented insight into local crystal structures and periodicity. Yet, the analysis of the long-range periodicity from the local imaging data, critical to correlation of functional properties and chemistry to the local crystallography, remains a challenge. Here, we introduce a Sliding Fast Fourier Transform (FFT) filter to analyze atomically resolved images of in-situ grown La5/8Ca3/8MnO3 films. We demonstrate the ability of sliding FFT algorithm to differentiate two sub-lattices, resulting from a mixed-terminated surface. Principal Component Analysis (PCA) and Independent Component Analysis (ICA) of themore » Sliding FFT dataset reveal the distinct changes in crystallography, step edges and boundaries between the multiple sub-lattices. The method is universal for images with any periodicity, and is especially amenable to atomically resolved probe and electron-microscopy data for rapid identification of the sub-lattices present.« less

Deformation behavior and mechanical analysis of vertically aligned carbon nanotube (VACNT) bundles

NASA Astrophysics Data System (ADS)

Hutchens, Shelby B.

Vertically aligned carbon nanotubes (VACNTs) serve as integral components in a variety of applications including MEMS devices, energy absorbing materials, dry adhesives, light absorbing coatings, and electron emitters, all of which require structural robustness. It is only through an understanding of VACNT's structural mechanical response and local constitutive stress-strain relationship that future advancements through rational design may take place. Even for applications in which the structural response is not central to device performance, VACNTs must be sufficiently robust and therefore knowledge of their microstructure-property relationship is essential. This thesis first describes the results of in situ uniaxial compression experiments of 50 micron diameter cylindrical bundles of these complex, hierarchical materials as they undergo unusual deformation behavior. Most notably they deform via a series of localized folding events, originating near the bundle base, which propagate laterally and collapse sequentially from bottom to top. This deformation mechanism accompanies an overall foam-like stress-strain response having elastic, plateau, and densification regimes with the addition of undulations in the stress throughout the plateau regime that correspond to the sequential folding events. Microstructural observations indicate the presence of a strength gradient, due to a gradient in both tube density and alignment along the bundle height, which is found to play a key role in both the sequential deformation process and the overall stress-strain response. Using the complicated structural response as both motivation and confirmation, a finite element model based on a viscoplastic solid is proposed. This model is characterized by a flow stress relation that contains an initial peak followed by strong softening and successive hardening. Analysis of this constitutive relation results in capture of the sequential buckling phenomenon and a strength gradient effect. This combination of experimental and modeling approaches motivates discussion of the particular microstructural mechanisms and local material behavior that govern the non-trivial energy absorption via sequential, localized buckle formation in the VACNT bundles.

Program on Earth Observation Data Management Systems (EODMS)

NASA Technical Reports Server (NTRS)

Eastwood, L. F., Jr.; Gohagan, J. K.; Hill, C. T.; Morgan, R. P.; Hays, T. R.; Ballard, R. J.; Crnkovick, G. R.; Schaeffer, M. A.

1976-01-01

An assessment was made of the needs of a group of potential users of satellite remotely sensed data (state, regional, and local agencies) involved in natural resources management in five states, and alternative data management systems to satisfy these needs are outlined. Tasks described include: (1) a comprehensive data needs analysis of state and local users; (2) the design of remote sensing-derivable information products that serve priority state and local data needs; (3) a cost and performance analysis of alternative processing centers for producing these products; (4) an assessment of the impacts of policy, regulation and government structure on implementing large-scale use of remote sensing technology in this community of users; and (5) the elaboration of alternative institutional arrangements for operational Earth Observation Data Management Systems (EODMS). It is concluded that an operational EODMS will be of most use to state, regional, and local agencies if it provides a full range of information services -- from raw data acquisition to interpretation and dissemination of final information products.

Application of LANDSAT satellite imagery for iron ore prospecting in the western desert of Egypt

NASA Technical Reports Server (NTRS)

Elshazly, E. M.; Abdel-Hady, M. A.; Elghawaby, M. A.; Khawasik, S. M. (Principal Investigator)

1977-01-01

The author has identified the following significant results. The delineation of the geological units and geological structures through image interpretation, corroborated by field observations and structural analysis, led to the discovery of new iron ore deposits. A new locality for iron ore deposition, namely Gebel Qalamun, was discovered, as well as new occurrences within the already known iron ore region of Bahariya Oasis.

Converging evidence for abnormalities of the prefrontal cortex and evaluation of midsagittal structures in pediatric PTSD: an MRI study

PubMed Central

Carrion, Victor G.; Weems, Carl F.; Watson, Christa; Eliez, Stephan; Menon, Vinod; Reiss, Allan L.

2009-01-01

Objective Volumetric imaging research has shown abnormal brain morphology in posttraumatic stress disorder (PTSD) when compared to controls. We present results on a study of brain morphology in the prefrontal cortex (PFC) and midline structures, via indices of gray matter volume and density, in pediatric PTSD. We hypothesized that both methods would demonstrate aberrant morphology in the PFC. Further, we hypothesized aberrant brainstem anatomy and reduced corpus collosum volume in children with PTSD. Methods Twenty-four children (aged 7-14) with history of interpersonal trauma and 24 age, and gender matched controls underwent structural magnetic resonance imaging. Images of the PFC and midline brain structures were first analyzed using volumetric image analysis. The PFC data were then compared with whole-brain voxel-based techniques using statistical parametric mapping (SPM). Results The PTSD group showed significant increased gray matter volume in the right and left inferior and superior quadrants of the prefrontal cortex and smaller gray matter volume in pons, and posterior vermis areas by volumetric image analysis. The voxel-byvoxel group comparisons demonstrated increased gray matter density mostly localized to ventral PFC as compared to the control group. Conclusions Abnormal frontal lobe morphology, as revealed by separate-complementary image analysis methods, and reduced pons and posterior vermis areas are associated with pediatric PTSD. Voxel-based morphometry may help to corroborate and further localize data obtained by volume of interest methods in PTSD. PMID:19349151

Introduction and application of the multiscale coefficient of variation analysis.

PubMed

Abney, Drew H; Kello, Christopher T; Balasubramaniam, Ramesh

2017-10-01

Quantifying how patterns of behavior relate across multiple levels of measurement typically requires long time series for reliable parameter estimation. We describe a novel analysis that estimates patterns of variability across multiple scales of analysis suitable for time series of short duration. The multiscale coefficient of variation (MSCV) measures the distance between local coefficient of variation estimates within particular time windows and the overall coefficient of variation across all time samples. We first describe the MSCV analysis and provide an example analytical protocol with corresponding MATLAB implementation and code. Next, we present a simulation study testing the new analysis using time series generated by ARFIMA models that span white noise, short-term and long-term correlations. The MSCV analysis was observed to be sensitive to specific parameters of ARFIMA models varying in the type of temporal structure and time series length. We then apply the MSCV analysis to short time series of speech phrases and musical themes to show commonalities in multiscale structure. The simulation and application studies provide evidence that the MSCV analysis can discriminate between time series varying in multiscale structure and length.

The organization of the cone photoreceptor mosaic measured in the living human retina

PubMed Central

Sawides, Lucie; de Castro, Alberto; Burns, Stephen A.

2016-01-01

The cone photoreceptors represent the initial fundamental sampling step in the acquisition of visual information. While recent advances in adaptive optics have provided increasingly precise estimates of the packing density and spacing of the cone photoreceptors in the living human retina, little is known about the local cone arrangement beyond a tendency towards hexagonal packing. We analyzed the cone mosaic in data from 10 normal subjects. A technique was applied to calculate the local average cone mosaic structure which allowed us to determine the hexagonality, spacing and orientation of local regions. Using cone spacing estimates, we find the expected decrease in cone density with retinal eccentricity and higher densities along the horizontal meridians as opposed to the vertical meridians. Orientation analysis reveals an asymmetry in the local cone spacing of the hexagonal packing, with cones having a larger local spacing along the horizontal direction. This horizontal/vertical asymmetry is altered at eccentricities larger than 2 degrees in the superior meridian and 2.5 degrees in the inferior meridian. Analysis of hexagon orientations in the central 1.4° of the retina show a tendency for orientation to be locally coherent, with orientation patches consisting of between 35 and 240 cones. PMID:27353225

Measuring local genetic variability in populations of codling moth (Lepidoptera: Tortricidae) across an unmanaged and commercial orchard interface.

PubMed

Fuentes-Contreras, Eduardo; Basoalto, Esteban; Franck, Pierre; Lavandero, Blas; Knight, Alan L; Ramírez, Claudio C

2014-04-01

The genetic structure of adult codling moth, Cydia pomonella (L.), populations was characterized both inside a managed apple, Malus domestica Borkdhausen, orchard and in surrounding unmanaged hosts and nonhost trees in central Chile during 2006-2007. Adult males were collected using an array of sex pheromone-baited traps. Five microsatellite genetic markers were used to study the population genetic structure across both spatial (1-100 ha) and temporal (generations within a season) gradients. Analysis of molecular variance (AMOVA) found a significant, but weak, association in both the spatial and temporal genetic structures. Discriminant analysis also found significant differentiation between the first and second generation for traps located either inside or outside the managed orchard. The Bayesian assignment test detected three genetic clusters during each of the two generations, which corresponded to different areas within the unmanaged and managed apple orchard interface. The lack of a strong spatial structure at a local scale was hypothesized to be because of active adult movement between the managed and unmanaged hosts and the asymmetry in the insecticide selection pressure inside and outside the managed habitats. These data highlight the importance of developing area-wide management programs that incorporate management tactics effective at the landscape level for successful codling moth control.

Time domain structures in a colliding magnetic flux rope experiment

NASA Astrophysics Data System (ADS)

Tang, Shawn Wenjie; Gekelman, Walter; Dehaas, Timothy; Vincena, Steve; Pribyl, Patrick

2017-10-01

Electron phase-space holes, regions of positive potential on the scale of the Debye length, have been observed in auroras as well as in laboratory experiments. These potential structures, also known as Time Domain Structures (TDS), are packets of intense electric field spikes that have significant components parallel to the local magnetic field. In an ongoing investigation at UCLA, TDS were observed on the surface of two magnetized flux ropes produced within the Large Plasma Device (LAPD). A barium oxide (BaO) cathode was used to produce an 18 m long magnetized plasma column and a lanthanum hexaboride (LaB6) source was used to create 11 m long kink unstable flux ropes. Using two probes capable of measuring the local electric and magnetic fields, correlation analysis was performed on tens of thousands of these structures and their propagation velocities, probability distribution function and spatial distribution were determined. The TDS became abundant as the flux ropes collided and appear to emanate from the reconnection region in between them. In addition, a preliminary analysis of the permutation entropy and statistical complexity of the data suggests that the TDS signals may be chaotic in nature. Work done at the Basic Plasma Science Facility (BaPSF) at UCLA which is supported by DOE and NSF.

The vibro-acoustic response and analysis of a full-scale aircraft fuselage section for interior noise reduction.

PubMed

Herdic, Peter C; Houston, Brian H; Marcus, Martin H; Williams, Earl G; Baz, Amr M

2005-06-01

The surface and interior response of a Cessna Citation fuselage section under three different forcing functions (10-1000 Hz) is evaluated through spatially dense scanning measurements. Spatial Fourier analysis reveals that a point force applied to the stiffener grid provides a rich wavenumber response over a broad frequency range. The surface motion data show global structural modes (approximately < 150 Hz), superposition of global and local intrapanel responses (approximately 150-450 Hz), and intrapanel motion alone (approximately > 450 Hz). Some evidence of Bloch wave motion is observed, revealing classical stop/pass bands associated with stiffener periodicity. The interior response (approximately < 150 Hz) is dominated by global structural modes that force the interior cavity. Local intrapanel responses (approximately > 150 Hz) of the fuselage provide a broadband volume velocity source that strongly excites a high density of interior modes. Mode coupling between the structural response and the interior modes appears to be negligible due to a lack of frequency proximity and mismatches in the spatial distribution. A high degree-of-freedom finite element model of the fuselage section was developed as a predictive tool. The calculated response is in good agreement with the experimental result, yielding a general model development methodology for accurate prediction of structures with moderate to high complexity.

Enhanced vibronic interaction caused by local lattice symmetry lowering in the (Fe, Mg)As2 ternary system

NASA Astrophysics Data System (ADS)

Pishtshev, A.; Rubin, P.

2018-04-01

By means of periodic density functional theory (DFT) electronic structure calculations, we investigate iron-site doping effects in a structural model of bulk FeAs2. Simulations performed within the projector augmented-wave method-Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) functional scheme reveal that the impacts of the two stoichiometric substitutions Fe → Mg and Fe → Ni are radically different with respect to the structural and electronic behavior of the dopants. In particular, unlike the Ni dopant, the Mg dopant incorporated in FeAs2 occupies a noncentral equilibrium position characterized by an off-center displacement from the reference higher-symmetry position. Analysis of the respective electron and vibrational factors allows us to explain this result in terms of the local pseudo Jahn-Teller effect (pJTE). On the basis of DFT calculations, we deduce which electron orbitals and lattice vibrational modes are appropriate for promoting the local instability at the origin of the pJTE. Quantitative evaluations of the pJTE parameters performed within the polyatomic formalism of an effective tight-binding model show that it is just the enhanced vibronic interaction in the Mg-[FeAs6] cluster that is responsible for the local lattice symmetry breaking.

Efficient organ localization using multi-label convolutional neural networks in thorax-abdomen CT scans

NASA Astrophysics Data System (ADS)

Efrain Humpire-Mamani, Gabriel; Arindra Adiyoso Setio, Arnaud; van Ginneken, Bram; Jacobs, Colin

2018-04-01

Automatic localization of organs and other structures in medical images is an important preprocessing step that can improve and speed up other algorithms such as organ segmentation, lesion detection, and registration. This work presents an efficient method for simultaneous localization of multiple structures in 3D thorax-abdomen CT scans. Our approach predicts the location of multiple structures using a single multi-label convolutional neural network for each orthogonal view. Each network takes extra slices around the current slice as input to provide extra context. A sigmoid layer is used to perform multi-label classification. The output of the three networks is subsequently combined to compute a 3D bounding box for each structure. We used our approach to locate 11 structures of interest. The neural network was trained and evaluated on a large set of 1884 thorax-abdomen CT scans from patients undergoing oncological workup. Reference bounding boxes were annotated by human observers. The performance of our method was evaluated by computing the wall distance to the reference bounding boxes. The bounding boxes annotated by the first human observer were used as the reference standard for the test set. Using the best configuration, we obtained an average wall distance of 3.20~+/-~7.33 mm in the test set. The second human observer achieved 1.23~+/-~3.39 mm. For all structures, the results were better than those reported in previously published studies. In conclusion, we proposed an efficient method for the accurate localization of multiple organs. Our method uses multiple slices as input to provide more context around the slice under analysis, and we have shown that this improves performance. This method can easily be adapted to handle more organs.

Radical-Driven Silicon Surface Passivation for Organic-Inorganic Hybrid Photovoltaics

NASA Astrophysics Data System (ADS)

Chandra, Nitish

The advent of metamaterials has increased the complexity of possible light-matter interactions, creating gaps in knowledge and violating various commonly used approximations and rendering some common mathematical frameworks incomplete. Our forward scattering experiments on metallic shells and cavities have created a need for a rigorous geometry-based analysis of scattering problems and more rigorous current distribution descriptions in the volume of the scattering object. In order to build an accurate understanding of these interactions, we have revisited the fundamentals of Maxwell's equations, electromagnetic potentials and boundary conditions to build a bottom-up geometry-based analysis of scattering. Individual structures or meta-atoms can be designed to localize the incident electromagnetic radiation in order to create a change in local constitutive parameters and possible nonlinear responses. Hence, in next generation engineered materials, an accurate determination of current distribution on the surface and in the structure's volume play an important role in describing and designing desired properties. Multipole expansions of the exact current distribution determined using principles of differential geometry provides an elegant way to study these local interactions of meta-atoms. The dynamics of the interactions can be studied using the behavior of the polarization and magnetization densities generated by localized current densities interacting with the electromagnetic potentials associated with the incident waves. The multipole method combined with propagation of electromagnetic potentials can be used to predict a large variety of linear and nonlinear physical phenomena. This has been demonstrated in experiments that enable the analog detection of sources placed at subwavelength separation by using time reversal of observed signals. Time reversal is accomplished by reversing the direction of the magnetic dipole in bianisotropic metasurfaces while simultaneously providing a method to reduce the losses often observed when light interacts with meta-structures.

Widespread signatures of local mRNA folding structure selection in four Dengue virus serotypes

PubMed Central

2015-01-01

Background It is known that mRNA folding can affect and regulate various gene expression steps both in living organisms and in viruses. Previous studies have recognized functional RNA structures in the genome of the Dengue virus. However, these studies usually focused either on the viral untranslated regions or on very specific and limited regions at the beginning of the coding sequences, in a limited number of strains, and without considering evolutionary selection. Results Here we performed the first large scale comprehensive genomics analysis of selection for local mRNA folding strength in the Dengue virus coding sequences, based on a total of 1,670 genomes and 4 serotypes. Our analysis identified clusters of positions along the coding regions that may undergo a conserved evolutionary selection for strong or weak local folding maintained across different viral variants. Specifically, 53-66 clusters for strong folding and 49-73 clusters for weak folding (depending on serotype) aggregated of positions with a significant conservation of folding energy signals (related to partially overlapping local genomic regions) were recognized. In addition, up to 7% of these positions were found to be conserved in more than 90% of the viral genomes. Although some of the identified positions undergo frequent synonymous / non-synonymous substitutions, the selection for folding strength therein is preserved, and thus cannot be trivially explained based on sequence conservation alone. Conclusions The fact that many of the positions with significant folding related signals are conserved among different Dengue variants suggests that a better understanding of the mRNA structures in the corresponding regions may promote the development of prospective anti- Dengue vaccination strategies. The comparative genomics approach described here can be employed in the future for detecting functional regions in other pathogens with very high mutations rates. PMID:26449467

Individual analysis of inter and intragrain defects in electrically characterized polycrystalline silicon nanowire TFTs by multicomponent dark-field imaging based on nanobeam electron diffraction two-dimensional mapping

NASA Astrophysics Data System (ADS)

Asano, Takanori; Takaishi, Riichiro; Oda, Minoru; Sakuma, Kiwamu; Saitoh, Masumi; Tanaka, Hiroki

2018-04-01

We visualize the grain structures for individual nanosized thin film transistors (TFTs), which are electrically characterized, with an improved data processing technique for the dark-field image reconstruction of nanobeam electron diffraction maps. Our individual crystal analysis gives the one-to-one correspondence of TFTs with different grain boundary structures, such as random and coherent boundaries, to the characteristic degradations of ON-current and threshold voltage. Furthermore, the local crystalline uniformity inside a single grain is detected as the difference in diffraction intensity distribution.

Data structures supporting multi-region adaptive isogeometric analysis

NASA Astrophysics Data System (ADS)

Perduta, Anna; Putanowicz, Roman

2018-01-01

Since the first paper published in 2005 Isogeometric Analysis (IGA) has gained strong interest and found applications in many engineering problems. Despite the advancement of the method, there are still far fewer software implementations comparing to Finite Element Method. The paper presents an approach to the development of data structures that can support multi-region IGA with local mesh refinement (patch-based) and possible application in IGA-FEM models. The purpose of this paper is to share original design concepts, that authors have created while developing an IGA package, which other researchers may find beneficial for their own simulation codes.

Distinct Correlation Structure Supporting a Rate-Code for Sound Localization in the Owl’s Auditory Forebrain

PubMed Central

2017-01-01

Abstract While a topographic map of auditory space exists in the vertebrate midbrain, it is absent in the forebrain. Yet, both brain regions are implicated in sound localization. The heterogeneous spatial tuning of adjacent sites in the forebrain compared to the midbrain reflects different underlying circuitries, which is expected to affect the correlation structure, i.e., signal (similarity of tuning) and noise (trial-by-trial variability) correlations. Recent studies have drawn attention to the impact of response correlations on the information readout from a neural population. We thus analyzed the correlation structure in midbrain and forebrain regions of the barn owl’s auditory system. Tetrodes were used to record in the midbrain and two forebrain regions, Field L and the downstream auditory arcopallium (AAr), in anesthetized owls. Nearby neurons in the midbrain showed high signal and noise correlations (RNCs), consistent with shared inputs. As previously reported, Field L was arranged in random clusters of similarly tuned neurons. Interestingly, AAr neurons displayed homogeneous monotonic azimuth tuning, while response variability of nearby neurons was significantly less correlated than the midbrain. Using a decoding approach, we demonstrate that low RNC in AAr restricts the potentially detrimental effect it can have on information, assuming a rate code proposed for mammalian sound localization. This study harnesses the power of correlation structure analysis to investigate the coding of auditory space. Our findings demonstrate distinct correlation structures in the auditory midbrain and forebrain, which would be beneficial for a rate-code framework for sound localization in the nontopographic forebrain representation of auditory space. PMID:28674698

The STAGS computer code

NASA Technical Reports Server (NTRS)

Almroth, B. O.; Brogan, F. A.

1978-01-01

Basic information about the computer code STAGS (Structural Analysis of General Shells) is presented to describe to potential users the scope of the code and the solution procedures that are incorporated. Primarily, STAGS is intended for analysis of shell structures, although it has been extended to more complex shell configurations through the inclusion of springs and beam elements. The formulation is based on a variational approach in combination with local two dimensional power series representations of the displacement components. The computer code includes options for analysis of linear or nonlinear static stress, stability, vibrations, and transient response. Material as well as geometric nonlinearities are included. A few examples of applications of the code are presented for further illustration of its scope.

Quantum phase transitions and local magnetism in Mott insulators: A local probe investigation using muons, neutrons, and photons

NASA Astrophysics Data System (ADS)

Frandsen, Benjamin A.

Mott insulators are materials in which strong correlations among the electrons induce an unconventional insulating state. Rich interplay between the structural, magnetic, and electronic degrees of freedom resulting from the electron correlation can lead to unusual complexity of Mott materials on the atomic scale, such as microscopically heterogeneous phases or local structural correlations that deviate significantly from the average structure. Such behavior must be studied by suitable experimental techniques, i.e. "local probes", that are sensitive to this local behavior rather than just the bulk, average properties. In this thesis, I will present results from our studies of multiple families of Mott insulators using two such local probes: muon spin relaxation (muSR), a probe of local magnetism; and pair distribution function (PDF) analysis of x-ray and neutron total scattering, a probe of local atomic structure. In addition, I will present the development of magnetic pair distribution function analysis, a novel method for studying local magnetic correlations that is highly complementary to the muSR and atomic PDF techniques. We used muSR to study the phase transition from Mott insulator to metal in two archetypal Mott insulating systems: RENiO3 (RE = rare earth element) and V2O3. In both of these systems, the Mott insulating state can be suppressed by tuning a nonthermal parameter, resulting in a "quantum" phase transition at zero temperature from the Mott insulating state to a metallic state. In RENiO3, this occurs through variation of the rare-earth element in the chemical composition; in V 2O3, through the application of hydrostatic pressure. Our results show that the metallic and Mott insulating states unexpectedly coexist in phase-separated regions across a large portion of parameter space near the Mott quantum phase transition and that the magnitude of the ordered antiferromagnetic moment remains constant across the phase diagram until it is abruptly destroyed at the quantum phase transition. Taken together, these findings point unambiguously to a first-order quantum phase transition in these systems. We also conducted x-ray and neutron PDF experiments, which suggest that the distinct atomic structures associated with the insulating and metallic phases similarly coexist near the quantum phase transition. These results have significant implications for our understanding of the Mott metal-insulator quantum phase transition in real materials. The second part of this thesis centers on the derivation and development of the magnetic pair distribution function (mPDF) technique and its application to the antiferromagnetic Mott insulator MnO. The atomic PDF method involves Fourier transforming the x-ray or neutron total scattering intensity from reciprocal space into real space to directly reveal the local atomic correlations in a material, which may deviate significantly from the average crystallographic structure of that material. Likewise, the mPDF method involves Fourier transforming the magnetic neutron total scattering intensity to probe the local correlations of magnetic moments in the material, which may exist on short length scales even when the material has no long-range magnetic order. After deriving the fundamental mPDF equations and providing a proof-of-principle by recovering the known magnetic structure of antiferromagnetic MnO, we used this technique to investigate the short-range magnetic correlations that persist well into the paramagnetic phase of MnO. By combining the mPDF measurements with ab initio calculations of the spin-spin correlation function in paramagnetic MnO, we were able to quantitatively account for the observed mPDF. We also used the mPDF data to evaluate competing ab initio theories, thereby resolving some longstanding questions about the magnetic exchange interactions in MnO.

Structural analysis of a ship on global aspect using ANSYS

NASA Astrophysics Data System (ADS)

Rahman, M. Muzibur; Kamol, Rajia Sultana; Islam, Reyana

2017-12-01

Ship is a complex geometry which undergoes a combination of loadings such as hydrostatic, hydrodynamic, wind, wave etc. at sea and thus adequate strength in a ship has always been one of the most challenging tasks for the ship designers. International Maritime Organization (IMO) and classification societies are providing the standards to ensure the adequacy of strength for the ship against all demands throughout its service life. Thus, structural analysis is needed to assess the overall strength of hull, and the means in this regard are based on finite element method which may be applied either local or global aspect of the ship. This paper is an attempt to carry out the structural analysis of a ship in global aspect using ANSYS software to locate the most stress concentration and deformed area, which will have ultimate effect on fatigue fracture.

Satellite-based prediction of rainfall interception by tropical forest stands of a human-dominated landscape in Central Sulawesi, Indonesia

NASA Astrophysics Data System (ADS)

Nieschulze, Jens; Erasmi, Stefan; Dietz, Johannes; Hölscher, Dirk

2009-01-01

SummaryRainforest conversion to other land use types drastically alters the hydrological cycle in which changes in rainfall interception contribute significantly to the observed differences. However, little is known about the effects of more gradual changes in forest structure and at regional scales. We studied land use types ranging from natural forest over selectively-logged forest to cacao agroforest in a lower montane region in Central Sulawesi, Indonesia, and tested the suitability of high-resolution optical satellite imagery for modeling observed interception patterns. Investigated characteristics indicating canopy structure were mean and standard deviation of reflectance values, local maxima, and self-similarity measures based on the grey level co-occurrence matrix and geostatistical variogram analysis. Previously studied and published rainfall interception data comprised twelve plots and median values per land use type ranged from 30% in natural forest to 18% in cacao agroforests. A linear regression model with local maxima, mean contrast and normalized digital vegetation index (NDVI) as regressors was able to explain more than 84% ( Radj2) of the variation encountered in the data. Other investigated characteristics did not prove significant in the regression analysis. The model yielded stable results with respect to cross-validation and also produced realistic values and spatial patterns when applied at the landscape level (783.6 ha). High values of interception were rare and localized in natural forest stands distant to villages, whereas low interception characterized the intensively used sites close to settlements. We conclude that forest use intensity significantly reduced rainfall interception and satellite image analysis can successfully be applied for its regional prediction, and most forest in the study region has already been subject to human-induced structural changes.