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Sample records for aligned graphic structure

  1. Graphics processing unit-based alignment of protein interaction networks.

    PubMed

    Xie, Jiang; Zhou, Zhonghua; Ma, Jin; Xiang, Chaojuan; Nie, Qing; Zhang, Wu

    2015-08-01

    Network alignment is an important bridge to understanding human protein-protein interactions (PPIs) and functions through model organisms. However, the underlying subgraph isomorphism problem complicates and increases the time required to align protein interaction networks (PINs). Parallel computing technology is an effective solution to the challenge of aligning large-scale networks via sequential computing. In this study, the typical Hungarian-Greedy Algorithm (HGA) is used as an example for PIN alignment. The authors propose a HGA with 2-nearest neighbours (HGA-2N) and implement its graphics processing unit (GPU) acceleration. Numerical experiments demonstrate that HGA-2N can find alignments that are close to those found by HGA while dramatically reducing computing time. The GPU implementation of HGA-2N optimises the parallel pattern, computing mode and storage mode and it improves the computing time ratio between the CPU and GPU compared with HGA when large-scale networks are considered. By using HGA-2N in GPUs, conserved PPIs can be observed, and potential PPIs can be predicted. Among the predictions based on 25 common Gene Ontology terms, 42.8% can be found in the Human Protein Reference Database. Furthermore, a new method of reconstructing phylogenetic trees is introduced, which shows the same relationships among five herpes viruses that are obtained using other methods. PMID:26243827

  2. Alignments of RNA structures.

    PubMed

    Blin, Guillaume; Denise, Alain; Dulucq, Serge; Herrbach, Claire; Touzet, Hélène

    2010-01-01

    We describe a theoretical unifying framework to express the comparison of RNA structures, which we call alignment hierarchy. This framework relies on the definition of common supersequences for arc-annotated sequences and encompasses the main existing models for RNA structure comparison based on trees and arc-annotated sequences with a variety of edit operations. It also gives rise to edit models that have not been studied yet. We provide a thorough analysis of the alignment hierarchy, including a new polynomial-time algorithm and an NP-completeness proof. The polynomial-time algorithm involves biologically relevant edit operations such as pairing or unpairing nucleotides. It has been implemented in a software, called gardenia, which is available at the Web server http://bioinfo.lifl.fr/RNA/gardenia. PMID:20431150

  3. Learning the Structure of Mixed Graphical Models

    PubMed Central

    Lee, Jason D.; Hastie, Trevor J.

    2014-01-01

    We consider the problem of learning the structure of a pairwise graphical model over continuous and discrete variables. We present a new pairwise model for graphical models with both continuous and discrete variables that is amenable to structure learning. In previous work, authors have considered structure learning of Gaussian graphical models and structure learning of discrete models. Our approach is a natural generalization of these two lines of work to the mixed case. The penalization scheme involves a novel symmetric use of the group-lasso norm and follows naturally from a particular parametrization of the model. Supplementary materials for this paper are available online. PMID:26085782

  4. GATA: A graphic alignment tool for comparative sequenceanalysis

    SciTech Connect

    Nix, David A.; Eisen, Michael B.

    2005-01-01

    Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dotplot analysis is often used to estimate non-coding sequence relatedness. Yet dot plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments.

  5. Protein structure alignment beyond spatial proximity

    PubMed Central

    Wang, Sheng; Ma, Jianzhu; Peng, Jian; Xu, Jinbo

    2013-01-01

    Protein structure alignment is a fundamental problem in computational structure biology. Many programs have been developed for automatic protein structure alignment, but most of them align two protein structures purely based upon geometric similarity without considering evolutionary and functional relationship. As such, these programs may generate structure alignments which are not very biologically meaningful from the evolutionary perspective. This paper presents a novel method DeepAlign for automatic pairwise protein structure alignment. DeepAlign aligns two protein structures using not only spatial proximity of equivalent residues (after rigid-body superposition), but also evolutionary relationship and hydrogen-bonding similarity. Experimental results show that DeepAlign can generate structure alignments much more consistent with manually-curated alignments than other automatic tools especially when proteins under consideration are remote homologs. These results imply that in addition to geometric similarity, evolutionary information and hydrogen-bonding similarity are essential to aligning two protein structures. PMID:23486213

  6. Combining Multiple Pairwise Structure-based Alignments

    SciTech Connect

    2014-11-12

    CombAlign is a new Python code that generates a gapped, one-to-many, multiple structure-based sequence alignment(MSSA) given a set of pairwise structure-based alignments. In order to better define regions of similarity among related protein structures, it is useful to detect the residue-residue correspondences among a set of pairwise structure alignments. Few codes exist for constructing a one-to-many, multiple sequence alignment derived from a set of structure alignments, and we perceived a need for creating a new tool for combing pairwise structure alignments that would allow for insertion of gaps in the reference structure.

  7. BarraCUDA - a fast short read sequence aligner using graphics processing units

    PubMed Central

    2012-01-01

    Background With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. Findings Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. Conclusions BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available from http://seqbarracuda.sf.net PMID:22244497

  8. Structural analysis of aligned RNAs.

    PubMed

    Voss, Björn

    2006-01-01

    The knowledge about classes of non-coding RNAs (ncRNAs) is growing very fast and it is mainly the structure which is the common characteristic property shared by members of the same class. For correct characterization of such classes it is therefore of great importance to analyse the structural features in great detail. In this manuscript I present RNAlishapes which combines various secondary structure analysis methods, such as suboptimal folding and shape abstraction, with a comparative approach known as RNA alignment folding. RNAlishapes makes use of an extended thermodynamic model and covariance scoring, which allows to reward covariation of paired bases. Applying the algorithm to a set of bacterial trp-operon leaders using shape abstraction it was able to identify the two alternating conformations of this attenuator. Besides providing in-depth analysis methods for aligned RNAs, the tool also shows a fairly well prediction accuracy. Therefore, RNAlishapes provides the community with a powerful tool for structural analysis of classes of RNAs and is also a reasonable method for consensus structure prediction based on sequence alignments. RNAlishapes is available for online use and download at http://rna.cyanolab.de. PMID:17020924

  9. Method for protein structure alignment

    DOEpatents

    Blankenbecler, Richard; Ohlsson, Mattias; Peterson, Carsten; Ringner, Markus

    2005-02-22

    This invention provides a method for protein structure alignment. More particularly, the present invention provides a method for identification, classification and prediction of protein structures. The present invention involves two key ingredients. First, an energy or cost function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. Second, a minimization of the energy or cost function by an iterative method, where in each iteration (1) a mean field method is employed for the assignment variables and (2) exact rotation and/or translation of atomic coordinates is performed, weighted with the corresponding assignment variables.

  10. Combining Multiple Pairwise Structure-based Alignments

    2014-11-12

    CombAlign is a new Python code that generates a gapped, one-to-many, multiple structure-based sequence alignment(MSSA) given a set of pairwise structure-based alignments. In order to better define regions of similarity among related protein structures, it is useful to detect the residue-residue correspondences among a set of pairwise structure alignments. Few codes exist for constructing a one-to-many, multiple sequence alignment derived from a set of structure alignments, and we perceived a need for creating a newmore » tool for combing pairwise structure alignments that would allow for insertion of gaps in the reference structure.« less

  11. Modelling structured data with Probabilistic Graphical Models

    NASA Astrophysics Data System (ADS)

    Forbes, F.

    2016-05-01

    Most clustering and classification methods are based on the assumption that the objects to be clustered are independent. However, in more and more modern applications, data are structured in a way that makes this assumption not realistic and potentially misleading. A typical example that can be viewed as a clustering task is image segmentation where the objects are the pixels on a regular grid and depend on neighbouring pixels on this grid. Also, when data are geographically located, it is of interest to cluster data with an underlying dependence structure accounting for some spatial localisation. These spatial interactions can be naturally encoded via a graph not necessarily regular as a grid. Data sets can then be modelled via Markov random fields and mixture models (e.g. the so-called MRF and Hidden MRF). More generally, probabilistic graphical models are tools that can be used to represent and manipulate data in a structured way while modeling uncertainty. This chapter introduces the basic concepts. The two main classes of probabilistic graphical models are considered: Bayesian networks and Markov networks. The key concept of conditional independence and its link to Markov properties is presented. The main problems that can be solved with such tools are described. Some illustrations are given associated with some practical work.

  12. The Alignment of Galaxy Structures

    NASA Astrophysics Data System (ADS)

    Biernacka, M.; Panko, E.; Bajan, K.; Godłowski, W.; Flin, P.

    2015-11-01

    We analyzed the orientation of the sample of ACO galaxy clusters. We examined the alignment in a subsample of 1056 galaxy structures taken from the Panko-Flin (2006) Catalog with known BM morphological types. We were looking for a correlation between the orientation of the cluster and the positions of neighboring clusters. The Binggeli effect (the excess of small values of the Δθ angles between the direction toward neighboring clusters and the cluster position angle) is observed, having a range up to about 45 h-1 Mpc. The strongest effect was found for elongated BM type I clusters. This is probably connected with the origins of the supergiant galaxy and with cluster formation along a long filament or plane in a supercluster.

  13. Structural Alignment Sensor Feasibility Demonstration

    NASA Technical Reports Server (NTRS)

    Anderson, R. H.; Huang, C. C.; Hodor, J. R.

    1978-01-01

    A structural alignment sensor (SAS) was developed for use with large deployable antenna systems for contour measurement and/or active control. The SAS is a laser ranging system using frequency modulation and accurate phase measurement to determine distance. Work was done with a CO2 and HeNe laser. The capability of the SAS to measure antenna rib contours was studied over ranges of 50 meters to a resolution of 100 microns. Initial resolution data was taken with the CO2 system. This data shows that it will indeed meet the SAS requirements. The development of the HeNe system was initiated because it offers substantial improvement in size, weight, and power over the CO2 system. The final demonstration was made with the HeNe system and it too showed that the SAS requirements could be met with this alternate approach. The projection of these results to a conceptual design for a flight system and its application are described.

  14. CARNA--alignment of RNA structure ensembles.

    PubMed

    Sorescu, Dragos Alexandru; Möhl, Mathias; Mann, Martin; Backofen, Rolf; Will, Sebastian

    2012-07-01

    Due to recent algorithmic progress, tools for the gold standard of comparative RNA analysis, namely Sankoff-style simultaneous alignment and folding, are now readily applicable. Such approaches, however, compare RNAs with respect to a simultaneously predicted, single, nested consensus structure. To make multiple alignment of RNAs available in cases, where this limitation of the standard approach is critical, we introduce a web server that provides a complete and convenient interface to the RNA structure alignment tool 'CARNA'. This tool uniquely supports RNAs with multiple conserved structures per RNA and aligns pseudoknots intrinsically; these features are highly desirable for aligning riboswitches, RNAs with conserved folding pathways, or pseudoknots. We represent structural input and output information as base pair probability dot plots; this provides large flexibility in the input, ranging from fixed structures to structure ensembles, and enables immediate visual analysis of the results. In contrast to conventional Sankoff-style approaches, 'CARNA' optimizes all structural similarities in the input simultaneously, for example across an entire RNA structure ensemble. Even compared with already costly Sankoff-style alignment, 'CARNA' solves an intrinsically much harder problem by applying advanced, constraint-based, algorithmic techniques. Although 'CARNA' is specialized to the alignment of RNAs with several conserved structures, its performance on RNAs in general is on par with state-of-the-art general-purpose RNA alignment tools, as we show in a Bralibase 2.1 benchmark. The web server is freely available at http://rna.informatik.uni-freiburg.de/CARNA. PMID:22689637

  15. DUC-Curve, a highly compact 2D graphical representation of DNA sequences and its application in sequence alignment

    NASA Astrophysics Data System (ADS)

    Li, Yushuang; Liu, Qian; Zheng, Xiaoqi

    2016-08-01

    A highly compact and simple 2D graphical representation of DNA sequences, named DUC-Curve, is constructed through mapping four nucleotides to a unit circle with a cyclic order. DUC-Curve could directly detect nucleotide, di-nucleotide compositions and microsatellite structure from DNA sequences. Moreover, it also could be used for DNA sequence alignment. Taking geometric center vectors of DUC-Curves as sequence descriptor, we perform similarity analysis on the first exons of β-globin genes of 11 species, oncogene TP53 of 27 species and twenty-four Influenza A viruses, respectively. The obtained reasonable results illustrate that the proposed method is very effective in sequence comparison problems, and will at least play a complementary role in classification and clustering problems.

  16. On comparing two structured RNA multiple alignments.

    PubMed

    Patel, Vandanaben; Wang, Jason T L; Setia, Shefali; Verma, Anurag; Warden, Charles D; Zhang, Kaizhong

    2010-12-01

    We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple alignments in the blocks. Unlike many other tools that can perform pairwise alignment of either single sequences or structures only, BlockMatch takes into account the characteristics of all the sequences in the blocks along with their consensus structures during the alignment process, thus being able to achieve a high-quality alignment result. We apply BlockMatch to phylogeny reconstruction on a set of 5S rRNA sequences taken from fifteen bacteria species. Experimental results showed that the phylogenetic tree generated by our method is more accurate than the tree constructed based on the widely used ClustalW tool. The BlockMatch algorithm is implemented into a web server, accessible at http://bioinformatics.njit.edu/blockmatch. A jar file of the program is also available for download from the web server. PMID:21121021

  17. DoSA: Database of Structural Alignments.

    PubMed

    Mahajan, Swapnil; Agarwal, Garima; Iftekhar, Mohammed; Offmann, Bernard; de Brevern, Alexandre G; Srinivasan, Narayanaswamy

    2013-01-01

    Protein structure alignment is a crucial step in protein structure-function analysis. Despite the advances in protein structure alignment algorithms, some of the local conformationally similar regions are mislabeled as structurally variable regions (SVRs). These regions are not well superimposed because of differences in their spatial orientations. The Database of Structural Alignments (DoSA) addresses this gap in identification of local structural similarities obscured in global protein structural alignments by realigning SVRs using an algorithm based on protein blocks. A set of protein blocks is a structural alphabet that abstracts protein structures into 16 unique local structural motifs. DoSA provides unique information about 159,780 conformationally similar and 56,140 conformationally dissimilar SVRs in 74 705 pairwise structural alignments of homologous proteins. The information provided on conformationally similar and dissimilar SVRs can be helpful to model loop regions. It is also conceivable that conformationally similar SVRs with conserved residues could potentially contribute toward functional integrity of homologues, and hence identifying such SVRs could be helpful in understanding the structural basis of protein function. Database URL: http://bo-protscience.fr/dosa/ PMID:23846594

  18. Graphics

    ERIC Educational Resources Information Center

    Post, Susan

    1975-01-01

    An art teacher described an elective course in graphics which was designed to enlarge a student's knowledge of value, color, shape within a shape, transparency, line and texture. This course utilized the technique of working a multi-colored print from a single block that was first introduced by Picasso. (Author/RK)

  19. CARNA—alignment of RNA structure ensembles

    PubMed Central

    Sorescu, Dragoş Alexandru; Möhl, Mathias; Mann, Martin; Backofen, Rolf; Will, Sebastian

    2012-01-01

    Due to recent algorithmic progress, tools for the gold standard of comparative RNA analysis, namely Sankoff-style simultaneous alignment and folding, are now readily applicable. Such approaches, however, compare RNAs with respect to a simultaneously predicted, single, nested consensus structure. To make multiple alignment of RNAs available in cases, where this limitation of the standard approach is critical, we introduce a web server that provides a complete and convenient interface to the RNA structure alignment tool ‘CARNA’. This tool uniquely supports RNAs with multiple conserved structures per RNA and aligns pseudoknots intrinsically; these features are highly desirable for aligning riboswitches, RNAs with conserved folding pathways, or pseudoknots. We represent structural input and output information as base pair probability dot plots; this provides large flexibility in the input, ranging from fixed structures to structure ensembles, and enables immediate visual analysis of the results. In contrast to conventional Sankoff-style approaches, ‘CARNA’ optimizes all structural similarities in the input simultaneously, for example across an entire RNA structure ensemble. Even compared with already costly Sankoff-style alignment, ‘CARNA’ solves an intrinsically much harder problem by applying advanced, constraint-based, algorithmic techniques. Although ‘CARNA’ is specialized to the alignment of RNAs with several conserved structures, its performance on RNAs in general is on par with state-of-the-art general-purpose RNA alignment tools, as we show in a Bralibase 2.1 benchmark. The web server is freely available at http://rna.informatik.uni-freiburg.de/CARNA. PMID:22689637

  20. DoSA: Database of Structural Alignments

    PubMed Central

    Mahajan, Swapnil; Agarwal, Garima; Iftekhar, Mohammed; Offmann, Bernard; de Brevern, Alexandre G.; Srinivasan, Narayanaswamy

    2013-01-01

    Protein structure alignment is a crucial step in protein structure–function analysis. Despite the advances in protein structure alignment algorithms, some of the local conformationally similar regions are mislabeled as structurally variable regions (SVRs). These regions are not well superimposed because of differences in their spatial orientations. The Database of Structural Alignments (DoSA) addresses this gap in identification of local structural similarities obscured in global protein structural alignments by realigning SVRs using an algorithm based on protein blocks. A set of protein blocks is a structural alphabet that abstracts protein structures into 16 unique local structural motifs. DoSA provides unique information about 159 780 conformationally similar and 56 140 conformationally dissimilar SVRs in 74 705 pairwise structural alignments of homologous proteins. The information provided on conformationally similar and dissimilar SVRs can be helpful to model loop regions. It is also conceivable that conformationally similar SVRs with conserved residues could potentially contribute toward functional integrity of homologues, and hence identifying such SVRs could be helpful in understanding the structural basis of protein function. Database URL: http://bo-protscience.fr/dosa/ PMID:23846594

  1. Multiple structure alignment with msTALI

    PubMed Central

    2012-01-01

    Background Multiple structure alignments have received increasing attention in recent years as an alternative to multiple sequence alignments. Although multiple structure alignment algorithms can potentially be applied to a number of problems, they have primarily been used for protein core identification. A method that is capable of solving a variety of problems using structure comparison is still absent. Here we introduce a program msTALI for aligning multiple protein structures. Our algorithm uses several informative features to guide its alignments: torsion angles, backbone Cα atom positions, secondary structure, residue type, surface accessibility, and properties of nearby atoms. The algorithm allows the user to weight the types of information used to generate the alignment, which expands its utility to a wide variety of problems. Results msTALI exhibits competitive results on 824 families from the Homstrad and SABmark databases when compared to Matt and Mustang. We also demonstrate success at building a database of protein cores using 341 randomly selected CATH domains and highlight the contribution of msTALI compared to the CATH classifications. Finally, we present an example applying msTALI to the problem of detecting hinges in a protein undergoing rigid-body motion. Conclusions msTALI is an effective algorithm for multiple structure alignment. In addition to its performance on standard comparison databases, it utilizes clear, informative features, allowing further customization for domain-specific applications. The C++ source code for msTALI is available for Linux on the web at http://ifestos.cse.sc.edu/mstali. PMID:22607234

  2. Alignment Pins for Assembling and Disassembling Structures

    NASA Technical Reports Server (NTRS)

    Campbell, Oliver C.

    2008-01-01

    Simple, easy-to-use, highly effective tooling has been devised for maintaining alignment of bolt holes in mating structures during assembly and disassembly of the structures. The tooling was originally used during removal of a body flap from the space shuttle Atlantis, in which misalignments during removal of the last few bolts could cause the bolts to bind in their holes. By suitably modifying the dimensions of the tooling components, the basic design of the tooling can readily be adapted to other structures that must be maintained in alignment. The tooling includes tapered, internally threaded alignment pins designed to fit in the bolt holes in one of the mating structures, plus a draw bolt and a cup that are used to install or remove each alignment pin. In preparation for disassembly of two mating structures, external supports are provided to prevent unintended movement of the structures. During disassembly of the structures, as each bolt that joins the structures is removed, an alignment pin is installed in its place. Once all the bolts have been removed and replaced with pins, the pins maintain alignment as the structures are gently pushed or pulled apart on the supports. In assembling the two structures, one reverses the procedure described above: pins are installed in the bolt holes, the structures are pulled or pushed together on the supports, then the pins are removed and replaced with bolts. The figure depicts the tooling and its use. To install an alignment pin in a bolt hole in a structural panel, the tapered end of the pin is inserted from one side of the panel, the cup is placed over the pin on the opposite side of the panel, the draw bolt is inserted through the cup and threaded into the pin, the draw bolt is tightened to pull the pin until the pin is seated firmly in the hole, then the draw bolt and cup are removed, leaving the pin in place. To remove an alignment pin, the cup is placed over the pin on the first-mentioned side of the panel, the draw

  3. Algorithms for Graphic Display of Sentence Dependency Structures.

    ERIC Educational Resources Information Center

    Craven, Timothy C.

    1991-01-01

    Discussion of graph-drawing algorithms compares and evaluates five algorithms for generated automatic graphic display of sentence dependency structures that have been implemented in the TEXTNET text structure management system. Evaluation criteria are discussed, and a test of the algorithms with a database of newspaper articles is described. (16…

  4. Algorithms, applications, and challenges of protein structure alignment.

    PubMed

    Ma, Jianzhu; Wang, Sheng

    2014-01-01

    As a fundamental problem in computational structure biology, protein structure alignment has attracted the focus of the community for more than 20 years. While the pairwise structure alignment could be applied to measure the similarity between two proteins, which is a first step for homology search and fold space construction, the multiple structure alignment could be used to understand evolutionary conservation and divergence from a family of protein structures. Structure alignment is an NP-hard problem, which is only computationally tractable by using heuristics. Three levels of heuristics for pairwise structure alignment have been proposed, from the representations of protein structure, the perspectives of viewing protein as a rigid-body or flexible, to the scoring functions as well as the search algorithms for the alignment. For multiple structure alignment, the fourth level of heuristics is applied on how to merge all input structures to a multiple structure alignment. In this review, we first present a small survey of current methods for protein pairwise and multiple alignment, focusing on those that are publicly available as web servers. In more detail, we also discuss the advancements on the development of the new approaches to increase the pairwise alignment accuracy, to efficiently and reliably merge input structures to the multiple structure alignment. Finally, besides broadening the spectrum of the applications of structure alignment for protein template-based prediction, we also list several open problems that need to be solved in the future, such as the large complex alignment and the fast database search. PMID:24629187

  5. GraSPI (Graphical Structured Packing Interface)

    2004-06-10

    GraSPI is a collection of macros (computer programs) written to work in concert with Fluent Inc. software GAMBIT and FLUENT for modeling and design of structured packing columns used in the chemical industry (the application focus is in distillation but other applications such as gas absorbers, and other chemical contactors can also be analyzed). GraSPI is an accessory to GAMBIT and FLUENT that drives the process of complex geometry creation, domain setup, and mesh generation.more » In addition, GraSPI manages automatic flow analysis in the aforementioned domain via either serial or parallel computing using FLUENT. A library of typical commercial structured packing elements is included in GraSPI, so is the capability for user-defined creation of new packings.« less

  6. LABVIEW graphical user interface for precision multichannel alignment of Raman lidar at Jet Propulsion Laboratory, Table Mountain Facility.

    PubMed

    Aspey, R A; McDermid, I S; Leblanc, T; Howe, J W; Walsh, T D

    2008-09-01

    The Jet Propulsion Laboratory operates lidar systems at Table Mountain Facility (TMF), California (34.4 degrees N, 117.7 degrees W) and Mauna Loa Observatory, Hawaii (19.5 degrees N, 155.6 degrees W) under the framework of the Network for the Detection of Atmospheric Composition Change. To complement these systems a new Raman lidar has been developed at TMF with particular attention given to optimizing water vapor profile measurements up to the tropopause and lower stratosphere. The lidar has been designed for accuracies of 5% up to 12 km in the free troposphere and a detection capability of <5 ppmv. One important feature of the lidar is a precision alignment system using range resolved data from eight Licel transient recorders, allowing fully configurable alignment via a LABVIEW/C++ graphical user interface (GUI). This allows the lidar to be aligned on any channel while simultaneously displaying signals from other channels at configurable altitude/bin combinations. The general lidar instrumental setup and the details of the alignment control system, data acquisition, and GUI alignment software are described. Preliminary validation results using radiosonde and lidar intercomparisons are briefly presented. PMID:19044439

  7. DAPS: Database of Aligned Protein Structures

    DOE Data Explorer

    Mallick, Parag; Rice, Danny; Eisenberg, David

    DAPS is based on the FSSP, DSSP, PDB and CATH databases. There also exists a subset of DAPS known as DDAPS (also pronounced DAPS) - Database of Distant Aligned Protein Structures. It is a database of structures that have low sequence similarity but share a similar fold. There are a number of filters used to make the DDAPS list more useful. The algorithm requires that an FSSP file exists for one of the members of a pair and that the other member is listed in that FSSP file. It requires that each member of the pair be within the CATH database and share a common CAT classification. It also requires that the secondary structure can be determined by DSSP. How is DAPS constructed? We begin with the set of all chains from the current release of the PDB. An all on all search is done on the list to find pairs that have the same fold acoording to both the FSSP and CATH databases and clustered into groups by a representative structure (representative structures have less than 25% sequence identity to each other). For each protein pair, regions aligned by the DALI program are extracted from the corresponding FSSP file, or recomputed using DALI-lite. In domain DAPS, only regions that are called "domains" by CATH are included in the alignment. The amino acid type, secondary structure type, and solvent accessibility are extracted from the DSSP file and written pairwise into the database. DAPS is updated with updates of CATH.[Taken from http://nihserver.mbi.ucla.edu/DAPS/daps_help.html

  8. Alignment issues of the SLC linac accelerating structure

    SciTech Connect

    Seeman, J.T.; Adolphsen, C.; Decker, F.J.; Fischer, G.; Hodgson, J.; Pennacchi, R.; Perkins, C.; Pietryka, M.

    1991-05-01

    The accelerating structure of the Stanford Linear Collider (SLC) is required to be aligned to 100--200 {mu}m rms. Alignment at such a level will reduce transverse wakefield effects sufficiently so that only a small emittance enlargement of the beam is expected during acceleration to 50 GeV with up to 7 {times} 10{sup 10} particles per bunch. This report describes many aspects of the alignment including global alignment, local alignment, construction of the accelerating cavities, active controls of the structure alignment, external constraints, temperature and airflow effects, and alignment stability. 9 refs., 8 figs.

  9. Effects of Discourse Structure Graphic Organizers on EFL Reading Comprehension

    ERIC Educational Resources Information Center

    Jiang, Xiangying

    2012-01-01

    This study investigated the effects of a 16-week reading instruction program with discourse structure graphic organizers (DSGOs) on the development of English reading comprehension among college-level English as a Foreign Language (EFL) students. A total of 340 first and third semester students of non-English majors at a Chinese university…

  10. R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

    PubMed Central

    Rahrig, Ryan R.; Leontis, Neocles B.; Zirbel, Craig L.

    2010-01-01

    Motivation: Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the ‘local alignment’ graph. Results: The algorithm is implemented in a program suite and web server called ‘R3D Align’. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments. Availability: R3D Align is freely available through a web server http://rna.bgsu.edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: r-rahrig@onu.edu PMID:20929913

  11. Implementation of a parallel protein structure alignment service on cloud.

    PubMed

    Hung, Che-Lun; Lin, Yaw-Ling

    2013-01-01

    Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. PMID:23671842

  12. Implementation of a Parallel Protein Structure Alignment Service on Cloud

    PubMed Central

    Hung, Che-Lun; Lin, Yaw-Ling

    2013-01-01

    Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. PMID:23671842

  13. Anisotropic fiber alignment in composite structures

    DOEpatents

    Graham, A.L.; Mondy, L.A.; Guell, D.C.

    1993-11-16

    High strength material composite structures are formed with oriented fibers to provide controlled anisotropic fibers. Fibers suspended in non-dilute concentrations (e.g., up to 20 volume percent for fibers having an aspect ratio of 20) in a selected medium are oriented by moving an axially spaced array of elements in the direction of desired fiber alignment. The array elements are generally perpendicular to the desired orientation. The suspension medium may also include sphere-like particles where the resulting material is a ceramic. 5 figures.

  14. Anisotropic fiber alignment in composite structures

    DOEpatents

    Graham, Alan L.; Mondy, Lisa A.; Guell, David C.

    1993-01-01

    High strength material composite structures are formed with oriented fibers to provide controlled anisotropic fibers. Fibers suspended in non-dilute concentrations (e.g., up to 20 volume percent for fibers having an aspect ratio of 20) in a selected medium are oriented by moving an axially spaced array of elements in the direction of desired fiber alignment. The array elements are generally perpendicular to the desired orientation. The suspension medium may also include sphere-like particles where the resulting material is a ceramic.

  15. Connectivity independent protein-structure alignment: a hierarchical approach

    PubMed Central

    Kolbeck, Bjoern; May, Patrick; Schmidt-Goenner, Tobias; Steinke, Thomas; Knapp, Ernst-Walter

    2006-01-01

    Background Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of secondary structure elements (SSE) but differ in the underlying polypeptide chain connectivity (non-sequential SSE connectivity). Results We perform protein-structure alignment using a two-level hierarchical approach implemented in the program GANGSTA. On the first level, pair contacts and relative orientations between SSEs (i.e. α-helices and β-strands) are maximized with a genetic algorithm (GA). On the second level residue pair contacts from the best SSE alignments are optimized. We have tested the method on visually optimized structure alignments of protein pairs (pairwise mode) and for database scans. For a given protein structure, our method is able to detect significant structural similarity of functionally important folds with non-sequential SSE connectivity. The performance for structure alignments with strictly sequential SSE connectivity is comparable to that of other structure alignment methods. Conclusion As demonstrated for several applications, GANGSTA finds meaningful protein-structure alignments independent of the SSE connectivity. GANGSTA is able to detect structural similarity of protein folds that are assigned to different superfamilies but nevertheless possess similar structures and perform related functions, even if these proteins differ in SSE connectivity. PMID:17118190

  16. Local Structural Alignment of RNA with Affine Gap Model

    NASA Astrophysics Data System (ADS)

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

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

  17. Refinement by shifting secondary structure elements improves sequence alignments.

    PubMed

    Tong, Jing; Pei, Jimin; Otwinowski, Zbyszek; Grishin, Nick V

    2015-03-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

  18. Refinement by shifting secondary structure elements improves sequence alignments

    PubMed Central

    Tong, Jing; Pei, Jimin; Otwinowski, Zbyszek; Grishin, Nick V.

    2015-01-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

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

    PubMed

    Menke, Matthew; Berger, Bonnie; Cowen, Lenore

    2008-01-01

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

  20. FlexSnap: Flexible Non-sequential Protein Structure Alignment

    PubMed Central

    2010-01-01

    Background Proteins have evolved subject to energetic selection pressure for stability and flexibility. Structural similarity between proteins that have gone through conformational changes can be captured effectively if flexibility is considered. Topologically unrelated proteins that preserve secondary structure packing interactions can be detected if both flexibility and Sequential permutations are considered. We propose the FlexSnap algorithm for flexible non-topological protein structural alignment. Results The effectiveness of FlexSnap is demonstrated by measuring the agreement of its alignments with manually curated non-sequential structural alignments. FlexSnap showed competitive results against state-of-the-art algorithms, like DALI, SARF2, MultiProt, FlexProt, and FATCAT. Moreover on the DynDom dataset, FlexSnap reported longer alignments with smaller rmsd. Conclusions We have introduced FlexSnap, a greedy chaining algorithm that reports both sequential and non-sequential alignments and allows twists (hinges). We assessed the quality of the FlexSnap alignments by measuring its agreements with manually curated non-sequential alignments. On the FlexProt dataset, FlexSnap was competitive to state-of-the-art flexible alignment methods. Moreover, we demonstrated the benefits of introducing hinges by showing significant improvements in the alignments reported by FlexSnap for the structure pairs for which rigid alignment methods reported alignments with either low coverage or large rmsd. Availability An implementation of the FlexSnap algorithm will be made available online at http://www.cs.rpi.edu/~zaki/software/flexsnap. PMID:20047669

  1. Confinement and Structural Changes in Vertically Aligned Dust Structures

    NASA Astrophysics Data System (ADS)

    Hyde, Truell

    2013-10-01

    In physics, confinement is known to influence collective system behavior. Examples include coulomb crystal variants such as those formed from ions or dust particles (classical), electrons in quantum dots (quantum) and the structural changes observed in vertically aligned dust particle systems formed within a glass box placed on the lower electrode of a Gaseous Electronics Conference (GEC) rf reference cell. Recent experimental studies have expanded the above to include the biological domain by showing that the stability and dynamics of proteins confined through encapsulation and enzyme molecules placed in inorganic cavities such as those found in biosensors are also directly influenced by their confinement. In this paper, the self-assembly and subsequent collective behavior of structures formed from n, charged dust particles interacting with one another and located within a glass box placed on the lower, powered electrode of a GEC rf reference cell is discussed. Self-organized formation of vertically aligned one-dimensional chains, two-dimensional zigzag structures, and three-dimensional helical structures of triangular, quadrangular, pentagonal, hexagonal, and heptagonal symmetries are shown to occur. System evolution is shown to progress from one-dimensional chain structures, through a zigzag transition to a two-dimensional, spindle like structures, and then to various three-dimensional, helical structures exhibiting various symmetries. Stable configurations are shown to be strongly dependent upon system confinement. The critical conditions for structural transitions as well as the basic symmetry exhibited by the one-, two-, and three-dimensional structures that subsequently develop will be shown to be in good agreement with molecular dynamics simulations.

  2. Interactive computer graphics system for structural sizing and analysis of aircraft structures

    NASA Technical Reports Server (NTRS)

    Bendavid, D.; Pipano, A.; Raibstein, A.; Somekh, E.

    1975-01-01

    A computerized system for preliminary sizing and analysis of aircraft wing and fuselage structures was described. The system is based upon repeated application of analytical program modules, which are interactively interfaced and sequence-controlled during the iterative design process with the aid of design-oriented graphics software modules. The entire process is initiated and controlled via low-cost interactive graphics terminals driven by a remote computer in a time-sharing mode.

  3. Structural Alignment of RNA with Complex Pseudoknot Structure

    NASA Astrophysics Data System (ADS)

    Wong, Thomas K. F.; Lam, T. W.; Sung, Wing-Kin; Yiu, S. M.

    The secondary structure of an ncRNA molecule is known to play an important role in its biological functions. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, existing algorithms cannot handle complex pseudoknot structures which are found in nature. In this paper, we propose algorithms to handle two types of complex pseudoknots: simple non-standard pseudoknots and recursive pseudoknots. Although our methods are not designed for general pseudoknots, it already cover all known ncRNAs in both Rfam and PseudoBase databases. A preliminary evaluation on our algorithms show that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA.

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

    PubMed

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

    2012-11-01

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

  5. Recursive dynamic programming for adaptive sequence and structure alignment

    SciTech Connect

    Thiele, R.; Zimmer, R.; Lengauer, T.

    1995-12-31

    We propose a new alignment procedure that is capable of aligning protein sequences and structures in a unified manner. Recursive dynamic programming (RDP) is a hierarchical method which, on each level of the hierarchy, identifies locally optimal solutions and assembles them into partial alignments of sequences and/or structures. In contrast to classical dynamic programming, RDP can also handle alignment problems that use objective functions not obeying the principle of prefix optimality, e.g. scoring schemes derived from energy potentials of mean force. For such alignment problems, RDP aims at computing solutions that are near-optimal with respect to the involved cost function and biologically meaningful at the same time. Towards this goal, RDP maintains a dynamic balance between different factors governing alignment fitness such as evolutionary relationships and structural preferences. As in the RDP method gaps are not scored explicitly, the problematic assignment of gap cost parameters is circumvented. In order to evaluate the RDP approach we analyse whether known and accepted multiple alignments based on structural information can be reproduced with the RDP method.

  6. iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2.

    PubMed

    Yang, Chung-Han; Shih, Cheng-Ting; Chen, Kun-Tze; Lee, Po-Han; Tsai, Ping-Han; Lin, Jian-Cheng; Yen, Ching-Yu; Lin, Tiao-Yin; Lu, Chin Lung

    2016-07-01

    Since its first release in 2010, iPARTS has become a valuable tool for globally or locally aligning two RNA 3D structures. It was implemented by a structural alphabet (SA)-based approach, which uses an SA of 23 letters to reduce RNA 3D structures into 1D sequences of SA letters and applies traditional sequence alignment to these SA-encoded sequences for determining their global or local similarity. In this version, we have re-implemented iPARTS into a new web server iPARTS2 by constructing a totally new SA, which consists of 92 elements with each carrying both information of base and backbone geometry for a representative nucleotide. This SA is significantly different from the one used in iPARTS, because the latter consists of only 23 elements with each carrying only the backbone geometry information of a representative nucleotide. Our experimental results have shown that iPARTS2 outperforms its previous version iPARTS and also achieves better accuracy than other popular tools, such as SARA, SETTER and RASS, in RNA alignment quality and function prediction. iPARTS2 takes as input two RNA 3D structures in the PDB format and outputs their global or local alignments with graphical display. iPARTS2 is now available online at http://genome.cs.nthu.edu.tw/iPARTS2/. PMID:27185896

  7. Alignment and defect structures in oriented phosphatidylcholine multilayers.

    PubMed Central

    Asher, S A; Pershan, P S

    1979-01-01

    The alignment of dilauryl-, dimyristoyl-, and dipalmitoylphosphatidylcholine at various water concentrations into large oriented monodomain multilayers by annealing at elevated temperatures (Powers and Clark, 1975, Proc. Natl. Acad. Sci. U.S.A. 72:840; Powers and Pershan. 1977. Biophys. J. 20:137) is accompanied by the formation and subsequent dissolution of various defect structures. Some of these defects appear similar to those observed in thermotropic and other lyotropic liquid crystals, reflecting the lamellar structure of these materials. The formation and evolution of defects during the alignment of the lipids into the defect-free, monodomain, multilamellar geometry is studied using polarized microscopy. A combination of polarized and dark-field microscopy facilitated characterization of the defects; specific structural models are proposed. A new alignment technique involving compression and dilation of the lipid, which effects sample alignment at temperatures that are lower than those required by the Powers technique, is described. Lower temperature alignment avoids thermal decomposition that will sometimes occur if the lipid is maintained at elevated temperatures for prolonged periods. With this technique, samples (80 micrometer thick) of dilaurylphosphatidylcholine with 20% water by weight were aligned at room temperature. Images FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 FIGURE 7 FIGURE 8 FIGURE 9 FIGURE 10 FIGURE 11 FIGURE 12 FIGURE 13 FIGURE 14 FIGURE 15 PMID:263691

  8. Proteins comparison through probabilistic optimal structure local alignment

    PubMed Central

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

    2014-01-01

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

  9. SAS-Pro: Simultaneous Residue Assignment and Structure Superposition for Protein Structure Alignment

    PubMed Central

    Shah, Shweta B.; Sahinidis, Nikolaos V.

    2012-01-01

    Protein structure alignment is the problem of determining an assignment between the amino-acid residues of two given proteins in a way that maximizes a measure of similarity between the two superimposed protein structures. By identifying geometric similarities, structure alignment algorithms provide critical insights into protein functional similarities. Existing structure alignment tools adopt a two-stage approach to structure alignment by decoupling and iterating between the assignment evaluation and structure superposition problems. We introduce a novel approach, SAS-Pro, which addresses the assignment evaluation and structure superposition simultaneously by formulating the alignment problem as a single bilevel optimization problem. The new formulation does not require the sequentiality constraints, thus generalizing the scope of the alignment methodology to include non-sequential protein alignments. We employ derivative-free optimization methodologies for searching for the global optimum of the highly nonlinear and non-differentiable RMSD function encountered in the proposed model. Alignments obtained with SAS-Pro have better RMSD values and larger lengths than those obtained from other alignment tools. For non-sequential alignment problems, SAS-Pro leads to alignments with high degree of similarity with known reference alignments. The source code of SAS-Pro is available for download at http://eudoxus.cheme.cmu.edu/saspro/SAS-Pro.html. PMID:22662161

  10. ASH structure alignment package: Sensitivity and selectivity in domain classification

    PubMed Central

    Standley, Daron M; Toh, Hiroyuki; Nakamura, Haruki

    2007-01-01

    Background Structure alignment methods offer the possibility of measuring distant evolutionary relationships between proteins that are not visible by sequence-based analysis. However, the question of how structural differences and similarities ought to be quantified in this regard remains open. In this study we construct a training set of sequence-unique CATH and SCOP domains, from which we develop a scoring function that can reliably identify domains with the same CATH topology and SCOP fold classification. The score is implemented in the ASH structure alignment package, for which the source code and a web service are freely available from the PDBj website . Results The new ASH score shows increased selectivity and sensitivity compared with values reported for several popular programs using the same test set of 4,298,905 structure pairs, yielding an area of .96 under the receiver operating characteristic (ROC) curve. In addition, weak sequence homologies between similar domains are revealed that could not be detected by BLAST sequence alignment. Also, a subset of domain pairs is identified that exhibit high similarity, even though their CATH and SCOP classification differs. Finally, we show that the ranking of alignment programs based solely on geometric measures depends on the choice of the quality measure. Conclusion ASH shows high selectivity and sensitivity with regard to domain classification, an important step in defining distantly related protein sequence families. Moreover, the CPU cost per alignment is competitive with the fastest programs, making ASH a practical option for large-scale structure classification studies. PMID:17407606

  11. SRP-RNA sequence alignment and secondary structure.

    PubMed Central

    Larsen, N; Zwieb, C

    1991-01-01

    The secondary structures of the RNAs from the signal recognition particle, termed SRP-RNA, were derived buy comparative analyses of an alignment of 39 sequences. The models are minimal in that only base pairs are included for which there is comparative evidence. The structures represent refinements of earlier versions and include a new short helix. PMID:1707519

  12. A Graphical Method for Assessing the Identification of Linear Structural Equation Models

    ERIC Educational Resources Information Center

    Eusebi, Paolo

    2008-01-01

    A graphical method is presented for assessing the state of identifiability of the parameters in a linear structural equation model based on the associated directed graph. We do not restrict attention to recursive models. In the recent literature, methods based on graphical models have been presented as a useful tool for assessing the state of…

  13. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

    PubMed

    Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

    2013-07-01

    The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/. PMID:23716643

  14. Impact of Information Technology Governance Structures on Strategic Alignment

    ERIC Educational Resources Information Center

    Gordon, Fitzroy R.

    2013-01-01

    This dissertation is a study of the relationship between Information Technology (IT) strategic alignment and IT governance structure within the organization. This dissertation replicates Asante (2010) among a different population where the prior results continue to hold, the non-experimental approach explored two research questions but include two…

  15. Crowdsourcing RNA structural alignments with an online computer game.

    PubMed

    Waldispühl, Jérôme; Kam, Arthur; Gardner, Paul P

    2015-01-01

    The annotation and classification of ncRNAs is essential to decipher molecular mechanisms of gene regulation in normal and disease states. A database such as Rfam maintains alignments, consensus secondary structures, and corresponding annotations for RNA families. Its primary purpose is the automated, accurate annotation of non-coding RNAs in genomic sequences. However, the alignment of RNAs is computationally challenging, and the data stored in this database are often subject to improvements. Here, we design and evaluate Ribo, a human-computing game that aims to improve the accuracy of RNA alignments already stored in Rfam. We demonstrate the potential of our techniques and discuss the feasibility of large scale collaborative annotation and classification of RNA families. PMID:25592593

  16. A Stochastic Evolutionary Model for Protein Structure Alignment and Phylogeny

    PubMed Central

    Challis, Christopher J.; Schmidler, Scott C.

    2012-01-01

    We present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model, and mutations follow a standard substitution matrix, whereas backbone atoms diffuse in three-dimensional space according to an Ornstein–Uhlenbeck process. The model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully accounting for uncertainty. The inclusion of structural information enables phylogenetic inference on time scales not previously attainable with sequence evolution models. The model also provides a tool for testing evolutionary hypotheses and improving our understanding of protein structural evolution. PMID:22723302

  17. Comparison of protein structures using 3D profile alignment.

    PubMed

    Suyama, M; Matsuo, Y; Nishikawa, K

    1997-01-01

    A novel method for protein structure comparison using 3D profile alignment is presented. The 3D profile is a position-dependent scoring matrix derived from three-dimensional structures and is basically used to estimate sequence-structure compatibility for prediction of protein structure. Our idea is to compare two 3D profiles using a dynamic programming algorithm to obtain optimal alignment and a similarity score between them. When the 3D profile of hemoglobin was compared with each of the profiles in the library, which contained 325 profiles of representative structures, all the profiles of other globins were detected with relatively high scores, and proteins in the same structural class followed the globins. Exhaustive comparison of 3D profiles in the library was also performed to depict protein relatedness in the structure space. Using multidimensional scaling, a planar projection of points in the protein structure space revealed an overall grouping in terms of structural classes, i.e., all-alpha, all-beta, alpha/beta, and alpha+beta. These results differ in implication from those obtained by the conventional structure-structure comparison method. Differences are discussed with respect to the structural divergence of proteins in the course of molecular evolution. PMID:9071025

  18. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures

    PubMed Central

    Rahrig, Ryan R.; Petrov, Anton I.; Leontis, Neocles B.; Zirbel, Craig L.

    2013-01-01

    The R3D Align web server provides online access to ‘RNA 3D Align’ (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/. PMID:23716643

  19. Interactive computer graphics and its role in control system design of large space structures

    NASA Technical Reports Server (NTRS)

    Reddy, A. S. S. R.

    1985-01-01

    This paper attempts to show the relevance of interactive computer graphics in the design of control systems to maintain attitude and shape of large space structures to accomplish the required mission objectives. The typical phases of control system design, starting from the physical model such as modeling the dynamics, modal analysis, and control system design methodology are reviewed and the need of the interactive computer graphics is demonstrated. Typical constituent parts of large space structures such as free-free beams and free-free plates are used to demonstrate the complexity of the control system design and the effectiveness of the interactive computer graphics.

  20. Structure based alignment and clustering of proteins (STRALCP)

    DOEpatents

    Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

    2013-06-18

    Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

  1. MacPASCO - A Macintosh-based, interactive graphic preprocessor for structural analysis and sizing

    NASA Technical Reports Server (NTRS)

    Lucas, S. H.; Davis, R. C.

    1991-01-01

    MacPASCO, an interactive, graphic preprocessor for panel design is described. MacPASCO creates input for PASCO, an existing computer code for structural analysis and optimization of longitudinal stiffened composite panels. By using a graphical user interface, MacPASCO simplifies the specification of panel geometry and reduces user input errors, thus making the modeling and analysis of panel designs more efficient. The user draws the initial structural geometry on the computer screen, then uses a combination of graphic and text inputs to: refine the structural geometry, specify information required for analysis such as panel load conditions, and define design variables and constraints for minimum-mass optimization. Composite panel design is an ideal application because the graphical user interface can: serve as a visual aid, eliminate the tedious aspects of text-based input, and eliminate many sources of input errors.

  2. Information Technology (IT) Strategic Alignment: A Correlational Study between the Impact of IT Governance Structures and IT Strategic Alignment

    ERIC Educational Resources Information Center

    Asante, Keith K.

    2010-01-01

    This dissertation explored the extent to which Information Technology (IT) strategic alignment are impacted by IT governance structures. The study discusses several strategic alignment and IT governance literature that presents a gap in the literature domain. Subsequent studies researched issues surrounding why organizations are not able to align…

  3. mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet.

    PubMed

    Léonard, Sylvain; Joseph, Agnel Praveen; Srinivasan, Narayanaswamy; Gelly, Jean-Christophe; de Brevern, Alexandre G

    2014-04-01

    The increasing number of available protein structures requires efficient tools for multiple structure comparison. Indeed, multiple structural alignments are essential for the analysis of function, evolution and architecture of protein structures. For this purpose, we proposed a new web server called multiple Protein Block Alignment (mulPBA). This server implements a method based on a structural alphabet to describe the backbone conformation of a protein chain in terms of dihedral angles. This 'sequence-like' representation enables the use of powerful sequence alignment methods for primary structure comparison, followed by an iterative refinement of the structural superposition. This approach yields alignments superior to most of the rigid-body alignment methods and highly comparable with the flexible structure comparison approaches. We implement this method in a web server designed to do multiple structure superimpositions from a set of structures given by the user. Outputs are given as both sequence alignment and superposed 3D structures visualized directly by static images generated by PyMol or through a Jmol applet allowing dynamic interaction. Multiple global quality measures are given. Relatedness between structures is indicated by a distance dendogram. Superimposed structures in PDB format can be also downloaded, and the results are quickly obtained. mulPBA server can be accessed at www.dsimb.inserm.fr/dsimb_tools/mulpba/ . PMID:23659291

  4. A graphically oriented specification language for automatic code generation. GRASP/Ada: A Graphical Representation of Algorithms, Structure, and Processes for Ada, phase 1

    NASA Technical Reports Server (NTRS)

    Cross, James H., II; Morrison, Kelly I.; May, Charles H., Jr.; Waddel, Kathryn C.

    1989-01-01

    The first phase of a three-phase effort to develop a new graphically oriented specification language which will facilitate the reverse engineering of Ada source code into graphical representations (GRs) as well as the automatic generation of Ada source code is described. A simplified view of the three phases of Graphical Representations for Algorithms, Structure, and Processes for Ada (GRASP/Ada) with respect to three basic classes of GRs is presented. Phase 1 concentrated on the derivation of an algorithmic diagram, the control structure diagram (CSD) (CRO88a) from Ada source code or Ada PDL. Phase 2 includes the generation of architectural and system level diagrams such as structure charts and data flow diagrams and should result in a requirements specification for a graphically oriented language able to support automatic code generation. Phase 3 will concentrate on the development of a prototype to demonstrate the feasibility of this new specification language.

  5. Structural magnetic loss of vertical aligned carbon fibres

    NASA Astrophysics Data System (ADS)

    Hong, Wen; Xiao, Peng; Luo, Heng

    2013-06-01

    The electromagnetic spectroscopy of vertical aligned carbon fibres (VACF) reinforced epoxy resin has been performed in the frequency range from 8.2 to 12.4 GHz. The composite was prepared by conventional epoxy polymerization. The results indicate VACF could possess magnetic loss and the structural magnetic properties could be tailored by adjusting the forest structure. The corresponding mechanism of the structural magnetic properties is proposed by the Faradays' law of induction. The structural magnetism is further confirmed by measuring VACF reinforced Al2O3 composites in 1073 K environment. The measurement agrees well with the trend predicted by the parallel fibres model. These results represent a crucial step towards high temperature microwave absorber design and open a new avenue for realizing magnetic losses in the dielectric material.

  6. Relational, Structural, and Semantic Analysis of Graphical Representations and Concept Maps

    ERIC Educational Resources Information Center

    Ifenthaler, Dirk

    2010-01-01

    The demand for good instructional environments presupposes valid and reliable analytical instruments for educational research. This paper introduces the "SMD Technology" (Surface, Matching, Deep Structure), which measures relational, structural, and semantic levels of graphical representations and concept maps. The reliability and validity of the…

  7. Electronic structure of spatially aligned graphene nanoribbons on Au(788).

    PubMed

    Linden, S; Zhong, D; Timmer, A; Aghdassi, N; Franke, J H; Zhang, H; Feng, X; Müllen, K; Fuchs, H; Chi, L; Zacharias, H

    2012-05-25

    We report on a bottom-up approach of the selective and precise growth of subnanometer wide straight and chevron-type armchair nanoribbons (GNRs) on a stepped Au(788) surface using different specific molecular precursors. This process creates spatially well-aligned GNRs, as characterized by STM. High-resolution direct and inverse photoemission spectroscopy of occupied and unoccupied states allows the determination of the energetic position and momentum dispersion of electronic states revealing the existence of band gaps of several electron volts for straight 7-armchair, 13-armchair, and chevron-type GNRs in the electronic structure. PMID:23003288

  8. A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers.

    PubMed

    Martin, Jeffrey W; Yan, Anthony K; Bailey-Kellogg, Chris; Zhou, Pei; Donald, Bruce R

    2011-06-01

    High-resolution structure determination of homo-oligomeric protein complexes remains a daunting task for NMR spectroscopists. Although isotope-filtered experiments allow separation of intermolecular NOEs from intramolecular NOEs and determination of the structure of each subunit within the oligomeric state, degenerate chemical shifts of equivalent nuclei from different subunits make it difficult to assign intermolecular NOEs to nuclei from specific pairs of subunits with certainty, hindering structural analysis of the oligomeric state. Here, we introduce a graphical method, DISCO, for the analysis of intermolecular distance restraints and structure determination of symmetric homo-oligomers using residual dipolar couplings. Based on knowledge that the symmetry axis of an oligomeric complex must be parallel to an eigenvector of the alignment tensor of residual dipolar couplings, we can represent distance restraints as annuli in a plane encoding the parameters of the symmetry axis. Oligomeric protein structures with the best restraint satisfaction correspond to regions of this plane with the greatest number of overlapping annuli. This graphical analysis yields a technique to characterize the complete set of oligomeric structures satisfying the distance restraints and to quantitatively evaluate the contribution of each distance restraint. We demonstrate our method for the trimeric E. coli diacylglycerol kinase, addressing the challenges in obtaining subunit assignments for distance restraints. We also demonstrate our method on a dimeric mutant of the immunoglobulin-binding domain B1 of streptococcal protein G to show the resilience of our method to ambiguous atom assignments. In both studies, DISCO computed oligomer structures with high accuracy despite using ambiguously assigned distance restraints. PMID:21413097

  9. GRASS: a server for the graphical representation and analysis of structures.

    PubMed Central

    Nayal, M.; Hitz, B. C.; Honig, B.

    1999-01-01

    GRASS (Graphical Representation and Analysis of Structures Server), a new web-based server, is described. GRASS exploits many of the features of the GRASP program and is designed to provide interactive molecular graphics and quantitative analysis tools with a simple interface over the World-Wide Web. Using GRASS, it is now possible to view many surface features of biological macromolecules on either standard workstations used in macromolecular analysis or personal computers. The result is a World-Wide Web-based, platform-independent, easily used tool for macromolecular visualization and structure analysis. PMID:10091670

  10. Structural re-alignment in an immunologic surface region of ricin A chain

    SciTech Connect

    Zemla, A T; Zhou, C E

    2007-07-24

    We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connecting the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.

  11. A rapid protein structure alignment algorithm based on a text modeling technique

    PubMed Central

    Razmara, Jafar; Deris, Safaai; Parvizpour, Sepideh

    2011-01-01

    Structural alignment of proteins is widely used in various fields of structural biology. In order to further improve the quality of alignment, we describe an algorithm for structural alignment based on text modelling techniques. The technique firstly superimposes secondary structure elements of two proteins and then, models the 3D-structure of the protein in a sequence of alphabets. These sequences are utilized by a step-by-step sequence alignment procedure to align two protein structures. A benchmark test was organized on a set of 200 non-homologous proteins to evaluate the program and compare it to state of the art programs, e.g. CE, SAL, TM-align and 3D-BLAST. On average, the results of all-against-all structure comparison by the program have a competitive accuracy with CE and TM-align where the algorithm has a high running speed like 3D-BLAST. PMID:21814392

  12. Parallel Block Structured Adaptive Mesh Refinement on Graphics Processing Units

    SciTech Connect

    Beckingsale, D. A.; Gaudin, W. P.; Hornung, R. D.; Gunney, B. T.; Gamblin, T.; Herdman, J. A.; Jarvis, S. A.

    2014-11-17

    Block-structured adaptive mesh refinement is a technique that can be used when solving partial differential equations to reduce the number of zones necessary to achieve the required accuracy in areas of interest. These areas (shock fronts, material interfaces, etc.) are recursively covered with finer mesh patches that are grouped into a hierarchy of refinement levels. Despite the potential for large savings in computational requirements and memory usage without a corresponding reduction in accuracy, AMR adds overhead in managing the mesh hierarchy, adding complex communication and data movement requirements to a simulation. In this paper, we describe the design and implementation of a native GPU-based AMR library, including: the classes used to manage data on a mesh patch, the routines used for transferring data between GPUs on different nodes, and the data-parallel operators developed to coarsen and refine mesh data. We validate the performance and accuracy of our implementation using three test problems and two architectures: an eight-node cluster, and over four thousand nodes of Oak Ridge National Laboratory’s Titan supercomputer. Our GPU-based AMR hydrodynamics code performs up to 4.87× faster than the CPU-based implementation, and has been scaled to over four thousand GPUs using a combination of MPI and CUDA.

  13. MALIDUP: a database of manually constructed structure alignments for duplicated domain pairs.

    PubMed

    Cheng, Hua; Kim, Bong-Hyun; Grishin, Nick V

    2008-03-01

    We describe MALIDUP (manual alignments of duplicated domains), a database of 241 pairwise structure alignments for homologous domains originated by internal duplication within the same polypeptide chain. Since duplicated domains within a protein frequently diverge in function and thus in sequence, this would be the first database of structurally similar homologs that is not strongly biased by sequence or functional similarity. Our manual alignments in most cases agree with the automatic structural alignments generated by several commonly used programs. This carefully constructed database could be used in studies on protein evolution and as a reference for testing structure alignment programs. The database is available at http://prodata.swmed.edu/malidup. PMID:17932926

  14. The Graphic Representation of Structure in Similarity/Dissimilarity Matrices: Alternative Methods.

    ERIC Educational Resources Information Center

    Rudnitsky, Alan N.

    Three approaches to the graphic representation of similarity and dissimilarity matrices are compared and contrasted. Specifically, Kruskal's multidimensional scaling, Johnson's hierarchical clustering, and Waern's graphing techniques are employed to depict, in two dimensions, data representing the structure of a set of botanical concepts. Each of…

  15. An adaptive structure data acquisition system using a graphical-based programming language

    NASA Technical Reports Server (NTRS)

    Baroth, Edmund C.; Clark, Douglas J.; Losey, Robert W.

    1992-01-01

    An example of the implementation of data fusion using a PC and a graphical programming language is discussed. A schematic of the data acquisition system and user interface panel for an adaptive structure test are presented. The computer programs (a series of icons 'wired' together) are also discussed. The way in which using graphical-based programming software to control a data acquisition system can simplify analysis of data, promote multidisciplinary interaction, and provide users a more visual key to understanding their data are shown.

  16. PROMALS3D web server for accurate multiple protein sequence and structure alignments.

    PubMed

    Pei, Jimin; Tang, Ming; Grishin, Nick V

    2008-07-01

    Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/. PMID:18503087

  17. Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.

    PubMed

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

    2012-09-01

    Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a 1D sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. PMID:22676903

  18. Higher-order derivative correlations and the alignment of small-scale structures in isotropic numerical turbulence

    NASA Technical Reports Server (NTRS)

    Kerr, R. A.

    1983-01-01

    In a three dimensional simulation higher order derivative correlations, including skewness and flatness factors, are calculated for velocity and passive scalar fields and are compared with structures in the flow. The equations are forced to maintain steady state turbulence and collect statistics. It is found that the scalar derivative flatness increases much faster with Reynolds number than the velocity derivative flatness, and the velocity and mixed derivative skewness do not increase with Reynolds number. Separate exponents are found for the various fourth order velocity derivative correlations, with the vorticity flatness exponent the largest. Three dimensional graphics show strong alignment between the vorticity, rate of strain, and scalar-gradient fields. The vorticity is concentrated in tubes with the scalar gradient and the largest principal rate of strain aligned perpendicular to the tubes. Velocity spectra, in Kolmogorov variables, collapse to a single curve and a short minus 5/3 spectral regime is observed.

  19. Band alignment of ultra-thin hetero-structure ZnO/TiO{sub 2} junction

    SciTech Connect

    Shen, Kai; Wu, Kunjie; Wang, Deliang

    2014-03-01

    Graphical abstract: - Highlights: • Band alignment at the ZnO/TiO{sub 2} hetero-structural interface with different ZnO coating thickness was studied. • The valence band offset was decreased with increased ZnO coating layer thickness. • The interface dipole was responsible for the decreased band offset. - Abstract: The band alignment at the ZnO/TiO{sub 2} hetero-structure interface was measured by high resolution X-ray photoelectron spectroscopy. The valence band offset (E{sub ZnO}−E{sub TiO{sub 2}}){sub Valence} was linearly changed from 0.27 to 0.01 eV at the interface with increased ZnO coating thickness from 0.7 to 7 nm. The interface dipole presented at the ZnO/TiO{sub 2} interface was responsible for the decreased band offset. The band alignment of the ZnO/TiO{sub 2} heterojunction is a type II alignment.

  20. PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL

    PubMed Central

    2012-01-01

    Background In recent years, an exponential growing number of tools for protein sequence analysis, editing and modeling tasks have been put at the disposal of the scientific community. Despite the vast majority of these tools have been released as open source software, their deep learning curves often discourages even the most experienced users. Results A simple and intuitive interface, PyMod, between the popular molecular graphics system PyMOL and several other tools (i.e., [PSI-]BLAST, ClustalW, MUSCLE, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modeling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks. Sequence similarity searches, multiple sequence and structural alignments generation and editing, and even the possibility to merge sequence and structure alignments have been implemented in PyMod, with the aim of creating a simple, yet powerful tool for sequence and structure analysis and building of homology models. Conclusions PyMod represents a new tool for the analysis and the manipulation of protein sequences and structures. The ease of use, integration with many sequence retrieving and alignment tools and PyMOL, one of the most used molecular visualization system, are the key features of this tool. Source code, installation instructions, video tutorials and a user's guide are freely available at the URL http://schubert.bio.uniroma1.it/pymod/index.html PMID:22536966

  1. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and 3-dimensional structural information

    PubMed Central

    Pei, Jimin; Grishin, Nick V.

    2015-01-01

    SUMMARY Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of 3-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D web server and package are available at http://prodata.swmed.edu/PROMALS3D. PMID:24170408

  2. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.

    PubMed

    Pei, Jimin; Grishin, Nick V

    2014-01-01

    Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D. PMID:24170408

  3. A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications.

    PubMed

    Tyagi, Manoj; Gowri, Venkataraman S; Srinivasan, Narayanaswamy; de Brevern, Alexandre G; Offmann, Bernard

    2006-10-01

    Analysis of protein structures based on backbone structural patterns known as structural alphabets have been shown to be very useful. Among them, a set of 16 pentapeptide structural motifs known as protein blocks (PBs) has been identified and upon which backbone model of most protein structures can be built. PBs allows simplification of 3D space onto 1D space in the form of sequence of PBs. Here, for the first time, substitution probabilities of PBs in a large number of aligned homologous protein structures have been studied and are expressed as a simplified 16 x 16 substitution matrix. The matrix was validated by benchmarking how well it can align sequences of PBs rather like amino acid alignment to identify structurally equivalent regions in closely or distantly related proteins using dynamic programming approach. The alignment results obtained are very comparable to well established structure comparison methods like DALI and STAMP. Other interesting applications of the matrix have been investigated. We first show that, in variable regions between two superimposed homologous proteins, one can distinguish between local conformational differences and rigid-body displacement of a conserved motif by comparing the PBs and their substitution scores. Second, we demonstrate, with the example of aspartic proteinases, that PBs can be efficiently used to detect the lobe/domain flexibility in the multidomain proteins. Lastly, using protein kinase as an example, we identify regions of conformational variations and rigid body movements in the enzyme as it is changed to the active state from an inactive state. PMID:16894618

  4. Word aligned bitmap compression method, data structure, and apparatus

    DOEpatents

    Wu, Kesheng; Shoshani, Arie; Otoo, Ekow

    2004-12-14

    The Word-Aligned Hybrid (WAH) bitmap compression method and data structure is a relatively efficient method for searching and performing logical, counting, and pattern location operations upon large datasets. The technique is comprised of a data structure and methods that are optimized for computational efficiency by using the WAH compression method, which typically takes advantage of the target computing system's native word length. WAH is particularly apropos to infrequently varying databases, including those found in the on-line analytical processing (OLAP) industry, due to the increased computational efficiency of the WAH compressed bitmap index. Some commercial database products already include some version of a bitmap index, which could possibly be replaced by the WAH bitmap compression techniques for potentially increased operation speed, as well as increased efficiencies in constructing compressed bitmaps. Combined together, this technique may be particularly useful for real-time business intelligence. Additional WAH applications may include scientific modeling, such as climate and combustion simulations, to minimize search time for analysis and subsequent data visualization.

  5. Reconstruction of three-dimensional molecular structure from diffraction of laser-aligned molecules.

    PubMed

    Yang, Jie; Makhija, Varun; Kumarappan, Vinod; Centurion, Martin

    2014-07-01

    Diffraction from laser-aligned molecules has been proposed as a method for determining 3-D molecular structures in the gas phase. However, existing structural retrieval algorithms are limited by the imperfect alignment in experiments and the rotational averaging in 1-D alignment. Here, we demonstrate a two-step reconstruction comprising a genetic algorithm that corrects for the imperfect alignment followed by an iterative phase retrieval method in cylindrical coordinates. The algorithm was tested with simulated diffraction patterns. We show that the full 3-D structure of trifluorotoluene, an asymmetric-top molecule, can be reconstructed with atomic resolution. PMID:26798781

  6. 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

  7. Presenting your structures: the CCP4mg molecular-graphics software

    PubMed Central

    McNicholas, S.; Potterton, E.; Wilson, K. S.; Noble, M. E. M.

    2011-01-01

    CCP4mg is a molecular-graphics program that is designed to give rapid access to both straightforward and complex static and dynamic representations of macromolecular structures. It has recently been updated with a new interface that provides more sophisticated atom-selection options and a wizard to facilitate the generation of complex scenes. These scenes may contain a mixture of coordinate-derived and abstract graphical objects, including text objects, arbitrary vectors, geometric objects and imported images, which can enhance a picture and eliminate the need for subsequent editing. Scene descriptions can be saved to file and transferred to other molecules. Here, the substantially enhanced version 2 of the program, with a new underlying GUI toolkit, is described. A built-in rendering module produces publication-quality images. PMID:21460457

  8. Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures

    PubMed Central

    Kolodny, Rachel; Koehl, Patrice; Levitt, Michael

    2009-01-01

    We report the largest and most comprehensive comparison of protein structural alignment methods. Specifically, we evaluate six publicly available structure alignment programs: SSAP, STRUCTAL, DALI, LSQMAN, CE and SSM by aligning all 8,581,970 protein structure pairs in a test set of 2930 protein domains specially selected from CATH v.2.4 to ensure sequence diversity. We consider an alignment good if it matches many residues, and the two substructures are geometrically similar. Even with this definition, evaluating structural alignment methods is not straightforward. At first, we compared the rates of true and false positives using receiver operating characteristic (ROC) curves with the CATH classification taken as a gold standard. This proved unsatisfactory in that the quality of the alignments is not taken into account: sometimes a method that finds less good alignments scores better than a method that finds better alignments. We correct this intrinsic limitation by using four different geometric match measures (SI, MI, SAS, and GSAS) to evaluate the quality of each structural alignment. With this improved analysis we show that there is a wide variation in the performance of different methods; the main reason for this is that it can be difficult to find a good structural alignment between two proteins even when such an alignment exists. We find that STRUCTAL and SSM perform best, followed by LSQMAN and CE. Our focus on the intrinsic quality of each alignment allows us to propose a new method, called “Best-of-All” that combines the best results of all methods. Many commonly used methods miss 10–50% of the good Best-of-All alignments. By putting existing structural alignments into proper perspective, our study allows better comparison of protein structures. By highlighting limitations of existing methods, it will spur the further development of better structural alignment methods. This will have significant biological implications now that structural

  9. Interactive Computer Graphics for Performance-Structure-Oriented CAI. Technical Report No. 73.

    ERIC Educational Resources Information Center

    Rigney, Joseph W.; And Others

    Two different uses of interactive graphics in computer-assisted instruction are described. Interactive graphics may be used as substitutes for physical devices and operations. An example is simulation of operating on man/machine interfaces, substituting interactive graphics for controls, indicators, and indications. Interactive graphics may also…

  10. An interactive NASTRAN preprocessor. [graphic display of undeformed structure using CDC 6000 series computer

    NASA Technical Reports Server (NTRS)

    Smith, W. W.

    1973-01-01

    A Langley Research Center version of NASTRAN Level 15.1.0 designed to provide the analyst with an added tool for debugging massive NASTRAN input data is described. The program checks all NASTRAN input data cards and displays on a CRT the graphic representation of the undeformed structure. In addition, the program permits the display and alteration of input data and allows reexecution without physically resubmitting the job. Core requirements on the CDC 6000 computer are approximately 77,000 octal words of central memory.

  11. Learning a structured graphical model with boosted top-down features for ultrasound image segmentation.

    PubMed

    Hao, Zhihui; Wang, Qiang; Wang, Xiaotao; Kim, Jung Bae; Hwang, Youngkyoo; Cho, Baek Hwan; Guo, Ping; Lee, Won Ki

    2013-01-01

    A key problem for many medical image segmentation tasks is the combination of different-level knowledge. We propose a novel scheme of embedding detected regions into a superpixel based graphical model, by which we achieve a full leverage on various image cues for ultrasound lesion segmentation. Region features are mapped into a higher-dimensional space via a boosted model to become well controlled. Parameters for regions, superpixels and a new affinity term are learned simultaneously within the framework of structured learning. Experiments on a breast ultrasound image data set confirm the effectiveness of the proposed approach as well as our two novel modules. PMID:24505670

  12. RNA global alignment in the joint sequence–structure space using elastic shape analysis

    PubMed Central

    Laborde, Jose; Robinson, Daniel; Klassen, Eric; Zhang, Jinfeng

    2013-01-01

    The functions of RNAs, like proteins, are determined by their structures, which, in turn, are determined by their sequences. Comparison/alignment of RNA molecules provides an effective means to predict their functions and understand their evolutionary relationships. For RNA sequence alignment, most methods developed for protein and DNA sequence alignment can be directly applied. RNA 3-dimensional structure alignment, on the other hand, tends to be more difficult than protein structure alignment due to the lack of regular secondary structures as observed in proteins. Most of the existing RNA 3D structure alignment methods use only the backbone geometry and ignore the sequence information. Using both the sequence and backbone geometry information in RNA alignment may not only produce more accurate classification, but also deepen our understanding of the sequence–structure–function relationship of RNA molecules. In this study, we developed a new RNA alignment method based on elastic shape analysis (ESA). ESA treats RNA structures as three dimensional curves with sequence information encoded on additional dimensions so that the alignment can be performed in the joint sequence–structure space. The similarity between two RNA molecules is quantified by a formal distance, geodesic distance. Based on ESA, a rigorous mathematical framework can be built for RNA structure comparison. Means and covariances of full structures can be defined and computed, and probability distributions on spaces of such structures can be constructed for a group of RNAs. Our method was further applied to predict functions of RNA molecules and showed superior performance compared with previous methods when tested on benchmark datasets. The programs are available at http://stat.fsu.edu/ ∼jinfeng/ESA.html. PMID:23585278

  13. Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling

    PubMed Central

    Wang, Sheng; Peng, Jian; Xu, Jinbo

    2011-01-01

    Motivation: Building an accurate alignment of a large set of distantly related protein structures is still very challenging. Results: This article presents a novel method 3DCOMB that can generate a multiple structure alignment (MSA) with not only as many conserved cores as possible, but also high-quality pairwise alignments. 3DCOMB is unique in that it makes use of both local and global structure environments, combined by a statistical learning method, to accurately identify highly similar fragment blocks (HSFBs) among all proteins to be aligned. By extending the alignments of these HSFBs, 3DCOMB can quickly generate an accurate MSA without using progressive alignment. 3DCOMB significantly excels others in aligning distantly related proteins. 3DCOMB can also generate correct alignments for functionally similar regions among proteins of very different structures while many other MSA tools fail. 3DCOMB is useful for many real-world applications. In particular, it enables us to find out that there is still large improvement room for multiple template homology modeling while several other MSA tools fail to do so. Availability: 3DCOMB is available at http://ttic.uchicago.edu/~jinbo/software.htm. Contact: jinboxu@gmail.com Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:21791532

  14. Multilayer photo-aligned thin-film structure for polarizing photonics.

    PubMed

    Zhao, C X; Fan, F; Du, T; Chigrinov, V G; Kwok, H S

    2015-07-01

    In this Letter, an advanced multilayer photo-aligned liquid crystal polymer (LCP) thin-film structure with multiple optical functions is introduced. Within each LCP layer, a spatially distribution of local optical axes can be controlled by a patterned photo-alignment layer. As an embodiment of the proposed structure, a two-layer structure with pixelated controlled light-propagation directions and polarizations has been studied, which has shown the potential to be used as a photomask for generating multi-domain photo-alignment structures with a single exposure step. The combination of the multilayer structure with patterned photo-alignment technology provides a new perspective of designing optical structures for polarizing photonics applications. PMID:26125350

  15. Dynamic Programming Used to Align Protein Structures with a Spectrum Is Robust

    PubMed Central

    Holder, Allen; Simon, Jacqueline; Strauser, Jonathon; Taylor, Jonathan; Shibberu, Yosi

    2013-01-01

    Several efficient algorithms to conduct pairwise comparisons among large databases of protein structures have emerged in the recent literature. The central theme is the design of a measure between the Cα atoms of two protein chains, from which dynamic programming is used to compute an alignment. The efficiency and efficacy of these algorithms allows large-scale computational studies that would have been previously impractical. The computational study herein shows that the structural alignment algorithm eigen-decomposition alignment with the spectrum (EIGAs) is robust against both parametric and structural variation. PMID:24833226

  16. Imaging of alignment and structural changes of carbon disulfide molecules using ultrafast electron diffraction.

    PubMed

    Yang, Jie; Beck, Joshua; Uiterwaal, Cornelis J; Centurion, Martin

    2015-01-01

    Imaging the structure of molecules in transient-excited states remains a challenge due to the extreme requirements for spatial and temporal resolution. Ultrafast electron diffraction from aligned molecules provides atomic resolution and allows for the retrieval of structural information without the need to rely on theoretical models. Here we use ultrafast electron diffraction from aligned molecules and femtosecond laser mass spectrometry to investigate the dynamics in carbon disulfide following the interaction with an intense femtosecond laser pulse. We observe that the degree of alignment reaches an upper limit at laser intensities below the ionization threshold, and find evidence of structural deformation, dissociation and ionization at higher laser intensities. PMID:26337631

  17. POSA: a user-driven, interactive multiple protein structure alignment server

    PubMed Central

    Li, Zhanwen; Natarajan, Padmaja; Ye, Yuzhen; Hrabe, Thomas; Godzik, Adam

    2014-01-01

    POSA (Partial Order Structure Alignment), available at http://posa.godziklab.org, is a server for multiple protein structure alignment introduced in 2005 (Ye,Y. and Godzik,A. (2005) Multiple flexible structure alignment using partial order graphs. Bioinformatics, 21, 2362–2369). It is free and open to all users, and there is no login requirement, albeit there is an option to register and store results in individual, password-protected directories. In the updated POSA server described here, we introduce two significant improvements. First is an interface allowing the user to provide additional information by defining segments that anchor the alignment in one or more input structures. This interface allows users to take advantage of their intuition and biological insights to improve the alignment and guide it toward a biologically relevant solution. The second improvement is an interactive visualization with options that allow the user to view all superposed structures in one window (a typical solution for visualizing results of multiple structure alignments) or view them individually in a series of synchronized windows with extensive, user-controlled visualization options. The user can rotate structure(s) in any of the windows and study similarities or differences between structures clearly visible in individual windows. PMID:24838569

  18. Structural anisotropy of magnetically aligned single wall carbon nanotube films

    SciTech Connect

    Smith, B. W.; Benes, Z.; Luzzi, D. E.; Fischer, J. E.; Walters, D. A.; Casavant, M. J.; Schmidt, J.; Smalley, R. E.

    2000-07-31

    Thick films of aligned single wall carbon nanotubes and ropes have been produced by filtration/deposition from suspension in strong magnetic fields. We measured mosaic distributions of rope orientations in the film plane, for samples of different thicknesses. For an {approx}1 {mu}m film the full width at half maximum (FWHM) derived from electron diffraction is 25 degree sign -28 degree sign . The FWHM of a thicker film ({approx}7 {mu}m) measured by x-ray diffraction is slightly broader, 35{+-}3 degree sign . Aligned films are denser than ordinary filter-deposited ones, and much denser than as-grown material. Optimization of the process is expected to yield smaller FWHMs and higher densities. (c) 2000 American Institute of Physics.

  19. Heteroepitaxial formation of aligned mesostructured silica films with large structural periodicities from mixed surfactant systems.

    PubMed

    Hayase, Saeko; Kanno, Yosuke; Watanabe, Masatoshi; Takahashi, Masahiko; Kuroda, Kazuyuki; Miyata, Hirokatsu

    2013-06-11

    Liquid-crystal phases consisting of cylindrical micelles of amphiphilic block copolymers and silica precursors are epitaxially built up on aligned surface micelles formed by an alkyl-PEO surfactant, Brij56, irrespective of the large difference in the intrinsic structural periodicities resulting in the formation of fully aligned mesostructured silica films with large lattice constants. Brij56 works as an alignment controlling agent on rubbing-treated polyimide through selective adsorption from a precursor solution containing the two surfactants, a block copolymer and Brij56, through strong hydrophobic interactions to form an anisotropic surface micelle structure. Aligned mesostructured silica layers with larger periodicities, which dominantly consist of block copolymers, form on these aligned surface micelles by gradually changing the vertical periodicity keeping the lateral intermicelle distance constant. This can be regarded as a kind of heteroepitaxy because the lattice constant at the surface is different from that of the bulk of the film. On the basis of this new concept, highly aligned mesostructured silica films with structural periodicities as large as 10 nm are successfully formed, which has never been achieved when the block copolymers are used alone as the structure-directing agent. The periodicity of the aligned films can precisely be controlled by an appropriate choice of block copolymers and the mixing ratio of the two surfactants, which increases the opportunity for applications of these films with highly anisotropic mesoscale structure. PMID:23721098

  20. Acceleration of the GAMESS-UK electronic structure package on graphical processing units.

    PubMed

    Wilkinson, Karl A; Sherwood, Paul; Guest, Martyn F; Naidoo, Kevin J

    2011-07-30

    The approach used to calculate the two-electron integral by many electronic structure packages including generalized atomic and molecular electronic structure system-UK has been designed for CPU-based compute units. We redesigned the two-electron compute algorithm for acceleration on a graphical processing unit (GPU). We report the acceleration strategy and illustrate it on the (ss|ss) type integrals. This strategy is general for Fortran-based codes and uses the Accelerator compiler from Portland Group International and GPU-based accelerators from Nvidia. The evaluation of (ss|ss) type integrals within calculations using Hartree Fock ab initio methods and density functional theory are accelerated by single and quad GPU hardware systems by factors of 43 and 153, respectively. The overall speedup for a single self consistent field cycle is at least a factor of eight times faster on a single GPU compared with that of a single CPU. PMID:21541963

  1. Imaging the electronic structure of valence orbitals in the XUV ionization of aligned molecules

    NASA Astrophysics Data System (ADS)

    Rouzée, Arnaud; Harvey, Alex G.; Kelkensberg, Freek; Brambila, Danilo; Kiu Siu, Wing; Gademann, Georg; Smirnova, Olga; Vrakking, Marc J. J.

    2014-06-01

    We present measurements of photoelectron angular distributions (PADs) for the ionization of aligned CO2 molecules by an extreme ultraviolet laser pulse (17-45 eV) that is produced via high-harmonic generation, and that is polarized perpendicularly to the alignment laser axis. Differential PADs are recorded by taking the difference between two measurements for aligned and anti-aligned molecules. The results are compared with ab initio multi-channel R-matrix calculations, which are extended to include the computation of PADs. The calculations agree very well with the experiment, and are resolved with respect to the internal state of the ion and the polarization of the ionizing laser field relative to the molecular frame. For a sufficiently high, but experimentally achievable degree of alignment, the nodal structure of the molecular orbital becomes visible in the PAD.

  2. Modeling and diagnosis of structural systems through sparse dynamic graphical models

    NASA Astrophysics Data System (ADS)

    Bornn, Luke; Farrar, Charles R.; Higdon, David; Murphy, Kevin P.

    2016-06-01

    Since their introduction into the structural health monitoring field, time-domain statistical models have been applied with considerable success. Current approaches still have several flaws, however, as they typically ignore the structure of the system, using individual sensor data for modeling and diagnosis. This paper introduces a Bayesian framework containing much of the previous work with autoregressive models as a special case. In addition, the framework allows for natural inclusion of structural knowledge through the form of prior distributions on the model parameters. Acknowledging the need for computational efficiency, we extend the framework through the use of decomposable graphical models, exploiting sparsity in the system to give models that are simple to fit and understand. This sparsity can be specified from knowledge of the system, from the data itself, or through a combination of the two. Using both simulated and real data, we demonstrate the capability of the model to capture the dynamics of the system and to provide clear indications of structural change and damage. We also demonstrate how learning the sparsity in the system gives insight into the structure's physical properties.

  3. Self-consistently optimized statistical mechanical energy functions for sequence structure alignment.

    PubMed Central

    Koretke, K. K.; Luthey-Schulten, Z.; Wolynes, P. G.

    1996-01-01

    A quantitative form of the principle of minimal frustration is used to obtain from a database analysis statistical mechanical energy functions and gap parameters for aligning sequences to three-dimensional structures. The analysis that partially takes into account correlations in the energy landscape improves upon the previous approximations of Goldstein et al. (1994, 1995) (Goldstein R, Luthey-Schulten Z, Wolynes P, 1994, Proceedings of the 27th Hawaii International Conference on System Sciences. Los Alamitos, California: IEEE Computer Society Press. pp 306-315; Goldstein R, Luthey-Schulten Z, Wolynes P, 1995, In: Elber R, ed. New developments in theoretical studies of proteins. Singapore: World Scientific). The energy function allows for ordering of alignments based on the compatibility of a sequence to be in a given structure (i.e., lowest energy) and therefore removes the necessity of using percent identity or similarity as scoring parameters. The alignments produced by the energy function on distant homologues with low percent identity (less than 21%) are generally better than those generated with evolutionary information. The lowest energy alignment generated with the energy function for sequences containing prosite signatures but unknown structures is a structure containing the same prosite signature, providing a check on the robustness of the algorithm. Finally, the energy function can make use of known experimental evidence as constraints within the alignment algorithm to aid in finding the correct structural alignment. PMID:8762136

  4. Pairwise Sequence Alignment Library

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprintmore » that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.« less

  5. Pairwise Sequence Alignment Library

    SciTech Connect

    Jeff Daily, PNNL

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  6. Structure and ionic conductivity of well-aligned polycrystalline sodium titanogallate grown by reactive diffusion

    SciTech Connect

    Hasegawa, Ryo; Okabe, Momoko; Asaka, Toru; Ishizawa, Nobuo; Fukuda, Koichiro

    2015-09-15

    We prepared the b-axis-oriented polycrystalline Na{sub 0.85}Ti{sub 0.51}Ga{sub 4.37}O{sub 8} (NTGO) embedded in Ga{sub 2}O{sub 3}-doped Na{sub 2}Ti{sub 4}O{sub 9} matrix using the reactive diffusion technique. When the sandwich-type Ga{sub 2}TiO{sub 5}/NaGaO{sub 2}/Ga{sub 2}TiO{sub 5} diffusion couple was heated at 1323 K for 24 h, the NTGO polycrystal was readily formed in the presence of a liquid phase. The resulting polycrystalline material was characterized by X-ray diffractometry, electron microscopy and impedance spectroscopy. We mechanically processed the annealed diffusion couple and obtained the thin-plate electrolyte consisting mostly of the grain-aligned NTGO polycrystal. The ionic conductivity (σ) of the electrolyte along the common b-axis direction steadily increased from 1.3×10{sup −4} to 7.3×10{sup −3} S/cm as the temperature increased from 573 to 1073 K. There was a slope change at ca. 792 K for the Arrhenius plot of σ; the activation energies were 0.39 eV above this temperature and 0.57 eV below it. The NTGO showed the crystal structure (space group C2/m) with substantial positional disordering of one of the two Ga sites. The Na{sup +} ions occupied ca. 43% of the Wyckoff position 4i site, the deficiency of which would contribute to the relatively high ionic conductivity along the b-axis. The reactive diffusion could be widely applicable as the novel technique to the preparation of grain-aligned ceramics of multi-component systems. - Graphical abstract: We have prepared the b-axis-oriented Na{sub 0.85}Ti{sub 0.51}Ga{sub 4.37}O{sub 8} polycrystal embedded in Ga{sub 2}O{sub 3}-doped Na{sub 2}Ti{sub 4}O{sub 9} matrix by the heat treatment of sandwich-type diffusion couple of Ga{sub 2}TiO{sub 5}/NaGaO{sub 2}/Ga{sub 2}TiO{sub 5}. The resulting Na{sub 0.85}Ti{sub 0.51}Ga{sub 4.37}O{sub 8} electrolyte showed the ionic conductivity ranging from 1.3×10{sup −4} S/cm at 573 K to 7.3×10{sup −3} S/cm at 1073 K. - Highlights: • The b

  7. Exploratory graphical models of functional and structural connectivity patterns for Alzheimer's Disease diagnosis

    PubMed Central

    Ortiz, Andrés; Munilla, Jorge; Álvarez-Illán, Ignacio; Górriz, Juan M.; Ramírez, Javier

    2015-01-01

    Alzheimer's Disease (AD) is the most common neurodegenerative disease in elderly people. Its development has been shown to be closely related to changes in the brain connectivity network and in the brain activation patterns along with structural changes caused by the neurodegenerative process. Methods to infer dependence between brain regions are usually derived from the analysis of covariance between activation levels in the different areas. However, these covariance-based methods are not able to estimate conditional independence between variables to factor out the influence of other regions. Conversely, models based on the inverse covariance, or precision matrix, such as Sparse Gaussian Graphical Models allow revealing conditional independence between regions by estimating the covariance between two variables given the rest as constant. This paper uses Sparse Inverse Covariance Estimation (SICE) methods to learn undirected graphs in order to derive functional and structural connectivity patterns from Fludeoxyglucose (18F-FDG) Position Emission Tomography (PET) data and segmented Magnetic Resonance images (MRI), drawn from the ADNI database, for Control, MCI (Mild Cognitive Impairment Subjects), and AD subjects. Sparse computation fits perfectly here as brain regions usually only interact with a few other areas. The models clearly show different metabolic covariation patters between subject groups, revealing the loss of strong connections in AD and MCI subjects when compared to Controls. Similarly, the variance between GM (Gray Matter) densities of different regions reveals different structural covariation patterns between the different groups. Thus, the different connectivity patterns for controls and AD are used in this paper to select regions of interest in PET and GM images with discriminative power for early AD diagnosis. Finally, functional an structural models are combined to leverage the classification accuracy. The results obtained in this work show the

  8. Seed selection strategy in global network alignment without destroying the entire structures of functional modules

    PubMed Central

    2012-01-01

    Background Network alignment is one of the most common biological network comparison methods. Aligning protein-protein interaction (PPI) networks of different species is of great important to detect evolutionary conserved pathways or protein complexes across species through the identification of conserved interactions, and to improve our insight into biological systems. Global network alignment (GNA) problem is NP-complete, for which only heuristic methods have been proposed so far. Generally, the current GNA methods fall into global heuristic seed-and-extend approaches. These methods can not get the best overall consistent alignment between networks for the opinionated local seed. Furthermore These methods are lost in maximizing the number of aligned edges between two networks without considering the original structures of functional modules. Methods We present a novel seed selection strategy for global network alignment by constructing the pairs of hub nodes of networks to be aligned into multiple seeds. Beginning from every hub seed and using the membership similarity of nodes to quantify to what extent the nodes can participate in functional modules associated with current seed topologically we align the networks by modules. By this way we can maintain the functional modules are not damaged during the heuristic alignment process. And our method is efficient in resolving the fatal problem of most conventional algorithms that the initialization selected seeds have a direct influence on the alignment result. The similarity measures between network nodes (e.g., proteins) include sequence similarity, centrality similarity, and dynamic membership similarity and our algorithm can be called Multiple Hubs-based Alignment (MHA). Results When applying our seed selection strategy to several pairs of real PPI networks, it is observed that our method is working to strike a balance, extending the conserved interactions while maintaining the functional modules unchanged. In

  9. Symbolic and graphical representation scheme for sensors deployed in large-scale structures.

    PubMed

    Park, Hyo Seon; Shin, Yunah; Choi, Se Woon; Kim, Yousok

    2013-01-01

    As wireless sensor network (WSN)-based structural health monitoring (SHM) systems are increasingly being employed in civil infrastructures and building structures, the management of large numbers of sensing devices and the large amount of data acquired from WSNs will become increasingly difficult unless systematic expressions of the sensor network are provided. This study introduces a practical WSN for SHM that consists of sensors, wireless sensor nodes, repeater nodes, master nodes, and monitoring servers. This study also proposes a symbolic and graphical representation scheme (SGRS) for this system, in which the communication relationships and respective location information of the distributed sensing components are expressed in a concise manner. The SGRS was applied to the proposed WSN, which is employed in an actual large-scale irregular structure in which three types of sensors (75 vibrating wire strain gauges, 10 inclinometers, and three laser displacement sensors) and customized wireless sensor nodes are installed. The application results demonstrate that prompt identification of sensing units and effective management of the distributed sensor network can be realized from the SGRS. The results also demonstrate the superiority of the SGRS over conventional expression methods in which a box diagram or tree diagram representing the ID of sensors and data loggers is used. PMID:23912426

  10. Symbolic and Graphical Representation Scheme for Sensors Deployed in Large-Scale Structures

    PubMed Central

    Park, Hyo Seon; Shin, Yunah; Choi, Se Woon; Kim, Yousok

    2013-01-01

    As wireless sensor network (WSN)-based structural health monitoring (SHM) systems are increasingly being employed in civil infrastructures and building structures, the management of large numbers of sensing devices and the large amount of data acquired from WSNs will become increasingly difficult unless systematic expressions of the sensor network are provided. This study introduces a practical WSN for SHM that consists of sensors, wireless sensor nodes, repeater nodes, master nodes, and monitoring servers. This study also proposes a symbolic and graphical representation scheme (SGRS) for this system, in which the communication relationships and respective location information of the distributed sensing components are expressed in a concise manner. The SGRS was applied to the proposed WSN, which is employed in an actual large-scale irregular structure in which three types of sensors (75 vibrating wire strain gauges, 10 inclinometers, and three laser displacement sensors) and customized wireless sensor nodes are installed. The application results demonstrate that prompt identification of sensing units and effective management of the distributed sensor network can be realized from the SGRS. The results also demonstrate the superiority of the SGRS over conventional expression methods in which a box diagram or tree diagram representing the ID of sensors and data loggers is used. PMID:23912426

  11. Simultaneous Bayesian Estimation of Alignment and Phylogeny under a Joint Model of Protein Sequence and Structure

    PubMed Central

    Herman, Joseph L.; Challis, Christopher J.; Novák, Ádám; Hein, Jotun; Schmidler, Scott C.

    2014-01-01

    For sequences that are highly divergent, there is often insufficient information to infer accurate alignments, and phylogenetic uncertainty may be high. One way to address this issue is to make use of protein structural information, since structures generally diverge more slowly than sequences. In this work, we extend a recently developed stochastic model of pairwise structural evolution to multiple structures on a tree, analytically integrating over ancestral structures to permit efficient likelihood computations under the resulting joint sequence–structure model. We observe that the inclusion of structural information significantly reduces alignment and topology uncertainty, and reduces the number of topology and alignment errors in cases where the true trees and alignments are known. In some cases, the inclusion of structure results in changes to the consensus topology, indicating that structure may contain additional information beyond that which can be obtained from sequences. We use the model to investigate the order of divergence of cytoglobins, myoglobins, and hemoglobins and observe a stabilization of phylogenetic inference: although a sequence-based inference assigns significant posterior probability to several different topologies, the structural model strongly favors one of these over the others and is more robust to the choice of data set. PMID:24899668

  12. Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.

    PubMed

    Washietl, Stefan; Bernhart, Stephan H; Kellis, Manolis

    2014-01-01

    Many biologically important RNA structures are conserved in evolution leading to characteristic mutational patterns. RNAalifold is a widely used program to predict consensus secondary structures in multiple alignments by combining evolutionary information with traditional energy-based RNA folding algorithms. Here we describe the theory and applications of the RNAalifold algorithm. Consensus secondary structure prediction not only leads to significantly more accurate structure models, but it also allows to study structural conservation of functional RNAs. PMID:24639158

  13. How Students "Unpack" the Structure of a Word Problem: Graphic Representations and Problem Solving

    ERIC Educational Resources Information Center

    Edens, Kellah; Potter, Ellen

    2008-01-01

    This research investigated how fourth and fifth grade students spontaneously "unpacked" a word problem when generating a graphic representation to aid in problem solution. Relationships among the type of graphic representation produced, spatial visualization, drawing ability, gender, and problem solving also were examined and described.…

  14. Magnetic field-aligned coupling effects on ionospheric plasma structure

    NASA Technical Reports Server (NTRS)

    Heelis, R. A.; Vickrey, J. F.

    1990-01-01

    This paper presents a mathematical description of the electrical coupling and dynamics of plasma structure in the E and F regions. The scale size dependence of the electric field coupling along the magnetic field is examined for a realistic background ionosphere and atmosphere. It is shown that, while normalized potentials map reciprocally between two altitudes, the potential disturbance caused by a fixed amplitude plasma density perturbation does not. The magnitude of electrostatic potential created by structured ionization is also shown to be strongly dependent on the altitude of the structure. The role of diffusion parallel to the magnetic field in the redistribution and decay of plasma structure is illustrated.

  15. Pathological tendons maintain sufficient aligned fibrillar structure on ultrasound tissue characterization (UTC).

    PubMed

    Docking, S I; Cook, J

    2016-06-01

    Structural disorganization in the tendon is associated with tendinopathy, with little research investigating whether disorganization overwhelms the overall structural integrity of the tendon. This study investigated the mean cross-sectional area (CSA) of aligned fibrillar structure as detected by ultrasound tissue characterization (UTC) in the pathological and normal Achilles and patellar tendons. Ninety-one participants had their Achilles and/or patellar tendons scanned using UTC to capture a three-dimensional image of the tendon and allow a semi-quantification of the echopattern. The mean CSA of aligned fibrillar structure (echo type I + II) and disorganized structure (echo type III + IV) was calculated based on UTC algorithms. Each tendon was classified as either pathological or normal based solely on gray-scale ultrasound. The mean CSA of aligned fibrillar structure was significantly greater (P ≤ 0.001) in the pathological tendon compared with the normal tendon, despite the pathological tendon containing greater amounts of disorganized structure (P ≤ 0.001). A significant relationship was observed between the mean CSA of disorganized structure and anteroposterior diameter of the Achilles (R(2)  = 0.587) and patellar (R(2)  = 0.559) tendons. This study is the first to show that pathological tendons have sufficient levels of aligned fibrillar structure. Pathological tendons may compensate for areas of disorganization by increasing in tendon thickness. PMID:26059532

  16. Alignment and structural control of nitrogen-doped carbon nanotubes by utilizing precursor concentration effect.

    PubMed

    Deng, Weina; Chen, Xiaohua; Chen, Xian; Liu, Zheng; Zeng, Ying; Hu, Aiping; Xiong, Yina; Li, Zhe; Tang, Qunli

    2014-11-28

    Nitrogen-doped carbon nanotubes (NCNTs) were prepared using a simple ultrasonic spray pyrolysis method. The precursor concentration effect was examined to effectively control alignment, open tip and diameter of the NCNTs by changing xylene/cyclohexylamine ratio. The structure and morphology of the resultant NCNTs were characterized by scanning electron microscopy, transmission electron microscopy and x-ray photoelectron spectroscopy. The degree of alignment and the diameter of the NCNTs increased as the xylene/cyclohexylamine precursor mixture was changed from 0 to 35% cyclohexylamine. This precursor composition also caused a large number of open-ended nanotubes to form with graphite layers inside the cavities of the NCNTs. However, further increase cyclohexylamine content in the precursor reduced the degree of alignment and diameter of the NCNTs. We demonstrate control over the NCNT alignment and diameter, along with the formation of open-ended nanotube tips, and propose a growth mechanism to understand how these properties are interlinked. PMID:25369800

  17. Homeotropically aligning phase separated columnar structures for fabrication of flexible electrooptical devices

    NASA Astrophysics Data System (ADS)

    Acharya, Bharat R.; Choi, Hyunchul; Srinivasarao, Mohan; Kumar, Satyendra

    2011-11-01

    A method of achieving homeotropic alignment of liquid crystals (LCs) by ultraviolet light induced phase separation of LC from its mixture with photo-curable pre-polymer is reported. Vertical polymer columns and micro-fibrils developed during the phase separation promote homeotropic alignment of the LC director (i.e., alignment perpendicular to the LC-substrate interface), suitable for devices based on LCs possessing negative dielectric anisotropy. These vertical structures extend between two substrates and permit the fabrication of highly flexible electro-optical devices with high contrast coupled with fast response times. This simple single-step technique eliminates the need for the traditional polymer alignment layer pre-deposited on substrates.

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

    PubMed Central

    Rose, Dominic; Backofen, Rolf

    2012-01-01

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

  19. Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications

    PubMed Central

    Cvicek, Vaclav; Goddard, William A.; Abrol, Ravinder

    2016-01-01

    The understanding of G-protein coupled receptors (GPCRs) is undergoing a revolution due to increased information about their signaling and the experimental determination of structures for more than 25 receptors. The availability of at least one receptor structure for each of the GPCR classes, well separated in sequence space, enables an integrated superfamily-wide analysis to identify signatures involving the role of conserved residues, conserved contacts, and downstream signaling in the context of receptor structures. In this study, we align the transmembrane (TM) domains of all experimental GPCR structures to maximize the conserved inter-helical contacts. The resulting superfamily-wide GpcR Sequence-Structure (GRoSS) alignment of the TM domains for all human GPCR sequences is sufficient to generate a phylogenetic tree that correctly distinguishes all different GPCR classes, suggesting that the class-level differences in the GPCR superfamily are encoded at least partly in the TM domains. The inter-helical contacts conserved across all GPCR classes describe the evolutionarily conserved GPCR structural fold. The corresponding structural alignment of the inactive and active conformations, available for a few GPCRs, identifies activation hot-spot residues in the TM domains that get rewired upon activation. Many GPCR mutations, known to alter receptor signaling and cause disease, are located at these conserved contact and activation hot-spot residue positions. The GRoSS alignment places the chemosensory receptor subfamilies for bitter taste (TAS2R) and pheromones (Vomeronasal, VN1R) in the rhodopsin family, known to contain the chemosensory olfactory receptor subfamily. The GRoSS alignment also enables the quantification of the structural variability in the TM regions of experimental structures, useful for homology modeling and structure prediction of receptors. Furthermore, this alignment identifies structurally and functionally important residues in all human GPCRs

  20. Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications.

    PubMed

    Cvicek, Vaclav; Goddard, William A; Abrol, Ravinder

    2016-03-01

    The understanding of G-protein coupled receptors (GPCRs) is undergoing a revolution due to increased information about their signaling and the experimental determination of structures for more than 25 receptors. The availability of at least one receptor structure for each of the GPCR classes, well separated in sequence space, enables an integrated superfamily-wide analysis to identify signatures involving the role of conserved residues, conserved contacts, and downstream signaling in the context of receptor structures. In this study, we align the transmembrane (TM) domains of all experimental GPCR structures to maximize the conserved inter-helical contacts. The resulting superfamily-wide GpcR Sequence-Structure (GRoSS) alignment of the TM domains for all human GPCR sequences is sufficient to generate a phylogenetic tree that correctly distinguishes all different GPCR classes, suggesting that the class-level differences in the GPCR superfamily are encoded at least partly in the TM domains. The inter-helical contacts conserved across all GPCR classes describe the evolutionarily conserved GPCR structural fold. The corresponding structural alignment of the inactive and active conformations, available for a few GPCRs, identifies activation hot-spot residues in the TM domains that get rewired upon activation. Many GPCR mutations, known to alter receptor signaling and cause disease, are located at these conserved contact and activation hot-spot residue positions. The GRoSS alignment places the chemosensory receptor subfamilies for bitter taste (TAS2R) and pheromones (Vomeronasal, VN1R) in the rhodopsin family, known to contain the chemosensory olfactory receptor subfamily. The GRoSS alignment also enables the quantification of the structural variability in the TM regions of experimental structures, useful for homology modeling and structure prediction of receptors. Furthermore, this alignment identifies structurally and functionally important residues in all human GPCRs

  1. A Visual Graphic Tool to Support the Production of Simple Sentence Structures in a Student with Learning Disability

    ERIC Educational Resources Information Center

    Valiquette, Christine; Gerin-Lajoie, Anne-Marie; Sutton, Ann

    2006-01-01

    A tool was devised to improve spoken syntax through manipulation of graphic symbols. The participant, a French-speaking 11-year-old girl with general learning disability, learned to produce subject-verb-object (SVOn) sentences and transform them into a subject-object-verb (SOpV) structure in which the object becomes pronominal in a preverbal…

  2. Alignment of quasar polarizations with large-scale structures

    NASA Astrophysics Data System (ADS)

    Hutsemékers, D.; Braibant, L.; Pelgrims, V.; Sluse, D.

    2014-12-01

    We have measured the optical linear polarization of quasars belonging to Gpc scale quasar groups at redshift z ~ 1.3. Out of 93 quasars observed, 19 are significantly polarized. We found that quasar polarization vectors are either parallel or perpendicular to the directions of the large-scale structures to which they belong. Statistical tests indicate that the probability that this effect can be attributed to randomly oriented polarization vectors is on the order of 1%. We also found that quasars with polarization perpendicular to the host structure preferentially have large emission line widths while objects with polarization parallel to the host structure preferentially have small emission line widths. Considering that quasar polarization is usually either parallel or perpendicular to the accretion disk axis depending on the inclination with respect to the line of sight, and that broader emission lines originate from quasars seen at higher inclinations, we conclude that quasar spin axes are likely parallel to their host large-scale structures. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under program ID 092.A-0221.Table 1 is available in electronic form at http://www.aanda.org

  3. The Alignment of Technology and Structure through Roles and Networks.

    ERIC Educational Resources Information Center

    Barley, Stephen R.

    1990-01-01

    Building on Nagel's theory of social structure, this paper argues that the microsocial dynamics occasioned by new technologies systematically reverberate up levels of analysis. This theory is illustrated by ethnographic and sociometric data drawn from a study comparing usage of traditional and computerized imaging devices in two radiology…

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

    DOEpatents

    Zemla, Adam T.

    2011-09-20

    A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

  5. Mask aligner lithography for TSV-structures using a double-sided (structured) photomask

    NASA Astrophysics Data System (ADS)

    Weichelt, T.; Stuerzebecher, L.; Zeitner, U. D.

    2015-03-01

    Through-silicon vias (TSV) are important for wafer level packaging (WLP) as they provide patterning holes through thick silicon dies to integrate and interconnect devices which are stacked in z-direction. For economic processing TSV fabrication primarily needs to be cost-effective including especially a high throughput. Furthermore, a lithography process for TSV has to be stable enough to allow patterning on pre-structured substrates with inhomogeneous topography. This can be addressed by an exposure process which offers a large depth of focus. We have developed a mask-aligner lithography process based on the use of a double-sided photomask to realize aerial images which meet these constraints.

  6. TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison

    PubMed Central

    2012-01-01

    Background In structural biology, similarity analysis of protein structure is a crucial step in studying the relationship between proteins. Despite the considerable number of techniques that have been explored within the past two decades, the development of new alternative methods is still an active research area due to the need for high performance tools. Results In this paper, we present TS-AMIR, a Topology String Alignment Method for Intensive Rapid comparison of protein structures. The proposed method works in two stages: In the first stage, the method generates a topology string based on the geometric details of secondary structure elements, and then, utilizes an n-gram modelling technique over entropy concept to capture similarities in these strings. This initial correspondence map between secondary structure elements is submitted to the second stage in order to obtain the alignment at the residue level. Applying the Kabsch method, a heuristic step-by-step algorithm is adopted in the second stage to align the residues, resulting in an optimal rotation matrix and minimized RMSD. The performance of the method was assessed in different information retrieval tests and the results were compared with those of CE and TM-align, representing two geometrical tools, and YAKUSA, 3D-BLAST and SARST as three representatives of linear encoding schemes. It is shown that the method obtains a high running speed similar to that of the linear encoding schemes. In addition, the method runs about 800 and 7200 times faster than TM-align and CE respectively, while maintaining a competitive accuracy with TM-align and CE. Conclusions The experimental results demonstrate that linear encoding techniques are capable of reaching the same high degree of accuracy as that achieved by geometrical methods, while generally running hundreds of times faster than conventional programs. PMID:22336468

  7. Computer Graphics.

    ERIC Educational Resources Information Center

    Halpern, Jeanne W.

    1970-01-01

    Computer graphics have been called the most exciting development in computer technology. At the University of Michigan, three kinds of graphics output equipment are now being used: symbolic printers, line plotters or drafting devices, and cathode-ray tubes (CRT). Six examples are given that demonstrate the range of graphics use at the University.…

  8. Enzyme structure captures four cysteines aligned for disulfide relay

    PubMed Central

    Gat, Yair; Vardi-Kilshtain, Alexandra; Grossman, Iris; Major, Dan Thomas; Fass, Deborah

    2014-01-01

    Thioredoxin superfamily proteins introduce disulfide bonds into substrates, catalyze the removal of disulfides, and operate in electron relays. These functions rely on one or more dithiol/disulfide exchange reactions. The flavoenzyme quiescin sulfhydryl oxidase (QSOX), a catalyst of disulfide bond formation with an interdomain electron transfer step in its catalytic cycle, provides a unique opportunity for exploring the structural environment of enzymatic dithiol/disulfide exchange. Wild-type Rattus norvegicus QSOX1 (RnQSOX1) was crystallized in a conformation that juxtaposes the two redox-active di-cysteine motifs in the enzyme, presenting the entire electron-transfer pathway and proton-transfer participants in their native configurations. As such a state cannot generally be enriched and stabilized for analysis, RnQSOX1 gives unprecedented insight into the functional group environments of the four cysteines involved in dithiol/disulfide exchange and provides the framework for analysis of the energetics of electron transfer in the presence of the bound flavin adenine dinucleotide cofactor. Hybrid quantum mechanics/molecular mechanics (QM/MM) free energy simulations based on the X-ray crystal structure suggest that formation of the interdomain disulfide intermediate is highly favorable and secures the flexible enzyme in a state from which further electron transfer via the flavin can occur. PMID:24888638

  9. A data-mining approach for multiple structural alignment of proteins.

    PubMed

    Siu, Wing-Yan; Mamoulis, Nikos; Yiu, Siu-Ming; Chan, Ho-Leung

    2010-01-01

    Comparing the 3D structures of proteins is an important but computationally hard problem in bioinformatics. In this paper, we propose studying the problem when much less information or assumptions are available. We model the structural alignment of proteins as a combinatorial problem. In the problem, each protein is simply a set of points in the 3D space, without sequence order information, and the objective is to discover all large enough alignments for any subset of the input. We propose a data-mining approach for this problem. We first perform geometric hashing of the structures such that points with similar locations in the 3D space are hashed into the same bin in the hash table. The novelty is that we consider each bin as a coincidence group and mine for frequent patterns, which is a well-studied technique in data mining. We observe that these frequent patterns are already potentially large alignments. Then a simple heuristic is used to extend the alignments if possible. We implemented the algorithm and tested it using real protein structures. The results were compared with existing tools. They showed that the algorithm is capable of finding conserved substructures that do not preserve sequence order, especially those existing in protein interfaces. The algorithm can also identify conserved substructures of functionally similar structures within a mixture with dissimilar ones. The running time of the program was smaller or comparable to that of the existing tools. PMID:21079664

  10. Molecular Graphics and Chemistry.

    ERIC Educational Resources Information Center

    Weber, Jacques; And Others

    1992-01-01

    Explains molecular graphics, i.e., the application of computer graphics techniques to investigate molecular structure, function, and interaction. Structural models and molecular surfaces are discussed, and a theoretical model that can be used for the evaluation of intermolecular interaction energies for organometallics is described. (45…

  11. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    SciTech Connect

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R

    2007-12-10

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  12. DR-TAMAS: Diffeomorphic Registration for Tensor Accurate Alignment of Anatomical Structures.

    PubMed

    Irfanoglu, M Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B; Sadeghi, Neda; Thomas, Cibu P; Pierpaoli, Carlo

    2016-05-15

    In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM. PMID:26931817

  13. Aligning USGS senior leadership structure with the USGS science strategy

    USGS Publications Warehouse

    U.S. Geological Survey

    2010-01-01

    The U.S. Geological Survey (USGS) is realigning its management and budget structure to further enhance the work of its science programs and their interdisciplinary focus areas related to the USGS Science Strategy as outlined in 'Facing Tomorrow's Challenges-U.S. Geological Survey Science in the Decade 2007-2017' (U.S. Geological Survey, 2007). In 2007, the USGS developed this science strategy outlining major natural-science issues facing the Nation and focusing on areas where natural science can make a substantial contribution to the well being of the Nation and the world. These areas include global climate change, water resources, natural hazards, energy and minerals, ecosystems, and data integration.

  14. IMAT graphics manual

    NASA Technical Reports Server (NTRS)

    Stockwell, Alan E.; Cooper, Paul A.

    1991-01-01

    The Integrated Multidisciplinary Analysis Tool (IMAT) consists of a menu driven executive system coupled with a relational database which links commercial structures, structural dynamics and control codes. The IMAT graphics system, a key element of the software, provides a common interface for storing, retrieving, and displaying graphical information. The IMAT Graphics Manual shows users of commercial analysis codes (MATRIXx, MSC/NASTRAN and I-DEAS) how to use the IMAT graphics system to obtain high quality graphical output using familiar plotting procedures. The manual explains the key features of the IMAT graphics system, illustrates their use with simple step-by-step examples, and provides a reference for users who wish to take advantage of the flexibility of the software to customize their own applications.

  15. Alignment tolerance of accelerating structures and corrections for future linear colliders

    SciTech Connect

    Kubo, K.; Adolphsen, C.; Bane, K.L.F.; Raubenheimer, T.O.; Thompson, K.A.

    1995-06-01

    The alignment tolerance of accelerating structures is estimated by tracking simulations. Both single-bunch and multi-bunch effects are taken into account. Correction schemes for controlling the single and multi-bunch emittance growth in the case of large misalignment are also tested by simulations.

  16. Spin Alignments of Spiral Galaxies within the Large-scale Structure from SDSS DR7

    NASA Astrophysics Data System (ADS)

    Zhang, Youcai; Yang, Xiaohu; Wang, Huiyuan; Wang, Lei; Luo, Wentao; Mo, H. J.; van den Bosch, Frank C.

    2015-01-01

    Using a sample of spiral galaxies selected from the Sloan Digital Sky Survey Data Release 7 and Galaxy Zoo 2, we investigate the alignment of spin axes of spiral galaxies with their surrounding large-scale structure, which is characterized by the large-scale tidal field reconstructed from the data using galaxy groups above a certain mass threshold. We find that the spin axes only have weak tendencies to be aligned with (or perpendicular to) the intermediate (or minor) axis of the local tidal tensor. The signal is the strongest in a cluster environment where all three eigenvalues of the local tidal tensor are positive. Compared to the alignments between halo spins and the local tidal field obtained in N-body simulations, the above observational results are in best agreement with those for the spins of inner regions of halos, suggesting that the disk material traces the angular momentum of dark matter halos in the inner regions.

  17. SPIN ALIGNMENTS OF SPIRAL GALAXIES WITHIN THE LARGE-SCALE STRUCTURE FROM SDSS DR7

    SciTech Connect

    Zhang, Youcai; Yang, Xiaohu; Luo, Wentao; Wang, Huiyuan; Wang, Lei; Mo, H. J.; Van den Bosch, Frank C. E-mail: xyang@sjtu.edu.cn

    2015-01-01

    Using a sample of spiral galaxies selected from the Sloan Digital Sky Survey Data Release 7 and Galaxy Zoo 2, we investigate the alignment of spin axes of spiral galaxies with their surrounding large-scale structure, which is characterized by the large-scale tidal field reconstructed from the data using galaxy groups above a certain mass threshold. We find that the spin axes only have weak tendencies to be aligned with (or perpendicular to) the intermediate (or minor) axis of the local tidal tensor. The signal is the strongest in a cluster environment where all three eigenvalues of the local tidal tensor are positive. Compared to the alignments between halo spins and the local tidal field obtained in N-body simulations, the above observational results are in best agreement with those for the spins of inner regions of halos, suggesting that the disk material traces the angular momentum of dark matter halos in the inner regions.

  18. Modulation of alignment and differentiation of skeletal myoblasts by submicron ridges/grooves surface structure.

    PubMed

    Wang, Peng-Yuan; Yu, Hung-Te; Tsai, Wei-Bor

    2010-06-01

    Alignment and fusion of myoblasts into parallel arrays of multinucleated myotubes are critical in skeletal muscle tissue engineering. It is well known that contact guidance by grooves/ridges structures induces myoblasts to align and to migrate along the anisotropic direction. In this study, two series of grooved substrata with different widths (450 and 900 nm) and different depths (100, 350, and 550 nm) were studied on their effects on myoblast adhesion, proliferation, and differentiation into myotubes. We found that C2C12 cells were aligned and elongated along the direction of grooves. Groove depth was more influential on cellular morphology, proliferation, and differentiation than groove width. While cell proliferation was retarded on the grooved surfaces especially on the substrate with 900/550 nm (width/depth), differentiation was also enhanced on the patterned surfaces compared to the flat control. Our results demonstrated the potential of grooved substrata with submicron scale in skeletal muscle tissue engineering. PMID:20148416

  19. Arc-Second Alignment of International X-Ray Observatory Mirror Segments in a Fixed Structure

    NASA Technical Reports Server (NTRS)

    Evans, Tyler, C.; Chan, Kai-Wing; Saha, Timo T.

    2010-01-01

    The optics for the International X-Ray Observatory (IXO) require alignment and integration of about fourteen thousand thin mirror segments to achieve the mission goal of 3.0 square meters of effective area at 1.25 keV with an angular resolution of five arc-seconds. These mirror segments are 0.4 mm thick, and 200 to 400 mm in size, which makes it hard to meet the strict angular resolution requirement of 5 arc-seconds for the telescope. This paper outlines the precise alignment, verification testing, and permanent bonding techniques developed at NASA's Goddard Space Flight Center (GSFC). These techniques are used to overcome the challenge of transferring thin mirror segments from a temporary mount to a fixed structure with arc-second alignment and minimal figure distortion. Recent advances in technology development in addition to the automation of several processes have produced significant results. Recent advances in the mirror fixture process known as the suspension mount has allowed for a mirror to be mounted to a fixture with minimal distortion. Once on the fixture, mirror segments have been aligned to around 5 arc-seconds which is halfway to the goal of 2.5 arc-seconds per mirror segment. This paper will highlight the recent advances in alignment, testing, and permanent bonding techniques as well as the results they have produced.

  20. Structurally controlled and aligned tight gas reservoir compartmentalization in the San Juan and Piceance Basins

    SciTech Connect

    Decker, A.D.; Kuuskraa, V.A.; Klawitter, A.L.

    1995-10-01

    Recurrent basement faulting is the primary controlling mechanism for aligning and compartmentalizing upper Cretaceous aged tight gas reservoirs of the San Juan and Piceance Basins. Northwest trending structural lineaments that formed in conjunction with the Uncompahgre Highlands have profoundly influenced sedimentation trends and created boundaries for gas migration; sealing and compartmentalizing sedimentary packages in both basins. Fractures which formed over the structural lineaments provide permeability pathways which allowing gas recovery from otherwise tight gas reservoirs. Structural alignments and associated reservoir compartments have been accurately targeted by integrating advanced remote sensing imagery, high resolution aeromagnetics, seismic interpretation, stratigraphic mapping and dynamic structural modelling. This unifying methodology is a powerful tool for exploration geologists and is also a systematic approach to tight gas resource assessment in frontier basins.

  1. Application of graphically oriented programming to imaging of structure deterioration of historic glass by optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Sylwestrzak, Marcin; Kwiatkowska, Ewa A.; Karaszkiewicz, Pawel; Iwanicka, Magdalena; Targowski, Piotr

    2009-07-01

    Optical Coherence Tomography (OCT) is an interferometric method utilising light of low temporal coherence for noninvasive structural imaging of objects weakly absorbing and scattering light. In this contribution, using various examples of images of objects made of glass affected by the atmospheric corrosion and/or by crizzling, we demonstrate a software developed in our laboratory specifically for 3D OCT imaging of samples with a fine structure. For this task we employed the OpenGL platform (Open Graphics Library), an Application Programming Interface (API) for writing applications dedicated to interactive 3D computer graphics. In our application we have utilized texture rendering with a modulation of transparency and a colour as a function of elevation.

  2. Design Graphics

    NASA Technical Reports Server (NTRS)

    1990-01-01

    A mathematician, David R. Hedgley, Jr. developed a computer program that considers whether a line in a graphic model of a three-dimensional object should or should not be visible. Known as the Hidden Line Computer Code, the program automatically removes superfluous lines and displays an object from a specific viewpoint, just as the human eye would see it. An example of how one company uses the program is the experience of Birdair which specializes in production of fabric skylights and stadium covers. The fabric called SHEERFILL is a Teflon coated fiberglass material developed in cooperation with DuPont Company. SHEERFILL glazed structures are either tension structures or air-supported tension structures. Both are formed by patterned fabric sheets supported by a steel or aluminum frame or cable network. Birdair uses the Hidden Line Computer Code, to illustrate a prospective structure to an architect or owner. The program generates a three- dimensional perspective with the hidden lines removed. This program is still used by Birdair and continues to be commercially available to the public.

  3. Improved liquid crystal pretilt angles by patterned dual alignment coating structures.

    PubMed

    Wu, G M; Chien, H W; Chen, C N; Lin, C Y; Huang, J A; Zeng, H L

    2010-07-01

    The pretilt angles for the optically compensated bend (OCB) mode liquid crystals have been improved using novel patterned dual alignment coating structures in this study. The transition from the splay configuration to the bend configuration can thus be effectively reduced. The dual alignment coating structures consisted of a horizontal alignment polyimide (PI) and a patterned vertical alignment liquid crystal polymer (LCP). Three patterning masks were designed for the photolithography process. The pretilt angles were demonstrated to be increased to 34 degrees for the triangle lattice array-patterned cells. It became 31 degrees for the square lattice array-patterned cells, and 24 degrees for the honeycomb lattice array-patterned cells. The improved pretilt angles were illustrated by the force balance model that can be predicted by the LCP area ratio. The effective control over the pretilt angle could improve the response time to 2 ms when the voltage was ramped up to 5.5 V for the OCB mode liquid crystal devices. PMID:21128462

  4. NATURAL graphics

    NASA Technical Reports Server (NTRS)

    Jones, R. H.

    1984-01-01

    The hardware and software developments in computer graphics are discussed. Major topics include: system capabilities, hardware design, system compatibility, and software interface with the data base management system.

  5. Business Graphics

    NASA Technical Reports Server (NTRS)

    1987-01-01

    Genigraphics Corporation's Masterpiece 8770 FilmRecorder is an advanced high resolution system designed to improve and expand a company's in-house graphics production. GRAFTIME/software package was designed to allow office personnel with minimal training to produce professional level graphics for business communications and presentations. Products are no longer being manufactured.

  6. Graphic Storytelling

    ERIC Educational Resources Information Center

    Thompson, John

    2009-01-01

    Graphic storytelling is a medium that allows students to make and share stories, while developing their art communication skills. American comics today are more varied in genre, approach, and audience than ever before. When considering the impact of Japanese manga on the youth, graphic storytelling emerges as a powerful player in pop culture. In…

  7. Research Update: The electronic structure of hybrid perovskite layers and their energetic alignment in devices

    NASA Astrophysics Data System (ADS)

    Olthof, Selina

    2016-09-01

    In recent years, the interest in hybrid organic-inorganic perovskites has increased at a rapid pace due to their tremendous success in the field of thin film solar cells. This area closely ties together fundamental solid state research and device application, as it is necessary to understand the basic material properties to optimize the performances and open up new areas of application. In this regard, the energy levels and their respective alignment with adjacent charge transport layers play a crucial role. Currently, we are lacking a detailed understanding about the electronic structure and are struggling to understand what influences the alignment, how it varies, or how it can be intentionally modified. This research update aims at giving an overview over recent results regarding measurements of the electronic structure of hybrid perovskites using photoelectron spectroscopy to summarize the present status.

  8. Arc-Second Alignment of International X-Ray Observatory Mirror Segments in a Fixed Structure

    NASA Technical Reports Server (NTRS)

    Evans, Tyler C.; Chan, Kai-Wing; Saha, Timo T.

    2010-01-01

    The optics for the International X-Ray Observatory (IXO) require alignment and integration of about fourteen thousand thin mirror segments to achieve the mission goal of 3.0 square meters of effective area at 1.25 keV with an angular resolution of five arc-seconds. These mirror segments are 0.4 mm thick, and 200 to 400 mm in size, which makes it hard not to impart distortion at the subare- second level. This paper outlines the precise alignment, verification testing, and permanent bonding techniques developed at NASA's Goddard Space Flight Center (GSFC). These techniques are used to overcome the challenge of transferring thin mirror segments from a temporary mount to a fixed structure with arc-second alignment and minimal figure distortion. Recent advances in technology development in addition to the automation of several processes have produced significant results. This paper will highlight the recent advances in alignment, testing, and permanent bonding techniques as well as the results they have produced.

  9. Arc Second Alignment of International X-Ray Observatory Mirror Segments in a Fixed Structure

    NASA Technical Reports Server (NTRS)

    Evans, Tyler C.; Chan, Kai-Wing

    2009-01-01

    The optics for the International X-Ray Observatory (IXO) require alignment and integration of about fourteen thousand thin mirror segments to achieve the mission goal of 3.0 square meters of effective area at 1.25 keV with an angular resolution of five arc seconds. These mirror segments are 0.4mm thick, and 200 to 400mm in size, which makes it hard not to impart distortion at the subarc second level. This paper outlines the precise alignment, verification testing, and permanent bonding techniques developed at NASA's Goddard Space Flight Center (GSFC). These techniques are used to overcome the challenge of transferring thin mirror segments from a temporary mount to a fixed structure with arc second alignment and minimal figure distortion. Recent advances in technology development in addition to the automation of several processes have produced significant results. This paper will highlight the recent advances in alignment, testing, and permanent bonding techniques as well as the results they have produced.

  10. Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation

    PubMed Central

    Sharma, Virag; Elghafari, Anas; Hiller, Michael

    2016-01-01

    Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes. PMID:27016733

  11. Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation.

    PubMed

    Sharma, Virag; Elghafari, Anas; Hiller, Michael

    2016-06-20

    Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes. PMID:27016733

  12. SG2PS (structural geology to postscript converter) - A graphical solution for brittle structural data evaluation and paleostress calculation

    NASA Astrophysics Data System (ADS)

    Sasvári, Ágoston; Baharev, Ali

    2014-05-01

    The aim of this work was to create an open source cross platform application to process brittle structural geological data with seven paleostress inversion algorithms published by different authors and formerly not available within a single desktop application. The tool facilitates separate processing and plotting of different localities, data types and user made groups, using the same single input file. Simplified data input is supported, requiring as small amount of data as possible. Data rotation to correct for bedding tilting, rotation with paleomagnetic declination and k-means clustering are available. RUP and ANG stress estimators calculation and visualization, resolved shear direction display and Mohr circle stress visualization are available. RGB-colored vector graphical outputs are automatically generated in Encapsulated PostScript and Portable Document Format. Stereographical displays on great circle or pole point plot, equal area or equal angle net and upper or lower hemisphere projections are implemented. Rose plots displaying dip direction or strike, with dip angle distribution of the input data set are available. This tool is ideal for preliminary data interpretation on the field (quick processing and visualization in seconds); the implemented methods can be regularly used in the daily academic and industrial work as well. The authors' goal was to create an open source and self-contained desktop application that does not require any additional third party framework (such as .NET) or the Java Virtual Machine. The software has a clear and highly modular structure enabling good code portability, easy maintainability, reusability and extensibility. A Windows installer is publicly available and the program is also fully functional on Linux. The Mac OS X port should be feasible with minimal effort. The install file with test and demo data sets, detailed manual, and links to the GitHub repositories are available on the regularly updated website www.sg2ps.eu.

  13. 1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap.

    PubMed

    Caprara, Alberto; Carr, Robert; Istrail, Sorin; Lancia, Giuseppe; Walenz, Brian

    2004-01-01

    Protein structure comparison is a fundamental problem for structural genomics, with applications to drug design, fold prediction, protein clustering, and evolutionary studies. Despite its importance, there are very few rigorous methods and widely accepted similarity measures known for this problem. In this paper we describe the last few years of developments on the study of an emerging measure, the contact map overlap (CMO), for protein structure comparison. A contact map is a list of pairs of residues which lie in three-dimensional proximity in the protein's native fold. Although this measure is in principle computationally hard to optimize, we show how it can in fact be computed with great accuracy for related proteins by integer linear programming techniques. These methods have the advantage of providing certificates of near-optimality by means of upper bounds to the optimal alignment value. We also illustrate effective heuristics, such as local search and genetic algorithms. We were able to obtain for the first time optimal alignments for large similar proteins (about 1,000 residues and 2,000 contacts) and used the CMO measure to cluster proteins in families. The clusters obtained were compared to SCOP classification in order to validate the measure. Extensive computational experiments showed that alignments which are off by at most 10% from the optimal value can be computed in a short time. Further experiments showed how this measure reacts to the choice of the threshold defining a contact and how to choose this threshold in a sensible way. PMID:15072687

  14. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

    PubMed

    Cannone, Jamie J; Sweeney, Blake A; Petrov, Anton I; Gutell, Robin R; Zirbel, Craig L; Leontis, Neocles

    2015-07-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960

  15. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server

    PubMed Central

    Cannone, Jamie J.; Sweeney, Blake A.; Petrov, Anton I.; Gutell, Robin R.; Zirbel, Craig L.; Leontis, Neocles

    2015-01-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960

  16. STAR3D: a stack-based RNA 3D structural alignment tool

    PubMed Central

    Ge, Ping; Zhang, Shaojie

    2015-01-01

    The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time. PMID:26184875

  17. STAR3D: a stack-based RNA 3D structural alignment tool.

    PubMed

    Ge, Ping; Zhang, Shaojie

    2015-11-16

    The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time. PMID:26184875

  18. Representation of Gravity-Aligned Scene Structure in Ventral Pathway Visual Cortex.

    PubMed

    Vaziri, Siavash; Connor, Charles E

    2016-03-21

    The ventral visual pathway in humans and non-human primates is known to represent object information, including shape and identity [1]. Here, we show the ventral pathway also represents scene structure aligned with the gravitational reference frame in which objects move and interact. We analyzed shape tuning of recently described macaque monkey ventral pathway neurons that prefer scene-like stimuli to objects [2]. Individual neurons did not respond to a single shape class, but to a variety of scene elements that are typically aligned with gravity: large planes in the orientation range of ground surfaces under natural viewing conditions, planes in the orientation range of ceilings, and extended convex and concave edges in the orientation range of wall/floor/ceiling junctions. For a given neuron, these elements tended to share a common alignment in eye-centered coordinates. Thus, each neuron integrated information about multiple gravity-aligned structures as they would be seen from a specific eye and head orientation. This eclectic coding strategy provides only ambiguous information about individual structures but explicit information about the environmental reference frame and the orientation of gravity in egocentric coordinates. In the ventral pathway, this could support perceiving and/or predicting physical events involving objects subject to gravity, recognizing object attributes like animacy based on movement not caused by gravity, and/or stabilizing perception of the world against changes in head orientation [3-5]. Our results, like the recent discovery of object weight representation [6], imply that the ventral pathway is involved not just in recognition, but also in physical understanding of objects and scenes. PMID:26923785

  19. Studies on structure-based sequence alignment and phylogenies of beta-lactamases.

    PubMed

    Salahuddin, Parveen; Khan, Asad U

    2014-01-01

    The β-lactamases enzymes cleave the amide bond in β-lactam ring, rendering β-lactam antibiotics harmless to bacteria. In this communication we have studied structure-function relationship and phylogenies of class A, B and D beta-lactamases using structure-based sequence alignment and phylip programs respectively. The data of structure-based sequence alignment suggests that in different isolates of TEM-1, mutations did not occur at or near sequence motifs. Since deletions are reported to be lethal to structure and function of enzyme. Therefore, in these variants antibiotic hydrolysis profile and specificity will be affected. The alignment data of class A enzyme SHV-1, CTX-M-15, class D enzyme, OXA-10, and class B enzyme VIM-2 and SIM-1 show sequence motifs along with other part of polypeptide are essentially conserved. These results imply that conformations of betalactamases are close to native state and possess normal hydrolytic activities towards beta-lactam antibiotics. However, class B enzyme such as IMP-1 and NDM-1 are less conserved than other class A and D studied here because mutation and deletions occurred at critically important region such as active site. Therefore, the structure of these beta-lactamases will be altered and antibiotic hydrolysis profile will be affected. Phylogenetic studies suggest that class A and D beta-lactamases including TOHO-1 and OXA-10 respectively evolved by horizontal gene transfer (HGT) whereas other member of class A such as TEM-1 evolved by gene duplication mechanism. Taken together, these studies justify structure-function relationship of beta-lactamases and phylogenetic studies suggest these enzymes evolved by different mechanisms. PMID:24966539

  20. Studies on structure-based sequence alignment and phylogenies of beta-lactamases

    PubMed Central

    Salahuddin, Parveen; Khan, Asad U

    2014-01-01

    The β-lactamases enzymes cleave the amide bond in β-lactam ring, rendering β-lactam antibiotics harmless to bacteria. In this communication we have studied structure-function relationship and phylogenies of class A, B and D beta-lactamases using structure-based sequence alignment and phylip programs respectively. The data of structure-based sequence alignment suggests that in different isolates of TEM-1, mutations did not occur at or near sequence motifs. Since deletions are reported to be lethal to structure and function of enzyme. Therefore, in these variants antibiotic hydrolysis profile and specificity will be affected. The alignment data of class A enzyme SHV-1, CTX-M-15, class D enzyme, OXA-10, and class B enzyme VIM-2 and SIM-1 show sequence motifs along with other part of polypeptide are essentially conserved. These results imply that conformations of betalactamases are close to native state and possess normal hydrolytic activities towards beta-lactam antibiotics. However, class B enzyme such as IMP-1 and NDM-1 are less conserved than other class A and D studied here because mutation and deletions occurred at critically important region such as active site. Therefore, the structure of these beta-lactamases will be altered and antibiotic hydrolysis profile will be affected. Phylogenetic studies suggest that class A and D beta-lactamases including TOHO-1 and OXA-10 respectively evolved by horizontal gene transfer (HGT) whereas other member of class A such as TEM-1 evolved by gene duplication mechanism. Taken together, these studies justify structure-function relationship of beta-lactamases and phylogenetic studies suggest these enzymes evolved by different mechanisms. PMID:24966539

  1. Brightness enhancement of ITO/GaN LEDs by self-aligned micro-net structures

    NASA Astrophysics Data System (ADS)

    Chang, Kow-Ming; Chu, Jiunn-Yi; Cheng, Chao-Chen; Chu, Chen-Fu

    2005-05-01

    Arrays of square and hexagonal holes of various dimensions were patterned on indium-tin-oxide (ITO)/GaN light-emitting diodes (LEDs) using the self-aligned method to increase the light extraction area and shorten the optical paths. The hole region was etched to give the sidewall of the active layer a sloped profile, and it was passivated by SiOxNy films to extract more light. The self-aligned micro-net LED is at least 10% brighter than the conventional structure in the normal direction without loss of operating voltage or leakage current. The ratio of luminescence to total output power is increased by 25% at a current density of 100 A/cm2. Moreover, varying the hole dimensions and the designed density increased the peak external quantum efficiency by 5% at a current of 3 mA. The greater axial luminescence and the higher external quantum efficiency make LEDs self-aligned micro-net structures quite useful in surface-mounting and low-power-consuming devices, such as cellular phones.

  2. Energy level alignment at the interfaces in a multilayer organic light-emitting diode structure

    NASA Astrophysics Data System (ADS)

    Olthof, S.; Meerheim, R.; Schober, M.; Leo, K.

    2009-06-01

    We use photoelectron spectroscopy to study the electronic structure and energy level alignment throughout an organic light-emitting diode. The structure under investigation is a state-of-the-art long-living red phosphorescent device composed of doped charge-injection layers, charge-blocking layers, and an emission layer. By consecutively building up the whole device, the key parameters of every interface are measured. Our results show that the doped layers have a significant influence on the device energetics, especially in controlling the built-in potential, and that there are mostly only small dipoles present at the interfaces of the intrinsic organic layers.

  3. Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

    DOE PAGESBeta

    Wang, Xu; Le, Anh -Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

    2016-03-30

    We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. Lastly, amore » simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method.« less

  4. Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

    NASA Astrophysics Data System (ADS)

    Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

    2016-03-01

    We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method.

  5. Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

    PubMed Central

    Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

    2016-01-01

    We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method. PMID:27025410

  6. Unwinding of the uniform lying helix structure in cholesteric liquid crystals next to a spatially uniform aligning surface.

    PubMed

    Salter, Patrick S; Carbone, Giovanni; Jewell, Sharon A; Elston, Steve J; Raynes, Peter

    2009-10-01

    The symmetry of the cholesteric uniform lying helix (ULH) structure, where the helix axis is aligned in a single direction parallel to the device substrates, is not compatible with a uniform surface alignment and an unwinding of the helical structure is expected at the interface. Fluorescence confocal polarizing microscopy experiments are performed on the interface between a bulk ULH and a uniform aligning surface (for both planar and homeotropic alignments). The results are analyzed in the framework of a finite difference numerical simulation based on the Frank elastic distortion, to determine relevant director structures. An optical model is introduced to predict three-dimensional fluorescence profiles for the structures. Comparison of experimental and theoretical results shows that the equilibrium structure of the system involves a continuous unwinding of the helix close to the surface. PMID:19905325

  7. Thermoresponsive composite hydrogels with aligned macroporous structure by ice-templated assembly

    PubMed Central

    Bai, Hao; Polini, Alessandro; Delattre, Benjamin; Tomsia, Antoni P.

    2014-01-01

    Natural tissues, such as bone, tendon, and muscle, have well defined hierarchical structures, which are crucial for their biological and mechanical functions. However, mimicking these structural features still remains a great challenge. In this study, we use ice-templated assembly and UV-initiated cryo-polymerization to fabricate a novel kind of composite hydrogel which have both aligned macroporous structure at micrometer scale and a nacre-like layered structure at nanoscale. Such hydrogels are macroporous, thermoresponsive, and exhibit excellent mechanical performance (tough and high stretchable), attractive properties that are of significant impact on the wide applications of composite hydrogels, especially as tissue-engineering scaffolds. The fabrication method in this study including freeze-casting and cryo-polymerization can also be applied to other materials, which makes it promising for designing and developing smart and multifunctional composite hydrogels with hierar chical structures. PMID:24489436

  8. Quasistatic electric field structures and field-aligned currents in the polar cusp region

    NASA Astrophysics Data System (ADS)

    Jacobsen, Knut; Moen, Joran; Pedersen, Arne

    2010-05-01

    Quasistatic electric field structures in the vicinity of the cusp have been studied using Cluster data. There are two categories of electric potential structures, S-shaped and U-shaped. In previous studies in the nightside auroral region, the S-shaped potential was uniquely related to the boundary transition between low density and high density plasma regimes, leading to the conclusion that the electric field profile depends on whether the plasma populations on each side of the boundary can support intense field-aligned and Pedersen currents. In this study in the dayside cusp this is not the case, and a different explanation has to be sought. Most electric field structures are associated with the start of the cusp ion dispersion or with injection signatures within the cusp, and the field-aligned currents associated with these structures are found to be consistent with the cusp currents expected for the IMF By polarity at the time. This indicates that the electric field structures are generated by the cusp current system, or modified by the cusp current system to be consistent with the required currents. Furthermore, we provide firm evidence for the dayside Region 1 current to be located on open field lines, which have been postulated but to our knowledge heretofore not experimentally verified.

  9. Electronic structure and band alignment at an epitaxial spinel/perovskite heterojunction.

    PubMed

    Qiao, Liang; Li, Wei; Xiao, Haiyan; Meyer, Harry M; Liang, Xuelei; Nguyen, N V; Weber, William J; Biegalski, Michael D

    2014-08-27

    The electronic properties of solid-solid interfaces play critical roles in a variety of technological applications. Recent advances of film epitaxy and characterization techniques have demonstrated a wealth of exotic phenomena at interfaces of oxide materials, which are critically dependent on the alignment of their energy bands across the interface. Here we report a combined photoemission and electrical investigation of the electronic structures across a prototypical spinel/perovskite heterojunction. Energy-level band alignment at an epitaxial Co3O4/SrTiO3(001) heterointerface indicates a chemically abrupt, type I heterojunction without detectable band bending at both the film and substrate. The unexpected band alignment for this typical p-type semiconductor on SrTiO3 is attributed to its intrinsic d-d interband excitation, which significantly narrows the fundamental band gap between the top of the valence band and the bottom of the conduction band. The formation of the type I heterojunction with a flat-band state results in a simultaneous confinement of both electrons and holes inside the Co3O4 layer, thus rendering the epitaxial Co3O4/SrTiO3(001) heterostructure to be a very promising material for high-efficiency luminescence and optoelectronic device applications. PMID:25075939

  10. Giant piezoresistivity in aligned carbon nanotube nanocomposite: account for nanotube structural distortion at crossed tunnel junctions.

    PubMed

    Gong, S; Zhu, Z H

    2015-01-28

    High piezoresistivity is critical for multifunctional carbon nanotube polymer composites with sensing capability. By developing a new percolation network model, this work reveals theoretically that a giant piezoresistivity in the composites can be potentially achieved by controlled nanotube alignment resulting from field based alignment techniques. The tube-tube and/or tube-matrix interaction in conjunction with the aligned carbon nanotube networks are fully considered in the newly proposed model. The structural distortion of nanotubes is determined self-consistently by minimizing the pseudo-potential energy at crossed-tube junctions based on the Lennard-Jones potential and simulation of coarse grain molecular dynamics. The tunneling transport through crossed-tube junctions is calculated by the Landauer-Büttiker formula with empirical fitting by first-principle calculation. The simulation results also reveal that the piezoresistivity can be further improved by using low carbon nanotube loadings near the percolation threshold, carbon nanotubes with a small aspect ratio, high intrinsic conductivity and polymers with a small Poisson's ratio. This giant piezoresistive effect offers a tremendously promising future, which needs further thorough exploration. PMID:25492244

  11. Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences.

    PubMed

    Roder, Cornelia; Bayer, Till; Aranda, Manuel; Kruse, Maren; Voolstra, Christian R

    2015-07-01

    The significance of bacteria for eukaryotic functioning is increasingly recognized. Coral reef ecosystems critically rely on the relationship between coral hosts and their intracellular photosynthetic dinoflagellates, but the role of the associated bacteria remains largely theoretical. Here, we set out to relate coral-associated bacterial communities of the fungid host species Ctenactis echinata to environmental settings (geographic location, substrate cover, summer/winter, nutrient and suspended matter concentrations) and coral host abundance. We show that bacterial diversity of C. echinata aligns with ecological differences between sites and that coral colonies sampled at the species' preferred habitats are primarily structured by one bacterial taxon (genus Endozoicomonas) representing more than 60% of all bacteria. In contrast, host microbiomes from lower populated coral habitats are less structured and more diverse. Our study demonstrates that the content and structure of the coral microbiome aligns with environmental differences and denotes habitat adequacy. Availability of a range of coral host habitats might be important for the conservation of distinct microbiome structures and diversity. PMID:26018191

  12. Environmental constraints shaping constituent order in emerging communication systems: Structural iconicity, interactive alignment and conventionalization.

    PubMed

    Christensen, Peer; Fusaroli, Riccardo; Tylén, Kristian

    2016-01-01

    Where does linguistic structure come from? Recent gesture elicitation studies have indicated that constituent order (corresponding to for instance subject-verb-object, or SVO in English) may be heavily influenced by human cognitive biases constraining gesture production and transmission. Here we explore the alternative hypothesis that syntactic patterns are motivated by multiple environmental and social-interactional constraints that are external to the cognitive domain. In three experiments, we systematically investigate different motivations for structure in the gestural communication of simple transitive events. The first experiment indicates that, if participants communicate about different types of events, manipulation events (e.g. someone throwing a cake) and construction events (e.g. someone baking a cake), they spontaneously and systematically produce different constituent orders, SOV and SVO respectively, thus following the principle of structural iconicity. The second experiment shows that participants' choice of constituent order is also reliably influenced by social-interactional forces of interactive alignment, that is, the tendency to re-use an interlocutor's previous choice of constituent order, thus potentially overriding affordances for iconicity. Lastly, the third experiment finds that the relative frequency distribution of referent event types motivates the stabilization and conventionalization of a single constituent order for the communication of different types of events. Together, our results demonstrate that constituent order in emerging gestural communication systems is shaped and stabilized in response to multiple external environmental and social factors: structural iconicity, interactive alignment and distributional frequency. PMID:26402649

  13. Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.

    PubMed

    Theis, Corinna; Höner Zu Siederdissen, Christian; Hofacker, Ivo L; Gorodkin, Jan

    2013-12-01

    Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general interest in matching structural modules known from one molecule to other molecules for which the 3D structure is not known yet. We have created a pipeline, metaRNAmodules, which completely automates extracting putative modules from the FR3D database and mapping of such modules to Rfam alignments to obtain comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22 495 3D modules in all PDB files results in 977 internal loop and 17 hairpin modules with clear discriminatory power. Many of these modules describe only minor variants of each other. Indeed, mapping of the modules onto Rfam families results in 35 unique locations in 11 different families. The metaRNAmodules pipeline source for the internal loop modules is available at http://rth.dk/resources/mrm. PMID:24005040

  14. Conservation success as a function of good alignment of social and ecological structures and processes.

    PubMed

    Bodin, Orjan; Crona, Beatrice; Thyresson, Matilda; Golz, Anna-Lea; Tengö, Maria

    2014-10-01

    How to create and adjust governing institutions so that they align (fit) with complex ecosystem processes and structures across scales is an issue of increasing concern in conservation. It is argued that lack of such social-ecological fit makes governance and conservation difficult, yet progress in explicitly defining and rigorously testing what constitutes a good fit has been limited. We used a novel modeling approach and data from case studies of fishery and forest conservation to empirically test presumed relationships between conservation outcomes and certain patterns of alignment of social-ecological interdependences. Our approach made it possible to analyze conservation outcome on a systems level while also providing information on how individual actors are positioned in the complex web of social-ecological interdependencies. We found that when actors who shared resources were also socially linked, conservation at the level of the whole social-ecological system was positively affected. When the scales at which individual actors used resources and the scale at which ecological resources were interconnected to other ecological resources were aligned through tightened feedback loops, conservation outcome was better than when they were not aligned. The analysis of individual actors' positions in the web of social-ecological interdependencies was helpful in understanding why a system has a certain level of social-ecological fit. Results of analysis of positions showed that different actors contributed in very different ways to achieve a certain fit and revealed some underlying difference between the actors, for example in terms of actors' varying rights to access and use different ecological resources. PMID:24779516

  15. Quasistatic electric field structures and field-aligned currents in the polar cusp region

    NASA Astrophysics Data System (ADS)

    Jacobsen, K. S.; Moen, J. I.; Pedersen, A.

    2010-10-01

    Cluster data have been examined for quasi-stationary electric field structures and field-aligned currents (FACs) in the vicinity of the dayside cusp region. We have related the measurements to the Region 1/Region 2 (R1/R2) current system and the cusp current system. It has been theoretically proposed that the dayside R1 current may be located on open field lines, and experimental evidence has been shown for R1 currents partially on open field lines. We document that R1 currents may flow entirely on open field lines. The electric field structures are found to occur at plasma density gradients in the cusp. They are associated with strong FACs with current directions that are consistent with the cusp currents. This indicates that the electric field structures are closely coupled to the cusp current system. The electric equipotential structures linking the perpendicular electric fields seen at Cluster altitudes to field-aligned electric fields at lower altitudes fall into one of two categories: S shape or U shape. Both types are found at both the equatorward edge of the cusp ion dispersion and at the equatorward edge of injection events within the cusp. Previous studies in the nightside auroral region attributed the S-shaped potential structures to the boundary transition between the low-density polar cap and the high-density plasma sheet, concluding that the shape of the electric potential structure depends on whether the plasma populations on each side of the structure can support intense currents. This explanation is not applicable for the S-shaped structures observed in the dayside cusp region.

  16. Multiple Amino Acid Sequence Alignment Nitrogenase Component 1: Insights into Phylogenetics and Structure-Function Relationships

    PubMed Central

    Howard, James B.; Kechris, Katerina J.; Rees, Douglas C.; Glazer, Alexander N.

    2013-01-01

    Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 α- and β-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as “core” for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf) yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification provides the bases

  17. Global universe anisotropy probed by the alignment of structures in the cosmic microwave background.

    PubMed

    Wiaux, Y; Vielva, P; Martínez-González, E; Vandergheynst, P

    2006-04-21

    We question the global universe isotropy by probing the alignment of local structures in the cosmic microwave background (CMB) radiation. The original method proposed relies on a steerable wavelet decomposition of the CMB signal on the sphere. The analysis of the first-year Wilkinson Microwave Anisotropy Probe data identifies a mean preferred plane with a normal direction close to the CMB dipole axis, and a mean preferred direction in this plane, very close to the ecliptic poles axis. Previous statistical anisotropy results are thereby synthesized, but further analyses are still required to establish their origin. PMID:16712146

  18. A Dynamic 3D Graphical Representation for RNA Structure Analysis and Its Application in Non-Coding RNA Classification

    PubMed Central

    Dong, Xiaoqing; Fang, Yiliang; Wang, Kejing; Zhu, Lijuan; Wang, Ke; Huang, Tao

    2016-01-01

    With the development of new technologies in transcriptome and epigenetics, RNAs have been identified to play more and more important roles in life processes. Consequently, various methods have been proposed to assess the biological functions of RNAs and thus classify them functionally, among which comparative study of RNA structures is perhaps the most important one. To measure the structural similarity of RNAs and classify them, we propose a novel three dimensional (3D) graphical representation of RNA secondary structure, in which an RNA secondary structure is first transformed into a characteristic sequence based on chemical property of nucleic acids; a dynamic 3D graph is then constructed for the characteristic sequence; and lastly a numerical characterization of the 3D graph is used to represent the RNA secondary structure. We tested our algorithm on three datasets: (1) Dataset I consisting of nine RNA secondary structures of viruses, (2) Dataset II consisting of complex RNA secondary structures including pseudo-knots, and (3) Dataset III consisting of 18 non-coding RNA families. We also compare our method with other nine existing methods using Dataset II and III. The results demonstrate that our method is better than other methods in similarity measurement and classification of RNA secondary structures. PMID:27213271

  19. A Dynamic 3D Graphical Representation for RNA Structure Analysis and Its Application in Non-Coding RNA Classification.

    PubMed

    Zhang, Yi; Huang, Haiyun; Dong, Xiaoqing; Fang, Yiliang; Wang, Kejing; Zhu, Lijuan; Wang, Ke; Huang, Tao; Yang, Jialiang

    2016-01-01

    With the development of new technologies in transcriptome and epigenetics, RNAs have been identified to play more and more important roles in life processes. Consequently, various methods have been proposed to assess the biological functions of RNAs and thus classify them functionally, among which comparative study of RNA structures is perhaps the most important one. To measure the structural similarity of RNAs and classify them, we propose a novel three dimensional (3D) graphical representation of RNA secondary structure, in which an RNA secondary structure is first transformed into a characteristic sequence based on chemical property of nucleic acids; a dynamic 3D graph is then constructed for the characteristic sequence; and lastly a numerical characterization of the 3D graph is used to represent the RNA secondary structure. We tested our algorithm on three datasets: (1) Dataset I consisting of nine RNA secondary structures of viruses, (2) Dataset II consisting of complex RNA secondary structures including pseudo-knots, and (3) Dataset III consisting of 18 non-coding RNA families. We also compare our method with other nine existing methods using Dataset II and III. The results demonstrate that our method is better than other methods in similarity measurement and classification of RNA secondary structures. PMID:27213271

  20. Helical structures in vertically aligned dust particle chains in a complex plasma.

    PubMed

    Hyde, Truell W; Kong, Jie; Matthews, Lorin S

    2013-05-01

    Self-assembly of structures from vertically aligned, charged dust particle bundles within a glass box placed on the lower, powered electrode of a Gaseous Electronics Conference rf reference cell were produced and examined experimentally. Self-organized formation of one-dimensional vertical chains, two-dimensional zigzag structures, and three-dimensional helical structures of triangular, quadrangular, pentagonal, hexagonal, and heptagonal symmetries are shown to occur. System evolution is shown to progress from a one-dimensional chain structure, through a zigzag transition to a two-dimensional, spindlelike structure, and then to various three-dimensional, helical structures exhibiting multiple symmetries. Stable configurations are found to be dependent upon the system confinement, γ(2)=(ω(0h)/ω(0v))(2) (where ω(0h,v) are the horizontal and vertical dust resonance frequencies), the total number of particles within a bundle, and the rf power. For clusters having fixed numbers of particles, the rf power at which structural phase transitions occur is repeatable and exhibits no observable hysteresis. The critical conditions for these structural phase transitions as well as the basic symmetry exhibited by the one-, two-, and three-dimensional structures that subsequently develop are in good agreement with the theoretically predicted configurations of minimum energy determined employing molecular dynamics simulations for charged dust particles confined in a prolate, spheroidal potential as presented theoretically by Kamimura and Ishihara [Kamimura and Ishihara, Phys. Rev. E 85, 016406 (2012)]. PMID:23767642

  1. Photochemical manipulation of microparticles on azobenzene-doped liquid-crystal films with homogeneous or homeotropic alignment structures

    NASA Astrophysics Data System (ADS)

    Yamamoto, Takahiro; Yoshida, Masaru

    2012-10-01

    In this study, we investigated self-organized structures and photoinduced motions of microparticles on azobenzenedoped liquid crystal (LC) films with homogeneous or homeotropic alignment structures. In the case of homogeneous alignment, the microparticles formed linear chains oriented along the direction of the bulk LC alignment at air-LC interface in the initial state. Upon irradiation with ultra-violet (UV) light, the linear chains gathered into the irradiated area and formed closely-packed aggregates. The assembled chains diffused outside the irradiated area to reform the chains upon irradiation with visible light. In contrast, on the homeotropically aligned LC films, pseudo-hexagonal lattice structures of microparticles with long interparticle distances have been organized in the initial state. The particles exhibited photoinduced motions in directions opposite to those observed on the homogeneously aligned LC films. Upon irradiation with UV light, lattice structures were expanded by a particle motion away from the photoirradiated area. Irradiation with visible light then induced contraction of lattice structures based on a particle motion toward the irradiated area. The photoinduced particle motions depending on LC alignments would be explained by macroscopic convective flow or deformation of LC surface induced by cis-trans photoisomerization of azobenzene dopant.

  2. Protalign: a 3-dimensional protein alignment assessment tool.

    PubMed

    Meads, D; Hansen, M D; Pang, A

    1999-01-01

    Protein fold recognition (sometimes called threading) is the prediction of a protein's 3-dimensional shape based on its similarity to a protein of known structure. Fold predictions are low resolution; that is, no effort is made to rotate the protein's component amino acid side chains into their correct spatial orientations. The goal is simply to recognize the protein family member that most closely resembles the target sequence of unknown structure and to create a sensible alignment of the target to the known structure (i.e., a structure-sequence alignment). To facilitate this type of structure prediction, we have designed a low resolution molecular graphics tool. ProtAlign introduces the ability to interact with and edit alignments directly in the 3-dimensional structure as well as in the usual 2-dimensional layout. It also contains several functions and features to help the user assess areas within the alignment. ProtAlign implements an open pipe architecture to allow other programs to access its molecular graphics capabilities. In addition, it is capable of "driving" other programs. Because amino acid side chain orientation is not relevant in fold recognition, we represent amino acid residues as abstract shapes or glyphs much like Lego (tm) blocks and we borrow techniques from comparative flow visualization using streamlines to provide clean depictions of the entire protein model. By creating a low resolution representation of protein structure, we are able to at least double the amount of information on the screen. At the same time, we create a view that is not as busy as the corresponding representations using traditional high resolution visualization methods which show detailed atomic structure. This eliminates distracting and possibly misleading visual clutter resulting from the mapping of protein alignment information onto a high resolution display of the known structure. This molecular graphics program is implemented in Open GL to facilitate porting to

  3. A bifunctional spin label reports the structural topology of phospholamban in magnetically-aligned bicelles.

    PubMed

    McCaffrey, Jesse E; James, Zachary M; Svensson, Bengt; Binder, Benjamin P; Thomas, David D

    2016-01-01

    We have applied a bifunctional spin label and EPR spectroscopy to determine membrane protein structural topology in magnetically-aligned bicelles, using monomeric phospholamban (PLB) as a model system. Bicelles are a powerful tool for studying membrane proteins by NMR and EPR spectroscopies, where magnetic alignment yields topological constraints by resolving the anisotropic spectral properties of nuclear and electron spins. However, EPR bicelle studies are often hindered by the rotational mobility of monofunctional Cys-linked spin labels, which obscures their orientation relative to the protein backbone. The rigid and stereospecific TOAC label provides high orientational sensitivity but must be introduced via solid-phase peptide synthesis, precluding its use in large proteins. Here we show that a bifunctional methanethiosulfonate spin label attaches rigidly and stereospecifically to Cys residues at i and i+4 positions along PLB's transmembrane helix, thus providing orientational resolution similar to that of TOAC, while being applicable to larger membrane proteins for which synthesis is impractical. Computational modeling and comparison with NMR data shows that these EPR experiments provide accurate information about helix tilt relative to the membrane normal, thus establishing a robust method for determining structural topology in large membrane proteins with a substantial advantage in sensitivity over NMR. PMID:26720587

  4. Alignment structures and diffraction properties of chiral nematic liquid crystal cells with periodically patterned photoalignment films

    NASA Astrophysics Data System (ADS)

    Sasaki, Tomoyuki; Shimura, Rei; Kawai, Kotaro; Noda, Kohei; Sakamoto, Moritsugu; Kawatsuki, Nobuhiro; Ono, Hiroshi

    2016-01-01

    Liquid crystal (LC) cells with periodic alignment distributions were fabricated using chiral nematic LCs (N*LCs), which were prepared using mixtures of a nematic LC and a chiral dopant, along with photoreactive liquid crystalline polymer (PLCP) films. Periodic structures were formed by polarization holographic recording in the PLCP films. The director distribution in each cell depended on the ratio of chiral dopant present, i.e., the inherent helical pitch of the N*LCs. These periodic alignment structures with line defects in the LC grating cells were well explained on the basis of the elastic continuum theory of the N*LCs and the photoalignment effect of the PLCP films. The diffraction properties of the grating LC cells were also investigated using a polarized visible laser. The observed intensity and polarization states of the diffracted beams were consistent with theoretical ones calculated using the director distribution models. Our results clarify that the diffraction properties of the grating LC cells can be controlled by the helical pitch of the N*LCs.

  5. A bifunctional spin label reports the structural topology of phospholamban in magnetically-aligned bicelles

    NASA Astrophysics Data System (ADS)

    McCaffrey, Jesse E.; James, Zachary M.; Svensson, Bengt; Binder, Benjamin P.; Thomas, David D.

    2016-01-01

    We have applied a bifunctional spin label and EPR spectroscopy to determine membrane protein structural topology in magnetically-aligned bicelles, using monomeric phospholamban (PLB) as a model system. Bicelles are a powerful tool for studying membrane proteins by NMR and EPR spectroscopies, where magnetic alignment yields topological constraints by resolving the anisotropic spectral properties of nuclear and electron spins. However, EPR bicelle studies are often hindered by the rotational mobility of monofunctional Cys-linked spin labels, which obscures their orientation relative to the protein backbone. The rigid and stereospecific TOAC label provides high orientational sensitivity but must be introduced via solid-phase peptide synthesis, precluding its use in large proteins. Here we show that a bifunctional methanethiosulfonate spin label attaches rigidly and stereospecifically to Cys residues at i and i + 4 positions along PLB's transmembrane helix, thus providing orientational resolution similar to that of TOAC, while being applicable to larger membrane proteins for which synthesis is impractical. Computational modeling and comparison with NMR data shows that these EPR experiments provide accurate information about helix tilt relative to the membrane normal, thus establishing a robust method for determining structural topology in large membrane proteins with a substantial advantage in sensitivity over NMR.

  6. Robot graphic simulation testbed

    NASA Technical Reports Server (NTRS)

    Cook, George E.; Sztipanovits, Janos; Biegl, Csaba; Karsai, Gabor; Springfield, James F.

    1991-01-01

    The objective of this research was twofold. First, the basic capabilities of ROBOSIM (graphical simulation system) were improved and extended by taking advantage of advanced graphic workstation technology and artificial intelligence programming techniques. Second, the scope of the graphic simulation testbed was extended to include general problems of Space Station automation. Hardware support for 3-D graphics and high processing performance make high resolution solid modeling, collision detection, and simulation of structural dynamics computationally feasible. The Space Station is a complex system with many interacting subsystems. Design and testing of automation concepts demand modeling of the affected processes, their interactions, and that of the proposed control systems. The automation testbed was designed to facilitate studies in Space Station automation concepts.

  7. Design and prototyping of self-centering optical single-mode fiber alignment structures

    NASA Astrophysics Data System (ADS)

    Ebraert, Evert; Gao, Fei; Beri, Stefano; Watté, Jan; Thienpont, Hugo; Van Erps, Jürgen

    2016-06-01

    The European Commission’s goal of providing each European household with at least a 30 Mb s‑1 Internet connection by 2020 would be facilitated by a widespread deployment of fibre-to-the-home, which would in turn be sped up by the development of connector essential components, such as high-precision alignment features. Currently, the performance of state-of-the-art physical contact optical fiber connectors is limited by the tolerance on the cladding of standard telecom-grade single-mode fiber (SMF), which is typically smaller than  ±1 μm. We propose to overcome this limit by developing micro-spring-based self-centering alignment structures (SCAS) for SMF-connectors. We design these alignment structures with robustness and low-cost replication in mind, allowing for large-scale deployment. Both theoretical and finite element analysis (FEA) models are used to determine the optimal dimensions of the beams of which the micro-springs of the SCAS are comprised. Two topologies of the SCAS, consisting of three and four micro-springs respectively, are investigated for two materials: polysulfone (PSU) and polyetherimide (PEI). These materials hold great potential for high-performance fiber connectors while being compatible with low-cost production and with the harsh environmental operation conditions of those connectors. The theory and FEA agree well (<3% difference) for a simple micro-spring. When including a pedestal on the micro-spring (to bring it further away from the fiber) and for shorter spring lengths the agreement worsens. This is due to spring compression effects not being taken into account in our theoretical model. Prototypes are successfully fabricated using deep proton writing and subsequently characterized. The controlled insertion of an SMF in the SCAS is investigated and we determine that a force of 0.11 N is required. The fiber insertion also causes an out-of-plane deformation of the micro-springs in the SCAS of about 7 μm, which is no problem

  8. Improving the alignment of a large telescope structure using thermographic measurements

    NASA Astrophysics Data System (ADS)

    Enriquez, Rogerio; Smith, David R.

    2004-09-01

    While many telescopes employ some form of thermal monitoring and control to reach their surface accuracy and pointing specifications, such thermal systems are generally not available during field erection of the telescope structure. This presents a problem for large structures, because their size results in structural members with long time constants and substantial total deformations. These characteristics can potentially result in the development of significant thermal gradients across the structure or even across the width of a member. The resulting temperature variations complicate the alignment of critical features, including the main axes. As a result, it would be advantageous to monitor the thermal behavior of a large telescope structure during its construction. In the past, such monitoring was made difficult because of the size of the structure, continuing construction work, or rugged field conditions. However, with the advent of affordable field-ready thermal imaging systems, it is now possible to perform such monitoring. In this paper, we present thermal images of the alidade structure of the Large Millimeter-wave Telescope (LMT/GTM) at its site at 4600m on the top of Volcan Sierra Negra in central Mexico. We present images of typical thermal distributions for different times of day, and compare them with basic analytical models. Finally, we use the thermal imaging results to predict the effects of the temperature distribution on the location of the azimuth bogie connections and the elevation axis.

  9. Simultaneous alignment and folding of 28S rRNA sequences uncovers phylogenetic signal in structure variation.

    PubMed

    Letsch, Harald O; Greve, Carola; Kück, Patrick; Fleck, Günther; Stocsits, Roman R; Misof, Bernhard

    2009-12-01

    Secondary structure models of mitochondrial and nuclear (r)RNA sequences are frequently applied to aid the alignment of these molecules in phylogenetic analyses. Additionally, it is often speculated that structure variation of (r)RNA sequences might profitably be used as phylogenetic markers. The benefit of these approaches depends on the reliability of structure models. We used a recently developed approach to show that reliable inference of large (r)RNA secondary structures as a prerequisite of simultaneous sequence and structure alignment is feasible. The approach iteratively establishes local structure constraints of each sequence and infers fully folded individual structures by constrained MFE optimization. A comparison of structure edit distances of individual constraints and fully folded structures showed pronounced phylogenetic signal in fully folded structures. As model sequences we characterized secondary structures of 28S rRNA sequences of selected insects and examined their phylogenetic signal according to established phylogenetic hypotheses. PMID:19654047

  10. Photoelectron spectroscopic study of band alignment of polymer/ZnO photovoltaic device structure

    SciTech Connect

    Nagata, T.; Chikyow, T.; Oh, S.; Wakayama, Y.; Yamashita, Y.; Yoshikawa, H.; Kobayashi, K.; Ikeno, N.

    2013-01-28

    Using x-ray photoelectron spectroscopy, we investigated the band alignment of a Ag/poly(3-hexylthiophene-2,5-diyl) (P3HT)/ZnO photovoltaic structure. At the P3HT/ZnO interface, a band bending of P3HT and a short surface depletion layer of ZnO were observed. The offset between the highest occupied molecular orbital of P3HT and the conduction band minimum of ZnO at the interface contributed to the open circuit voltage (Voc) was estimated to be approximately 1.5 {+-} 0.1 eV, which was bigger than that of the electrically measured effective Voc of P3HT/ZnO photovoltaic devices, meaning that the P3HT/ZnO photovoltaic structure has the potential to provide improved photovoltaic properties.

  11. REIONIZATION SIMULATIONS POWERED BY GRAPHICS PROCESSING UNITS. I. ON THE STRUCTURE OF THE ULTRAVIOLET RADIATION FIELD

    SciTech Connect

    Aubert, Dominique; Teyssier, Romain

    2010-11-20

    We present a set of cosmological simulations with radiative transfer in order to model the reionization history of the universe from z = 18 down to z = 6. Galaxy formation and the associated star formation are followed self-consistently with gas and dark matter dynamics using the RAMSES code, while radiative transfer is performed as a post-processing step using a moment-based method with the M1 closure relation in the ATON code. The latter has been ported to a multiple Graphics Processing Unit (GPU) architecture using the CUDA language together with the MPI library, resulting in an overall acceleration that allows us to tackle radiative transfer problems at a significantly higher resolution than previously reported: 1024{sup 3} + 2 levels of refinement for the hydrodynamic adaptive grid and 1024{sup 3} for the radiative transfer Cartesian grid. We reach a typical acceleration factor close to 100x when compared to the CPU version, allowing us to perform 1/4 million time steps in less than 3000 GPU hr. We observe good convergence properties between our different resolution runs for various volume- and mass-averaged quantities such as neutral fraction, UV background, and Thomson optical depth, as long as the effects of finite resolution on the star formation history are properly taken into account. We also show that the neutral fraction depends on the total mass density, in a way close to the predictions of photoionization equilibrium, as long as the effect of self-shielding are included in the background radiation model. Although our simulation suite has reached unprecedented mass and spatial resolution, we still fail in reproducing the z {approx} 6 constraints on the neutral fraction of hydrogen and the intensity of the UV background. In order to account for unresolved density fluctuations, we have modified our chemistry solver with a simple clumping factor model. Using our most spatially resolved simulation (12.5 Mpc h {sup -1} with 1024{sup 3} particles) to

  12. Vertically aligned P(VDF-TrFE) core-shell structures on flexible pillar arrays

    PubMed Central

    Choi, Yoon-Young; Yun, Tae Gwang; Qaiser, Nadeem; Paik, Haemin; Roh, Hee Seok; Hong, Jongin; Hong, Seungbum; Han, Seung Min; No, Kwangsoo

    2015-01-01

    PVDF and P(VDF-TrFE) nano- and micro- structures have been widely used due to their potential applications in several fields, including sensors, actuators, vital sign transducers, and energy harvesters. In this study, we developed vertically aligned P(VDF-TrFE) core-shell structures using high modulus polyurethane acrylate (PUA) pillars as the support structure to maintain the structural integrity. In addition, we were able to improve the piezoelectric effect by 1.85 times from 40 ± 2 to 74 ± 2 pm/V when compared to the thin film counterpart, which contributes to the more efficient current generation under a given stress, by making an effective use of the P(VDF-TrFE) thin top layer as well as the side walls. We attribute the enhancement of piezoelectric effects to the contributions from the shell component and the strain confinement effect, which was supported by our modeling results. We envision that these organic-based P(VDF-TrFE) core-shell structures will be used widely as 3D sensors and power generators because they are optimized for current generations by utilizing all surface areas, including the side walls of core-shell structures. PMID:26040539

  13. Vertically aligned P(VDF-TrFE) core-shell structures on flexible pillar arrays

    SciTech Connect

    Choi, Yoon-Young; Yun, Tae Gwang; Qaiser, Nadeem; Paik, Haemin; Roh, Hee Seok; Hong, Jongin; Hong, Seungbum; Han, Seung Min; No, Kwangsoo

    2015-06-04

    PVDF and P(VDF-TrFE) nano- and micro- structures are widely used due to their potential applications in several fields, including sensors, actuators, vital sign transducers, and energy harvesters. In this study, we developed vertically aligned P(VDF-TrFE) core-shell structures using high modulus polyurethane acrylate (PUA) pillars as the support structure to maintain the structural integrity. In addition, we were able to improve the piezoelectric effect by 1.85 times from 40 ± 2 to 74 ± 2 pm/V when compared to the thin film counterpart, which contributes to the more efficient current generation under a given stress, by making an effective use of the P(VDF-TrFE) thin top layer as well as the side walls. We attribute the enhancement of piezoelectric effects to the contributions from the shell component and the strain confinement effect, which was supported by our modeling results. We envision that these organic-based P(VDF-TrFE) core-shell structures will be used widely as 3D sensors and power generators because they are optimized for current generations by utilizing all surface areas, including the side walls of core-shell structures.

  14. Vertically aligned P(VDF-TrFE) core-shell structures on flexible pillar arrays

    DOE PAGESBeta

    Choi, Yoon-Young; Yun, Tae Gwang; Qaiser, Nadeem; Paik, Haemin; Roh, Hee Seok; Hong, Jongin; Hong, Seungbum; Han, Seung Min; No, Kwangsoo

    2015-06-04

    PVDF and P(VDF-TrFE) nano- and micro- structures are widely used due to their potential applications in several fields, including sensors, actuators, vital sign transducers, and energy harvesters. In this study, we developed vertically aligned P(VDF-TrFE) core-shell structures using high modulus polyurethane acrylate (PUA) pillars as the support structure to maintain the structural integrity. In addition, we were able to improve the piezoelectric effect by 1.85 times from 40 ± 2 to 74 ± 2 pm/V when compared to the thin film counterpart, which contributes to the more efficient current generation under a given stress, by making an effective use ofmore » the P(VDF-TrFE) thin top layer as well as the side walls. We attribute the enhancement of piezoelectric effects to the contributions from the shell component and the strain confinement effect, which was supported by our modeling results. We envision that these organic-based P(VDF-TrFE) core-shell structures will be used widely as 3D sensors and power generators because they are optimized for current generations by utilizing all surface areas, including the side walls of core-shell structures.« less

  15. Vertically aligned P(VDF-TrFE) core-shell structures on flexible pillar arrays.

    PubMed

    Choi, Yoon-Young; Yun, Tae Gwang; Qaiser, Nadeem; Paik, Haemin; Roh, Hee Seok; Hong, Jongin; Hong, Seungbum; Han, Seung Min; No, Kwangsoo

    2015-01-01

    PVDF and P(VDF-TrFE) nano- and micro- structures have been widely used due to their potential applications in several fields, including sensors, actuators, vital sign transducers, and energy harvesters. In this study, we developed vertically aligned P(VDF-TrFE) core-shell structures using high modulus polyurethane acrylate (PUA) pillars as the support structure to maintain the structural integrity. In addition, we were able to improve the piezoelectric effect by 1.85 times from 40 ± 2 to 74 ± 2 pm/V when compared to the thin film counterpart, which contributes to the more efficient current generation under a given stress, by making an effective use of the P(VDF-TrFE) thin top layer as well as the side walls. We attribute the enhancement of piezoelectric effects to the contributions from the shell component and the strain confinement effect, which was supported by our modeling results. We envision that these organic-based P(VDF-TrFE) core-shell structures will be used widely as 3D sensors and power generators because they are optimized for current generations by utilizing all surface areas, including the side walls of core-shell structures. PMID:26040539

  16. Identification of WD40 repeats by secondary structure-aided profile-profile alignment.

    PubMed

    Wang, Chuan; Dong, Xiaobao; Han, Lei; Su, Xiao-Dong; Zhang, Ziding; Li, Jinyan; Song, Jiangning

    2016-06-01

    A WD40 protein typically contains four or more repeats of ~40 residues ended with the Trp-Asp dipeptide, which folds into β-propellers with four β strands in each repeat. They often function as scaffolds for protein-protein interactions and are involved in numerous fundamental biological processes. Despite their important functional role, the "velcro" closure of WD40 propellers and the diversity of WD40 repeats make their identification a difficult task. Here we develop a new WD40 Repeat Recognition method (WDRR), which uses predicted secondary structure information to generate candidate repeat segments, and further employs a profile-profile alignment to identify the correct WD40 repeats from candidate segments. In particular, we design a novel alignment scoring function that combines dot product and BLOSUM62, thereby achieving a great balance of sensitivity and accuracy. Taking advantage of these strategies, WDRR could effectively reduce the false positive rate and accurately identify more remote homologous WD40 repeats with precise repeat boundaries. We further use WDRR to re-annotate the Pfam families in the β-propeller clan (CL0186) and identify a number of WD40 repeat proteins with high confidence across nine model organisms. The WDRR web server and the datasets are available at http://protein.cau.edu.cn/wdrr/. PMID:27021623

  17. Evaporation-based method for preparing gelatin foams with aligned tubular pore structures.

    PubMed

    Frazier, Shane D; Srubar, Wil V

    2016-05-01

    Gelatin-based foams with aligned tubular pore structures were prepared via liquid-to-gas vaporization of tightly bound water in dehydrated gelatin hydrogels. This study elucidates the mechanism of the foaming process by investigating the secondary (i.e., helical) structure, molecular interactions, and water content of gelatin films before and after foaming using X-ray diffraction, Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry and thermogravimetric analysis (TGA), respectively. Experimental data from gelatin samples prepared at various gelatin-to-water concentrations (5-30 wt.%) substantiate that resulting foam structures are similar in pore diameter (approximately 350 μm), shape, and density (0.05-0.22 g/cm(3)) to those fabricated using conventional methods (e.g., freeze-drying). Helical structures were identified in the films but were not evident in the foamed samples after vaporization (~150 °C), suggesting that the primary foaming mechanism is governed by the vaporization of water that is tightly bound in secondary structures (i.e., helices, β-turns, β-sheets) that are present in dehydrated gelatin films. FTIR and TGA data show that the foaming process leads to more disorder and reduced hydrogen bonding to hydroxyl groups in gelatin and that no thermal degradation of gelatin occurs before or after foaming. PMID:26952448

  18. Growth and structural discrimination of cortical neurons on randomly oriented and vertically aligned dense carbon nanotube networks

    PubMed Central

    Nick, Christoph; Yadav, Sandeep; Joshi, Ravi

    2014-01-01

    Summary The growth of cortical neurons on three dimensional structures of spatially defined (structured) randomly oriented, as well as on vertically aligned, carbon nanotubes (CNT) is studied. Cortical neurons are attracted towards both types of CNT nano-architectures. For both, neurons form clusters in close vicinity to the CNT structures whereupon the randomly oriented CNTs are more closely colonised than the CNT pillars. Neurons develop communication paths via neurites on both nanoarchitectures. These neuron cells attach preferentially on the CNT sidewalls of the vertically aligned CNT architecture instead than onto the tips of the individual CNT pillars. PMID:25247139

  19. Computer graphics and the graphic artist

    NASA Technical Reports Server (NTRS)

    Taylor, N. L.; Fedors, E. G.; Pinelli, T. E.

    1985-01-01

    A centralized computer graphics system is being developed at the NASA Langley Research Center. This system was required to satisfy multiuser needs, ranging from presentation quality graphics prepared by a graphic artist to 16-mm movie simulations generated by engineers and scientists. While the major thrust of the central graphics system was directed toward engineering and scientific applications, hardware and software capabilities to support the graphic artists were integrated into the design. This paper briefly discusses the importance of computer graphics in research; the central graphics system in terms of systems, software, and hardware requirements; the application of computer graphics to graphic arts, discussed in terms of the requirements for a graphic arts workstation; and the problems encountered in applying computer graphics to the graphic arts. The paper concludes by presenting the status of the central graphics system.

  20. The use of mould-templated surface structures for high-quality uniform-lying-helix liquid-crystal alignment

    NASA Astrophysics Data System (ADS)

    Outram, B. I.; Elston, S. J.; Tuffin, R.; Siemianowski, S.; Snow, B.

    2013-06-01

    The chiral-flexoelectrooptic effect in a Uniform Lying Helix (ULH) configuration provides a sub-millisecond in-plane rotation of the optic axis with the application of a transverse field. This enables displays with a wide viewing angle without costly in-plane-type electrodes. The salient challenge is one of alignment of the ULH, which is not topologically compatible with uniform alignment surface treatments. Here, we create a micro-grooved surface structure with features on the micron scale by using a replica-moulding technique. When the cell is assembled, the micro-grooves create channels, and using surface-energy considerations, we explain how and show experimentally that the channels align a cholesteric material in the ULH geometry with the helicoidal axis oriented parallel to the channels. The resultant alignment provides a high level of contrast between crossed polarizers and exhibits an electrooptic response with a switching time of the order of tens of microseconds.

  1. Wavelength dependence of high-harmonic yield from aligned molecules: roles of structure and electron dynamics

    NASA Astrophysics Data System (ADS)

    Li, Y. P.; Yu, S. J.; Duan, X. Y.; Shi, Y. Z.; Chen, Y. J.

    2016-04-01

    We study high-order harmonic generation (HHG) from aligned molecules {{{H}}}2+ by varying the laser wavelength from 400 to 2300 nm. Our simulations show that the wavelength dependence of the integrated HHG yield is influenced significantly by the molecular orientation. Our analyses reveal that the electronic dynamics and the interference effect relating to the molecular structure and orientation play a dominating role in the wavelength-orientation-dependent HHG yield. The wavelength scaling of the HHG yield associated with long and short electron trajectories is also addressed. We find the contribution of short trajectory scales vary differently for short and long laser wavelengths, which provides important suggestions for the experimental study of the HHG scaling law.

  2. Thin Films of a Main Chain Columnar Liquid Crystal: Studies of Structure, Phase Transitions and Alignment

    SciTech Connect

    Defaux, M.; DiMasi, E.; Vidal, Loic; Moller, Martin; Gearba, Raluca; Ivanov, Dimitri

    2009-03-22

    The structure of thin films of poly(di-n-propylsiloxane), PDPS, was studied with a combination of optical and atomic force microscopy, electron diffraction, and grazing incidence X-ray diffraction. Two different morphological features are observed in the mesomorphic films. The lamellar ribbons are composed of the chains oriented parallel to the plane of the substrate in which the reciprocal space 10 vector is vertical. The other feature with a circular symmetry, the cylindrite, contains the chains parallel to the substrate normal. The cylindrites and needles are essentially the same mesomorphic lamellae that develop differently under the conditions of confinement. The crystallization of PDPS films does not change the gross morphological features developed during the mesophase formation and mainly proceeds via epitaxial growth of the {alpha}-crystal on the parent mesophase. Spontaneous alignment of the mesomorphic PDPS films on the PTFE-rubbed substrates allows fabricating highly crystalline inorganic polymer surfaces oriented on the scale of centimeters.

  3. Dendrite-Free Lithium Deposition with Self-Aligned Nanorod Structure

    SciTech Connect

    Zhang, Yaohui; Qian, Jiangfeng; Xu, Wu; Russell, Selena M.; Chen, Xilin; Nasybulin, Eduard; Bhattacharya, Priyanka; Engelhard, Mark H.; Mei, Donghai; Cao, Ruiguo; Ding, Fei; Cresce, Arthur V.; Xu, Kang; Zhang, Jiguang

    2014-12-10

    Suppressing lithium (Li) dendrite growth is one of the most critical challenges for the development of Li metal batteries. We recently proposed a novel self-healing electrostatic shield (SHES) mechanism which can fundamentally change the Li deposition behavior and lead to the growth of dendrite-free Li films. Here, we report for the first time that the as-deposited dendrite-free Li films grown with assistance of SHES additive are actually composed of highly-aligned and compacted Li nanorods with hemispherical tips. Both surface and cross sectional morphology evolution of the Li films during repeated Li deposition/stripping processes were systematically investigated. A new model has been established to explain the formation and evolution of the Li nanorods. A fundamental understanding on the internal structure and evolution of Li metal films may lead to new approaches to stabilize the long term cycling stability of Li metal anode.

  4. Exploring the limits of fold discrimination by structural alignment: A large scale benchmark using decoys of known fold

    PubMed Central

    Hollup, Siv Midtun; Sadowski, Michael I.; Jonassen, Inge; Taylor, William R.

    2011-01-01

    Protein structure comparison by pairwise alignment is commonly used to identify highly similar substructures in pairs of proteins and provide a measure of structural similarity based on the size and geometric similarity of the match. These scores are routinely applied in analyses of protein fold space under the assumption that high statistical significance is equivalent to a meaningful relationship, however the truth of this assumption has previously been difficult to test since there is a lack of automated methods which do not rely on the same underlying principles. As a resolution to this we present a method based on the use of topological descriptions of global protein structure, providing an independent means to assess the ability of structural alignment to maintain meaningful structural correspondances on a large scale. Using a large set of decoys of specified global fold we benchmark three widely used methods for structure comparison, SAP, TM-align and DALI, and test the degree to which this assumption is justified for these methods. Application of a topological edit distance measure to provide a scale of the degree of fold change shows that while there is a broad correlation between high structural alignment scores and low edit distances there remain many pairs of highly significant score which differ by core strand swaps and therefore are structurally different on a global level. Possible causes of this problem and its meaning for present assessments of protein fold space are discussed. PMID:21704264

  5. Optical and structural properties of amorphous Se x Te100- x aligned nanorods

    NASA Astrophysics Data System (ADS)

    Al-Agel, Faisal A.

    2013-12-01

    In the present work, we report studies on optical and structural phenomenon in as-deposited thin films composed of aligned nanorods of amorphous Se x Te100- x ( x = 3, 6, 9, and 12). In structural studies, field emission scanning electron microscopic (FESEM) images suggest that these thin films contain high yield of aligned nanorods. These nanorods show a completely amorphous nature, which is verified by X-ray diffraction patterns of these thin films. Optical studies include the measurement of spectral dependence of absorption, reflection, and transmission of these thin films, respectively. On the basis of optical absorption data, a direct optical band gap is observed. This observation of a direct optical band gap in these nanorods is interesting as chalcogenides normally show an indirect band gap, and due to this reason, these materials could not become very popular for semiconducting devices. Therefore, this is an important report and will open up new directions for the application of these materials in semiconducting devices. The value of this optical band gap is found to decrease with the increase in selenium (Se) concentration. The reflection and absorption data are employed to estimate the values of optical constants (extinction coefficient ( k) and refractive index ( n)). From the spectral dependence of these optical constants, it is found that the values of refractive index ( n) increase, whereas the values of extinction coefficient ( k) decrease with the increase in photon energy. The real and imaginary parts of dielectric constants calculated with the values of extinction coefficient ( k) and refractive index ( n), are found to vary with photon energy and dopant concentration.

  6. Relating field-aligned beams to inverted-V structures and visible auroras

    NASA Astrophysics Data System (ADS)

    Lee, E.; Parks, G. K.; Fu, S. Y.; Fillingim, M.; Cui, Y. B.; Hong, J.; Dandouras, I.; Rème, H.

    2015-10-01

    The ion composition experiment on Cluster measures 3-D distributions in one spin of the spacecraft (4 s). These distributions often measure field-aligned ion beams (H+, He+ and O+) accelerated out of the ionosphere. The standard model of these beams relies on a quasi-static U-shaped potential model. The beams contain important information about the structure and distribution of the U-shaped potential structures. For example, a simple beam with a narrow velocity range tells us that the particles are accelerated going through a quasi-static U-shaped potential structure localized in space. A more complex beam with a large range of velocities varying smoothly (a few tens of kilometers per second to > 100 km s-1) tells us that the potential structure is extended and distributed along the magnetic field. The Cluster experiment has now revealed new features about the beams. Some beams are broken into many individual structures each with their own velocity. The U-shaped potential model would interpret the new features in terms of particles accelerated by narrow isolated potential structures maintained over an extended region of the magnetic field. Another interpretation is that these features arise as Cluster traverses toward the center of a small-scale U-shaped potential region detecting particles accelerated on different equipotential contours. The estimate of the distance of the adjacent contours is ~ 590-610 m at a Cluster height of ~ 3.5 RE. The observed dimensions map to ~ 295-305 m in the ionosphere, suggesting Cluster has measured the potential structure of an auroral arc.

  7. Neural Schematics as a unified formal graphical representation of large-scale Neural Network Structures.

    PubMed

    Ehrlich, Matthias; Schüffny, René

    2013-01-01

    One of the major outcomes of neuroscientific research are models of Neural Network Structures (NNSs). Descriptions of these models usually consist of a non-standardized mixture of text, figures, and other means of visual information communication in print media. However, as neuroscience is an interdisciplinary domain by nature, a standardized way of consistently representing models of NNSs is required. While generic descriptions of such models in textual form have recently been developed, a formalized way of schematically expressing them does not exist to date. Hence, in this paper we present Neural Schematics as a concept inspired by similar approaches from other disciplines for a generic two dimensional representation of said structures. After introducing NNSs in general, a set of current visualizations of models of NNSs is reviewed and analyzed for what information they convey and how their elements are rendered. This analysis then allows for the definition of general items and symbols to consistently represent these models as Neural Schematics on a two dimensional plane. We will illustrate the possibilities an agreed upon standard can yield on sampled diagrams transformed into Neural Schematics and an example application for the design and modeling of large-scale NNSs. PMID:24167490

  8. Neural Schematics as a unified formal graphical representation of large-scale Neural Network Structures

    PubMed Central

    Ehrlich, Matthias; Schüffny, René

    2013-01-01

    One of the major outcomes of neuroscientific research are models of Neural Network Structures (NNSs). Descriptions of these models usually consist of a non-standardized mixture of text, figures, and other means of visual information communication in print media. However, as neuroscience is an interdisciplinary domain by nature, a standardized way of consistently representing models of NNSs is required. While generic descriptions of such models in textual form have recently been developed, a formalized way of schematically expressing them does not exist to date. Hence, in this paper we present Neural Schematics as a concept inspired by similar approaches from other disciplines for a generic two dimensional representation of said structures. After introducing NNSs in general, a set of current visualizations of models of NNSs is reviewed and analyzed for what information they convey and how their elements are rendered. This analysis then allows for the definition of general items and symbols to consistently represent these models as Neural Schematics on a two dimensional plane. We will illustrate the possibilities an agreed upon standard can yield on sampled diagrams transformed into Neural Schematics and an example application for the design and modeling of large-scale NNSs. PMID:24167490

  9. A study of self-aligned doped channel MOSFET structure for low power and low 1/f noise operation

    NASA Astrophysics Data System (ADS)

    Yoshitomi, Takashi; Kimijima, Hideki; Ishizuka, Shinnichiro; Miyahara, Yasunori; Ohguro, Tatsuya; Morifuji, Eiji; Morimoto, Toyota; Sasaki Momose, Hisayo; Katsumata, Yasuhiro; Iwai, Hiroshi

    1999-07-01

    A self-Aligned Doped Channel (SADC) is proposed and investigated for the first time. In the SADC process, the channel doping process is carried out by using solid phase diffusion from the gate; hence the doping region is fully self-aligned to the gate, and the junction capacitance can be reduced. In addition, the implantation damage in the channel is reduced. We obtained 0.25 μm gate length nMOSFETs with low noise and low power consumption by using the SADC structure. Hence, this structure is attractive for small geometry RF CMOS devices.

  10. Structure-thermal property correlation of aligned silicon dioxide nanorod arrays

    NASA Astrophysics Data System (ADS)

    Zhu, Jie; Zhu, Yu; Wu, Xuewang; Song, Helun; Zhang, Yaohui; Wang, Xiaojia

    2016-06-01

    Quantitative characterization of thermal properties of nanorod (NR) arrays appears to be challenging due to the complex combination of high volume of air voids, anisotropy, and structural non-uniformity. This work investigates the structure-thermal property correlation of arrays consisting of either vertically aligned or slanted silicon dioxide (SiO2) NRs, fabricated by the dynamic shadowing growth technique. We apply the frequency-dependent time-domain thermoreflectance method to quantify the thermal properties of SiO2 NR arrays that may possess inhomogeneity along the depth direction. The effective thermal conductivities of four SiO2 NR array films and one reference capping layer for the SiO2 NR array are obtained. The impact of the structure on the effective thermal conductivities of the SiO2 NR array is discussed. The lowest effective thermal conductivity among all samples in this work is found to be 0.13 W m-1 K-1 for the slanted NR array. We attribute the reduction in the effective thermal conductivity of the NR array to the discontinuous nature of SiO2 NRs, which reduces the density of the thermal transport channels and thus prevents heat flux from propagating downwards along the through-plane direction. The results from this work facilitate the potential applications of NR-array-based thermal insulators for micro-thermal devices.

  11. Dendrite-free lithium deposition with self-aligned nanorod structure.

    PubMed

    Zhang, Yaohui; Qian, Jiangfeng; Xu, Wu; Russell, Selena M; Chen, Xilin; Nasybulin, Eduard; Bhattacharya, Priyanka; Engelhard, Mark H; Mei, Donghai; Cao, Ruiguo; Ding, Fei; Cresce, Arthur V; Xu, Kang; Zhang, Ji-Guang

    2014-12-10

    Suppressing lithium (Li) dendrite growth is one of the most critical challenges for the development of Li metal batteries. Here, we report for the first time the growth of dendrite-free lithium films with a self-aligned and highly compacted nanorod structure when the film was deposited in the electrolyte consisting of 1.0 M LiPF6 in propylene carbonate with 0.05 M CsPF6 as an additive. Evolution of both the surface and the cross-sectional morphologies of the Li films during repeated Li deposition/stripping processes were systematically investigated. It is found that the formation of the compact Li nanorod structure is preceded by a solid electrolyte interphase (SEI) layer formed on the surface of the substrate. Electrochemical analysis indicates that an initial reduction process occurred at ∼ 2.05 V vs Li/Li(+) before Li deposition is responsible for the formation of the initial SEI, while the X-ray photoelectron spectroscopy indicates that the presence of CsPF6 additive can largely enhance the formation of LiF in this initial SEI. Hence, the smooth Li deposition in Cs(+)-containing electrolyte is the result of a synergistic effect of Cs(+) additive and preformed SEI layer. A fundamental understanding on the composition, internal structure, and evolution of Li metal films may lead to new approaches to stabilize the long-term cycling stability of Li metal and other metal anodes for energy storage applications. PMID:25419865

  12. Determination of material constants of vertically aligned carbon nanotube structures in compressions.

    PubMed

    Li, Yupeng; Kang, Junmo; Choi, Jae-Boong; Nam, Jae-Do; Suhr, Jonghwan

    2015-06-19

    Different chemical vapour deposition (CVD) fabrication conditions lead to a wide range of variation in the microstructure and morphologies of carbon nanotubes (CNTs), which actually determine the compressive mechanical properties of CNTs. However, the underlying relationship between the structure/morphology and mechanical properties of CNTs is not fully understood. In this study, we characterized and compared the structural and morphological properties of three kinds of vertically aligned carbon nanotube (VACNT) arrays from different CVD fabrication methods and performed monotonic compressive tests for each VACNT array. The compressive stress-strain responses and plastic deformation were first compared and analyzed with nanotube buckling behaviours. To quantify the compressive properties of the VACNT arrays, a strain density energy function was used to determine their intrinsic material constants. Then, the structural and morphological effects on the quantified material constants of the VACNTs were statistically investigated and analogized to cellular materials with an open-cell model. The statistical analysis shows that density, defect degree, and the moment of inertia of the CNTs are key factors in the improvement of the compressive mechanical properties of VACNT arrays. This approach could allow a model-driven CNT synthesis for engineering their mechanical behaviours. PMID:26011574

  13. Determination of material constants of vertically aligned carbon nanotube structures in compressions

    NASA Astrophysics Data System (ADS)

    Li, Yupeng; Kang, Junmo; Choi, Jae-Boong; Nam, Jae-Do; Suhr, Jonghwan

    2015-06-01

    Different chemical vapour deposition (CVD) fabrication conditions lead to a wide range of variation in the microstructure and morphologies of carbon nanotubes (CNTs), which actually determine the compressive mechanical properties of CNTs. However, the underlying relationship between the structure/morphology and mechanical properties of CNTs is not fully understood. In this study, we characterized and compared the structural and morphological properties of three kinds of vertically aligned carbon nanotube (VACNT) arrays from different CVD fabrication methods and performed monotonic compressive tests for each VACNT array. The compressive stress-strain responses and plastic deformation were first compared and analyzed with nanotube buckling behaviours. To quantify the compressive properties of the VACNT arrays, a strain density energy function was used to determine their intrinsic material constants. Then, the structural and morphological effects on the quantified material constants of the VACNTs were statistically investigated and analogized to cellular materials with an open-cell model. The statistical analysis shows that density, defect degree, and the moment of inertia of the CNTs are key factors in the improvement of the compressive mechanical properties of VACNT arrays. This approach could allow a model-driven CNT synthesis for engineering their mechanical behaviours.

  14. Structure and Characterization of Vertically Aligned Single-Walled Carbon Nanotube Bundles

    DOE PAGESBeta

    Márquez, Francisco; López, Vicente; Morant, Carmen; Roque-Malherbe, Rolando; Domingo, Concepción; Elizalde, Eduardo; Zamora, Félix

    2010-01-01

    Arrmore » ays of vertically aligned single-walled carbon nanotube bundles, SWCNTs, have been synthesized by simple alcohol catalytic chemical vapor deposition process, carried out at 800°C. The formed SWCNTs are organized in small groups perpendicularly aligned and attached to the substrate. These small bundles show a constant diameter of ca. 30 nm and are formed by the adhesion of no more than twenty individual SWCNTs perfectly aligned along their length.« less

  15. eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models

    PubMed Central

    Brylinski, Michal

    2014-01-01

    Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-scale benchmarking calculations using adenine-binding pockets in crystal structures demonstrate that eMatchSite generates accurate alignments for almost three times more protein pairs than SOIPPA. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. For example, the percentage of correctly aligned pairs of adenine-binding sites in weakly homologous protein models is only 4–9% lower than those aligned using crystal structures. This represents a significant improvement over other algorithms, e.g. the performance of eMatchSite in recognizing similar binding sites is 6% and 13% higher than that of SiteEngine using high- and moderate-quality protein models, respectively. Constructing biologically correct alignments using predicted ligand binding sites in protein models opens up the possibility to investigate drug-protein interaction networks for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite. PMID

  16. Structure and ionic conductivity of well-aligned polycrystalline sodium titanogallate grown by reactive diffusion

    NASA Astrophysics Data System (ADS)

    Hasegawa, Ryo; Okabe, Momoko; Asaka, Toru; Ishizawa, Nobuo; Fukuda, Koichiro

    2015-09-01

    We prepared the b-axis-oriented polycrystalline Na0.85Ti0.51Ga4.37O8 (NTGO) embedded in Ga2O3-doped Na2Ti4O9 matrix using the reactive diffusion technique. When the sandwich-type Ga2TiO5/NaGaO2/Ga2TiO5 diffusion couple was heated at 1323 K for 24 h, the NTGO polycrystal was readily formed in the presence of a liquid phase. The resulting polycrystalline material was characterized by X-ray diffractometry, electron microscopy and impedance spectroscopy. We mechanically processed the annealed diffusion couple and obtained the thin-plate electrolyte consisting mostly of the grain-aligned NTGO polycrystal. The ionic conductivity (σ) of the electrolyte along the common b-axis direction steadily increased from 1.3×10-4 to 7.3×10-3 S/cm as the temperature increased from 573 to 1073 K. There was a slope change at ca. 792 K for the Arrhenius plot of σ; the activation energies were 0.39 eV above this temperature and 0.57 eV below it. The NTGO showed the crystal structure (space group C2/m) with substantial positional disordering of one of the two Ga sites. The Na+ ions occupied ca. 43% of the Wyckoff position 4i site, the deficiency of which would contribute to the relatively high ionic conductivity along the b-axis. The reactive diffusion could be widely applicable as the novel technique to the preparation of grain-aligned ceramics of multi-component systems.

  17. PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.

    PubMed

    Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

    2015-10-01

    There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2) fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF(2) fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2) fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2) fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2) fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2) fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search. PMID:26469938

  18. PF2 fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps

    PubMed Central

    Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

    2015-01-01

    There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF2 fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF2 fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF2 fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF2 fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF2 fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF2 fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search. PMID:26469938

  19. Method of making self-aligned lightly-doped-drain structure for MOS transistors

    DOEpatents

    Weiner, Kurt H.; Carey, Paul G.

    2001-01-01

    A process for fabricating lightly-doped-drains (LDD) for short-channel metal oxide semiconductor (MOS) transistors. The process utilizes a pulsed laser process to incorporate the dopants, thus eliminating the prior oxide deposition and etching steps. During the process, the silicon in the source/drain region is melted by the laser energy. Impurities from the gas phase diffuse into the molten silicon to appropriately dope the source/drain regions. By controlling the energy of the laser, a lightly-doped-drain can be formed in one processing step. This is accomplished by first using a single high energy laser pulse to melt the silicon to a significant depth and thus the amount of dopants incorporated into the silicon is small. Furthermore, the dopants incorporated during this step diffuse to the edge of the MOS transistor gate structure. Next, many low energy laser pulses are used to heavily dope the source/drain silicon only in a very shallow region. Because of two-dimensional heat transfer at the MOS transistor gate edge, the low energy pulses are inset from the region initially doped by the high energy pulse. By computer control of the laser energy, the single high energy laser pulse and the subsequent low energy laser pulses are carried out in a single operational step to produce a self-aligned lightly-doped-drain-structure.

  20. Effect of molecular structure and packing density of an azo self-assembled monolayer on liquid crystal alignment.

    PubMed

    Vengatesan, M R; Lee, Seung-Ho; Son, Jong-Ho; Lim, Jeong-Ku; Song, Jang Kun

    2013-10-01

    We studied the alignment of liquid crystals (LCs) on a photo-switchable azo-containing self-assembled monolayer (azo-SAM) with different packing densities and molecular structures. The packing density of the azo-SAM substrates was varied by changing the dipping time of the substrate in azosilane monomers solution (2mM in toluene). The thickness of the monolayer on the silicon substrate increased as the dipping time was increased. The relative surface packing density on the glass substrates was estimated from the surface energies of the azo-SAM. The photo-induced dynamics of liquid crystal alignment on the azo-SAM significantly varied according to the packing density of the azo-SAM and the structure of the azo-SAM molecules. The azo-SAM from long octyloxy chain-terminated azosilane (azo-S1) possessed stable homeotropic alignment even after photobuffing, while the azo-SAM from short methyl group-terminated azosilane monomer (azo-S2) showed photo-switchable homeotropic and planar alignments. However, when the packing density was increased to an excessive degree, even the azo-SAM from azo-S2 exhibited stable homeotropic alignment regardless of photobuffing. PMID:23871311

  1. Pitch Accent Alignment in Romance: Primary and Secondary Associations with Metrical Structure

    ERIC Educational Resources Information Center

    Prieto, Pilar; D'Imperio, Mariapaola; Fivela, Barbara Gili

    2005-01-01

    The article describes the contrastive possibilities of alignment of high accents in three Romance varieties, namely, Central Catalan, Neapolitan Italian, and Pisa Italian. The Romance languages analyzed in this article provide crucial evidence that small differences in alignment in rising accents should be encoded phonologically. To account for…

  2. European hospital reforms in times of crisis: aligning cost containment needs with plans for structural redesign?

    PubMed

    Clemens, Timo; Michelsen, Kai; Commers, Matt; Garel, Pascal; Dowdeswell, Barrie; Brand, Helmut

    2014-07-01

    Hospitals have become a focal point for health care reform strategies in many European countries during the current financial crisis. It has been called for both, short-term reforms to reduce costs and long-term changes to improve the performance in the long run. On the basis of a literature and document analysis this study analyses how EU member states align short-term and long-term pressures for hospital reforms in times of the financial crisis and assesses the EU's influence on the national reform agenda. The results reveal that there has been an emphasis on cost containment measures rather than embarking on structural redesign of the hospital sector and its position within the broader health care system. The EU influences hospital reform efforts through its enhanced economic framework governance which determines key aspects of the financial context for hospitals in some countries. In addition, the EU health policy agenda which increasingly addresses health system questions stimulates the process of structural hospital reforms by knowledge generation, policy advice and financial incentives. We conclude that successful reforms in such a period would arguably need to address both the organisational and financing sides to hospital care. Moreover, critical to structural reform is a widely held acknowledgement of shortfalls in the current system and belief that new models of hospital care can deliver solutions to overcome these deficits. Advancing the structural redesign of the hospital sector while pressured to contain cost in the short-term is not an easy task and only slowly emerging in Europe. PMID:24703855

  3. Multiple genome alignment for identifying the core structure among moderately related microbial genomes

    PubMed Central

    Uchiyama, Ikuo

    2008-01-01

    Background Identifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult when more distantly related genomes are compared. Here, we consider the core structure as a set of sufficiently long segments in which gene orders are conserved so that they are likely to have been inherited mainly through vertical transfer, and developed a method for identifying the core structure by finding the order of pre-identified orthologous groups (OGs) that maximally retains the conserved gene orders. Results The method was applied to genome comparisons of two well-characterized families, Bacillaceae and Enterobacteriaceae, and identified their core structures comprising 1438 and 2125 OGs, respectively. The core sets contained most of the essential genes and their related genes, which were primarily included in the intersection of the two core sets comprising around 700 OGs. The definition of the genomic core based on gene order conservation was demonstrated to be more robust than the simpler approach based only on gene conservation. We also investigated the core structures in terms of G+C content homogeneity and phylogenetic congruence, and found that the core genes primarily exhibited the expected characteristic, i.e., being indigenous and sharing the same history, more than the non-core genes. Conclusion The results demonstrate that our strategy of genome alignment based on gene order conservation can provide an effective approach to identify the genomic core among moderately related microbial genomes. PMID:18976470

  4. Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs).

    PubMed

    Ganesan, Narayan; Bauer, Brad A; Lucas, Timothy R; Patel, Sandeep; Taufer, Michela

    2011-11-15

    We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the particle mesh Ewald method (PME) for solution of Poisson's Equation for the electrostatic potential under periodic boundary conditions. We discuss elements of our implementation of the PME algorithm on GPUs as well as pertinent performance issues. We proceed to show results of simulations of extended lipid bilayer systems using our program, FEN ZI. We performed simulations of DMPC bilayer systems consisting of 17,004, 68,484, and 273,936 atoms in explicit solvent. We present bilayer structural properties (atomic number densities, electron density profiles), deuterium order parameters (S(CD)), electrostatic properties (dipole potential, water dipole moments), and orientational properties of water. Predicted properties demonstrate excellent agreement with experiment and previous all-atom molecular dynamics simulations. We observe no statistically significant differences in calculated structural or electrostatic properties for different system sizes, suggesting the small bilayer simulations (less than 100 lipid molecules) provide equivalent representation of structural and electrostatic properties associated with significantly larger systems (over 1000 lipid molecules). We stress that the three system size representations will have differences in other properties such as surface capillary wave dynamics or surface tension related effects that are not probed in the current study. The latter properties are inherently dependent on system size. This contribution suggests the suitability of applying emerging GPU technologies to studies of an important class of biological environments, that of lipid bilayers and their associated integral

  5. Interactive computer graphics displays for hierarchical data structures. [Description of THESGRAF, in FORTRAN IV for CDC and IBM computers

    SciTech Connect

    Cahn, D.F.; Murano, C.V.

    1980-05-01

    An interactive computer graphical display program was developed as an aid to user visualization and manipulation of hierarchically structured data systems such as thesauri. In the present configuration, a thesaurus term and its primary and secondary conceptual neighbors are presented to the user in tree graph form on a CRT; the user then designates, via light pen or keyboard, any of the neighbors as the next term of interest and receives a new display centered on this term. By successive specification of broader, narrower, and related terms, the user can course rapidly through the thesaurus space and refine his search file. At any stage, he deals with a term-centered, conceptually meaningful picture of a localized portion of the thesaurus, and is freed from the artificial difficulties of handling the traditional alphabetized thesaurus. Intentional limitation of the associative range of each display frame, and the use of color, case, and interconnecting vectors to encode relationships among terms, enhance interpretability of the display. Facile movement through the term space, provided by interactive computation, allows the display to remain simple, and is an essential element of the system. 3 figures.

  6. Bioinspired modification of h-BN for high thermal conductive composite films with aligned structure.

    PubMed

    Shen, Heng; Guo, Jing; Wang, Hao; Zhao, Ning; Xu, Jian

    2015-03-18

    With the development of microelectronic technology, the demand of insulating electronic encapsulation materials with high thermal conductivity is ever growing and much attractive. Surface modification of chemical inert h-BN is yet a distressing issue which hinders its applications in thermal conductive composites. Here, dopamine chemistry has been used to achieve the facile surface modification of h-BN microplatelets by forming a polydopamine (PDA) shell on its surface. The successful and effective preparation of h-BN@PDA microplatelets has been confirmed by SEM, EDS, TEM, Raman spectroscopy, and TGA investigations. The PDA coating increases the dispersibility of the filler and enhances its interaction with PVA matrix as well. Based on the combination of surface modification and doctor blading, composite films with aligned h-BN@PDA are fabricated. The oriented fillers result in much higher in-plane thermal conductivities than the films with disordered structures produced by casting or using the pristine h-BN. The thermal conductivity is as high as 5.4 W m(-1) K(-1) at 10 vol % h-BN@PDA loading. The procedure is eco-friendly, easy handling, and suitable for the practical application in large scale. PMID:25707681

  7. Liquid crystallinity driven highly aligned large graphene oxide composites

    SciTech Connect

    Lee, Kyung Eun; Oh, Jung Jae; Yun, Taeyeong; Kim, Sang Ouk

    2015-04-15

    Graphene is an emerging graphitic carbon materials, consisting of sp{sup 2} hybridized two dimensinal honeycomb structure. It has been widely studied to incorporate graphene with polymer to utilize unique property of graphene and reinforce electrical, mechanical and thermal property of polymer. In composite materials, orientation control of graphene significantly influences the property of composite. Until now, a few method has been developed for orientation control of graphene within polymer matrix. Here, we demonstrate facile fabrication of high aligned large graphene oxide (LGO) composites in polydimethylsiloxane (PDMS) matrix exploiting liquid crystallinity. Liquid crystalline aqueous dispersion of LGO is parallel oriented within flat confinement geometry. Freeze-drying of the aligned LGO dispersion and subsequent infiltration with PDMS produce highly aligned LGO/PDMS composites. Owing to the large shape anisotropy of LGO, liquid crystalline alignment occurred at low concentration of 2 mg/ml in aqueous dispersion, which leads to the 0.2 wt% LGO loaded composites. - Graphical abstract: Liquid crystalline LGO aqueous dispersions are spontaneous parallel aligned between geometric confinement for highly aligned LGO/polymer composite fabrication. - Highlights: • A simple fabrication method for highly aligned LGO/PDMS composites is proposed. • LGO aqueous dispersion shows nematic liquid crystalline phase at 0.8 mg/ml. • In nematic phase, LGO flakes are highly aligned by geometric confinement. • Infiltration of PDMS into freeze-dried LGO allows highly aligned LGO/PDMS composites.

  8. Hierarchical structures of aligned carbon nanotubes as low-density energy-dissipative materials

    NASA Astrophysics Data System (ADS)

    Raney, Jordan R.

    Carbon nanotubes (CNTs) are known to have remarkable properties, such as a specific strength two orders of magnitude higher than that of steel. It has remained a challenge, however, to achieve useful bulk properties from CNTs. Toward that goal, here we develop low-density bulk materials (0.1-0.4 g cm-3) entirely or nearly entirely from CNTs. These consist of nominally-aligned arrays of CNTs that display a dissipative compressive response, with a notable stress-strain hysteresis. The compressive properties of CNT arrays are examined in detail. This analysis reveals interesting features in the mechanical response, such as strain localization (resulting from a gradient in physical properties along the height), recovery after compression, non-linear viscoelasticity, and behavior under repeated compression that depends on the strain of previous cycles (similar to the Mullins effect in rubbers). We observe that in compression the energy dissipation of these materials is more than 200 times that of polymeric foams of comparable density. Next, materials based on CNT arrays are studied as exemplary of hierarchical materials (materials with distinct structure at multiple length scales). Hierarchical materials have pushed the limits of traditional material tradeoffs (e.g., the typical trend that increased strength requires increased weight). Techniques are developed to separately vary the structure of CNT arrays at nanometer, micrometer, and millimeter length scales, and the effects on the bulk material response are examined. Structure can be modified during CNT synthesis, such as by varying the composition of the flow gas or by manipulating the input rate of chemical precursors; it can also be modified post-synthesis, e.g., by the in situ synthesis of nanoparticles in the interstices of the CNT arrays or by the assembly of multilayer structures of multiple CNT arrays connected by polymeric or metallic interlayers. Finally, a mathematical model is applied to capture the

  9. ALIGNING JIG

    DOEpatents

    Culver, J.S.; Tunnell, W.C.

    1958-08-01

    A jig or device is described for setting or aligning an opening in one member relative to another member or structure, with a predetermined offset, or it may be used for measuring the amount of offset with which the parts have previously been sct. This jig comprises two blocks rabbeted to each other, with means for securing thc upper block to the lower block. The upper block has fingers for contacting one of the members to be a1igmed, the lower block is designed to ride in grooves within the reference member, and calibration marks are provided to determine the amount of offset. This jig is specially designed to align the collimating slits of a mass spectrometer.

  10. miR-Explore: Predicting MicroRNA Precursors by Class Grouping and Secondary Structure Positional Alignment

    PubMed Central

    Sebastian, Bram; Aggrey, Samuel E.

    2013-01-01

    MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expressions by targeting the mRNAs especially in the 3′UTR regions. The identification of miRNAs has been done by biological experiment and computational prediction. The computational prediction approach has been done using two major methods: comparative and noncomparative. The comparative method is dependent on the conservation of the miRNA sequences and secondary structure. The noncomparative method, on the other hand, does not rely on conservation. We hypothesized that each miRNA class has its own unique set of features; therefore, grouping miRNA by classes before using them as training data will improve sensitivity and specificity. The average sensitivity was 88.62% for miR-Explore, which relies on within miRNA class alignment, and 70.82% for miR-abela, which relies on global alignment. Compared with global alignment, grouping miRNA by classes yields a better sensitivity with very high specificity for pre-miRNA prediction even when a simple positional based secondary and primary structure alignment are used. PMID:23645986

  11. PROMUSE: a system for multi-media data presentation of protein structural alignments.

    PubMed

    Hansen, M D; Charp, E; Lodha, S; Meads, D; Pang, A

    1999-01-01

    We present and evaluate PROMUSE: an integrated visualization/sonification system for analyzing pairwise protein structural alignments (superpositions of two protein structures in three-dimensional space). We also explore how the use of sound can enhance the perception and recognition of specific aspects of the local environment at given positions in the represented molecular structure. Sonification presents several opportunities to researchers. For those with visual impairment, data sonification can be a useful alternative to visualization. Sonification can further serve to improve understanding of information in several ways. One use for data sonification is in tasks such as background monitoring, in which case sounds can be used to indicate thresholding events. With PROMUSE, data represented visually may be enhanced or disambiguated by adding sound to the presentation. This aspect of data representation is particularly important for showing features that are difficult to represent visually, due to occlusion or other factors. Another feature of our system is that by representing some variables through sound and others visually, the amount of information that may be represented simultaneously is extended. Our tool aims to augment the power of data visualization rather than replace it. To maximize the utility of our sonifications to represent data, we employed musical voices and melodic components with unique characteristics. We also used sound effects such as panning a voice to the left or right speaker and changing its volume to maximize the individuality of the sonification elements. By making the sonification parameters distinct, we allow the user to focus on those portions of the sonification necessary to resolve possible ambiguities in the visual display. Sonifications of low level data such as raw protein or DNA sequences tend to sound random, and not very musical. We chose instead to sonify an analysis of data features, and thereby present a higher level

  12. Droplet etching of deep nanoholes for filling with self-aligned complex quantum structures.

    PubMed

    Küster, Achim; Heyn, Christian; Ungeheuer, Arne; Juska, Gediminas; Tommaso Moroni, Stefano; Pelucchi, Emanuele; Hansen, Wolfgang

    2016-12-01

    Strain-free epitaxial quantum dots (QDs) are fabricated by a combination of Al local droplet etching (LDE) of nanoholes in AlGaAs surfaces and subsequent hole filling with GaAs. The whole process is performed in a conventional molecular beam epitaxy (MBE) chamber. Autocorrelation measurements establish single-photon emission from LDE QDs with a very small correlation function g ((2))(0)≃ 0.01 of the exciton emission. Here, we focus on the influence of the initial hole depth on the QD optical properties with the goal to create deep holes suited for filling with more complex nanostructures like quantum dot molecules (QDM). The depth of droplet etched nanoholes is controlled by the droplet material coverage and the process temperature, where a higher coverage or temperature yields deeper holes. The requirements of high quantum dot uniformity and narrow luminescence linewidth, which are often found in applications, set limits to the process temperature. At high temperatures, the hole depths become inhomogeneous and the linewidth rapidly increases beyond 640 °C. With the present process technique, we identify an upper limit of 40-nm hole depth if the linewidth has to remain below 100 μeV. Furthermore, we study the exciton fine-structure splitting which is increased from 4.6 μeV in 15-nm-deep to 7.9 μeV in 35-nm-deep holes. As an example for the functionalization of deep nanoholes, self-aligned vertically stacked GaAs QD pairs are fabricated by filling of holes with 35 nm depth. Exciton peaks from stacked dots show linewidths below 100 μeV which is close to that from single QDs. PMID:27255902

  13. Droplet etching of deep nanoholes for filling with self-aligned complex quantum structures

    NASA Astrophysics Data System (ADS)

    Küster, Achim; Heyn, Christian; Ungeheuer, Arne; Juska, Gediminas; Tommaso Moroni, Stefano; Pelucchi, Emanuele; Hansen, Wolfgang

    2016-06-01

    Strain-free epitaxial quantum dots (QDs) are fabricated by a combination of Al local droplet etching (LDE) of nanoholes in AlGaAs surfaces and subsequent hole filling with GaAs. The whole process is performed in a conventional molecular beam epitaxy (MBE) chamber. Autocorrelation measurements establish single-photon emission from LDE QDs with a very small correlation function g (2)(0)≃ 0.01 of the exciton emission. Here, we focus on the influence of the initial hole depth on the QD optical properties with the goal to create deep holes suited for filling with more complex nanostructures like quantum dot molecules (QDM). The depth of droplet etched nanoholes is controlled by the droplet material coverage and the process temperature, where a higher coverage or temperature yields deeper holes. The requirements of high quantum dot uniformity and narrow luminescence linewidth, which are often found in applications, set limits to the process temperature. At high temperatures, the hole depths become inhomogeneous and the linewidth rapidly increases beyond 640 °C. With the present process technique, we identify an upper limit of 40-nm hole depth if the linewidth has to remain below 100 μeV. Furthermore, we study the exciton fine-structure splitting which is increased from 4.6 μeV in 15-nm-deep to 7.9 μeV in 35-nm-deep holes. As an example for the functionalization of deep nanoholes, self-aligned vertically stacked GaAs QD pairs are fabricated by filling of holes with 35 nm depth. Exciton peaks from stacked dots show linewidths below 100 μeV which is close to that from single QDs.

  14. The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods.

    PubMed

    Letsch, Harald O; Kück, Patrick; Stocsits, Roman R; Misof, Bernhard

    2010-11-01

    The use of secondary structures has been advocated to improve both the alignment and the tree reconstruction processes of ribosomal RNA (rRNA) data sets. We used simulated and empirical rRNA data to test the impact of secondary structure consideration in both steps of molecular phylogenetic analyses. A simulation approach was used to generate realistic rRNA data sets based on real 16S, 18S, and 28S sequences and structures in combination with different branch length and topologies. Alignment and tree reconstruction performance of four recent structural alignment methods was compared with exclusively sequence-based approaches. As empirical data, we used a hexapod rRNA data set to study the influence of nucleotide interdependencies in sequence alignment and tree reconstruction. Structural alignment methods delivered significantly better sequence alignments compared with pure sequence-based methods. Also, structural alignment methods delivered better trees judged by topological congruence to simulation base trees. However, the advantage of structural alignments was less pronounced and even vanished in several instances. For simulated data, application of mixed RNA/DNA models to stems and loops, respectively, led to significantly shorter branches. The application of mixed RNA/DNA models in the hexapod analyses delivered partly implausible relationships. This can be interpreted as a stronger sensitivity of mixed model setups to nonphylogenetic signal. Secondary structure consideration clearly influenced sequence alignment and tree reconstruction of ribosomal genes. Although sequence alignment quality can considerably be improved by the use of secondary structure information, the application of mixed models in tree reconstructions needs further studies to understand the observed effects. PMID:20530152

  15. Kohonen map as a visualization tool for the analysis of protein sequences: multiple alignments, domains and segments of secondary structures.

    PubMed

    Hanke, J; Reich, J G

    1996-12-01

    The method of Kohonen maps, a special form of neural networks, was applied as a visualization tool for the analysis of protein sequence similarity. The procedure converts sequence (domains, aligned sequences, segments of secondary structure) into a characteristic signal matrix. This conversion depends on the property or replacement score vector selected by the user. Similar sequences have small distance in the signal space. The trained Kohonen network is functionally equivalent to an unsupervised non-linear cluster analyzer. Protein families, or aligned sequences, or segments of similar secondary structure, aggregate as clusters, and their proximity may be inspected on a color screen or on paper. Pull-down menus permit access to background information in the established text-oriented way. PMID:9021261

  16. Intermediate pre-tilt angle control by a composite alignment thin film structure for liquid crystal displays.

    PubMed

    Wu, G M; Chien, H W; Huang, J W; Zeng, H L

    2010-04-01

    We designed a patterned composite alignment thin film structure using a horizontal alignment polyimide (PI) layer and vertical alignment liquid crystal polymer (LCP) pillars. The LCP polymer precursor concentration was varied at 0-10% and the pillars were introduced by a photolithography process. Both single-sided and double-sided liquid crystal display cells were assembled for a series of electro-optical characterization techniques. The horizontal PI alignment layer alone had a designated control of the pre-tilt angle of 7 degrees after the prescribed mechanical rubbing process. The pre-tilt angle was improved to 24 degrees when the LCP precursor concentration was 5%. It was further increased to 61 degrees at the concentration of 10%. In addition, the study on the electrical response time and gray level variation demonstrated promising results for potential applications. The field-on response time was only 2.79 ms and the field-off response time was 0.35 ms for the double-sided liquid crystal display cells using a ramping voltage of 5.5 V. The effective control of the cell pre-tilt angle suggested that the display power consumption and response time would be greatly improved. PMID:20208122

  17. Three-Dimensional Structure of the Transmembrane Domain of Vpu from HIV-1 in Aligned Phospholipid Bicelles

    PubMed Central

    Park, Sang Ho; De Angelis, Anna A.; Nevzorov, Alexander A.; Wu, Chin H.; Opella, Stanley J.

    2006-01-01

    The three-dimensional backbone structure of the transmembrane domain of Vpu from HIV-1 was determined by solid-state NMR spectroscopy in two magnetically-aligned phospholipid bilayer environments (bicelles) that differed in their hydrophobic thickness. Isotopically labeled samples of Vpu2–30+, a 36-residue polypeptide containing residues 2–30 from the N-terminus of Vpu, were incorporated into large (q = 3.2 or 3.0) phospholipid bicelles composed of long-chain ether-linked lipids (14-O-PC or 16-O-PC) and short-chain lipids (6-O-PC). The protein-containing bicelles are aligned in the static magnetic field of the NMR spectrometer. Wheel-like patterns of resonances characteristic of tilted transmembrane helices were observed in two-dimensional 1H/15N PISEMA spectra of uniformly 15N-labeled Vpu2–30+ obtained on bicelle samples with their bilayer normals aligned perpendicular or parallel to the direction of the magnetic field. The NMR experiments were performed at a 1H resonance frequency of 900 MHz, and this resulted in improved data compared to lower-resonance frequencies. Analysis of the polarity-index slant-angle wheels and dipolar waves demonstrates the presence of a transmembrane α-helix spanning residues 8–25 in both 14-O-PC and 16-O-PC bicelles, which is consistent with results obtained previously in micelles by solution NMR and mechanically aligned lipid bilayers by solid-state NMR. The three-dimensional backbone structures were obtained by structural fitting to the orientation-dependent 15N chemical shift and 1H-15N dipolar coupling frequencies. Tilt angles of 30° and 21° are observed in 14-O-PC and 16-O-PC bicelles, respectively, which are consistent with the values previously determined for the same polypeptide in mechanically-aligned DMPC and DOPC bilayers. The difference in tilt angle in C14 and C16 bilayer environments is also consistent with previous results indicating that the transmembrane helix of Vpu responds to hydrophobic mismatch by

  18. Graphic displays of vector magnetograph data

    NASA Technical Reports Server (NTRS)

    Rabin, D. M.; West, E. A.

    1985-01-01

    Graphic displays that have proved useful in dealing with vector magnetograph data are summarized in three settings: real-time control, analysis, and final presentation. Among the topics discussed are: flexible, implicit data-scaling; geometrical transformations; methods of comparing fields (e.g., transverse vs. longitudinal; observed vs. computed; one time vs. another); displaying the magnitude and direction of the transverse field; minimizing the display time of serial graphics devices; graphic file structure; and graphic interaction with operators and observers.

  19. SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions.

    PubMed

    Jefferson, Emily R; Walsh, Thomas P; Roberts, Timothy J; Barton, Geoffrey J

    2007-01-01

    SNAPPI-DB, a high performance database of Structures, iNterfaces and Alignments of Protein-Protein Interactions, and its associated Java Application Programming Interface (API) is described. SNAPPI-DB contains structural data, down to the level of atom co-ordinates, for each structure in the Protein Data Bank (PDB) together with associated data including SCOP, CATH, Pfam, SWISSPROT, InterPro, GO terms, Protein Quaternary Structures (PQS) and secondary structure information. Domain-domain interactions are stored for multiple domain definitions and are classified by their Superfamily/Family pair and interaction interface. Each set of classified domain-domain interactions has an associated multiple structure alignment for each partner. The API facilitates data access via PDB entries, domains and domain-domain interactions. Rapid development, fast database access and the ability to perform advanced queries without the requirement for complex SQL statements are provided via an object oriented database and the Java Data Objects (JDO) API. SNAPPI-DB contains many features which are not available in other databases of structural protein-protein interactions. It has been applied in three studies on the properties of protein-protein interactions and is currently being employed to train a protein-protein interaction predictor and a functional residue predictor. The database, API and manual are available for download at: http://www.compbio.dundee.ac.uk/SNAPPI/downloads.jsp. PMID:17202171

  20. Photoinduced Directional Motions of Microparticles at Air-Liquid-Crystal Interfaces of Azobenzene-Doped Liquid-Crystal Films with Homeotropic or Homogeneous Alignment Structures

    NASA Astrophysics Data System (ADS)

    Yamamoto, Takahiro; Yoshida, Masaru

    2012-10-01

    We investigated the effects of liquid-crystal (LC) alignments on photoinduced motions of microparticles at air-LC interfaces of azobenzene-doped LC films. In homeotropically aligned LC films, the lattice spacings of pseudo-hexagonal structures of microparticles site-selectively exhibited reversible expansion or contraction on alternating irradiation with ultraviolet and visible light. The particle motions were probably driven by photochemical deformation of LC surfaces. In homogeneously aligned films, alternating irradiation induced macroscopic convective flows followed by rapid gathering or dispersion of linear chains of microparticles. Particle motions were significantly influenced by LC alignments as well as the light wavelength.

  1. Corneal Fibroblast Migration Patterns During Intrastromal Wound Healing Correlate With ECM Structure and Alignment

    PubMed Central

    Petroll, W. Matthew; Kivanany, Pouriska B.; Hagenasr, Daniela; Graham, Eric K.

    2015-01-01

    Purpose To assess keratocyte backscattering, alignment, morphology, and connectivity in vivo following a full-thickness corneal injury using the Heidelberg Retina Tomograph Rostock Cornea Module (HRT-RCM), and to correlate these findings with en bloc three-dimensional (3-D) confocal fluorescence and second harmonic generation (SHG) imaging. Methods Rabbit corneas were scanned in vivo both before and 3, 7, 14, and 28 days after transcorneal freeze injury (FI), which damages all corneal cell layers. Corneal tissue was also fixed and labeled for f-actin and nuclei en bloc, and imaged using 3-D confocal fluorescence microscopy and SHG imaging. Results Using the modified HRT-RCM, full-thickness scans of all cell layers were consistently obtained. Following FI, stromal cells repopulating the damaged tissue assumed an elongated fibroblastic morphology, and a significant increase in cellular light scattering was measured. This stromal haze gradually decreased as wound healing progressed. Parallel, interconnected streams of aligned corneal fibroblasts were observed both in vivo (from HRT-RCM reflection images) and ex vivo (from f-actin and nuclear labeling) during wound healing, particularly in the posterior cornea. Second harmonic generation imaging demonstrated that these cells were aligned parallel to the collagen lamellae. Conclusions The modified HRT-RCM allows in vivo measurements of sublayer thickness, assessment of cell morphology, alignment and connectivity, and estimation of stromal backscatter during wound healing. In this study, these in vivo observations led to the novel finding that the pattern of corneal fibroblast alignment is highly correlated with lamellar organization, suggesting contact guidance of intrastromal migration that may facilitate more rapid wound repopulation. PMID:26562169

  2. Inverse cascade in the structure of substorm aurora and non-linear dynamics of field-aligned current filaments

    NASA Astrophysics Data System (ADS)

    Kozelov, B. V.; Golovchanskaya, I. V.; Mingalev, O. V.

    2011-08-01

    We investigate time evolution of scaling index αA that characterizes auroral luminosity fluctuations at the beginning of substorm expansion. With the use of UVI images from the Polar satellite, it is shown that αA typically varies from values less than unity to ~1.5, increasing with breakup progress. Similar scaling features were previously reported for fluctuations at smaller scales from all-sky TV observations. If this signature is interpreted in terms of non-linear interactions between scales, it means that the power of small-scale fluctuations is transferred with time to larger scales, a kind of the inverse cascade. Scaling behavior in the aurora during substorm activity is compared with that in the field-aligned currents simulated numerically in the model of non-linear interactions of Alfvénic coherent structures, according to the Chang et al. (2004) scenario. This scenario also suggests an inverse cascade, manifesting in clustering of small-scale field-aligned current filaments of the same polarity and formation of "coarse-grained" structures of field-aligned currents.

  3. CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking

    PubMed Central

    Kim, Namhee; Laing, Christian; Wang, Jason T. L.; Schlick, Tamar

    2016-01-01

    RNA junctions are important structural elements of RNA molecules. They are formed when three or more helices come together in three-dimensional space. Recent studies have focused on the annotation and prediction of coaxial helical stacking (CHS) motifs within junctions. Here we exploit such predictions to develop an efficient alignment tool to handle RNA secondary structures with CHS motifs. Specifically, we build upon our Junction-Explorer software for predicting coaxial stacking and RNAJAG for modelling junction topologies as tree graphs to incorporate constrained tree matching and dynamic programming algorithms into a new method, called CHSalign, for aligning the secondary structures of RNA molecules containing CHS motifs. Thus, CHSalign is intended to be an efficient alignment tool for RNAs containing similar junctions. Experimental results based on thousands of alignments demonstrate that CHSalign can align two RNA secondary structures containing CHS motifs more accurately than other RNA secondary structure alignment tools. CHSalign yields a high score when aligning two RNA secondary structures with similar CHS motifs or helical arrangement patterns, and a low score otherwise. This new method has been implemented in a web server, and the program is also made freely available, at http://bioinformatics.njit.edu/CHSalign/. PMID:26789998

  4. Reconstruction of two-dimensional molecular structure with laser-induced electron diffraction from laser-aligned polyatomic molecules

    DOE PAGESBeta

    Yu, Chao; Wei, Hui; Wang, Xu; Le, Anh -Thu; Lu, Ruifeng; Lin, C. D.

    2015-10-27

    Imaging the transient process of molecules has been a basic way to investigate photochemical reactions and dynamics. Based on laser-induced electron diffraction and partial one-dimensional molecular alignment, here we provide two effective methods for reconstructing two-dimensional structure of polyatomic molecules. We demonstrate that electron diffraction images in both scattering angles and broadband energy can be utilized to retrieve complementary structure information, including positions of light atoms. Lastly, with picometre spatial resolution and the inherent femtosecond temporal resolution of lasers, laser-induced electron diffraction method offers significant opportunities for probing atomic motion in a large molecule in a typical pump-probe measurement.

  5. Simulation of a symmetric optical response from a hybrid-aligned structure of a dual-frequency nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Ivanov, A. V.; Vakulin, D. A.

    2015-12-01

    To create a hybrid-aligned structure of a dual-frequency nematic liquid crystal (LC), we have obtained an approximate analytical solution of the system of equations that describes the dynamics of reorientations of the director under the action of a control electric signal of an arbitrary shape. Formulas obtained have been used to simulate a symmetric optical response of the LC structure for a sinusoidal electric pulse. It has been shown that, in terms of the used approximations, the results of the analytical calculation agree well with results of computer simulation and with experiment in the case of small deformations of the LC layer.

  6. Reconstruction of two-dimensional molecular structure with laser-induced electron diffraction from laser-aligned polyatomic molecules

    PubMed Central

    Yu, Chao; Wei, Hui; Wang, Xu; Le, Anh-Thu; Lu, Ruifeng; Lin, C. D.

    2015-01-01

    Imaging the transient process of molecules has been a basic way to investigate photochemical reactions and dynamics. Based on laser-induced electron diffraction and partial one-dimensional molecular alignment, here we provide two effective methods for reconstructing two-dimensional structure of polyatomic molecules. We demonstrate that electron diffraction images in both scattering angles and broadband energy can be utilized to retrieve complementary structure information, including positions of light atoms. With picometre spatial resolution and the inherent femtosecond temporal resolution of lasers, laser-induced electron diffraction method offers significant opportunities for probing atomic motion in a large molecule in a typical pump-probe measurement. PMID:26503116

  7. Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures.

    PubMed

    Fu, Yinghan; Xu, Zhenjiang Zech; Lu, Zhi J; Zhao, Shan; Mathews, David H

    2015-01-01

    Recently, non-coding RNAs (ncRNAs) have been discovered with novel functions, and it has been appreciated that there is pervasive transcription of genomes. Moreover, many novel ncRNAs are not conserved on the primary sequence level. Therefore, de novo computational ncRNA detection that is accurate and efficient is desirable. The purpose of this study is to develop a ncRNA detection method based on conservation of structure in more than two genomes. A new method called Multifind, using Multilign, was developed. Multilign predicts the common secondary structure for multiple input sequences. Multifind then uses measures of structure conservation to estimate the probability that the input sequences are a conserved ncRNA using a classification support vector machine. Multilign is based on Dynalign, which folds and aligns two sequences simultaneously using a scoring scheme that does not include sequence identity; its structure prediction quality is therefore not affected by input sequence diversity. Additionally, ensemble defect was introduced to Multifind as an additional discriminating feature that quantifies the compactness of the folding space for a sequence. Benchmarks showed Multifind performs better than RNAz and LocARNATE+RNAz, a method that uses RNAz on structure alignments generated by LocARNATE, on testing sequences extracted from the Rfam database. For de novo ncRNA discovery in three genomes, Multifind and LocARNATE+RNAz had an advantage over RNAz in low similarity regions of genome alignments. Additionally, Multifind and LocARNATE+RNAz found different subsets of known ncRNA sequences, suggesting the two approaches are complementary. PMID:26075601

  8. Development of Accurate Structure for Mounting and Aligning Thin-Foil X-Ray Mirrors

    NASA Technical Reports Server (NTRS)

    Heilmann, Ralf K.

    2001-01-01

    The goal of this work was to improve the assembly accuracy for foil x-ray optics as produced by the high-energy astrophysics group at the NASA Goddard Space Flight Center. Two main design choices lead to an alignment concept that was shown to improve accuracy well within the requirements currently pursued by the Constellation-X Spectroscopy X-Ray Telescope (SXT).

  9. Detection and Alignment of 3D Domain Swapping Proteins Using Angle-Distance Image-Based Secondary Structural Matching Techniques

    PubMed Central

    Wang, Hsin-Wei; Hsu, Yen-Chu; Hwang, Jenn-Kang; Lyu, Ping-Chiang; Pai, Tun-Wen; Tang, Chuan Yi

    2010-01-01

    This work presents a novel detection method for three-dimensional domain swapping (DS), a mechanism for forming protein quaternary structures that can be visualized as if monomers had “opened” their “closed” structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer's and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are rarely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D) image transformations of secondary structural elements (SSEs), specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the detection of DS relationships. The Matthews correlation coefficient (MCC) and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high and stable for DS-related homologs with less than 10% sequence identities. In addition, the quality of its hinge

  10. Self-assembly of gold nanorods into vertically aligned, rectangular microplates with a supercrystalline structure

    NASA Astrophysics Data System (ADS)

    Xiao, Junyan; Li, Zhe; Ye, Xiaozhou; Ma, Yurong; Qi, Limin

    2013-12-01

    Vertically aligned, supercrystalline microplates with a well-defined rectangular shape were fabricated in a large area through self-assembly of gold nanorods by a novel bulk solution evaporation method. This evaporative self-assembly strategy involving continuous movement of the contact line can prevent the coffee-ring effect, thus allowing uniform deposition of discrete GNR superstructures over a large area and favoring the formation of GNR supercrystals with geometrically symmetric shapes. A mechanism based on the continuing nucleation and growth of smectic GNR superstructures accompanying the movement of the contact line was put forward for the formation of the unique GNR supercrystal arrays. Based on this mechanism, a micropatterned substrate was designed to control the nucleation location and growth direction, leading to the spontaneous self-assembly of nearly parallel arrays of vertically aligned, supercrystalline microplates of GNRs. The obtained rectangular-plate-shaped GNR supercrystals exhibited interesting anisotropic optical reflection properties, which were revealed by polarized light microscopy.Vertically aligned, supercrystalline microplates with a well-defined rectangular shape were fabricated in a large area through self-assembly of gold nanorods by a novel bulk solution evaporation method. This evaporative self-assembly strategy involving continuous movement of the contact line can prevent the coffee-ring effect, thus allowing uniform deposition of discrete GNR superstructures over a large area and favoring the formation of GNR supercrystals with geometrically symmetric shapes. A mechanism based on the continuing nucleation and growth of smectic GNR superstructures accompanying the movement of the contact line was put forward for the formation of the unique GNR supercrystal arrays. Based on this mechanism, a micropatterned substrate was designed to control the nucleation location and growth direction, leading to the spontaneous self-assembly of

  11. Angle-resolved x-ray absorption near edge structure study of vertically aligned single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Li, Zhongrui; Zhang, Liang; Resasco, Daniel E.; Mun, Bongjin Simon; Requejo, Félix G.

    2007-03-01

    Vertically aligned single-walled carbon nanotube (SWNT) forest was studied by using angular-dependent C K-edge x-ray absorption near edge structure (XANES) with linearly polarized x-ray beam. The XANES analysis found a crust of entangled nanotubes on top of the forest formed at the first stage of the forest growth, which shapes the morphology of the entire forest and constricts the nanotubes to grow to the same length. It indicates that this type of SWNT forest has a different growth mechanism from the multiwalled carbon nanotube forest.

  12. Foundations of statistical methods for multiple sequence alignment and structure prediction

    SciTech Connect

    Lawrence, C.

    1995-12-31

    Statistical algorithms have proven to be useful in computational molecular biology. Many statistical problems are most easily addressed by pretending that critical missing data are available. For some problems statistical inference in facilitated by creating a set of latent variables, none of whose variables are observed. A key observation is that conditional probabilities for the values of the missing data can be inferred by application of Bayes theorem to the observed data. The statistical framework described in this paper employs Boltzmann like models, permutated data likelihood, EM, and Gibbs sampler algorithms. This tutorial reviews the common statistical framework behind all of these algorithms largely in tabular or graphical terms, illustrates its application, and describes the biological underpinnings of the models used.

  13. Self-assembly of gold nanorods into vertically aligned, rectangular microplates with a supercrystalline structure.

    PubMed

    Xiao, Junyan; Li, Zhe; Ye, Xiaozhou; Ma, Yurong; Qi, Limin

    2014-01-21

    Vertically aligned, supercrystalline microplates with a well-defined rectangular shape were fabricated in a large area through self-assembly of gold nanorods by a novel bulk solution evaporation method. This evaporative self-assembly strategy involving continuous movement of the contact line can prevent the coffee-ring effect, thus allowing uniform deposition of discrete GNR superstructures over a large area and favoring the formation of GNR supercrystals with geometrically symmetric shapes. A mechanism based on the continuing nucleation and growth of smectic GNR superstructures accompanying the movement of the contact line was put forward for the formation of the unique GNR supercrystal arrays. Based on this mechanism, a micropatterned substrate was designed to control the nucleation location and growth direction, leading to the spontaneous self-assembly of nearly parallel arrays of vertically aligned, supercrystalline microplates of GNRs. The obtained rectangular-plate-shaped GNR supercrystals exhibited interesting anisotropic optical reflection properties, which were revealed by polarized light microscopy. PMID:24292548

  14. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

    PubMed Central

    Di Tommaso, Paolo; Moretti, Sebastien; Xenarios, Ioannis; Orobitg, Miquel; Montanyola, Alberto; Chang, Jia-Ming; Taly, Jean-François; Notredame, Cedric

    2011-01-01

    This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10 000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat. PMID:21558174

  15. GRASP/Ada: Graphical Representations of Algorithms, Structures, and Processes for Ada. The development of a program analysis environment for Ada: Reverse engineering tools for Ada, task 2, phase 3

    NASA Technical Reports Server (NTRS)

    Cross, James H., II

    1991-01-01

    The main objective is the investigation, formulation, and generation of graphical representations of algorithms, structures, and processes for Ada (GRASP/Ada). The presented task, in which various graphical representations that can be extracted or generated from source code are described and categorized, is focused on reverse engineering. The following subject areas are covered: the system model; control structure diagram generator; object oriented design diagram generator; user interface; and the GRASP library.

  16. Hot-embossing replication of self-centering optical fiber alignment structures prototyped by deep proton writing

    NASA Astrophysics Data System (ADS)

    Ebraert, Evert; Wissmann, Markus; Guttmann, Markus; Kolew, Alexander; Worgull, Matthias; Barié, Nicole; Schneider, Marc; Hofmann, Andreas; Beri, Stefano; Watté, Jan; Thienpont, Hugo; Van Erps, Jürgen

    2016-07-01

    This paper presents the hot-embossing replication of self-centering fiber alignment structures for high-precision, single-mode optical fiber connectors. To this end, a metal mold insert was fabricated by electroforming a polymer prototype patterned by means of deep proton writing (DPW). To achieve through-hole structures, we developed a postembossing process step to remove the residual layer inherently present in hot-embossed structures. The geometrical characteristics of the hot-embossed replicas are compared, before and after removal of the residual layer, with the DPW prototypes. Initial measurements on the optical performance of the replicas are performed. The successful replication of these components paves the way toward low-cost mass replication of DPW-fabricated prototypes in a variety of high-tech plastics.

  17. Precision alignment device

    DOEpatents

    Jones, N.E.

    1988-03-10

    Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam. 5 figs.

  18. Precision alignment device

    DOEpatents

    Jones, Nelson E.

    1990-01-01

    Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam.

  19. PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features.

    PubMed

    Gandhimathi, Arumugam; Ghosh, Pritha; Hariharaputran, Sridhar; Mathew, Oommen K; Sowdhamini, R

    2016-01-01

    Structure-based sequence alignment is an essential step in assessing and analysing the relationship of distantly related proteins. PASS2 is a database that records such alignments for protein domain superfamilies and has been constantly updated periodically. This update of the PASS2 version, named as PASS2.5, directly corresponds to the SCOPe 2.04 release. All SCOPe structural domains that share less than 40% sequence identity, as defined by the ASTRAL compendium of protein structures, are included. The current version includes 1977 superfamilies and has been assembled utilizing the structure-based sequence alignment protocol. Such an alignment is obtained initially through MATT, followed by a refinement through the COMPARER program. The JOY program has been used for structural annotations of such alignments. In this update, we have automated the protocol and focused on inclusion of new features such as mapping of GO terms, absolutely conserved residues among the domains in a superfamily and inclusion of PDBs, that are absent in SCOPe 2.04, using the HMM profiles from the alignments of the superfamily members and are provided as a separate list. We have also implemented a more user-friendly manner of data presentation and options for downloading more features. PASS2.5 version is available at http://caps.ncbs.res.in/pass2/. PMID:26553811

  20. PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features

    PubMed Central

    Gandhimathi, Arumugam; Ghosh, Pritha; Hariharaputran, Sridhar; Mathew, Oommen K.; Sowdhamini, R.

    2016-01-01

    Structure-based sequence alignment is an essential step in assessing and analysing the relationship of distantly related proteins. PASS2 is a database that records such alignments for protein domain superfamilies and has been constantly updated periodically. This update of the PASS2 version, named as PASS2.5, directly corresponds to the SCOPe 2.04 release. All SCOPe structural domains that share less than 40% sequence identity, as defined by the ASTRAL compendium of protein structures, are included. The current version includes 1977 superfamilies and has been assembled utilizing the structure-based sequence alignment protocol. Such an alignment is obtained initially through MATT, followed by a refinement through the COMPARER program. The JOY program has been used for structural annotations of such alignments. In this update, we have automated the protocol and focused on inclusion of new features such as mapping of GO terms, absolutely conserved residues among the domains in a superfamily and inclusion of PDBs, that are absent in SCOPe 2.04, using the HMM profiles from the alignments of the superfamily members and are provided as a separate list. We have also implemented a more user-friendly manner of data presentation and options for downloading more features. PASS2.5 version is available at http://caps.ncbs.res.in/pass2/. PMID:26553811

  1. Field Emission Characteristics of the Structure of Vertically Aligned Carbon Nanotube Bundles.

    PubMed

    Lin, Pao-Hung; Sie, Cong-Lin; Chen, Ching-An; Chang, Hsuan-Chen; Shih, Yi-Ting; Chang, Hsin-Yueh; Su, Wei-Jhih; Lee, Kuei-Yi

    2015-12-01

    In this study, we performed thermal chemical vapor deposition for growing vertically aligned carbon nanotube (VACNT) bundles for a field emitter and applied photolithography for defining the arrangement pattern to simultaneously compare square and hexagonal arrangements by using two ratios of the interbundle distance to the bundle height (R) of field emitters. The hexagon arrangement with R = 2 had the lowest turn-on electric field (E to) and highest enhancement factor, whereas the square arrangement with R = 3 had the most stable field emission (FE) characteristic. The number density can reveal the correlation to the lowest E to and highest enhancement factor more effectively than can the R or L. The fluorescent images of the synthesized VACNT bundles manifested the uniformity of FE currents. The results of our study indicate the feasibility of applying the VACNT field emitter arrangement to achieve optimal FE performance. PMID:26183388

  2. Spun-wrapped aligned nanofiber (SWAN) lithography for fabrication of micro/nano-structures on 3D objects.

    PubMed

    Ye, Zhou; Nain, Amrinder S; Behkam, Bahareh

    2016-07-01

    Fabrication of micro/nano-structures on irregularly shaped substrates and three-dimensional (3D) objects is of significant interest in diverse technological fields. However, it remains a formidable challenge thwarted by limited adaptability of the state-of-the-art nanolithography techniques for nanofabrication on non-planar surfaces. In this work, we introduce Spun-Wrapped Aligned Nanofiber (SWAN) lithography, a versatile, scalable, and cost-effective technique for fabrication of multiscale (nano to microscale) structures on 3D objects without restriction on substrate material and geometry. SWAN lithography combines precise deposition of polymeric nanofiber masks, in aligned single or multilayer configurations, with well-controlled solvent vapor treatment and etching processes to enable high throughput (>10(-7) m(2) s(-1)) and large-area fabrication of sub-50 nm to several micron features with high pattern fidelity. Using this technique, we demonstrate whole-surface nanopatterning of bulk and thin film surfaces of cubes, cylinders, and hyperbola-shaped objects that would be difficult, if not impossible to achieve with existing methods. We demonstrate that the fabricated feature size (b) scales with the fiber mask diameter (D) as b(1.5)∝D. This scaling law is in excellent agreement with theoretical predictions using the Johnson, Kendall, and Roberts (JKR) contact theory, thus providing a rational design framework for fabrication of systems and devices that require precisely designed multiscale features. PMID:27283144

  3. A Web Graphics Primer.

    ERIC Educational Resources Information Center

    Buchanan, Larry

    1999-01-01

    Discusses the basic technical concepts of using graphics in World Wide Web pages, including: color depth and dithering, dots-per-inch, image size, file types, Graphics Interchange Formats (GIFs), Joint Photographic Experts Group (JPEG), format, and software recommendations. (AEF)

  4. Self-centering fiber alignment structures for high-precision field installable single-mode fiber connectors

    NASA Astrophysics Data System (ADS)

    Van Erps, Jürgen; Ebraert, Evert; Gao, Fei; Vervaeke, Michael; Berghmans, Francis; Beri, Stefano; Watté, Jan; Thienpont, Hugo

    2014-05-01

    There is a steady increase in the demand for internet bandwidth, primarily driven by cloud services and high-definition video streaming. Europe's Digital Agenda states the ambitious objective that by 2020 all Europeans should have access to internet at speeds of 30Mb/s or above, with 50% or more of households subscribing to connections of 100Mb/s. Today however, internet access in Europe is mainly based on the first generation of broadband, meaning internet accessed over legacy telephone copper and TV cable networks. In recent years, Fiber-To-The-Home (FTTH) networks have been adopted as a replacement of traditional electrical connections for the `last mile' transmission of information at bandwidths over 1Gb/s. However, FTTH penetration is still very low (< 5%) in most major Western economies. The main reason for this is the high deployment cost of FTTH networks. Indeed, the success and adoption of optical access networks critically depend on the quality and reliability of connections between optical fibers. In particular a further reduction of insertion loss of field- installable connectors must be achieved without a significant increase in component cost. This requires precise alignment of fibers that can differ in terms of ellipticity, eccentricity or diameter and seems hardly achievable using today's widespread ferrule-based alignment systems. In this paper, we present a field-installable connector based on deflectable/compressible spring structures, providing a self-centering functionality for the fiber. This way, it can accommodate for possible fiber cladding diameter variations (the tolerance on the cladding diameter of G.652 fiber is typically +/-0.7μm). The mechanical properties of the cantilever are derived through an analytical approximation and a mathematical model of the spring constant, and finite element-based simulations are carried out to find the maximum first principal stress as well as the stress distribution distribution in the fiber alignment

  5. Graphics at DESY

    NASA Astrophysics Data System (ADS)

    Schilling, Peter K.

    1989-12-01

    After a short history of computer graphics at DESY the introduction of graphic workstations based on true and "quasi" standards is described. An overview of graphics hardware and software at DESY is given as well as the communication facilities used. Some remarks about current and future development finish the paper.

  6. Synthesis of Vertically-Aligned Single-Walled Carbon Nanotubes in Micro Structure of Atmospheric Pressure Non-Equilibrium Plasma

    NASA Astrophysics Data System (ADS)

    Ohnishi, Kuma; Nozaki, Tomohiro; Okazaki, Ken; Heberlein, Joachim; Kortshagen, Uwe

    Plasma enhanced chemical vapor deposition (PECVD) is recognized as one of the viable fabrication techniques of carbon nanotubes. The outstanding advantage of PECVD is that free-standing, vertically-aligned carbon nanotubes (VA-CNTs) are synthesized due to the electric field normal to the substrate. This feature draws intense attention for the fabrication of nanoelectronic devices such as high-resolution scanning nanoprobes, interconnects, and field emission devices. However, carbon nanotubes synthesized in PECVD are overwhelmingly carbon nanofibers (CNFs) or multi-walled carbon nanotubes (MWNTs) with measurable structural defects. Tremendous interest in the preparation and characterization of vertically-aligned single-walled carbon nanotubes (VA-SWNTs) and related applications had not been realized in the scope of PECVD until recently. Here we present a fabrication technique of high-purity vertically-aligned single-walled carbon nanotubes using atmospheric pressure plasma enhanced chemical vapor deposition. By now, we have developed the atmospheric pressure radio-frequency discharge (APRFD) for this purpose. Although densely mono-dispersed Fe-Co catalysts of a few nanometers is primarily responsible for VA-SWNT growth, carbon precipitation was virtually absent in the thermal CVD regime at 700°C. On the other hand, high-yield VA-SWNTs were grown at 4 μm min-1 by applying the atmospheric pressure radio-frequency discharge. The results proved that cathodic ion sheath adjacent to the substrates, where a large potential drop exists, also plays an essential role for the controlled growth of SWNTs, while ion damage to the VA-SWNTs is inherently avoided due to high collision frequency among molecules in atmospheric pressure. In this paper, operation regime of APRFD and tentative reaction mechanisms for VA-SWNT growth are discussed along with optical imaging of near substrate region of APRFD.

  7. Preparation of a novel structured catalyst based on aligned carbon nanotube arrays for a microchannel Fischer-Tropsch synthesis reactor

    SciTech Connect

    Chin, Ya-Huei; Hu, Jianli; Cao, Chunshe; Gao, Yufei; Wang, Yong

    2005-12-15

    A novel catalyst microstructure based on aligned multiwall carbon nanotube arrays was synthesized. Its advanced heat and mass transport characteristics coupled with high surface area led to superior performances for Fischer-Tropsch synthesis in a microchannel chemical reactor. The fabrication of such a novel catalyst structure first involved metalorganic chemical vapor deposition (MOCVD) growth of a dense Al2O3 thin film over FeCrAlY foam substrate to enhance adhesion between catalyst layer and metal substrate. Aligned arrays of multiwall carbon nanotubes were grown over the substrate by catalytic decomposition of ethylene. These nanotube bundles were directly attached to the FeCrAlY substrate through a thin layer of oxide thin film. When the outer surfaces of nanobundles were coated with a catalyst layer, a unique hierarchical catalyst structure with nanoporous interstitials between the bundles was created. Thus, engineered catalysts based on such a novel hierarchical structure minimizes mass transfer encountered in the gas-liquid-solid three phase reactions. In addition, high thermal conductivity of carbon nanotube and the direct attachment of these nanobundles to the metal foam allow efficient heat removal from catalytic sites. The advanced heat and mass transfer on this novel structured catalyst was demonstrated in Fischer-Tropsch synthesis in a microchannel fixed bed reactor. The presence of carbon nanotube arrays improved dispersion of active metals and reduced mass transfer limitation, leading to a factor of four enhancement of Fischer-Tropsch synthesis activity. The improved temperature control with the carbon nanotube arrays also allows the Fischer-Tropsch synthesis being operated at temperatures as high as 265 C without reaction runaway favoring methane formation.

  8. Alignment of the system's chief nursing officer: staff or direct line structure?

    PubMed

    Kerfoot, Karlene M; Luquire, Rosemary

    2012-01-01

    The role of the system chief nursing officer nationally and internationally has been traditionally structured as a staff model, a direct line model, or a hybrid that includes parts of each model. The choice of structure should be made after a thorough investigation of what outcomes the system wants this position to accomplish, developing the appropriate structure to achieve these outcomes, and then engaging a chief nursing officer with the skills indicated by the type of structure chosen. This article describes these 3 structures and the support infrastructure necessary for each model. PMID:22955221

  9. A class of monolayer metal halogenides MX2: Electronic structures and band alignments

    NASA Astrophysics Data System (ADS)

    Lu, Feng; Wang, Weichao; Luo, Xiaoguang; Xie, Xinjian; Cheng, Yahui; Dong, Hong; Liu, Hui; Wang, Wei-Hua

    2016-03-01

    With systematic first principles calculations, a class of monolayer metal halogenides MX2 (M = Mg, Ca, Zn, Cd, Ge, Pb; M = Cl, Br, I) has been proposed. Our study indicates that these monolayer materials are semiconductors with the band gaps ranging from 2.03 eV of ZnI2 to 6.08 eV of MgCl2. Overall, the band gap increases with the increase of the electronegativity of the X atom or the atomic number of the metal M. Meanwhile, the band gaps of monolayer MgX2 (X = Cl, Br) are direct while those of other monolayers are indirect. Based on the band edge curvatures, the derived electron (me) and hole (mh) effective masses of MX2 monolayers are close to their corresponding bulk values except that the me of CdI2 is three times larger and the mh for PbI2 is twice larger. Finally, the band alignments of all the studied MX2 monolayers are provided using the vacuum level as energy reference. These theoretical results may not only introduce the monolayer metal halogenides family MX2 into the emerging two-dimensional materials, but also provide insights into the applications of MX2 in future electronic, visible and ultraviolet optoelectronic devices.

  10. Polymer stabilized vertical alignment liquid crystal display: effect of monomer structures and their stabilizing characteristics

    NASA Astrophysics Data System (ADS)

    Kwon, You Ri; Choi, Young Eun; Wen, Pushen; Lee, Byeong Hoon; Kim, Jong Chan; Lee, Myong-Hoon; Jeong, Kwang-Un; Lee, Seung Hee

    2016-04-01

    A polymer-stabilized vertical alignment (PS-VA) mode using a new type of photoreactive monomer for polymer stabilization of the liquid crystal (LC) director was developed. Conventional reactive mesogens having a higher molecular weight than those of the host LC tend to aggregate and form large-sized polymer grains when exposed to ultraviolet (UV) light, subsequently deteriorating the quality of the dark state. To address these problems, bis(4-hydroxyphenyl) diacrylates were synthesized with four different linking groups as stabilizing monomers (SMs) which have molecular weights similar to that of the host LC. Their stabilizing characteristics with respect to the molecular size and polarity of SMs were evaluated by examining the electro-optic characteristics of LC cells after UV irradiation. The results showed that the SM containing a small linking group in size between biphenyls with high polarity was favored to achieve excellent polymer stabilization. The SM containing an ether linkage showed excellent electro-optic characteristics with no large-sized polymer grains even in the absence of a photo-initiator. Consequently, we anticipate that SMs, polar and smaller in size, can improve the electro-optic characteristics in PS-VA mode.

  11. Seeing the song: left auditory structures may track auditory-visual dynamic alignment.

    PubMed

    Mossbridge, Julia A; Grabowecky, Marcia; Suzuki, Satoru

    2013-01-01

    Auditory and visual signals generated by a single source tend to be temporally correlated, such as the synchronous sounds of footsteps and the limb movements of a walker. Continuous tracking and comparison of the dynamics of auditory-visual streams is thus useful for the perceptual binding of information arising from a common source. Although language-related mechanisms have been implicated in the tracking of speech-related auditory-visual signals (e.g., speech sounds and lip movements), it is not well known what sensory mechanisms generally track ongoing auditory-visual synchrony for non-speech signals in a complex auditory-visual environment. To begin to address this question, we used music and visual displays that varied in the dynamics of multiple features (e.g., auditory loudness and pitch; visual luminance, color, size, motion, and organization) across multiple time scales. Auditory activity (monitored using auditory steady-state responses, ASSR) was selectively reduced in the left hemisphere when the music and dynamic visual displays were temporally misaligned. Importantly, ASSR was not affected when attentional engagement with the music was reduced, or when visual displays presented dynamics clearly dissimilar to the music. These results appear to suggest that left-lateralized auditory mechanisms are sensitive to auditory-visual temporal alignment, but perhaps only when the dynamics of auditory and visual streams are similar. These mechanisms may contribute to correct auditory-visual binding in a busy sensory environment. PMID:24194873

  12. Seeing the Song: Left Auditory Structures May Track Auditory-Visual Dynamic Alignment

    PubMed Central

    Mossbridge, Julia A.; Grabowecky, Marcia; Suzuki, Satoru

    2013-01-01

    Auditory and visual signals generated by a single source tend to be temporally correlated, such as the synchronous sounds of footsteps and the limb movements of a walker. Continuous tracking and comparison of the dynamics of auditory-visual streams is thus useful for the perceptual binding of information arising from a common source. Although language-related mechanisms have been implicated in the tracking of speech-related auditory-visual signals (e.g., speech sounds and lip movements), it is not well known what sensory mechanisms generally track ongoing auditory-visual synchrony for non-speech signals in a complex auditory-visual environment. To begin to address this question, we used music and visual displays that varied in the dynamics of multiple features (e.g., auditory loudness and pitch; visual luminance, color, size, motion, and organization) across multiple time scales. Auditory activity (monitored using auditory steady-state responses, ASSR) was selectively reduced in the left hemisphere when the music and dynamic visual displays were temporally misaligned. Importantly, ASSR was not affected when attentional engagement with the music was reduced, or when visual displays presented dynamics clearly dissimilar to the music. These results appear to suggest that left-lateralized auditory mechanisms are sensitive to auditory-visual temporal alignment, but perhaps only when the dynamics of auditory and visual streams are similar. These mechanisms may contribute to correct auditory-visual binding in a busy sensory environment. PMID:24194873

  13. Leaf Extraction and Analysis Framework Graphical User Interface: Segmenting and Analyzing the Structure of Leaf Veins and Areoles1[W][OA

    PubMed Central

    Price, Charles A.; Symonova, Olga; Mileyko, Yuriy; Hilley, Troy; Weitz, Joshua S.

    2011-01-01

    Interest in the structure and function of physical biological networks has spurred the development of a number of theoretical models that predict optimal network structures across a broad array of taxonomic groups, from mammals to plants. In many cases, direct tests of predicted network structure are impossible given the lack of suitable empirical methods to quantify physical network geometry with sufficient scope and resolution. There is a long history of empirical methods to quantify the network structure of plants, from roots, to xylem networks in shoots and within leaves. However, with few exceptions, current methods emphasize the analysis of portions of, rather than entire networks. Here, we introduce the Leaf Extraction and Analysis Framework Graphical User Interface (LEAF GUI), a user-assisted software tool that facilitates improved empirical understanding of leaf network structure. LEAF GUI takes images of leaves where veins have been enhanced relative to the background, and following a series of interactive thresholding and cleaning steps, returns a suite of statistics and information on the structure of leaf venation networks and areoles. Metrics include the dimensions, position, and connectivity of all network veins, and the dimensions, shape, and position of the areoles they surround. Available for free download, the LEAF GUI software promises to facilitate improved understanding of the adaptive and ecological significance of leaf vein network structure. PMID:21057114

  14. Large area gold coated nano-needles fabricated by proximity mask aligner lithography for plasmonic AR-structures

    NASA Astrophysics Data System (ADS)

    Bourgin, Yannick; Michaelis, Dirk; Käsebier, Thomas; Dannberg, Peter; Zeitner, Uwe D.

    2016-04-01

    Mask-aligner (MA) lithography is a well-known method for the fabrication of micrometer sized structures on a substrate with a diameter up to 300 mm. In spite of a theoretical resolution below 200 nm, the minimum printable feature sized remained above 1μm due to diffraction effects and limit its utilization to advanced packaging, or MEMS fabrication. Recently, developments in the illumination system and mechanical parts (known as AMALTIH for Advanced MA LITHography) as well as mask design, have permitted to used diffractive based photo-mask, and then reach the resolution limit mentioned above. This opens the possibility to fabricate smaller structures, usually accessible only by ebeam lithography. We propose here to demonstrate a fast and robust fabrication method of large area plasmonic absorber structures based on 2D sub-micrometric (350 nm period) nano-needles in a transparent polymer on a glass substrate and coated with a 50 nm thick gold layer. The interaction of the incoming light with metallic structured surface leads to the small total reflections of the 0th order below 5 %, over a large spectral band (460-660 nm) and a large set of incidence angles with TE and TM polarizations. Those results demonstrate that our fabrication process is a step toward the implementation of plasmonic based effect structures for a wide range of application.

  15. VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program

    PubMed Central

    Yahyavi, Masoumeh; Falsafi-Zadeh, Sajad; Karimi, Zahra; Kalatarian, Giti; Galehdari, Hamid

    2014-01-01

    The investigation on the types of secondary structure (SS) of a protein is important. The evolution of secondary structures during molecular dynamics simulations is a useful parameter to analyze protein structures. Therefore, it is of interest to describe VMD-SS (a software program) for the identification of secondary structure elements and its trajectories during simulation for known structures available at the Protein Data Bank (PDB). The program helps to calculate (1) percentage SS, (2) SS occurrence in each residue, (3) percentage SS during simulation, and (4) percentage residues in all SS types during simulation. The VMD-SS plug-in was designed using TCL script and stride to calculate secondary structure features. Availability The database is available for free at http://science.scu.ac.ir/HomePage.aspx?TabID=13755 PMID:25258493

  16. Spun-wrapped aligned nanofiber (SWAN) lithography for fabrication of micro/nano-structures on 3D objects

    NASA Astrophysics Data System (ADS)

    Ye, Zhou; Nain, Amrinder S.; Behkam, Bahareh

    2016-06-01

    Fabrication of micro/nano-structures on irregularly shaped substrates and three-dimensional (3D) objects is of significant interest in diverse technological fields. However, it remains a formidable challenge thwarted by limited adaptability of the state-of-the-art nanolithography techniques for nanofabrication on non-planar surfaces. In this work, we introduce Spun-Wrapped Aligned Nanofiber (SWAN) lithography, a versatile, scalable, and cost-effective technique for fabrication of multiscale (nano to microscale) structures on 3D objects without restriction on substrate material and geometry. SWAN lithography combines precise deposition of polymeric nanofiber masks, in aligned single or multilayer configurations, with well-controlled solvent vapor treatment and etching processes to enable high throughput (>10-7 m2 s-1) and large-area fabrication of sub-50 nm to several micron features with high pattern fidelity. Using this technique, we demonstrate whole-surface nanopatterning of bulk and thin film surfaces of cubes, cylinders, and hyperbola-shaped objects that would be difficult, if not impossible to achieve with existing methods. We demonstrate that the fabricated feature size (b) scales with the fiber mask diameter (D) as b1.5 ~ D. This scaling law is in excellent agreement with theoretical predictions using the Johnson, Kendall, and Roberts (JKR) contact theory, thus providing a rational design framework for fabrication of systems and devices that require precisely designed multiscale features.Fabrication of micro/nano-structures on irregularly shaped substrates and three-dimensional (3D) objects is of significant interest in diverse technological fields. However, it remains a formidable challenge thwarted by limited adaptability of the state-of-the-art nanolithography techniques for nanofabrication on non-planar surfaces. In this work, we introduce Spun-Wrapped Aligned Nanofiber (SWAN) lithography, a versatile, scalable, and cost-effective technique for

  17. Mould insert fabrication of a single-mode fibre connector alignment structure optimized by justified partial metallization

    NASA Astrophysics Data System (ADS)

    Wissmann, Markus; Barié, Nicole; Guttmann, Markus; Schneider, Marc; Kolew, Alexander; Besser, Heino; Pfleging, Wilhelm; Hofmann, Andreas; Van Erps, Jürgen; Beri, Stefano; Watté, Jan

    2015-03-01

    For mass production of multiscale-optical components, microstructured moulding tools are needed. Metal tools are used for hot embossing or injection moulding of microcomponents made of a thermoplastic polymer. Microstructures with extremely tight specifications, e.g. low side wall roughness and high aspect ratios are generally made by lithographic procedures such as x-ray lithography or deep proton writing. However, these processes are unsuitable for low-cost mass production. An alternative manufacturing method of moulding tools has been developed at the Karlsruhe Institute of Technology (KIT). This article describes a mould insert fabrication and a new replication process for self-centring fibre alignment structures for low loss field installable single-mode fibre connectors, developed and fabricated by the Vrije Universiteit Brussel (VUB) in collaboration with TE Connectivity. These components are to be used in fibre-to-the-home networks and support the deployment and maintenance of fibre optic links. The special feature of this particular fibre connector is a self-centring fibre alignment, achieved by means of a through hole with deflectable cantilevers acting as micro-springs. The particular challenge is the electroforming of through holes with a centre hole diameter smaller than 125 µm. The fibre connector structure is prototyped by deep proton writing in polymethylmethacrylate and used as a sacrificial part. Using joining, physical vapour deposition and electroforming technology, a negative copy of the prototyped connector is transferred into nickel to be used as a moulding tool. The benefits of this replication technique are a rapid and economical fabrication of moulding tools with high-precision microstructures and a long tool life. With these moulding tools low-cost mass production is possible. We present the manufacturing chain we have established. Each individual manufacturing step of the mould insert fabrication will be shown in this report. The

  18. Structure and method for controlling band offset and alignment at a crystalline oxide-on-semiconductor interface

    DOEpatents

    McKee, Rodney A.; Walker, Frederick J.

    2003-11-25

    A crystalline oxide-on-semiconductor structure and a process for constructing the structure involves a substrate of silicon, germanium or a silicon-germanium alloy and an epitaxial thin film overlying the surface of the substrate wherein the thin film consists of a first epitaxial stratum of single atomic plane layers of an alkaline earth oxide designated generally as (AO).sub.n and a second stratum of single unit cell layers of an oxide material designated as (A'BO.sub.3).sub.m so that the multilayer film arranged upon the substrate surface is designated (AO).sub.n (A'BO.sub.3).sub.m wherein n is an integer repeat of single atomic plane layers of the alkaline earth oxide AO and m is an integer repeat of single unit cell layers of the A'BO.sub.3 oxide material. Within the multilayer film, the values of n and m have been selected to provide the structure with a desired electrical structure at the substrate/thin film interface that can be optimized to control band offset and alignment.

  19. Programming Language Software For Graphics Applications

    NASA Technical Reports Server (NTRS)

    Beckman, Brian C.

    1993-01-01

    New approach reduces repetitive development of features common to different applications. High-level programming language and interactive environment with access to graphical hardware and software created by adding graphical commands and other constructs to standardized, general-purpose programming language, "Scheme". Designed for use in developing other software incorporating interactive computer-graphics capabilities into application programs. Provides alternative to programming entire applications in C or FORTRAN, specifically ameliorating design and implementation of complex control and data structures typifying applications with interactive graphics. Enables experimental programming and rapid development of prototype software, and yields high-level programs serving as executable versions of software-design documentation.

  20. The TEKLIB graphic library

    NASA Technical Reports Server (NTRS)

    Bostic, S. W.

    1983-01-01

    TEKLIB is a library of procedures written in TI PASCAL to perform basic graphic tasks. TEKLIB was written to provide an interface between a graphics terminal and the TI 990. The TI 990 is used as a controller for the Finite Element Machine which is an array of microprocessors designed to solve problems by finite element methods in parallel. The use of TEKLIB provides a means of inputting data graphically and displaying output.

  1. Xtal-xplore-R: a graphical tool for exploring the residual function involved in crystal structure determination

    PubMed Central

    Simons, Jan Marten; Roth, Georg

    2015-01-01

    This work presents Xtal-xplore-R, a tool dedicated to the visualization of two-dimensional cuts through the multidimensional crystallographic residual function. It imports arbitrary crystal structures, generates artificial diffraction data, and calculates and investigates the residual function in parameter space. The program serves two major purposes. Firstly, it is part of a more general project dealing with structure determination via global optimization techniques. In this context, the tool is being used to systematically analyse characteristic universal features of the target function (residual function) which can be used to develop appropriate problem-specific heuristic optimization algorithms. Secondly, Xtal-xplore-R is intended as a didactic tool to visualize how changes in atom parameters affect the residual function and can be used to demonstrate manual structure optimization for simple crystal structures. PMID:26306094

  2. Alignment validation

    SciTech Connect

    ALICE; ATLAS; CMS; LHCb; Golling, Tobias

    2008-09-06

    The four experiments, ALICE, ATLAS, CMS and LHCb are currently under constructionat CERN. They will study the products of proton-proton collisions at the Large Hadron Collider. All experiments are equipped with sophisticated tracking systems, unprecedented in size and complexity. Full exploitation of both the inner detector andthe muon system requires an accurate alignment of all detector elements. Alignmentinformation is deduced from dedicated hardware alignment systems and the reconstruction of charged particles. However, the system is degenerate which means the data is insufficient to constrain all alignment degrees of freedom, so the techniques are prone to converging on wrong geometries. This deficiency necessitates validation and monitoring of the alignment. An exhaustive discussion of means to validate is subject to this document, including examples and plans from all four LHC experiments, as well as other high energy experiments.

  3. Interactive graphical computer-aided design system

    NASA Technical Reports Server (NTRS)

    Edge, T. M.

    1975-01-01

    System is used for design, layout, and modification of large-scale-integrated (LSI) metal-oxide semiconductor (MOS) arrays. System is structured around small computer which provides real-time support for graphics storage display unit with keyboard, slave display unit, hard copy unit, and graphics tablet for designer/computer interface.

  4. Homeotropic alignment and director structures in thin films of triphenylamine-based discotic liquid crystals controlled by supporting nanostructured substrates and surface confinement.

    PubMed

    Choudhury, Trirup Dutta; Rao, Nandiraju V S; Tenent, Robert; Blackburn, Jeffrey; Gregg, Brian; Smalyukh, Ivan I

    2011-02-01

    We explore the effects of nanoscale morphology of supporting solid substrates on alignment, defects, and director structures exhibited by thin films of triphenylamine-based discotic liquid crystals. Fluorescence confocal polarizing microscopy and intrinsic polarized fluorescence properties of studied molecules are used to visualize three-dimensional director fields in the liquid crystal films. We demonstrate that, by controlling surface anchoring on supporting or confining solid substrates such as those of carbon nanotube electrodes on glass plates, both uniform homeotropic and in-plane (edge-on) alignment and nonuniform structures with developable domains can be achieved for the same discotic liquid crystal material. PMID:21214228

  5. Evidence for a spin-aligned neutron-proton paired phase from the level structure of (92)Pd.

    PubMed

    Cederwall, B; Moradi, F Ghazi; Bäck, T; Johnson, A; Blomqvist, J; Clément, E; de France, G; Wadsworth, R; Andgren, K; Lagergren, K; Dijon, A; Jaworski, G; Liotta, R; Qi, C; Nyakó, B M; Nyberg, J; Palacz, M; Al-Azri, H; Algora, A; de Angelis, G; Ataç, A; Bhattacharyya, S; Brock, T; Brown, J R; Davies, P; Di Nitto, A; Dombrádi, Zs; Gadea, A; Gál, J; Hadinia, B; Johnston-Theasby, F; Joshi, P; Juhász, K; Julin, R; Jungclaus, A; Kalinka, G; Kara, S O; Khaplanov, A; Kownacki, J; La Rana, G; Lenzi, S M; Molnár, J; Moro, R; Napoli, D R; Singh, B S Nara; Persson, A; Recchia, F; Sandzelius, M; Scheurer, J-N; Sletten, G; Sohler, D; Söderström, P-A; Taylor, M J; Timár, J; Valiente-Dobón, J J; Vardaci, E; Williams, S

    2011-01-01

    Shell structure and magic numbers in atomic nuclei were generally explained by pioneering work that introduced a strong spin-orbit interaction to the nuclear shell model potential. However, knowledge of nuclear forces and the mechanisms governing the structure of nuclei, in particular far from stability, is still incomplete. In nuclei with equal neutron and proton numbers (N = Z), enhanced correlations arise between neutrons and protons (two distinct types of fermions) that occupy orbitals with the same quantum numbers. Such correlations have been predicted to favour an unusual type of nuclear superfluidity, termed isoscalar neutron-proton pairing, in addition to normal isovector pairing. Despite many experimental efforts, these predictions have not been confirmed. Here we report the experimental observation of excited states in the N = Z = 46 nucleus (92)Pd. Gamma rays emitted following the (58)Ni((36)Ar,2n)(92)Pd fusion-evaporation reaction were identified using a combination of state-of-the-art high-resolution γ-ray, charged-particle and neutron detector systems. Our results reveal evidence for a spin-aligned, isoscalar neutron-proton coupling scheme, different from the previous prediction. We suggest that this coupling scheme replaces normal superfluidity (characterized by seniority coupling) in the ground and low-lying excited states of the heaviest N = Z nuclei. Such strong, isoscalar neutron-proton correlations would have a considerable impact on the nuclear level structure and possibly influence the dynamics of rapid proton capture in stellar nucleosynthesis. PMID:21179086

  6. High school chemistry students' learning of the elements, structure, and periodicity of the periodic table: Contributions of inquiry-based activities and exemplary graphics

    NASA Astrophysics Data System (ADS)

    Roddy, Knight Phares, Jr.

    The main research question of this study was: How do selected high school chemistry students' understandings of the elements, structure, and periodicity of the Periodic Table change as they participate in a unit study consisting of inquiry-based activities emphasizing construction of innovative science graphics? The research question was answered using a multiple case study/mixed model design which employed elements of both qualitative and quantitative methodologies during data collection and analyses. The unit study was conducted over a six-week period with 11th -grade students enrolled in a chemistry class. A purposive sample of six students from the class was selected to participate in interviews and concept map coconstruction (Wandersee & Abrams, 1993) periodically across the study. The progress of the selected students of the case study was compared to the progress of the class as a whole. The students of the case study were also compared to a group of high school chemistry students at a comparative school. The results show that the students from both schools left traditional instruction on the periodic table (lecture and textbook activities) with a very limited understanding of the topic. It also revealed that the inquiry-based, visual approach of the unit study helped students make significant conceptual progress in their understanding of the periodic table. The pictorial periodic table (which features photographs of the elements), used in conjunction with the graphic technique of data mapping, enhanced students understanding of the patterns of the physical properties of the elements on the periodic table. The graphic technique of compound mapping helped students learn reactivity patterns between types and groups of elements on the periodic table. The recreation of the periodic table with element cards created from the pictorial periodic table helped students progress in their understanding of periodicity and its key concepts. The Periodic Table Literacy

  7. Alignment-Annotator web server: rendering and annotating sequence alignments

    PubMed Central

    Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

    2014-01-01

    Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

  8. Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

    PubMed

    Moriya, Yuki; Yamada, Takuji; Okuda, Shujiro; Nakagawa, Zenichi; Kotera, Masaaki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Goto, Susumu

    2016-03-28

    Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies that estimate the number of candidate enzyme genes, these studies required some additional information aside from the structures of metabolites such as gene expression and order in the genome. In this study, we developed a novel method to identify a candidate enzyme gene of a reaction using the chemical structures of the substrate-product pair (reactant pair). The proposed method is based on a search for similar reactant pairs in a reference database and offers ortholog groups that possibly mediate the given reaction. We applied the proposed method to two experimentally validated reactions. As a result, we confirmed that the histidine transaminase was correctly identified. Although our method could not directly identify the asparagine oxo-acid transaminase, we successfully found the paralog gene most similar to the correct enzyme gene. We also applied our method to infer candidate enzyme genes in the mesaconate pathway. The advantage of our method lies in the prediction of possible genes for orphan enzyme reactions where any associated gene sequences are not determined yet. We believe that this approach will facilitate experimental identification of genes for orphan enzymes. PMID:26822930

  9. Interplay between Self-Assembled Structures and Energy Level Alignment of Benzenediamine on Au(111) Surfaces

    NASA Astrophysics Data System (ADS)

    Li, Guo; Neaton, Jeffrey

    2015-03-01

    Using van der Waals-corrected density functional theory (DFT) calculations, we study the adsorption of benzene-diamine (BDA) molecules on Au(111) surfaces. We find that at low surface coverage, the adsorbed molecules prefer to stay isolated from each other in a monomer phase, due to the inter-molecular dipole-dipole repulsions. However, when the coverage rises above a critical value of 0.9nm-2, the adsorbed molecules aggregate into linear structures via hydrogen bonding between amine groups, consistent with recent experiments [Haxton, Zhou, Tamblyn, et al, Phys. Rev. Lett. 111, 265701 (2013)]. Moreover, we find that these linear structures at high density considerably reduces the Au work function (relative to a monomer phase). Due to reduced surface polarization effects, we estimate that the resonance energy of the highest occupied molecular orbital of the adsorbed BDA molecule relative to the Au Fermi level is significantly lower than the monomer phase by more than 0.5 eV, consistent with the experimental measurements [DellAngela, Kladnik, and Cossaro, et al., Nano Lett. 10, 2470 (2010)]. This work supported by DOE (the JCAP under Award Number DE-SC000499 and the Molecular Foundry of LBNL), and computational resources provided by NERSC.

  10. Graphics mini manual

    NASA Technical Reports Server (NTRS)

    Taylor, Nancy L.; Randall, Donald P.; Bowen, John T.; Johnson, Mary M.; Roland, Vincent R.; Matthews, Christine G.; Gates, Raymond L.; Skeens, Kristi M.; Nolf, Scott R.; Hammond, Dana P.

    1990-01-01

    The computer graphics capabilities available at the Center are introduced and their use is explained. More specifically, the manual identifies and describes the various graphics software and hardware components, details the interfaces between these components, and provides information concerning the use of these components at LaRC.

  11. Quantitative Graphics in Newspapers.

    ERIC Educational Resources Information Center

    Tankard, James W., Jr.

    The use of quantitative graphics in newspapers requires achieving a balance between being accurate and getting the attention of the reader. The statistical representations in newspapers are drawn by graphic designers whose key technique is fusion--the striking combination of two visual images. This technique often results in visual puns,…

  12. How Computer Graphics Work.

    ERIC Educational Resources Information Center

    Prosise, Jeff

    This document presents the principles behind modern computer graphics without straying into the arcane languages of mathematics and computer science. Illustrations accompany the clear, step-by-step explanations that describe how computers draw pictures. The 22 chapters of the book are organized into 5 sections. "Part 1: Computer Graphics in…

  13. gCOMBINE: A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes.

    PubMed

    Gil-Redondo, Rubén; Klett, Javier; Gago, Federico; Morreale, Antonio

    2010-01-01

    We present gCOMBINE, a Java-written graphical user interface (GUI) for performing comparative binding energy (COMBINE) analysis (Ortiz et al. J Med Chem 1995; 38:2681-2691) on a set of ligand-receptor complexeswith the aim of deriving highly informative quantitative structure-activity relationships. The essence of the method is to decompose the ligand-receptor interaction energies into a series of terms, explore the origins of the variance within the set using Principal Component Analysis, and then assign weights to selected ligandresidue interactions using partial least squares analysis to correlate with the experimental activities or binding affinities. The GUI allows plenty of interactivity and provides multiple plots representing the energy descriptors entering the analysis, scores, loadings, experimental versus predicted regression lines, and the evolution of parameterssuch as r(2) (correlation coefficient), q(2) (cross-validated r(2)), and prediction errors as the number of extracted latent variables increases. Other representative features include the implementation of a sigmoidal dielectric function for electrostatic energy calculations, alternative cross-validation procedures (leave-N-out and random groups), drawing of confidence ellipses, and the possibility to carry out several additional tasks such as optional truncation of positive interaction energy values and generation of ready-to-use PDB files containing information related to the importance for activity of individual protein residues. This information can be displayed and color-coded using a standard molecular graphics program such as PyMOL. It is expected that this user-friendly tool will expand the applicability of the COMBINE analysis method and encourage more groups to use it in their drug design research programs. PMID:19705486

  14. Usefulness of graphical invariants in quantitative structure-activity correlations of tuberculostatic drugs of the isonicotinic acid hydrazide type.

    PubMed

    Bagchi, Manish C; Maiti, Bhim C; Mills, Denise; Basak, Subhash C

    2004-04-01

    Quantitative structure-activity relationship (QSAR) studies have been performed for a series of 2-substituted isonicotinic acid hydrazides utilizing theoretical molecular descriptors. 223 topological (topostructural and topochemical) indices along with seven geometrical descriptors were computed for the prediction of antibacterial activity against Mycobacterium tuberculosis. Ridge-regression models assessed by cross-validated R2 have been formulated, and a comparative study on the relative effectiveness of physicochemical vis-à-vis theoretical molecular descriptors performed. The models developed clearly indicate the supremacy of structure-activity over property-activity relationships in the current study and can be used to evaluate the potential tuberculostatic activity of other INH derivatives, real or hypothetical. PMID:14691675

  15. Quick synthesis of highly aligned or randomly oriented nanofibrous structures composed of C60 molecules via self-assembly

    NASA Astrophysics Data System (ADS)

    Kurosu, Shunji; Fukuda, Takahiro; Maekawa, Toru

    2013-06-01

    Assemblies, which are composed of nanoparticles such as nanofibres, have been intensively studied in recent years. This has particularly been the case in the field of biomedicine, where the aim is to develop efficient methodologies for capturing and separating target biomolecules and cells and/or encouraging bio-chemical reactions, utilizing the extremely high surface area to volume ratio of assemblies. There is an urgent need for the development of a quick synthesis method of forming nanofibrous structures on the surface of biomedical microchips and devices for the investigation of the interactions between biomolecules/cells and the nanostructures. Here, we produce nanofibrous structures composed of C60 molecules, which are aligned in one direction or randomly oriented, by dissolving C60 molecules and sulphur in benzene and evaporating a droplet of the solution on a glass substrate under appropriate conditions. The synthesis time is as short as 30 s. Sulphur is extracted and nanofibres are crystallized by leaving them in supercritical carbon dioxide.

  16. Band alignment of vanadium oxide as an interlayer in a hafnium oxide-silicon gate stack structure

    NASA Astrophysics Data System (ADS)

    Zhu, Chiyu; Kaur, Manpuneet; Tang, Fu; Liu, Xin; Smith, David J.; Nemanich, Robert J.

    2012-10-01

    Vanadium oxide (VO2) is a narrow band gap material (Eg = 0.7 eV) with a thermally induced insulator-metal phase transition at ˜343 K and evidence of an electric field induced transition at T < 343 K. To explore the electronic properties of VO2, a sandwich structure was prepared with a 2 nm VO2 layer embedded between an oxidized Si(100) surface and a 2 nm hafnium oxide (HfO2) layer. The layer structure was confirmed with high resolution transmission electron microscopy. The electronic properties were characterized with x-ray and ultraviolet photoemission spectroscopy, and the band alignment was deduced on both n-type and p-type Si substrates. The valence band offset between VO2 and SiO2 is measured to be 4.0 eV. The valence band offset between HfO2 and VO2 is measured to be ˜3.4 eV. The band relation developed from these results demonstrates the potential for charge storage and switching for the embedded VO2 layer.

  17. The effect of high-temperature annealing on the structure and electrical properties of well-aligned carbon nanotubes

    SciTech Connect

    Gong Qianming . E-mail: gongqianming@mail.tsinghua.org.cn; Li Zhi; Wang Ye; Wu Bin; Zhang Zhengyi; Liang Ji

    2007-03-22

    Systematic work has been performed on the effect of high-temperature annealing on structural defects and impurities of well-aligned carbon nanotubes (ACNTs) in this paper. ACNTs had been prepared by CVD process with ferrocene as catalyst and then the as-grown samples were experienced heat treatment (HT) from 1800 to 3000 deg. C. X-ray diffraction, Raman spectroscopy and electron dispersive spectroscopy (EDS), etc., have been used to analyze the effect of annealing. Results indicate that some impurities can be removed once annealing temperature exceeds vaporization point of corresponding metal or non-metal. Desorption of O should be attributed to reduced active sites of dangling covalent bonds after heat treatment. Specious discrepancy about interlayer spacing resulted from XRD and Raman tests show that although high-temperature heat treatment can remove in-plane defects of carbon nanotubes greatly, interlayer spacing between graphene shells could not be reduced effectively because of the special concentric cylindrical structure of nanotubes. Electrical resistivity of ACNTs block is about three orders higher than that of copper even after HT at 3000 deg. C, and the anisotropy of electrical properties increased once experienced heat treatment at increased temperature.

  18. EINSTEIN Cluster Alignments Revisited

    NASA Astrophysics Data System (ADS)

    Chambers, S. W.; Melott, A. L.; Miller, C. J.

    2000-12-01

    We have examined whether the major axes of rich galaxy clusters tend to point (in projection) toward their nearest neighboring cluster. We used the data of Ulmer, McMillan and Kowalski, who used x-ray morphology to define position angles. Our cluster samples, with well measured redshifts and updated positions, were taken from the MX Northern Abell Cluster Survey. The usual Kolmogorov-Smirnov test shows no significant alignment signal for nonrandom angles for all separations less than 100 Mpc/h. Refining the null hypothesis, however, with the Wilcoxon rank-sum test, reveals a high confidence signal for alignment. This confidence is highest when we restrict our sample to small nearest neighbor separations. We conclude that we have identified a more powerful tool for testing cluster-cluster alignments. Moreover, there is a strong signal in the data for alignment, consistent with a picture of hierarchical cluster formation in which matter falls into clusters along large scale filamentary structures.

  19. Structure-based sequence alignment for the beta-trefoil subdomain of the clostridial neurotoxin family provides residue level information about the putative ganglioside binding site.

    PubMed

    Ginalski, K; Venclovas, C; Lesyng, B; Fidelis, K

    2000-09-29

    Clostridial neurotoxins embrace a family of extremely potent toxins comprised of tetanus toxin (TeNT) and seven different serotypes of botulinum toxin (BoNT/A-G). The beta-trefoil subdomain of the C-terminal part of the heavy chain (H(C)), responsible for ganglioside binding, is the most divergent region in clostridial neurotoxins with sequence identity as low as 15%. We re-examined the alignment between family sequences within this subdomain, since in this region all alignments published to date show obvious inconsistencies with the beta-trefoil fold. The final alignment was obtained by considering the general constraints imposed by this fold, and homology modeling studies based on the TeNT structure. Recently solved structures of BoNT/A confirm the validity of this structure-based approach. Taking into account biochemical data and crystal structures of TeNT and BoNT/A, we also re-examined the location of the putative ganglioside binding site and, using the new alignment, characterized this site in other BoNT serotypes. PMID:11018534

  20. Perception in statistical graphics

    NASA Astrophysics Data System (ADS)

    VanderPlas, Susan Ruth

    There has been quite a bit of research on statistical graphics and visualization, generally focused on new types of graphics, new software to create graphics, interactivity, and usability studies. Our ability to interpret and use statistical graphics hinges on the interface between the graph itself and the brain that perceives and interprets it, and there is substantially less research on the interplay between graph, eye, brain, and mind than is sufficient to understand the nature of these relationships. The goal of the work presented here is to further explore the interplay between a static graph, the translation of that graph from paper to mental representation (the journey from eye to brain), and the mental processes that operate on that graph once it is transferred into memory (mind). Understanding the perception of statistical graphics should allow researchers to create more effective graphs which produce fewer distortions and viewer errors while reducing the cognitive load necessary to understand the information presented in the graph. Taken together, these experiments should lay a foundation for exploring the perception of statistical graphics. There has been considerable research into the accuracy of numerical judgments viewers make from graphs, and these studies are useful, but it is more effective to understand how errors in these judgments occur so that the root cause of the error can be addressed directly. Understanding how visual reasoning relates to the ability to make judgments from graphs allows us to tailor graphics to particular target audiences. In addition, understanding the hierarchy of salient features in statistical graphics allows us to clearly communicate the important message from data or statistical models by constructing graphics which are designed specifically for the perceptual system.

  1. Support Vector Training of Protein Alignment Models

    PubMed Central

    Joachims, Thorsten; Elber, Ron; Pillardy, Jaroslaw

    2008-01-01

    Abstract Sequence to structure alignment is an important step in homology modeling of protein structures. Incorporation of features such as secondary structure, solvent accessibility, or evolutionary information improve sequence to structure alignment accuracy, but conventional generative estimation techniques for alignment models impose independence assumptions that make these features difficult to include in a principled way. In this paper, we overcome this problem using a Support Vector Machine (SVM) method that provides a well-founded way of estimating complex alignment models with hundred of thousands of parameters. Furthermore, we show that the method can be trained using a variety of loss functions. In a rigorous empirical evaluation, the SVM algorithm outperforms the generative alignment method SSALN, a highly accurate generative alignment model that incorporates structural information. The alignment model learned by the SVM aligns 50% of the residues correctly and aligns over 70% of the residues within a shift of four positions. PMID:18707536

  2. Reexamining X-mode suppression and fine structure in artificial E region field-aligned plasma density irregularities

    NASA Astrophysics Data System (ADS)

    Miceli, R. J.; Hysell, D. L.; Munk, J.; McCarrick, M.; Huba, J. D.

    2013-09-01

    Artificial field-aligned plasma density irregularities (FAIs) were generated in the E region of the ionosphere above the High Frequency Active Auroral Research Program facility during campaigns in May and August of 2012 and observed using a 30 MHz coherent scatter radar imager in Homer, Alaska. The purpose of this ionospheric modification experiment was to measure the threshold pump power required to excite thermal parametric instabilities by O-mode heating and to investigate the suppression of the FAIs by simultaneous X-mode heating. We find that the threshold pump power for irregularity excitation was consistent with theoretical predictions and increased by approximately a factor of 2 when X-mode heating was present. A modified version of the Another Model of the Ionosphere (SAMI2) ionospheric model was used to simulate the threshold experiments and suggested that the increase was entirely due to enhanced D region absorption associated with X-mode heating. Additionally, a remarkable degree of fine structure possibly caused by natural gradient drift instability in the heater-modified volume was observed in experiments performed during geomagnetically active conditions.

  3. Cryogenic performance of a high precision photogrammetry system for verification of the James Webb Space Telescope Integrated Science Instrument Module and associated ground support equipment structural alignment requirements

    NASA Astrophysics Data System (ADS)

    Nowak, Maria D.; Cleveland, Paul E.; Cofie, Emmanuel; Crane, J. Allen; Davila, Pamela S.; Eegholm, Bente H.; Hammond, Randolph P.; Heaney, James B.; Hylan, Jason E.; Johnston, John D.; Ohl, Raymond G.; Orndorff, Joseph D.; Osgood, Dean L.; Redman, Kevin W.; Sampler, Henry P.; Smee, Stephen A.; Stock, Joseph M.; Threat, Felix T.; Woodruff, Robert A.; Young, Philip J.

    2010-08-01

    The James Webb Space Telescope (JWST) is a general astrophysics mission which consists of a 6.6m diameter, segmented, deployable telescope for cryogenic IR space astronomy (~35K). The JWST Observatory architecture includes the Optical Telescope Element and the Integrated Science Instrument Module (ISIM) element that contains four science instruments (SI) including a Guider. The alignment philosophy of ISIM is such that the cryogenic changes in the alignment of the SI interfaces are captured in the ISIM alignment error budget. The SIs are aligned to the structure's coordinate system under ambient, clean room conditions using laser tracker and theodolite metrology. The ISIM structure is thermally cycled and temperature-induced structural changes are concurrently measured with a photogrammetry metrology system to ensure they are within requirements. We compare the ISIM photogrammetry system performance to the ISIM metrology requirements and describe the cryogenic data acquired to verify photogrammetry system level requirements, including measurement uncertainty. The ISIM photogrammetry system is the baseline concept for future tests involving the Optical Telescope Element (OTE) and Observatory level testing at Johnson Space Flight Center.

  4. Minerals and aligned collagen fibrils in tilapia fish scales: structural analysis using dark-field and energy-filtered transmission electron microscopy and electron tomography.

    PubMed

    Okuda, Mitsuhiro; Ogawa, Nobuhiro; Takeguchi, Masaki; Hashimoto, Ayako; Tagaya, Motohiro; Chen, Song; Hanagata, Nobutaka; Ikoma, Toshiyuki

    2011-10-01

    The mineralized structure of aligned collagen fibrils in a tilapia fish scale was investigated using transmission electron microscopy (TEM) techniques after a thin sample was prepared using aqueous techniques. Electron diffraction and electron energy loss spectroscopy data indicated that a mineralized internal layer consisting of aligned collagen fibrils contains hydroxyapatite crystals. Bright-field imaging, dark-field imaging, and energy-filtered TEM showed that the hydroxyapatite was mainly distributed in the hole zones of the aligned collagen fibrils structure, while needle-like materials composed of calcium compounds including hydroxyapatite existed in the mineralized internal layer. Dark-field imaging and three-dimensional observation using electron tomography revealed that hydroxyapatite and needle-like materials were mainly found in the matrix between the collagen fibrils. It was observed that hydroxyapatite and needle-like materials were preferentially distributed on the surface of the hole zones in the aligned collagen fibrils structure and in the matrix between the collagen fibrils in the mineralized internal layer of the scale. PMID:21899811

  5. Alignment fixture

    DOEpatents

    Bell, Grover C.; Gibson, O. Theodore

    1980-01-01

    A part alignment fixture is provided which may be used for precise variable lateral and tilt alignment relative to the fixture base of various shaped parts. The fixture may be used as a part holder for machining or inspection of parts or alignment of parts during assembly and the like. The fixture includes a precisely machined diameter disc-shaped hub adapted to receive the part to be aligned. The hub is nested in a guide plate which is adapted to carry two oppositely disposed pairs of positioning wedges so that the wedges may be reciprocatively positioned by means of respective micrometer screws. The sloping faces of the wedges contact the hub at respective quadrants of the hub periphery. The lateral position of the hub relative to the guide plate is adjusted by positioning the wedges with the associated micrometer screws. The tilt of the part is adjusted relative to a base plate, to which the guide plate is pivotally connected by means of a holding plate. Two pairs of oppositely disposed wedges are mounted for reciprocative lateral positioning by means of separate micrometer screws between flanges of the guide plate and the base plate. Once the wedges are positioned to achieve the proper tilt of the part or hub on which the part is mounted relative to the base plate, the fixture may be bolted to a machining, inspection, or assembly device.

  6. Developing a Graphical User Interface to Automate the Estimation and Prediction of Risk Values for Flood Protective Structures using Artificial Neural Network

    NASA Astrophysics Data System (ADS)

    Hasan, M.; Helal, A.; Gabr, M.

    2014-12-01

    In this project, we focus on providing a computer-automated platform for a better assessment of the potential failures and retrofit measures of flood-protecting earth structures, e.g., dams and levees. Such structures play an important role during extreme flooding events as well as during normal operating conditions. Furthermore, they are part of other civil infrastructures such as water storage and hydropower generation. Hence, there is a clear need for accurate evaluation of stability and functionality levels during their service lifetime so that the rehabilitation and maintenance costs are effectively guided. Among condition assessment approaches based on the factor of safety, the limit states (LS) approach utilizes numerical modeling to quantify the probability of potential failures. The parameters for LS numerical modeling include i) geometry and side slopes of the embankment, ii) loading conditions in terms of rate of rising and duration of high water levels in the reservoir, and iii) cycles of rising and falling water levels simulating the effect of consecutive storms throughout the service life of the structure. Sample data regarding the correlations of these parameters are available through previous research studies. We have unified these criteria and extended the risk assessment in term of loss of life through the implementation of a graphical user interface to automate input parameters that divides data into training and testing sets, and then feeds them into Artificial Neural Network (ANN) tool through MATLAB programming. The ANN modeling allows us to predict risk values of flood protective structures based on user feedback quickly and easily. In future, we expect to fine-tune the software by adding extensive data on variations of parameters.

  7. Structure of small-scale field-aligned currents at middle and low latitudes having lower atmospheric origin

    NASA Astrophysics Data System (ADS)

    Nakanishi, K.; Iyemori, T.; Luhr, H.; Aoyama, T.

    2014-12-01

    The CHAMP magnetic data indicate that small amplitude (1-5 nT) magnetic fluctuations with period around a few tens of seconds along the orbit exist globally and almost all the time. Characteristics of the magnetic fluctuations including seasonal dependence having geographical characteristics strongly suggest that they are the small-scale spatial structure of field-aligned currents with lower atmospheric origin (Nakanishi et al., 2014). We suppose that gravity waves generated by lower atmospheric disturbances propagate to the ionosphere and drive the E-layer dynamo. The currents in the ionosphere divert along the magnetic field into the other hemisphere and make a closed circuit. To confirm the above scenario and to find the scale of the current circuit in longitudinal direction, we use the magnetic data observed by the SWARM satellites. By analysis of the magnetic data observed by the SWARM satellites, the magnetic fluctuations as recorded earlier by CHAMP are confirmed to have the same characteristics i.e., the magnetic fluctuation is perpendicular to the geomagnetic field; the amplitude on the dayside is much larger than that on the nightside; towards the dip equator the period tends to get longer. Because the three Swarm satellites have various spatial relations in 3-D space between their orbits, we could easily confirm that the objective magnetic fluctuations are not temporal but spatial structures. The longitudinal scale seems to be of the order of 100 km. We shall show the above results and some other characteristics of the current circuit and discuss whether or not our suggested model fits the observed characteristics.

  8. Graphical models of residue coupling in protein families.

    PubMed

    Thomas, John; Ramakrishnan, Naren; Bailey-Kellogg, Chris

    2008-01-01

    Many statistical measures and algorithmic techniques have been proposed for studying residue coupling in protein families. Generally speaking, two residue positions are considered coupled if, in the sequence record, some of their amino acid type combinations are significantly more common than others. While the proposed approaches have proven useful in finding and describing coupling, a significant missing component is a formal probabilistic model that explicates and compactly represents the coupling, integrates information about sequence,structure, and function, and supports inferential procedures for analysis, diagnosis, and prediction.We present an approach to learning and using probabilistic graphical models of residue coupling. These models capture significant conservation and coupling constraints observable ina multiply-aligned set of sequences. Our approach can place a structural prior on considered couplings, so that all identified relationships have direct mechanistic explanations. It can also incorporate information about functional classes, and thereby learn a differential graphical model that distinguishes constraints common to all classes from those unique to individual classes. Such differential models separately account for class-specific conservation and family-wide coupling, two different sources of sequence covariation. They are then able to perform interpretable functional classification of new sequences, explaining classification decisions in terms of the underlying conservation and coupling constraints. We apply our approach in studies of both G protein-coupled receptors and PDZ domains, identifying and analyzing family-wide and class-specific constraints, and performing functional classification. The results demonstrate that graphical models of residue coupling provide a powerful tool for uncovering, representing, and utilizing significant sequence structure-function relationships in protein families. PMID:18451428

  9. A graphical ICU workstation.

    PubMed Central

    Higgins, S. B.; Jiang, K.; Swindell, B. B.; Bernard, G. R.

    1991-01-01

    A workstation designed to facilitate electronic charting in the intensive care unit is described. The system design incorporates a graphical, windows-based user interface. The system captures all data formerly recorded on the paper flowsheet including direct patient measurements, nursing assessment, patient care procedures, and nursing notes. It has the ability to represent charted data in a variety of graphical formats, thereby providing additional insights to facilitate the management of the critically ill patient. Initial nursing evaluation is described. PMID:1807712

  10. Flowfield computer graphics

    NASA Technical Reports Server (NTRS)

    Desautel, Richard

    1993-01-01

    The objectives of this research include supporting the Aerothermodynamics Branch's research by developing graphical visualization tools for both the branch's adaptive grid code and flow field ray tracing code. The completed research for the reporting period includes development of a graphical user interface (GUI) and its implementation into the NAS Flowfield Analysis Software Tool kit (FAST), for both the adaptive grid code (SAGE) and the flow field ray tracing code (CISS).

  11. Graphical Models via Univariate Exponential Family Distributions

    PubMed Central

    Yang, Eunho; Ravikumar, Pradeep; Allen, Genevera I.; Liu, Zhandong

    2016-01-01

    Undirected graphical models, or Markov networks, are a popular class of statistical models, used in a wide variety of applications. Popular instances of this class include Gaussian graphical models and Ising models. In many settings, however, it might not be clear which subclass of graphical models to use, particularly for non-Gaussian and non-categorical data. In this paper, we consider a general sub-class of graphical models where the node-wise conditional distributions arise from exponential families. This allows us to derive multivariate graphical model distributions from univariate exponential family distributions, such as the Poisson, negative binomial, and exponential distributions. Our key contributions include a class of M-estimators to fit these graphical model distributions; and rigorous statistical analysis showing that these M-estimators recover the true graphical model structure exactly, with high probability. We provide examples of genomic and proteomic networks learned via instances of our class of graphical models derived from Poisson and exponential distributions. PMID:27570498

  12. The Identification and Classification of Graphic Communication Technology.

    ERIC Educational Resources Information Center

    Fecik, John T.

    All graphic reproduction processes are a means of communication. The purpose of this study was to identify and classify common elements of graphic communication technology into a structure representing the various industrial techniques. Six graphic reproduction processes were identified as relief, intaglio, planography, screen process,…

  13. Software tool for the analysis and visualization of whole genome alignments

    2011-08-01

    GenomeVISTA is a tool which performs and displays pairwise and multiple whole genome DNA alignments. The tools provides a graphical user interface by which users can navigate alignments and multiple levels of resolution and get imformation about individual aligned regions. Users can load their own sequences into GenomeVISTA or view pre-computed alignments for genomes in the VISTA database.

  14. Understanding human functioning using graphical models

    PubMed Central

    2010-01-01

    Background Functioning and disability are universal human experiences. However, our current understanding of functioning from a comprehensive perspective is limited. The development of the International Classification of Functioning, Disability and Health (ICF) on the one hand and recent developments in graphical modeling on the other hand might be combined and open the door to a more comprehensive understanding of human functioning. The objective of our paper therefore is to explore how graphical models can be used in the study of ICF data for a range of applications. Methods We show the applicability of graphical models on ICF data for different tasks: Visualization of the dependence structure of the data set, dimension reduction and comparison of subpopulations. Moreover, we further developed and applied recent findings in causal inference using graphical models to estimate bounds on intervention effects in an observational study with many variables and without knowing the underlying causal structure. Results In each field, graphical models could be applied giving results of high face-validity. In particular, graphical models could be used for visualization of functioning in patients with spinal cord injury. The resulting graph consisted of several connected components which can be used for dimension reduction. Moreover, we found that the differences in the dependence structures between subpopulations were relevant and could be systematically analyzed using graphical models. Finally, when estimating bounds on causal effects of ICF categories on general health perceptions among patients with chronic health conditions, we found that the five ICF categories that showed the strongest effect were plausible. Conclusions Graphical Models are a flexible tool and lend themselves for a wide range of applications. In particular, studies involving ICF data seem to be suited for analysis using graphical models. PMID:20149230

  15. Image alignment

    DOEpatents

    Dowell, Larry Jonathan

    2014-04-22

    Disclosed is a method and device for aligning at least two digital images. An embodiment may use frequency-domain transforms of small tiles created from each image to identify substantially similar, "distinguishing" features within each of the images, and then align the images together based on the location of the distinguishing features. To accomplish this, an embodiment may create equal sized tile sub-images for each image. A "key" for each tile may be created by performing a frequency-domain transform calculation on each tile. A information-distance difference between each possible pair of tiles on each image may be calculated to identify distinguishing features. From analysis of the information-distance differences of the pairs of tiles, a subset of tiles with high discrimination metrics in relation to other tiles may be located for each image. The subset of distinguishing tiles for each image may then be compared to locate tiles with substantially similar keys and/or information-distance metrics to other tiles of other images. Once similar tiles are located for each image, the images may be aligned in relation to the identified similar tiles.

  16. Mesoscale field-aligned irregularity structures (FAIs) of airglow associated with medium-scale traveling ionospheric disturbances (MSTIDs)

    NASA Astrophysics Data System (ADS)

    Sun, Longchang; Xu, Jiyao; Wang, Wenbin; Yue, Xinan; Yuan, Wei; Ning, Baiqi; Zhang, Donghe; Meneses, F. C.

    2015-11-01

    In this paper, we report the evolution (generation, amplification, and dissipation) of optically observed mesoscale field-aligned irregularity structures (FAIs) (~150 km) associated with a medium-scale traveling ionospheric disturbance (MSTID) event. There have not been observations of mesoscale FAIs of airglow before. The mesoscale FAIs were generated in an airglow-depleted front of southwestward propagating MSTIDs that were simultaneously observed by an all-sky imager, a GPS monitor, and a digisonde around Xinglong (40.4°N, 30.5° magnetic latitude), China, on 17/18 February 2012. A normalized cross-correlation method has been used to obtain the velocities of mesoscale FAIs and MSTIDs. The mesoscale FAIs had an obvious northwestward relative velocity to main-body MSTIDs (about 87.0 m/s on average). The direction of this relative velocity was roughly parallel to the depleted fronts. Furthermore, the evolution of the mesoscale FAIs was mostly controlled by the intensity of the depleted fronts. Occurred in a highly elevated ionosphere that had a total electron content depletion associated with large negative airglow perturbations (-25%), the mesoscale FAIs grew rapidly when they experienced southeastward wind, which had a speed of about 100 m/s and were measured by a Fabry-Perot interferometer. A northeastward polarization electric field within a depleted airglow front can play a controlling role in the development of the mesoscale FAIs. The electric field can significantly elevate the ionosphere and move the mesoscale FAIs northwestward by the E × B drift. The processes for the generation and development of the polarization electric field and the mesoscale FAIs, however, need further study.

  17. Abnormal arrangement of a collagen/apatite extracellular matrix orthogonal to osteoblast alignment is constructed by a nanoscale periodic surface structure.

    PubMed

    Matsugaki, Aira; Aramoto, Gento; Ninomiya, Takafumi; Sawada, Hiroshi; Hata, Satoshi; Nakano, Takayoshi

    2015-01-01

    Morphological and directional alteration of cells is essential for structurally appropriate construction of tissues and organs. In particular, osteoblast alignment is crucial for the realization of anisotropic bone tissue microstructure. In this article, the orientation of a collagen/apatite extracellular matrix (ECM) was established by controlling osteoblast alignment using a surface geometry with nanometer-sized periodicity induced by laser ablation. Laser irradiation induced self-organized periodic structures (laser-induced periodic surface structures; LIPSS) with a spatial period equal to the wavelength of the incident laser on the surface of biomedical alloys of Ti-6Al-4V and Co-Cr-Mo. Osteoblast orientation was successfully induced parallel to the grating structure. Notably, both the fibrous orientation of the secreted collagen matrix and the c-axis of the produced apatite crystals were orientated orthogonal to the cell direction. To the best of our knowledge, this is the first report demonstrating that bone tissue anisotropy is controllable, including the characteristic organization of a collagen/apatite composite orthogonal to the osteoblast orientation, by controlling the cell alignment using periodic surface geometry. PMID:25453944

  18. A Graphical Physics Course

    NASA Astrophysics Data System (ADS)

    Wood, Roy C.

    2001-11-01

    There has been a desire in recent years to introduce physics to students at the middle school, or freshmen high school level. However, traditional physics courses involve a great deal of mathematics, and this makes physics unattractive to many of them. In the last few decades, courses have been developed with a focus that is more conceptual than mathematical, and is generally referred to as conceptual physics. These two types of courses emphasize two methods that physicist use to solve physics problems. However, there is a third, graphical method that is also useful, and complements mathematical and verbal reasoning. A course emphasizing graphical methods would deal with quantitative graphical diagrams, as well as qualitative diagrams. Examples of quantitative graphical diagrams are scaled force diagrams and scaled optical ray-tracing diagrams. A course based on this type of approach would involve measurements and uncertainties, and would involve active (hands-on) student participation suitable for younger students. This talk will discuss a graphical physics course, and its benefits to younger students.

  19. Segment alignment control system

    NASA Technical Reports Server (NTRS)

    Aubrun, JEAN-N.; Lorell, Ken R.

    1988-01-01

    The segmented primary mirror for the LDR will require a special segment alignment control system to precisely control the orientation of each of the segments so that the resulting composite reflector behaves like a monolith. The W.M. Keck Ten Meter Telescope will utilize a primary mirror made up of 36 actively controlled segments. Thus the primary mirror and its segment alignment control system are directly analogous to the LDR. The problems of controlling the segments in the face of disturbances and control/structures interaction, as analyzed for the TMT, are virtually identical to those for the LDR. The two systems are briefly compared.

  20. OAP- OFFICE AUTOMATION PILOT GRAPHICS DATABASE SYSTEM

    NASA Technical Reports Server (NTRS)

    Ackerson, T.

    1994-01-01

    The Office Automation Pilot (OAP) Graphics Database system offers the IBM PC user assistance in producing a wide variety of graphs and charts. OAP uses a convenient database system, called a chartbase, for creating and maintaining data associated with the charts, and twelve different graphics packages are available to the OAP user. Each of the graphics capabilities is accessed in a similar manner. The user chooses creation, revision, or chartbase/slide show maintenance options from an initial menu. The user may then enter or modify data displayed on a graphic chart. The cursor moves through the chart in a "circular" fashion to facilitate data entries and changes. Various "help" functions and on-screen instructions are available to aid the user. The user data is used to generate the graphics portion of the chart. Completed charts may be displayed in monotone or color, printed, plotted, or stored in the chartbase on the IBM PC. Once completed, the charts may be put in a vector format and plotted for color viewgraphs. The twelve graphics capabilities are divided into three groups: Forms, Structured Charts, and Block Diagrams. There are eight Forms available: 1) Bar/Line Charts, 2) Pie Charts, 3) Milestone Charts, 4) Resources Charts, 5) Earned Value Analysis Charts, 6) Progress/Effort Charts, 7) Travel/Training Charts, and 8) Trend Analysis Charts. There are three Structured Charts available: 1) Bullet Charts, 2) Organization Charts, and 3) Work Breakdown Structure (WBS) Charts. The Block Diagram available is an N x N Chart. Each graphics capability supports a chartbase. The OAP graphics database system provides the IBM PC user with an effective means of managing data which is best interpreted as a graphic display. The OAP graphics database system is written in IBM PASCAL 2.0 and assembler for interactive execution on an IBM PC or XT with at least 384K of memory, and a color graphics adapter and monitor. Printed charts require an Epson, IBM, OKIDATA, or HP Laser

  1. Ultrafast electron diffraction from aligned molecules

    SciTech Connect

    Centurion, Martin

    2015-08-17

    The aim of this project was to record time-resolved electron diffraction patterns of aligned molecules and to reconstruct the 3D molecular structure. The molecules are aligned non-adiabatically using a femtosecond laser pulse. A femtosecond electron pulse then records a diffraction pattern while the molecules are aligned. The diffraction patterns are then be processed to obtain the molecular structure.

  2. Vertically aligned nanostructure scanning probe microscope tips

    SciTech Connect

    Guillorn, Michael A.; Ilic, Bojan; Melechko, Anatoli V.; Merkulov, Vladimir I.; Lowndes, Douglas H.; Simpson, Michael L.

    2006-12-19

    Methods and apparatus are described for cantilever structures that include a vertically aligned nanostructure, especially vertically aligned carbon nanofiber scanning probe microscope tips. An apparatus includes a cantilever structure including a substrate including a cantilever body, that optionally includes a doped layer, and a vertically aligned nanostructure coupled to the cantilever body.

  3. Interactive computer graphics

    NASA Astrophysics Data System (ADS)

    Purser, K.

    1980-08-01

    Design layouts have traditionally been done on a drafting board by drawing a two-dimensional representation with section cuts and side views to describe the exact three-dimensional model. With the advent of computer graphics, a three-dimensional model can be created directly. The computer stores the exact three-dimensional model, which can be examined from any angle and at any scale. A brief overview of interactive computer graphics, how models are made and some of the benefits/limitations are described.

  4. Printer Graphics Package

    NASA Technical Reports Server (NTRS)

    Blanchard, D. C.

    1986-01-01

    Printer Graphics Package (PGP) is tool for making two-dimensional symbolic plots on line printer. PGP created to support development of Heads-Up Display (HUD) simulation. Standard symbols defined with HUD in mind. Available symbols include circle, triangle, quadrangle, window, line, numbers, and text. Additional symbols easily added or built up from available symbols.

  5. Computer Graphics Verification

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Video processing creates technical animation sequences using studio quality equipment to realistically represent fluid flow over space shuttle surfaces, helicopter rotors, and turbine blades.Computer systems Co-op, Tim Weatherford, performing computer graphics verification. Part of Co-op brochure.

  6. Mathematical Graphic Organizers

    ERIC Educational Resources Information Center

    Zollman, Alan

    2009-01-01

    As part of a math-science partnership, a university mathematics educator and ten elementary school teachers developed a novel approach to mathematical problem solving derived from research on reading and writing pedagogy. Specifically, research indicates that students who use graphic organizers to arrange their ideas improve their comprehension…

  7. Raster graphics display library

    NASA Technical Reports Server (NTRS)

    Grimsrud, Anders; Stephenson, Michael B.

    1987-01-01

    The Raster Graphics Display Library (RGDL) is a high level subroutine package that give the advanced raster graphics display capabilities needed. The RGDL uses FORTRAN source code routines to build subroutines modular enough to use as stand-alone routines in a black box type of environment. Six examples are presented which will teach the use of RGDL in the fastest, most complete way possible. Routines within the display library that are used to produce raster graphics are presented in alphabetical order, each on a separate page. Each user-callable routine is described by function and calling parameters. All common blocks that are used in the display library are listed and the use of each variable within each common block is discussed. A reference on the include files that are necessary to compile the display library is contained. Each include file and its purpose are listed. The link map for MOVIE.BYU version 6, a general purpose computer graphics display system that uses RGDL software, is also contained.

  8. Computing Graphical Confidence Bounds

    NASA Technical Reports Server (NTRS)

    Mezzacappa, M. A.

    1983-01-01

    Approximation for graphical confidence bounds is simple enough to run on programmable calculator. Approximation is used in lieu of numerical tables not always available, and exact calculations, which often require rather sizable computer resources. Approximation verified for collection of up to 50 data points. Method used to analyze tile-strength data on Space Shuttle thermal-protection system.

  9. Designing Award Winning Graphics.

    ERIC Educational Resources Information Center

    Kintigh, Cynthia

    1990-01-01

    Graphic designers, marketing specialists, and campus activities professionals who have won awards for the design of campus programing publicity offer tips in the process of designing successful promotional items, including ingredients of winning pieces and aspects of a productive designer-client relationship. (MSE)

  10. Comics & Graphic Novels

    ERIC Educational Resources Information Center

    Cleaver, Samantha

    2008-01-01

    Not so many years ago, comic books in school were considered the enemy. Students caught sneaking comics between the pages of bulky--and less engaging--textbooks were likely sent to the principal. Today, however, comics, including classics such as "Superman" but also their generally more complex, nuanced cousins, graphic novels, are not only…

  11. Graphic Novels: A Roundup.

    ERIC Educational Resources Information Center

    Kan, Katherine L.

    1994-01-01

    Reviews graphic novels for young adults, including five titles from "The Adventures of Tintin," a French series that often uses ethnic and racial stereotypes which reflect the time in which they were published, and "Wolverine," a Marvel comic character adventure. (Contains six references.) (LRW)

  12. IUS prerelease alignment

    NASA Technical Reports Server (NTRS)

    Evans, F. A.

    1978-01-01

    Space shuttle orbiter/IUS alignment transfer was evaluated. Although the orbiter alignment accuracy was originally believed to be the major contributor to the overall alignment transfer error, it was shown that orbiter alignment accuracy is not a factor affecting IUS alignment accuracy, if certain procedures are followed. Results are reported of alignment transfer accuracy analysis.

  13. Parallel Implementation of MAFFT on CUDA-Enabled Graphics Hardware.

    PubMed

    Zhu, Xiangyuan; Li, Kenli; Salah, Ahmad; Shi, Lin; Li, Keqin

    2015-01-01

    Multiple sequence alignment (MSA) constitutes an extremely powerful tool for many biological applications including phylogenetic tree estimation, secondary structure prediction, and critical residue identification. However, aligning large biological sequences with popular tools such as MAFFT requires long runtimes on sequential architectures. Due to the ever increasing sizes of sequence databases, there is increasing demand to accelerate this task. In this paper, we demonstrate how graphic processing units (GPUs), powered by the compute unified device architecture (CUDA), can be used as an efficient computational platform to accelerate the MAFFT algorithm. To fully exploit the GPU's capabilities for accelerating MAFFT, we have optimized the sequence data organization to eliminate the bandwidth bottleneck of memory access, designed a memory allocation and reuse strategy to make full use of limited memory of GPUs, proposed a new modified-run-length encoding (MRLE) scheme to reduce memory consumption, and used high-performance shared memory to speed up I/O operations. Our implementation tested in three NVIDIA GPUs achieves speedup up to 11.28 on a Tesla K20m GPU compared to the sequential MAFFT 7.015. PMID:26357090

  14. On the alignment space.

    PubMed

    Shen, Shi-Yi; Wang, Kui; Hu, Gang; Chen, Lu-Sheng; Zhang, Hua; Xia, Shu-Tao

    2005-01-01

    Sequences with generalized errors which are called mutations in bioinformatics and generalized error-correcting codes are studied in this paper. In the areas of bioinformatics, computer science and information theory, sequences with generalized errors are discussed respectively for different aims. Firstly, we give the definitions of alignment distance and Levenshtein distance by expansion sequences and discuss their properties and relations. Then the modular structure theory is introduced for strictly describe the expansion sequences. We show that the expansion modular structures of sequences form a Boolean algebra. As applications of the modular structure theory, we give a new and more strict proof of triangle inequality for alignment distance. At last, the definition and construction of generalized error-correcting codes are studied, and some optimal codes with small length are listed. PMID:17282158

  15. Infrared detectors and lasers operating in the 3-12 μm range using band-gap engineered structures with type II band-gap alignment

    NASA Astrophysics Data System (ADS)

    Swaminathan, Venkataraman; Little, John W.; Tober, Richard L.

    2006-02-01

    The Type II broken band-gap alignment in semiconductor structures wherein the conduction band minimum is in one semiconductor (e.g., InAs) and the valence band maximum is in another (e.g., GaInSb) offers certain unique advantages which can be utilized to realize band-gap engineered novel quantum electro-optic devices such as lasers and detectors. The advantages of the type II structures include reduced Auger recombination, extending the effective band-gap energy of materials wherein type I band-gap alignment would give rise to difficulties such as miscibility gap. In this paper we describe the work carried out at the Army Research Laboratory on type II semiconductor quantum electro-optic devices such as IR lasers and detectors operating in the 3-12 μm range. Specifically we will cover the progress made in GaSb based type II strained layer superlattice IR detectors and Interband Cascade IR Lasers. We will also present our recent work in self-assembled quantum dots which have type II band-gap alignment with the matrix material in which the dots are embedded.

  16. Teaching Geometry through Dynamic Modeling in Introductory Engineering Graphics.

    ERIC Educational Resources Information Center

    Wiebe, Eric N.; Branoff, Ted J.; Hartman, Nathan W.

    2003-01-01

    Examines how constraint-based 3D modeling can be used as a vehicle for rethinking instructional approaches to engineering design graphics. Focuses on moving from a mode of instruction based on the crafting by students and assessment by instructors of static 2D drawings and 3D models. Suggests that the new approach is better aligned with…

  17. Structural, electronic structure, and band alignment properties at epitaxial NiO/Al2O3 heterojunction evaluated from synchrotron based X-ray techniques

    NASA Astrophysics Data System (ADS)

    Singh, S. D.; Nand, Mangla; Das, Arijeet; Ajimsha, R. S.; Upadhyay, Anuj; Kamparath, Rajiv; Shukla, D. K.; Mukherjee, C.; Misra, P.; Rai, S. K.; Sinha, A. K.; Jha, S. N.; Phase, D. M.; Ganguli, Tapas

    2016-04-01

    The valence band offset value of 2.3 ± 0.2 eV at epitaxial NiO/Al2O3 heterojunction is determined from photoelectron spectroscopy experiments. Pulsed laser deposited thin film of NiO on Al2O3 substrate is epitaxially grown along [111] direction with two domain structures, which are in-plane rotated by 60° with respect to each other. Observation of Pendellosung oscillations around Bragg peak confirms high interfacial and crystalline quality of NiO layer deposited on Al2O3 substrate. Surface related feature in Ni 2p3/2 core level spectra along with oxygen K-edge soft X-ray absorption spectroscopy results indicates that the initial growth of NiO on Al2O3 substrate is in the form of islands, which merge to form NiO layer for the larger coverage. The value of conduction band offset is also evaluated from the measured values of band gaps of NiO and Al2O3 layers. A type-I band alignment at NiO and Al2O3 heterojunction is also obtained. The determined values of band offsets can be useful in heterojunction based light emitting devices.

  18. MUSE optical alignment procedure

    NASA Astrophysics Data System (ADS)

    Laurent, Florence; Renault, Edgard; Loupias, Magali; Kosmalski, Johan; Anwand, Heiko; Bacon, Roland; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dubois, Jean-Pierre; Dupuy, Christophe; Kelz, Andreas; Lizon, Jean-Louis; Nicklas, Harald; Parès, Laurent; Remillieux, Alban; Seifert, Walter; Valentin, Hervé; Xu, Wenli

    2012-09-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation VLT integral field spectrograph (1x1arcmin² Field of View) developed for the European Southern Observatory (ESO), operating in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently assembling and testing MUSE in the Integration Hall of the Observatoire de Lyon for the Preliminary Acceptance in Europe, scheduled for 2013. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic instrument mechanical structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2011, all MUSE subsystems were integrated, aligned and tested independently in each institute. After validations, the systems were shipped to the P.I. institute at Lyon and were assembled in the Integration Hall This paper describes the end-to-end optical alignment procedure of the MUSE instrument. The design strategy, mixing an optical alignment by manufacturing (plug and play approach) and few adjustments on key components, is presented. We depict the alignment method for identifying the optical axis using several references located in pupil and image planes. All tools required to perform the global alignment between each subsystem are described. The success of this alignment approach is demonstrated by the good results for the MUSE image quality. MUSE commissioning at the VLT (Very Large Telescope) is planned for 2013.

  19. The Evolution of North-South Aligned Auroral Forms into Auroral Torch Structures : The Generation of Omega Bands and Ps6 Pulsations via Flow Bursts.

    SciTech Connect

    Henderson, M. G.; Kepko, L.; Spence, H. E.; Connors, M.; Sigwarth, J. B.; Frank, L. A.; Singer, H. J.; Yumoto, K.

    2002-01-01

    Although auroral torch structures and omega bands have been observed and studied for decades, a satisfactory understanding of how they form has yet to be achieved. Using global auroral imager data, we show conclusively that the equatorward moving north-south (NS) aligned auroral forms that are ejected episodically from the poleward boundary can evolve directly into torch structures which contribute to a well-defined omega-band form. And that as a consequence, omega bands can be produced as a direct result of earthward-directed bursty bulk flows (BBFs).

  20. Band alignment and interfacial structure of ZnO/Si heterojunction with Al{sub 2}O{sub 3} and HfO{sub 2} as interlayers

    SciTech Connect

    Lu, Hong-Liang Yang, Ming; Xie, Zhang-Yi; Geng, Yang; Zhang, Yuan; Wang, Peng-Fei; Sun, Qing-Qing; Ding, Shi-Jin; Wei Zhang, David

    2014-04-21

    Energy band alignment of ZnO/Si heterojunction with thin interlayers Al{sub 2}O{sub 3} and HfO{sub 2} grown by atomic layer deposition has been studied using x-ray photoelectron spectroscopy. The valence band offsets of ZnO/Al{sub 2}O{sub 3} and ZnO/HfO{sub 2} heterojunctions have been determined to be 0.43 and 0.22 eV, respectively. Accordingly, the band alignment ZnO/Si heterojunction is then modified to be 0.34 and 0.50 eV through inserting a thin Al{sub 2}O{sub 3} and HfO{sub 2} layer, respectively. The feasibility to tune the band structure of ZnO/Si heterojunction by selecting a proper interlayer shows great advantage in improving the performance of the ZnO-based optoelectronic devices.

  1. Anisotropic electronic structure of in-plane aligned a-axis YBa2Cu3O7-δ thin films

    NASA Astrophysics Data System (ADS)

    Luo, C. W.; Chen, M. H.; Liu, S. J.; Wu, K. H.; Juang, J. Y.; Uen, T. M.; Lin, J.-Y.; Chen, J.-M.; Gou, Y. S.

    2003-09-01

    Polarization-dependent x-ray absorption near-edge spectra (XANES) of the O 1s has been measured on a highly in-plane aligned a-axis YBa2Cu3O7-δ (YBCO) thin film. The in-plane XANES, with the electric field E of the linearly polarized synchrotron light being parallel to the b or c axis of YBCO films (E//b or E//c) were obtained in a normal-incidence alignment. The XANES for E//a was then calculated from the data obtained by varying the angle. The results lend strong support to those obtained by using detwinned YBCO single crystals in all crystalline orientations, including the extrapolated c-axis spectra.

  2. Fusion bonding and alignment fixture

    DOEpatents

    Ackler, Harold D.; Swierkowski, Stefan P.; Tarte, Lisa A.; Hicks, Randall K.

    2000-01-01

    An improved vacuum fusion bonding structure and process for aligned bonding of large area glass plates, patterned with microchannels and access holes and slots, for elevated glass fusion temperatures. Vacuum pumpout of all the components is through the bottom platform which yields an untouched, defect free top surface which greatly improves optical access through this smooth surface. Also, a completely non-adherent interlayer, such as graphite, with alignment and location features is located between the main steel platform and the glass plate pair, which makes large improvements in quality, yield, and ease of use, and enables aligned bonding of very large glass structures.

  3. Graphic Grown Up

    ERIC Educational Resources Information Center

    Kim, Ann

    2009-01-01

    It's no secret that children and YAs are clued in to graphic novels (GNs) and that comics-loving adults are positively giddy that this format is getting the recognition it deserves. Still, there is a whole swath of library card-carrying grown-up readers out there with no idea where to start. Splashy movies such as "300" and "Spider-Man" and their…

  4. Graphical Contingency Analysis Tool

    SciTech Connect

    2010-03-02

    GCA is a visual analytic tool for power grid contingency analysis to provide more decision support for power grid operations. GCA allows power grid operators to quickly gain situational awareness of power grid by converting large amounts of operational data to graphic domain with a color contoured map; identify system trend and foresee and discern emergencies by performing trending analysis; identify the relationships between system configurations and affected assets by conducting clustering analysis; and identify the best action by interactively evaluate candidate actions.

  5. Space Spurred Computer Graphics

    NASA Technical Reports Server (NTRS)

    1983-01-01

    Dicomed Corporation was asked by NASA in the early 1970s to develop processing capabilities for recording images sent from Mars by Viking spacecraft. The company produced a film recorder which increased the intensity levels and the capability for color recording. This development led to a strong technology base resulting in sophisticated computer graphics equipment. Dicomed systems are used to record CAD (computer aided design) and CAM (computer aided manufacturing) equipment, to update maps and produce computer generated animation.

  6. Graphic engine resource management

    NASA Astrophysics Data System (ADS)

    Bautin, Mikhail; Dwarakinath, Ashok; Chiueh, Tzi-cker

    2008-01-01

    Modern consumer-grade 3D graphic cards boast a computation/memory resource that can easily rival or even exceed that of standard desktop PCs. Although these cards are mainly designed for 3D gaming applications, their enormous computational power has attracted developers to port an increasing number of scientific computation programs to these cards, including matrix computation, collision detection, cryptography, database sorting, etc. As more and more applications run on 3D graphic cards, there is a need to allocate the computation/memory resource on these cards among the sharing applications more fairly and efficiently. In this paper, we describe the design, implementation and evaluation of a Graphic Processing Unit (GPU) scheduler based on Deficit Round Robin scheduling that successfully allocates to every process an equal share of the GPU time regardless of their demand. This scheduler, called GERM, estimates the execution time of each GPU command group based on dynamically collected statistics, and controls each process's GPU command production rate through its CPU scheduling priority. Measurements on the first GERM prototype show that this approach can keep the maximal GPU time consumption difference among concurrent GPU processes consistently below 5% for a variety of application mixes.

  7. John Herschel's Graphical Method

    NASA Astrophysics Data System (ADS)

    Hankins, Thomas L.

    2011-01-01

    In 1833 John Herschel published an account of his graphical method for determining the orbits of double stars. He had hoped to be the first to determine such orbits, but Felix Savary in France and Johann Franz Encke in Germany beat him to the punch using analytical methods. Herschel was convinced, however, that his graphical method was much superior to analytical methods, because it used the judgment of the hand and eye to correct the inevitable errors of observation. Line graphs of the kind used by Herschel became common only in the 1830s, so Herschel was introducing a new method. He also found computation fatiguing and devised a "wheeled machine" to help him out. Encke was skeptical of Herschel's methods. He said that he lived for calculation and that the English would be better astronomers if they calculated more. It is difficult to believe that the entire Scientific Revolution of the 17th century took place without graphs and that only a few examples appeared in the 18th century. Herschel promoted the use of graphs, not only in astronomy, but also in the study of meteorology and terrestrial magnetism. Because he was the most prominent scientist in England, Herschel's advocacy greatly advanced graphical methods.

  8. Career Opportunities in Computer Graphics.

    ERIC Educational Resources Information Center

    Langer, Victor

    1983-01-01

    Reviews the impact of computer graphics on industrial productivity. Details the computer graphics technician curriculum at Milwaukee Area Technical College and the cooperative efforts of business and industry to fund and equip the program. (SK)

  9. Magnetic alignment of nickel-coated carbon fibers

    SciTech Connect

    Hao, Chuncheng; State Key Laboratory of Electrical Insulation and Power Equipment, Xi'an Jiaotong University, Xi'an, 710049 ; Li, Xiaojiao; Wang, Guizhen

    2011-11-15

    Graphical abstract: Carbon nanofibers were subjected to a two-step pretreatment, sensitization and activation. Carbon nanofibers were encapsulated by a uniform layer of nickel nanoparticles. The prepared composites are ferromagnetic and with a small value of coercivity. Upon such functionalization, the carbon nanofibers can be aligned in a relatively small external magnetic field. Highlights: {center_dot} A simple microwave-assisted procedure for the magnetic composite. {center_dot} Dense layer of nickel on pretreated carbon nanofibers. {center_dot} Ferromagnetic properties and low coercivity. {center_dot} A long-chain aligned structure under magnetic field. -- Abstract: Magnetic composites of nickel-coated carbon nanofibers have been successfully fabricated by employing a simple microwave-assisted procedure. The scanning electron microscopy images show that a complete and uniform nickel coating with mean size of 25 nm could be deposited on carbon fibers. Magnetization curves demonstrate that the prepared composites are ferromagnetic and that the coercivity is 96 Oe. The magnetic carbon nanofibers can be aligned as a long-chain structure in an external magnetic field.

  10. Effects of Phosphate Buffered Saline Concentration and Incubation Time on the Mechanical and Structural Properties of Electrochemically Aligned Collagen Threads

    PubMed Central

    Uquillas, Jorge Alfredo; Kishore, Vipuil; Akkus, Ozan

    2011-01-01

    A key step during the synthesis of collagen constructs is the incubation of monomeric collagen in phosphate buffer saline (PBS) to promote fibrillogenesis in the collagen network. Optimal PBS treatment conditions for monomeric collagen solutions to induce gelation are well established in the literature. Recently, a report in the literature[1] showed a novel method to fabricate highly oriented electrochemically aligned collagen (ELAC) threads which have orders of magnitude greater packing density than collagen gels. The optimal PBS treatment conditions for induction of D-banding pattern in such dense and anisotropic collagen network are unknown. This study aimed to optimize PBS treatment of ELAC threads by investigating the effect of phosphate ion concentration (0.5×, 1×, 5× or 10×) and incubation time (3, 12 or 96 hours) on the mechanical strength and ultrastructural organization by monotonic mechanical testing, small angle X-ray scattering and transmission electron microscopy. ELAC threads incubated in water (No PBS) served as the control. ELAC threads incubated in 1× PBS showed significantly higher extensibility compared to 0.5× or 10× PBS along with the presence of D-banded patterns with a periodicity of 63.83 nm. Incubation of ELAC threads in 1× PBS for 96 hours resulted in significantly higher ultimate stress compared to 3 or 12 hours. However, these threads lacked D-banding pattern. TEM showed no significant differences in the microfibril diameter distribution of ELAC threads treated with or without PBS. This indicates that microfibrils lacked D-banding following electrochemical alignment and the subsequent PBS treatment induced D-banding by reorganization within microfibrils. It was concluded that incubation of aligned collagen in 1× PBS for 12 hours results in mechanically competent, D-banded ELAC threads which can be used for the regeneration of load bearing tissues such as tendons and ligaments. PMID:21540522

  11. The interplay between interface structure, energy level alignment and chemical bonding strength at organic-metal interfaces.

    PubMed

    Willenbockel, M; Lüftner, D; Stadtmüller, B; Koller, G; Kumpf, C; Soubatch, S; Puschnig, P; Ramsey, M G; Tautz, F S

    2015-01-21

    What do energy level alignments at metal-organic interfaces reveal about the metal-molecule bonding strength? Is it permissible to take vertical adsorption heights as indicators of bonding strengths? In this paper we analyse 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA) on the three canonical low index Ag surfaces to provide exemplary answers to these questions. Specifically, we employ angular resolved photoemission spectroscopy for a systematic study of the energy level alignments of the two uppermost frontier states in ordered monolayer phases of PTCDA. Data are analysed using the orbital tomography approach. This allows the unambiguous identification of the orbital character of these states, and also the discrimination between inequivalent species. Combining this experimental information with DFT calculations and the generic Newns-Anderson chemisorption model, we analyse the alignments of highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO) with respect to the vacuum levels of bare and molecule-covered surfaces. This reveals clear differences between the two frontier states. In particular, on all surfaces the LUMO is subject to considerable bond stabilization through the interaction between the molecular π-electron system and the metal, as a consequence of which it also becomes occupied. Moreover, we observe a larger bond stabilization for the more open surfaces. Most importantly, our analysis shows that both the orbital binding energies of the LUMO and the overall adsorption heights of the molecule are linked to the strength of the chemical interaction between the molecular π-electron system and the metal, in the sense that stronger bonding leads to shorter adsorption heights and larger orbital binding energies. PMID:25475998

  12. Semiautomated improvement of RNA alignments

    PubMed Central

    Andersen, Ebbe S.; Lind-Thomsen, Allan; Knudsen, Bjarne; Kristensen, Susie E.; Havgaard, Jakob H.; Torarinsson, Elfar; Larsen, Niels; Zwieb, Christian; Sestoft, Peter; Kjems, Jørgen; Gorodkin, Jan

    2007-01-01

    We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its integrated analysis tools prevent the introduction of errors when doing alignment editing. SARSE readily connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster: the mir-399 RNA, vertebrate telomase RNA (vert-TR), bacterial transfer-messenger RNA (tmRNA), and the signal recognition particle (SRP) RNA. The general use of the method is illustrated by the ability to accommodate pseudoknots and handle even large and divergent RNA families. The open architecture of the SARSE editor makes it a flexible tool to improve all RNA alignments with relatively little human intervention. Online documentation and software are available at http://sarse.ku.dk. PMID:17804647

  13. Computer graphics in aerodynamic analysis

    NASA Technical Reports Server (NTRS)

    Cozzolongo, J. V.

    1984-01-01

    The use of computer graphics and its application to aerodynamic analyses on a routine basis is outlined. The mathematical modelling of the aircraft geometries and the shading technique implemented are discussed. Examples of computer graphics used to display aerodynamic flow field data and aircraft geometries are shown. A future need in computer graphics for aerodynamic analyses is addressed.

  14. Graphic Novels and School Libraries

    ERIC Educational Resources Information Center

    Rudiger, Hollis Margaret; Schliesman, Megan

    2007-01-01

    School libraries serving children and teenagers today should be committed to collecting graphic novels to the extent that their budgets allow. However, the term "graphic novel" is enough to make some librarians--not to mention administrators and parents--pause. Graphic novels are simply book-length comics. They can be works of fiction or…

  15. Low Cost Graphics. Second Edition.

    ERIC Educational Resources Information Center

    Tinker, Robert F.

    This manual describes the CALM TV graphics interface, a low-cost means of producing quality graphics on an ordinary TV. The system permits the output of data in graphic as well as alphanumeric form and the input of data from the face of the TV using a light pen. The integrated circuits required in the interface can be obtained from standard…

  16. Selecting Mangas and Graphic Novels

    ERIC Educational Resources Information Center

    Nylund, Carol

    2007-01-01

    The decision to add graphic novels, and particularly the Japanese styled called manga, was one the author has debated for a long time. In this article, the author shares her experience when she purchased graphic novels and mangas to add to her library collection. She shares how graphic novels and mangas have revitalized the library.

  17. GRASP/Ada (Graphical Representations of Algorithms, Structures, and Processes for Ada): The development of a program analysis environment for Ada. Reverse engineering tools for Ada, task 1, phase 2

    NASA Technical Reports Server (NTRS)

    Cross, James H., II

    1990-01-01

    The study, formulation, and generation of structures for Ada (GRASP/Ada) are discussed in this second phase report of a three phase effort. Various graphical representations that can be extracted or generated from source code are described and categorized with focus on reverse engineering. The overall goal is to provide the foundation for a CASE (computer-aided software design) environment in which reverse engineering and forward engineering (development) are tightly coupled. Emphasis is on a subset of architectural diagrams that can be generated automatically from source code with the control structure diagram (CSD) included for completeness.

  18. A self-consistent two-dimensional resistive fluid theory of field-aligned potential structures including charge separation and magnetic and velocity shear

    NASA Technical Reports Server (NTRS)

    Hesse, Michael; Birn, Joachim; Schindler, Karl

    1990-01-01

    A self-consistent two-fluid theory that includes the magnetic field and shear patterns is developed to model stationary electrostatic structures with field-aligned potential drops. Shear flow is also included in the theory since this seems to be a prominent feature of the structures of interest. In addition, Ohmic dissipation, a Hall term, and pressure gradients in a generalized Ohm's law, modified for cases without quasi-neutrality, are included. In the analytic theory, the electrostatic force is balanced by field-aligned pressure gradients (i.e., thermal effects in the direction of the magnetic field) and by pressure gradients and magnetic stresses in the perpendicular direction. Within this theory, simple examples of applications are presented to demonstrate the kind of solutions resulting from the model. The results show how the effects of charge separation and shear in the magnetic field and the velocity can be combined to form self-consistent structures such as are found to exist above the aurora, suggested also in association with solar flares.

  19. Graphical Contingency Analysis Tool

    2010-03-02

    GCA is a visual analytic tool for power grid contingency analysis to provide more decision support for power grid operations. GCA allows power grid operators to quickly gain situational awareness of power grid by converting large amounts of operational data to graphic domain with a color contoured map; identify system trend and foresee and discern emergencies by performing trending analysis; identify the relationships between system configurations and affected assets by conducting clustering analysis; and identifymore » the best action by interactively evaluate candidate actions.« less

  20. Graphical timeline editing

    NASA Technical Reports Server (NTRS)

    Meyer, Patrick E.; Jaap, John P.

    1994-01-01

    NASA's Experiment Scheduling Program (ESP), which has been used for approximately 12 Spacelab missions, is being enhanced with the addition of a Graphical Timeline Editor. The GTE Clipboard, as it is called, was developed to demonstrate new technology which will lead the development of International Space Station Alpha's Payload Planning System and support the remaining Spacelab missions. ESP's GTE Clipboard is developed in C using MIT's X Windows System X11R5 and follows OSF/Motif Style Guide Revision 1.2.

  1. Testing the tidal alignment model of galaxy intrinsic alignment

    SciTech Connect

    Blazek, Jonathan; Seljak, Uroš; McQuinn, Matthew E-mail: mmcquinn@berkeley.edu

    2011-05-01

    Weak gravitational lensing has become a powerful probe of large-scale structure and cosmological parameters. Precision weak lensing measurements require an understanding of the intrinsic alignment of galaxy ellipticities, which can in turn inform models of galaxy formation. It is hypothesized that elliptical galaxies align with the background tidal field and that this alignment mechanism dominates the correlation between ellipticities on cosmological scales (in the absence of lensing). We use recent large-scale structure measurements from the Sloan Digital Sky Survey to test this picture with several statistics: (1) the correlation between ellipticity and galaxy overdensity, w{sub g+}; (2) the intrinsic alignment auto-correlation functions; (3) the correlation functions of curl-free, E, and divergence-free, B, modes, the latter of which is zero in the linear tidal alignment theory; (4) the alignment correlation function, w{sub g}(r{sub p},θ), a recently developed statistic that generalizes the galaxy correlation function to account for the angle between the galaxy separation vector and the principle axis of ellipticity. We show that recent measurements are largely consistent with the tidal alignment model and discuss dependence on galaxy luminosity. In addition, we show that at linear order the tidal alignment model predicts that the angular dependence of w{sub g}(r{sub p},θ) is simply w{sub g+}(r{sub p})cos (2θ) and that this dependence is consistent with recent measurements. We also study how stochastic nonlinear contributions to galaxy ellipticity impact these statistics. We find that a significant fraction of the observed LRG ellipticity can be explained by alignment with the tidal field on scales ∼> 10 \\hMpc. These considerations are relevant to galaxy formation and evolution.

  2. DNA Align Editor: DNA Alignment Editor Tool

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The SNPAlignEditor is a DNA sequence alignment editor that runs on Windows platforms. The purpose of the program is to provide an intuitive, user-friendly tool for manual editing of multiple sequence alignments by providing functions for input, editing, and output of nucleotide sequence alignments....

  3. Adaptive control of molecular alignment

    SciTech Connect

    Horn, C.; Wollenhaupt, M.; Krug, M.; Baumert, T.; Nalda, R. de; Banares, L.

    2006-03-15

    We demonstrate control on nonadiabatic molecular alignment by using a spectrally phase-shaped laser pulse. An evolutionary algorithm in a closed feedback loop has been used in order to find pulse shapes that maximize a given effect. In particular, this scheme has been applied to the optimization of total alignment, and to the control of the temporal structure of the alignment transient within a revival. Asymmetric temporal pulse shapes have been found to be very effective for the latter and have been studied separately in a single-parameter control scheme. Our experimental results are supported by numerical simulations.

  4. The Digital Space Shuttle, 3D Graphics, and Knowledge Management

    NASA Technical Reports Server (NTRS)

    Gomez, Julian E.; Keller, Paul J.

    2003-01-01

    The Digital Shuttle is a knowledge management project that seeks to define symbiotic relationships between 3D graphics and formal knowledge representations (ontologies). 3D graphics provides geometric and visual content, in 2D and 3D CAD forms, and the capability to display systems knowledge. Because the data is so heterogeneous, and the interrelated data structures are complex, 3D graphics combined with ontologies provides mechanisms for navigating the data and visualizing relationships.

  5. Ultrasonic welding for fast bonding of self-aligned structures in lab-on-a-chip systems.

    PubMed

    Kistrup, K; Poulsen, C E; Hansen, M F; Wolff, A

    2015-05-01

    Ultrasonic welding is a rapid, promising bonding method for the bonding of polymer chips; yet its use is still limited. We present two lab-on-a-chip applications where ultrasonic welding can be preferably applied: (1) self-aligned gapless bonding of a two-part chip with a tolerance of 50 μm; (2) bonding of a large area shallow chamber (1.8 cm(2) × 150 μm). Using injection moulding combined with ultrasonic welding we achieved a total production and bonding time of 60 s per chip, and a batch of chips could be produced within a day going from design to finished chips. We believe that the technical solutions offered here can significantly help bridge the gap between academia and industry, where the differences in production methods and materials pose a challenge when transferring technology. PMID:25806857

  6. Probabilistic Graphical Model Representation in Phylogenetics

    PubMed Central

    Höhna, Sebastian; Heath, Tracy A.; Boussau, Bastien; Landis, Michael J.; Ronquist, Fredrik; Huelsenbeck, John P.

    2014-01-01

    Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis–Hastings or Gibbs sampling of the posterior distribution. [Computation; graphical models; inference; modularization; statistical phylogenetics; tree plate.] PMID:24951559

  7. Arrows: A Special Case of Graphic Communication.

    ERIC Educational Resources Information Center

    Hardin, Pris

    The purpose of this paper is to examine arrow design in relation to the type of pointing, connecting, or processing involved. Three possible approaches to the investigation of arrows as graphic communication include research: by arrow function, relating message structure to arrow design, and linking user expectations to arrow design. The following…

  8. Applications of Computer Graphics in Engineering

    NASA Technical Reports Server (NTRS)

    1975-01-01

    Various applications of interactive computer graphics to the following areas of science and engineering were described: design and analysis of structures, configuration geometry, animation, flutter analysis, design and manufacturing, aircraft design and integration, wind tunnel data analysis, architecture and construction, flight simulation, hydrodynamics, curve and surface fitting, gas turbine engine design, analysis, and manufacturing, packaging of printed circuit boards, spacecraft design.

  9. A sweet spot for highly efficient growth of vertically aligned single-walled carbon nanotube forests enabling their unique structures and properties

    NASA Astrophysics Data System (ADS)

    Chen, Guohai; Davis, Robert C.; Futaba, Don N.; Sakurai, Shunsuke; Kobashi, Kazufumi; Yumura, Motoo; Hata, Kenji

    2015-12-01

    We investigated the correlation between growth efficiency and structural parameters of single-walled carbon nanotube (SWCNT) forests and report the existence of a SWCNT ``sweet spot'' in the CNT diameter and spacing domain for highly efficient synthesis. Only within this region could SWCNTs be grown efficiently. Through the investigation of the growth rates for ~340 CNT forests spanning diameters from 1.3 to 8.0 nm and average spacing from 5 to 80 nm, this ``sweet spot'' was found to exist because highly efficient growth was constrained by several mechanistic boundaries that either hindered the formation or reduced the growth rate of SWCNT forests. Specifically, with increased diameter SWCNTs transitioned to multiwalled CNTs (multiwall border), small diameter SWCNTs could only be grown at low growth rates (low efficiency border), sparse SWCNTs lacked the requirements to vertically align (lateral growth border), and high density catalysts could not be prepared (high catalyst density border). As a result, the SWCNTs synthesized within this ``sweet spot'' possessed a unique set of characteristics vital for the development applications, such as large diameter, long, aligned, defective, and high specific surface area.We investigated the correlation between growth efficiency and structural parameters of single-walled carbon nanotube (SWCNT) forests and report the existence of a SWCNT ``sweet spot'' in the CNT diameter and spacing domain for highly efficient synthesis. Only within this region could SWCNTs be grown efficiently. Through the investigation of the growth rates for ~340 CNT forests spanning diameters from 1.3 to 8.0 nm and average spacing from 5 to 80 nm, this ``sweet spot'' was found to exist because highly efficient growth was constrained by several mechanistic boundaries that either hindered the formation or reduced the growth rate of SWCNT forests. Specifically, with increased diameter SWCNTs transitioned to multiwalled CNTs (multiwall border), small

  10. MUSE alignment onto VLT

    NASA Astrophysics Data System (ADS)

    Laurent, Florence; Renault, Edgard; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dupuy, Christophe; Jarno, Aurélien; Lizon, Jean-Louis; Migniau, Jean-Emmanuel; Nicklas, Harald; Piqueras, Laure

    2014-07-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation Very Large Telescope (VLT) integral field spectrograph developed for the European Southern Observatory (ESO). It combines a 1' x 1' field of view sampled at 0.2 arcsec for its Wide Field Mode (WFM) and a 7.5"x7.5" field of view for its Narrow Field Mode (NFM). Both modes will operate with the improved spatial resolution provided by GALACSI (Ground Atmospheric Layer Adaptive Optics for Spectroscopic Imaging), that will use the VLT deformable secondary mirror and 4 Laser Guide Stars (LGS) foreseen in 2015. MUSE operates in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently commissioning MUSE in the Very Large Telescope for the Preliminary Acceptance in Chile, scheduled for September, 2014. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2012 and 2013, all MUSE subsystems were integrated, aligned and tested to the P.I. institute at Lyon. After successful PAE in September 2013, MUSE instrument was shipped to the Very Large Telescope in Chile where that was aligned and tested in ESO integration hall at Paranal. After, MUSE was directly transported, fully aligned and without any optomechanical dismounting, onto VLT telescope where the first light was overcame the 7th of February, 2014. This paper describes the alignment procedure of the whole MUSE instrument with respect to the Very Large Telescope (VLT). It describes how 6 tons could be move with accuracy better than 0.025mm and less than 0.25 arcmin in order to reach alignment requirements. The success

  11. Graphical Model Theory for Wireless Sensor Networks

    SciTech Connect

    Davis, William B.

    2002-12-08

    Information processing in sensor networks, with many small processors, demands a theory of computation that allows the minimization of processing effort, and the distribution of this effort throughout the network. Graphical model theory provides a probabilistic theory of computation that explicitly addresses complexity and decentralization for optimizing network computation. The junction tree algorithm, for decentralized inference on graphical probability models, can be instantiated in a variety of applications useful for wireless sensor networks, including: sensor validation and fusion; data compression and channel coding; expert systems, with decentralized data structures, and efficient local queries; pattern classification, and machine learning. Graphical models for these applications are sketched, and a model of dynamic sensor validation and fusion is presented in more depth, to illustrate the junction tree algorithm.

  12. Study on effects of substrate temperature on growth and structure of alignment carbon nanotubes in plasma-enhanced hot filament chemical vapor deposition system

    NASA Astrophysics Data System (ADS)

    Dang, Chun; Wang, Tingzhi

    2006-11-01

    Alignment carbon nanotubes (ACNTs) were synthesized on silicon substrate coated with Ni catalyst film and Ta buffer layer by plasma-enhanced hot filament chemical vapor deposition using CH 4, NH 3, and H 2 as the reaction gas, and they were investigated by scanning electron microscopy and transmission electron microscopy. It is found that the diameter of the bamboo-structured ACNTs is increased from 62 to 177 nm when the substrate temperature was changed from 626 to 756 °C. Their growth rate is enhanced by the substrate temperature in a range of 626-683 °C and it is reversely reduced with the substrate temperature after the substrate temperature is over 683 °C. Beginning with wetting phenomenon, the effects of the substrate temperature on the structure and growth rate of the ACNTs are analyzed.

  13. [Hardware for graphics systems].

    PubMed

    Goetz, C

    1991-02-01

    In all personal computer applications, be it for private or professional use, the decision of which "brand" of computer to buy is of central importance. In the USA Apple computers are mainly used in universities, while in Europe computers of the so-called "industry standard" by IBM (or clones thereof) have been increasingly used for many years. Independently of any brand name considerations, the computer components purchased must meet the current (and projected) needs of the user. Graphic capabilities and standards, processor speed, the use of co-processors, as well as input and output devices such as "mouse", printers and scanners are discussed. This overview is meant to serve as a decision aid. Potential users are given a short but detailed summary of current technical features. PMID:2042260

  14. LONGLIB - A GRAPHICS LIBRARY

    NASA Technical Reports Server (NTRS)

    Long, D.

    1994-01-01

    This library is a set of subroutines designed for vector plotting to CRT's, plotters, dot matrix, and laser printers. LONGLIB subroutines are invoked by program calls similar to standard CALCOMP routines. In addition to the basic plotting routines, LONGLIB contains an extensive set of routines to allow viewport clipping, extended character sets, graphic input, shading, polar plots, and 3-D plotting with or without hidden line removal. LONGLIB capabilities include surface plots, contours, histograms, logarithm axes, world maps, and seismic plots. LONGLIB includes master subroutines, which are self-contained series of commonly used individual subroutines. When invoked, the master routine will initialize the plotting package, and will plot multiple curves, scatter plots, log plots, 3-D plots, etc. and then close the plot package, all with a single call. Supported devices include VT100 equipped with Selanar GR100 or GR100+ boards, VT125s, VT240s, VT220 equipped with Selanar SG220, Tektronix 4010/4014 or 4107/4109 and compatibles, and Graphon GO-235 terminals. Dot matrix printer output is available by using the provided raster scan conversion routines for DEC LA50, Printronix printers, and high or low resolution Trilog printers. Other output devices include QMS laser printers, Postscript compatible laser printers, and HPGL compatible plotters. The LONGLIB package includes the graphics library source code, an on-line help library, scan converter and meta file conversion programs, and command files for installing, creating, and testing the library. The latest version, 5.0, is significantly enhanced and has been made more portable. Also, the new version's meta file format has been changed and is incompatible with previous versions. A conversion utility is included to port the old meta files to the new format. Color terminal plotting has been incorporated. LONGLIB is written in FORTRAN 77 for batch or interactive execution and has been implemented on a DEC VAX series

  15. GFI - EASY PC GRAPHICS

    NASA Technical Reports Server (NTRS)

    Katz, R. B.

    1994-01-01

    Easy PC Graphics (GFI) is a graphical plot program that permits data to be easily and flexibly plotted. Data is input in a standard format which allows easy data entry and evaluation. Multiple dependent axes are also supported. The program may either be run in a stand alone mode or be embedded in the user's own software. Automatic scaling is built in for several logarithmic and decibel scales. New scales are easily incorporated into the code through the use of object-oriented programming techniques. For the autoscale routines and the actual plotting code, data is not retrieved directly from a file, but a "method" delivers the data, performing scaling as appropriate. Each object (variable) has state information which selects its own scaling. GFI is written in Turbo Pascal version 6.0 for IBM PC compatible computers running MS-DOS. The source code will only compile properly with the Turbo Pascal v. 6.0 or v. 7.0 compilers; however, an executable is provided on the distribution disk. This executable requires at least 64K of RAM and DOS 3.1 or higher, as well as an HP LaserJet printer to print output plots. The standard distribution medium for this program is one 5.25 inch 360K MS-DOS format diskette. The contents of the diskette are compressed using the PKWARE archiving tools. The utility to unarchive the files, PKUNZIP.EXE, is included. An electronic copy of the documentation is provided on the distribution medium in ASCII format. GFI was developed in 1993.

  16. Band alignments of InGaPN/GaPN quantum well structures on GaP and Si

    NASA Astrophysics Data System (ADS)

    Umeno, Kazuyuki; Kim, Sung Man; Furukawa, Yuzo; Yonezu, Hiroo; Wakahara, Akihiro

    2007-04-01

    We proposed a calculation method for the band alignment of a novel InGaPN/GaPN single-quantum well (SQW) on GaP and Si substrates. The calculation method composed the model-solid theory (MST) for the band edge shifts due to strain and the band anticrossing (BAC) model for a large band bowing of an InGaPN alloy due to N incorporation. The band alignments of the InGaPN/GaPN SQW with In compositions larger than 27% on GaP and Si substrates were investigated by the calculation method, whose QW could have a direct bandgap. The 18-K experimental photoluminescence (PL) peak energy of the InGaPN/GaPN SQW on a GaP substrate, which was grown by radiofrequency plasma-assisted molecular-beam epitaxy (RF-MBE), was in good agreement with the calculated transition energy between the first electron quantum level and the first heavy-hole quantum level. The conduction band offsets of the InGaPN/GaPN SQW with N compositions of 1-2% into the InGaPN well grown on GaP substrates were several dozens meV at the most, while the valence band offsets were 200-300 meV due to compressive strain increased by increasing In compositions. Therefore, larger N compositions of the InGaPN well were required to increase the conduction band offsets of the InGaPN/GaPN SQW for light-emitting devices. It was demonstrated that the type-I InGaPN/GaPN SQW with a direct bandgap could be obtained on Si substrates. Our calculation results showed that the appropriate In composition of the InGaPN well were 30-45% and N composition of the GaPN barrier 1-2%. The differences of N compositions around 3% between the InGaPN well and the GaPN barrier were required for realizing a conduction band offset of 300 meV.

  17. DspaceOgre 3D Graphics Visualization Tool

    NASA Technical Reports Server (NTRS)

    Jain, Abhinandan; Myin, Steven; Pomerantz, Marc I.

    2011-01-01

    This general-purpose 3D graphics visualization C++ tool is designed for visualization of simulation and analysis data for articulated mechanisms. Examples of such systems are vehicles, robotic arms, biomechanics models, and biomolecular structures. DspaceOgre builds upon the open-source Ogre3D graphics visualization library. It provides additional classes to support the management of complex scenes involving multiple viewpoints and different scene groups, and can be used as a remote graphics server. This software provides improved support for adding programs at the graphics processing unit (GPU) level for improved performance. It also improves upon the messaging interface it exposes for use as a visualization server.

  18. Joint estimation of multiple graphical models

    PubMed Central

    Guo, Jian; Levina, Elizaveta; Michailidis, George; Zhu, Ji

    2011-01-01

    Summary Gaussian graphical models explore dependence relationships between random variables, through the estimation of the corresponding inverse covariance matrices. In this paper we develop an estimator for such models appropriate for data from several graphical models that share the same variables and some of the dependence structure. In this setting, estimating a single graphical model would mask the underlying heterogeneity, while estimating separate models for each category does not take advantage of the common structure. We propose a method that jointly estimates the graphical models corresponding to the different categories present in the data, aiming to preserve the common structure, while allowing for differences between the categories. This is achieved through a hierarchical penalty that targets the removal of common zeros in the inverse covariance matrices across categories. We establish the asymptotic consistency and sparsity of the proposed estimator in the high-dimensional case, and illustrate its performance on a number of simulated networks. An application to learning semantic connections between terms from webpages collected from computer science departments is included. PMID:23049124

  19. Structure Determination of a Membrane Protein with Two Trans-membrane Helices in Aligned Phospholipid Bicelles by Solid-state NMR Spectroscopy

    PubMed Central

    De Angelis, Anna A.; Howell, Stanley C.; Nevzorov, Alexander A.; Opella, Stanley J.

    2011-01-01

    The structure of the membrane protein MerFt was determined in magnetically aligned phospholipid bicelles by solid-state NMR spectroscopy. With two trans-membrane helices and a 10-residue inter-helical loop, this truncated construct of the mercury transport membrane protein MerF has sufficient structural complexity to demonstrate the feasibility of determining the structures of polytopic membrane proteins in their native phospholipid bilayer environment under physiological conditions. PISEMA, SAMMY, and other double-resonance experiments were applied to uniformly and selectively 15N labeled samples to resolve and assign the backbone amide resonances, and to measure the associated 15N chemical shift and 1H-15N heteronuclear dipolar coupling frequencies as orientation constraints for structure calculations. 1H/13C/15N triple-resonance experiments were applied to selectively 13C′ and 15N labeled samples to complete the resonance assignments, especially for residues in the non-helical regions of the protein. A single resonance is observed for each labeled site in one- and two-dimensional spectra. Therefore, each residue has a unique conformation, and all protein molecules in the sample have the same three-dimensional structure and are oriented identically in planar phospholipid bilayers. Combined with the absence of significant intensity near the isotropic resonance frequency, this demonstrates that the entire protein, including the loop and terminal regions, has a well-defined, stable structure in phospholipid bilayers. PMID:16967977

  20. Big system: Interactive graphics for the engineer

    NASA Technical Reports Server (NTRS)

    Quenneville, C. E.

    1975-01-01

    The BCS Interactive Graphics System (BIG System) approach to graphics was presented, along with several significant engineering applications. The BIG System precompiler, the graphics support library, and the function requirements of graphics applications are discussed. It was concluded that graphics standardization and a device independent code can be developed to assure maximum graphic terminal transferability.

  1. Structural and optical characteristics of graphene quantum dots size-controlled and well-aligned on a large scale by polystyrene-nanosphere lithography

    NASA Astrophysics Data System (ADS)

    Duck Oh, Si; Kim, Jungkil; Lee, Dae Hun; Kim, Ju Hwan; Jang, Chan Wook; Kim, Sung; Choi, Suk-Ho

    2016-01-01

    Graphene quantum dots (GQDs) are one of the most attractive graphene nanostructures due to their potential optoelectronic device applications, but it is a challenge to accurately control the size and arrangement of GQDs. In this report, we fabricate well-aligned GQDs on a large area by polystyrene (PS)-nanosphere (NS) lithography and study their structural and optical properties. Single-layer graphene grown on a Cu foil by chemical vapour deposition is patterned by reactive ion etching employing aligned PS-NS arrays as an etching mask. The size (d) of the GQDs is controlled from 75 to 23 nm by varying the etching time, as proved by scanning electron microscopy and atomic force microscopy. This method is well valid for both rigid/flexible target substrates and even for multilayer graphene formed by piling up single layers. The absorption peak of the GQDs is blue-shifted with respect to that of a graphene sheet, and is sequentially shifted to higher energies by reducing d, consistent with the quantum confinement effect (QCE). The Raman D-to-G band intensity ratio shows an almost monotonic increase with decreasing d, resulting from the dominant contribution of the edge states at the periphery of smaller GQDs. The G-band frequency shows a three-step size-dependence: initial increase, interim saturation, and final decrease with decreasing d, thought to be caused by the competition between the QCE and edge-induced strain effect.

  2. Dynamics of Mental Model Construction from Text and Graphics

    ERIC Educational Resources Information Center

    Hochpöchler, Ulrike; Schnotz, Wolfgang; Rasch, Thorsten; Ullrich, Mark; Horz, Holger; McElvany, Nele; Baumert, Jürgen

    2013-01-01

    When students read for learning, they frequently are required to integrate text and graphics information into coherent knowledge structures. The following study aimed at analyzing how students deal with texts and how they deal with graphics when they try to integrate the two sources of information. Furthermore, the study investigated differences…

  3. Mage: A Tool for Developing Interactive Instructional Graphics

    ERIC Educational Resources Information Center

    Pavkovic, Stephen F.

    2005-01-01

    Mage is a graphics program developed for visualization of three-dimensional structures of proteins and other macromolecules. An application of the Mage program is reported here for developing interactive instructional graphics files (kinemages) of much smaller scale. Examples are given illustrating features of VSEPR models, permanent dipoles,…

  4. A Technical Communication Course in Graphics and Audiovisuals.

    ERIC Educational Resources Information Center

    Carson, David L.; Harkins, Craig

    1980-01-01

    Describes the development of a course in graphics and audiovisuals as they are applied in technical communication. Includes brief discussions of the course design, general course structure, course objectives, course content, student evaluation, and student reaction. Indicates that the course includes information on theory, graphics, audiovisuals,…

  5. Graphical programming of telerobotic tasks

    SciTech Connect

    Small, D.E.; McDonald, M.J.

    1996-11-01

    With a goal of producing faster, safer, and cheaper technologies for nuclear waste cleanup, Sandia is actively developing and extending intelligent systems technologies through the US Department of Energy Office of Technology Development (DOE OTD) Robotic Technology Development Program (RTDP). Graphical programming is a key technology for robotic waste cleanup that Sandia is developing for this goal. Graphical programming uses simulation such as TELEGRIP `on-line` to program and control robots. Characterized by its model-based control architecture, integrated simulation, `point-and-click` graphical user interfaces, task and path planning software, and network communications, Sandia`s Graphical Programming systems allow operators to focus on high-level robotic tasks rather than the low-level details. Use of scripted tasks, rather than customized programs minimizes the necessity of recompiling supervisory control systems and enhances flexibility. Rapid world-modelling technologies allow Graphical Programming to be used in dynamic and unpredictable environments including digging and pipe-cutting. This paper describes Sancho, Sandia`s most advanced graphical programming supervisory software. Sancho, now operational on several robot systems, incorporates all of Sandia`s recent advances in supervisory control. Graphical programming uses 3-D graphics models as intuitive operator interfaces to program and control complex robotic systems. The goal of the paper is to help the reader understand how Sandia implements graphical programming systems and which key features in Sancho have proven to be most effective.

  6. Evaluating Texts for Graphical Literacy Instruction: The Graphic Rating Tool

    ERIC Educational Resources Information Center

    Roberts, Kathryn L.; Brugar, Kristy A.; Norman, Rebecca R.

    2015-01-01

    In this article, we present the Graphical Rating Tool (GRT), which is designed to evaluate the graphical devices that are commonly found in content-area, non-fiction texts, in order to identify books that are well suited for teaching about those devices. We also present a "best of" list of science and social studies books, which includes…

  7. Cationic copper(II)-containing surfactants: molecular structures, film morphology, and influence on the alignment of nematic mesogens.

    PubMed

    Verani, Cláudio N; Driscoll, Jeffery; Keyes, Paul H; Heeg, Mary Jane

    2014-06-01

    We discuss the synthesis and amphiphilic behavior of the cationic metallosurfactants [(L(Py14))2Cu(II)ClO4]ClO4 (1), [(L(Py16))2Cu(II)ClO4]ClO4 (2), [(L(Py18))2Cu(II)ClO4]ClO4 (3), [(L(Py18))2Cu(II)NO3]NO3 (4), [(L(Py18))2Cu(II)Cl]Cl (5), and [(L(Py18))2Cu(II)Br]Br (6) obtained by treatment of the appropriate alkylaminemethyl-2-pyridine ligand containing tetra-, hexa-, or octadecyl chains with copper salts. These metallosurfactants show excellent agreement between infrared spectroscopic bands, spectrometric masses with isotopic patterns, and elemental composition. Single-crystal X-ray data available for 1, 2, 5 and the previously published 3 reveal a trigonal bipyramidal copper(II) ion bound at the basal plane to the amine and pyridine of each alkylaminemethylpyridine ligand and an anionic coligand to the apical position. Except for the surfactant with the shortest tetradecyl (C14) chain, these species yield Langmuir films with collapse pressures of 45-55 mN·m(-1) and average areas of ca. 50 Å(2). A plateau around 15 mN·m(-1) is observed for 3, 4, and 5 and associated with the formation of dendritic domains about 50 μm in size. Species 2 and 6 lack this plateau and show domains of ca. 5 μm. Once transferred onto solid substrates, the resulting Langmuir-Blodgett film of 3 at 18 mN·m(-1) influences the alignment of the nematic liquid crystal N-(4-methoxybenzylidene)-4-butylaniline. PMID:24813105

  8. Magnetically aligned iron oxide/gold nanoparticle-decorated carbon nanotube hybrid structure as a humidity sensor.

    PubMed

    Lee, Jaewook; Mulmi, Suresh; Thangadurai, Venkataraman; Park, Simon S

    2015-07-22

    Functionalized carbon nanotubes (f-CNTs), particularly CNTs decorated with nanoparticles (NPs), are of great interest because of their synergic effects, such as surface-enhanced Raman scattering, plasmonic resonance energy transfer, magnetoplasmonic, magnetoelectric, and magnetooptical effects. In general, research has focused on a single type of NP, such as a metal or metal oxide, that has been modified on a CNT surface. In this study, however, a new strategy is introduced for the decoration of two different NP types on CNTs. In order to improve the functionality of modified CNTs, we successfully prepared binary NP-decorated CNTs, namely, iron oxide/gold (Au) NP-decorated CNTs (IA-CNTs), which were created through two simple reactions in deionized water, without high temperature, high pressure, or harsh reducing agents. The physicochemical properties of IA-CNTs were characterized by ultraviolet/visible spectroscopy, Fourier transform infrared spectroscopy, a superconducting quantum interference device, scanning electron microscopy, and transmission electron microscopy. In this study, IA-CNTs were utilized to detect humidity. Magnetic IA-CNTs were aligned on interdigitated platinum electrodes under external magnetic fields to create a humidity-sensing channel, and its electrical conductivity was monitored. As the humidity increased, the electrical resistance of the sensor also increased. In comparison with various gases, for example, H2, O2, CO, CO2, SO2, and dry air, the IA-CNT-based humidity sensor exhibited high-selectivity performances. IA-CNTs also responded to heavy water (D2O), and it was established that the humidity detection mechanism had D2O-sensing capabilities. Further, the humidity from human out-breathing was also successfully detected by this system. In conclusion, these unique IA-CNTs exhibited potential application as gas detection materials. PMID:26112318

  9. Probabilistic graphical model representation in phylogenetics.

    PubMed

    Höhna, Sebastian; Heath, Tracy A; Boussau, Bastien; Landis, Michael J; Ronquist, Fredrik; Huelsenbeck, John P

    2014-09-01

    Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis-Hastings or Gibbs sampling of the posterior distribution. PMID:24951559

  10. Development of computer graphics

    SciTech Connect

    Nuttall, H.E.

    1989-07-01

    The purpose of this project was to screen and evaluate three graphics packages as to their suitability for displaying concentration contour graphs. The information to be displayed is from computer code simulations describing air-born contaminant transport. The three evaluation programs were MONGO (John Tonry, MIT, Cambridge, MA, 02139), Mathematica (Wolfram Research Inc.), and NCSA Image (National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign). After a preliminary investigation of each package, NCSA Image appeared to be significantly superior for generating the desired concentration contour graphs. Hence subsequent work and this report describes the implementation and testing of NCSA Image on both an Apple MacII and Sun 4 computers. NCSA Image includes several utilities (Layout, DataScope, HDF, and PalEdit) which were used in this study and installed on Dr. Ted Yamada`s Mac II computer. Dr. Yamada provided two sets of air pollution plume data which were displayed using NCSA Image. Both sets were animated into a sequential expanding plume series.

  11. Liquid crystal alignment on ion-beam-treated polyimide with a long alkyl side chain: near edge X-ray absorption fine structure spectroscopy analysis.

    PubMed

    Seo, Joo-Hong; Hwang, Soo Won; Song, Dong Han; Shin, Jae Hoon; Yoon, Tae-Hoon; Kim, Jae Chang; Yi, Mi Hye

    2009-02-19

    Liquid crystal alignment on ion-beam-treated polyimides with a long alkyl side chain was investigated using near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The long alkyl side chains and the asymmetric distribution and orientational order of the pi-bonds of the polyimide surface can be determined by analyzing the angular dependent resonance intensities of the NEXAFS measurements. Herein, we demonstrate that the pretilt angle of the LC cell made by our method decreases as more long alkyl side chains are destroyed. Additionally, the tilt direction of the LC molecules can be determined from the asymmetric distribution of pi-bonds of the polyimide created by the ion beam irradiation. PMID:19161281

  12. Oklahoma's Mobile Computer Graphics Laboratory.

    ERIC Educational Resources Information Center

    McClain, Gerald R.

    This Computer Graphics Laboratory houses an IBM 1130 computer, U.C.C. plotter, printer, card reader, two key punch machines, and seminar-type classroom furniture. A "General Drafting Graphics System" (GDGS) is used, based on repetitive use of basic coordinate and plot generating commands. The system is used by 12 institutions of higher education…

  13. Graphic Interfaces and Online Information.

    ERIC Educational Resources Information Center

    Percival, J. Mark

    1990-01-01

    Discusses the growing importance of the use of Graphic User Interfaces (GUIs) with microcomputers and online services. Highlights include the development of graphics interfacing with microcomputers; CD-ROM databases; an evaluation of HyperCard as a potential interface to electronic mail and online commercial databases; and future possibilities.…

  14. Computer Graphics and Physics Teaching.

    ERIC Educational Resources Information Center

    Bork, Alfred M.; Ballard, Richard

    New, more versatile and inexpensive terminals will make computer graphics more feasible in science instruction than before. This paper describes the use of graphics in physics teaching at the University of California at Irvine. Commands and software are detailed in established programs, which include a lunar landing simulation and a program which…

  15. REQUIREMENTS FOR GRAPHIC TEACHING MACHINES.

    ERIC Educational Resources Information Center

    HICKEY, ALBERT; AND OTHERS

    AN EXPERIMENT WAS REPORTED WHICH DEMONSTRATES THAT GRAPHICS ARE MORE EFFECTIVE THAN SYMBOLS IN ACQUIRING ALGEBRA CONCEPTS. THE SECOND PHASE OF THE STUDY DEMONSTRATED THAT GRAPHICS IN HIGH SCHOOL TEXTBOOKS WERE RELIABLY CLASSIFIED IN A MATRIX OF 480 FUNCTIONAL STIMULUS-RESPONSE CATEGORIES. SUGGESTIONS WERE MADE FOR EXTENDING THE CLASSIFICATION…

  16. Computer Graphics Evolution: A Survey.

    ERIC Educational Resources Information Center

    Gartel, Laurence M.

    1985-01-01

    The history of the field of computer graphics is discussed. In 1976 there were no institutions that offered any kind of study of computer graphics. Today electronic image-making is seen as a viable, legitimate art form, and courses are offered by many universities and colleges. (RM)

  17. Liquid crystal alignment in cylindrical microcapillaries

    NASA Astrophysics Data System (ADS)

    Chychłowski, M.; Yaroshchuk, O.; Kravchuk, R.; Woliński, T.

    2011-09-01

    A variety of alignment configurations of liquid crystals (LCs) inside the glassy cylindrical capillaries is realized by using alignment materials providing different anchoring. The radial configuration with central disclination line is obtained for homeotropic boundary conditions. In turn, the axial, transversal and tilted alignment structures are realized by using materials for planar anchoring. The uniformity and controlling of the latter structures were provided by photoalignment method. This approach can be further used to control LC alignment in the photonic crystal fibers recognized as advanced elements for different optical devices.

  18. Liquid crystal alignment in cylindrical microcapillaries

    NASA Astrophysics Data System (ADS)

    Chychłowski, M.; Yaroshchuk, O.; Kravchuk, R.; Woliński, T.

    2012-03-01

    A variety of alignment configurations of liquid crystals (LCs) inside the glassy cylindrical capillaries is realized by using alignment materials providing different anchoring. The radial configuration with central disclination line is obtained for homeotropic boundary conditions. In turn, the axial, transversal and tilted alignment structures are realized by using materials for planar anchoring. The uniformity and controlling of the latter structures were provided by photoalignment method. This approach can be further used to control LC alignment in the photonic crystal fibers recognized as advanced elements for different optical devices.

  19. Super VGA Primitives Graphics System.

    1992-05-14

    Version 00 These primitives are the lowest level routines needed to perform super VGA graphics on a PC. A sample main program is included that exercises the primitives. Both Lahey and Microsoft FORTRAN's have graphics libraries. However, the libraries do not support 256 color graphics at resolutions greater than 320x200. The primitives bypass these libraries while still conforming to standard usage of BIOS. The supported graphics modes depend upon the PC graphics card and itsmore » memory. Super VGA resolutions of 640x480 and 800x600 have been tested on an ATI VGA Wonder card with 512K memory and on several 80486 PC's (unknown manufacturers) at retail stores.« less

  20. Learning Layouts for Single-Page Graphic Designs.

    PubMed

    O'Donovan, Peter; Agarwala, Aseem; Hertzmann, Aaron

    2014-08-01

    This paper presents an approach for automatically creating graphic design layouts using a new energy-based model derived from design principles. The model includes several new algorithms for analyzing graphic designs, including the prediction of perceived importance, alignment detection, and hierarchical segmentation. Given the model, we use optimization to synthesize new layouts for a variety of single-page graphic designs. Model parameters are learned with Nonlinear Inverse Optimization (NIO) from a small number of example layouts. To demonstrate our approach, we show results for applications including generating design layouts in various styles, retargeting designs to new sizes, and improving existing designs. We also compare our automatic results with designs created using crowdsourcing and show that our approach performs slightly better than novice designers. PMID:26357371

  1. Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

    SciTech Connect

    Mohammadi, Shahin; Gleich, David F.; Kolda, Tamara G.; Grama, Ananth

    2015-11-01

    Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangular AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.

  2. Bio-inspired configurable multiscale extracellular matrix-like structures for functional alignment and guided orientation of cells.

    PubMed

    Bae, Won-Gyu; Kim, Jangho; Choung, Yun-Hoon; Chung, Yesol; Suh, Kahp Y; Pang, Changhyun; Chung, Jong Hoon; Jeong, Hoon Eui

    2015-11-01

    Inspired by the hierarchically organized protein fibers in extracellular matrix (ECM) as well as the physiological importance of multiscale topography, we developed a simple but robust method for the design and manipulation of precisely controllable multiscale hierarchical structures using capillary force lithography in combination with an original wrinkling technique. In this study, based on our proposed fabrication technology, we approached a conceptual platform that can mimic the hierarchically multiscale topographical and orientation cues of the ECM for controlling cell structure and function. We patterned the polyurethane acrylate-based nanotopography with various orientations on the microgrooves, which could provide multiscale topography signals of ECM to control single and multicellular morphology and orientation with precision. Using our platforms, we found that the structures and orientations of fibroblast cells were greatly influenced by the nanotopography, rather than the microtopography. We also proposed a new approach that enables the generation of native ECM having nanofibers in specific three-dimensional (3D) configurations by culturing fibroblast cells on the multiscale substrata. We suggest that our methodology could be used as efficient strategies for the design and manipulation of various functional platforms, including well-defined 3D tissue structures for advanced regenerative medicine applications. PMID:26285083

  3. Ground and CHAMP observations of field-aligned current circuits generated by lower atmospheric disturbances and expectations to the SWARM to clarify their three dimensional structure

    NASA Astrophysics Data System (ADS)

    Iyemori, Toshihiko; Nakanishi, Kunihito; Aoyama, Tadashi; Lühr, Hermann

    2014-05-01

    Acoustic gravity waves propagated to the ionosphere cause dynamo currents in the ionosphere. They divert along geomagnetic field lines of force to another hemisphere accompanying electric field and then flow in the ionosphere of another hemisphere by the electric field forming closed current circuits. The oscillating current circuits with the period of acoustic waves generate magnetic variations on the ground, and they are observed as long period geomagnetic pulsations. This effect has been detected during big earthquakes, strong typhoons, tornados etc. On a low-altitude satellite orbit, the spatial distribution (i.e., structure) of the current circuits along the satellite orbit should be detected as temporal magnetic oscillations, and the effect is confirmed by a CHAMP data analysis. On the spatial structure, in particular, in the longitudinal direction, it has been difficult to examine by a single satellite or from ground magnetic observations. The SWARM satellites will provide an unique opportunity to clarify the three dimensional structure of the field-aligned current circuits.

  4. Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments.

    PubMed

    Ortiz, A R; Kolinski, A; Skolnick, J

    1998-02-15

    Using a recently developed protein folding algorithm, a prediction of the tertiary structure of the KIX domain of the CREB binding protein is described. The method incorporates predicted secondary and tertiary restraints derived from multiple sequence alignments in a reduced protein model whose conformational space is explored by Monte Carlo dynamics. Secondary structure restraints are provided by the PHD secondary structure prediction algorithm that was modified for the presence of predicted U-turns, i.e., regions where the chain reverses global direction. Tertiary restraints are obtained via a two-step process: First, seed side-chain contacts are identified from a correlated mutation analysis, and then, a threading-based algorithm expands the number of these seed contacts. Blind predictions indicate that the KIX domain is a putative three-helix bundle, although the chirality of the bundle could not be uniquely determined. The expected root-mean-square deviation for the correct chirality of the KIX domain is between 5.0 and 6.2 A. This is to be compared with the estimate of 12.9 A that would be expected by a random prediction, using the model of F. Cohen and M. Sternberg (J. Mol. Biol. 138:321-333, 1980). PMID:9517544

  5. Markov Random Field Based Automatic Image Alignment for ElectronTomography

    SciTech Connect

    Moussavi, Farshid; Amat, Fernando; Comolli, Luis R.; Elidan, Gal; Downing, Kenneth H.; Horowitz, Mark

    2007-11-30

    Cryo electron tomography (cryo-ET) is the primary method for obtaining 3D reconstructions of intact bacteria, viruses, and complex molecular machines ([7],[2]). It first flash freezes a specimen in a thin layer of ice, and then rotates the ice sheet in a transmission electron microscope (TEM) recording images of different projections through the sample. The resulting images are aligned and then back projected to form the desired 3-D model. The typical resolution of biological electron microscope is on the order of 1 nm per pixel which means that small imprecision in the microscope's stage or lenses can cause large alignment errors. To enable a high precision alignment, biologists add a small number of spherical gold beads to the sample before it is frozen. These beads generate high contrast dots in the image that can be tracked across projections. Each gold bead can be seen as a marker with a fixed location in 3D, which provides the reference points to bring all the images to a common frame as in the classical structure from motion problem. A high accuracy alignment is critical to obtain a high resolution tomogram (usually on the order of 5-15nm resolution). While some methods try to automate the task of tracking markers and aligning the images ([8],[4]), they require user intervention if the SNR of the image becomes too low. Unfortunately, cryogenic electron tomography (or cryo-ET) often has poor SNR, since the samples are relatively thick (for TEM) and the restricted electron dose usually results in projections with SNR under 0 dB. This paper shows that formulating this problem as a most-likely estimation task yields an approach that is able to automatically align with high precision cryo-ET datasets using inference in graphical models. This approach has been packaged into a publicly available software called RAPTOR-Robust Alignment and Projection estimation for Tomographic Reconstruction.

  6. Graphical presentation of diagnostic information

    PubMed Central

    Whiting, Penny F; Sterne, Jonathan AC; Westwood, Marie E; Bachmann, Lucas M; Harbord, Roger; Egger, Matthias; Deeks, Jonathan J

    2008-01-01

    Background Graphical displays of results allow researchers to summarise and communicate the key findings of their study. Diagnostic information should be presented in an easily interpretable way, which conveys both test characteristics (diagnostic accuracy) and the potential for use in clinical practice (predictive value). Methods We discuss the types of graphical display commonly encountered in primary diagnostic accuracy studies and systematic reviews of such studies, and systematically review the use of graphical displays in recent diagnostic primary studies and systematic reviews. Results We identified 57 primary studies and 49 systematic reviews. Fifty-six percent of primary studies and 53% of systematic reviews used graphical displays to present results. Dot-plot or box-and- whisker plots were the most commonly used graph in primary studies and were included in 22 (39%) studies. ROC plots were the most common type of plot included in systematic reviews and were included in 22 (45%) reviews. One primary study and five systematic reviews included a probability-modifying plot. Conclusion Graphical displays are currently underused in primary diagnostic accuracy studies and systematic reviews of such studies. Diagnostic accuracy studies need to include multiple types of graphic in order to provide both a detailed overview of the results (diagnostic accuracy) and to communicate information that can be used to inform clinical practice (predictive value). Work is required to improve graphical displays, to better communicate the utility of a test in clinical practice and the implications of test results for individual patients. PMID:18405357

  7. Robust Gaussian Graphical Modeling via l1 Penalization

    PubMed Central

    Sun, Hokeun; Li, Hongzhe

    2012-01-01

    Summary Gaussian graphical models have been widely used as an effective method for studying the conditional independency structure among genes and for constructing genetic networks. However, gene expression data typically have heavier tails or more outlying observations than the standard Gaussian distribution. Such outliers in gene expression data can lead to wrong inference on the dependency structure among the genes. We propose a l1 penalized estimation procedure for the sparse Gaussian graphical models that is robustified against possible outliers. The likelihood function is weighted according to how the observation is deviated, where the deviation of the observation is measured based on its own likelihood. An efficient computational algorithm based on the coordinate gradient descent method is developed to obtain the minimizer of the negative penalized robustified-likelihood, where nonzero elements of the concentration matrix represents the graphical links among the genes. After the graphical structure is obtained, we re-estimate the positive definite concentration matrix using an iterative proportional fitting algorithm. Through simulations, we demonstrate that the proposed robust method performs much better than the graphical Lasso for the Gaussian graphical models in terms of both graph structure selection and estimation when outliers are present. We apply the robust estimation procedure to an analysis of yeast gene expression data and show that the resulting graph has better biological interpretation than that obtained from the graphical Lasso. PMID:23020775

  8. Nearest Alignment Space Termination

    2006-07-13

    Near Alignment Space Termination (NAST) is the Greengenes algorithm that matches up submitted sequences with the Greengenes database to look for similarities and align the submitted sequences based on those similarities.

  9. Photoluminescence and band edge alignment of C-induced Ge islands and related SiGeC structures

    NASA Astrophysics Data System (ADS)

    Schmidt, O. G.; Eberl, K.

    1998-11-01

    Growth of less than 2 monolayers Ge on a submonolayer amount of predeposited C on Si results in the formation of very small Ge quantum islands. In a photoluminescence study, we compare these C-induced Ge (CGe) dots with carefully chosen reference structures incorporating the same total amount of C and Ge but with different deposition orders and with varied C distribution below the Ge islands. Our investigations imply that the special combination of pregrown low surface mobility C and post-grown high surface mobility Ge constitutes a distinct microstructure within the SiGeC material system, causing dot formation at a very early stage and showing particularly intense photoluminescence signal. Moreover, structures combining CGe dots with Si1-yCy quantum wells are well explained by the model of spatially indirect type-II recombination within the CGe islands.

  10. Interfacial band alignment and structural properties of nanoscale TiO2 thin films for integration with epitaxial crystallographic oriented germanium

    NASA Astrophysics Data System (ADS)

    Jain, N.; Zhu, Y.; Maurya, D.; Varghese, R.; Priya, S.; Hudait, M. K.

    2014-01-01

    We have investigated the structural and band alignment properties of nanoscale titanium dioxide (TiO2) thin films deposited on epitaxial crystallographic oriented Ge layers grown on (100), (110), and (111)A GaAs substrates by molecular beam epitaxy. The TiO2 thin films deposited at low temperature by physical vapor deposition were found to be amorphous in nature, and high-resolution transmission electron microscopy confirmed a sharp heterointerface between the TiO2 thin film and the epitaxially grown Ge with no traceable interfacial layer. A comprehensive assessment on the effect of substrate orientation on the band alignment at the TiO2/Ge heterointerface is presented by utilizing x-ray photoelectron spectroscopy and spectroscopic ellipsometry. A band-gap of 3.33 ± 0.02 eV was determined for the amorphous TiO2 thin film from the Tauc plot. Irrespective of the crystallographic orientation of the epitaxial Ge layer, a sufficient valence band-offset of greater than 2 eV was obtained at the TiO2/Ge heterointerface while the corresponding conduction band-offsets for the aforementioned TiO2/Ge system were found to be smaller than 1 eV. A comparative assessment on the effect of Ge substrate orientation revealed a valence band-offset relation of ΔEV(100) > ΔEV(111) > ΔEV(110) and a conduction band-offset relation of ΔEC(110) > ΔEC(111) > ΔEC(100). These band-offset parameters are of critical importance and will provide key insight for the design and performance analysis of TiO2 for potential high-κ dielectric integration and for future metal-insulator-semiconductor contact applications with next generation of Ge based metal-oxide field-effect transistors.

  11. Robust and exact structural variation detection with paired-end and soft-clipped alignments: SoftSV compared with eight algorithms.

    PubMed

    Bartenhagen, Christoph; Dugas, Martin

    2016-01-01

    Structural variation (SV) plays an important role in genetic diversity among the population in general and specifically in diseases such as cancer. Modern next-generation sequencing (NGS) technologies provide paired-end sequencing data at high depth with increasing read lengths. This development enabled the analysis of split-reads to detect SV breakpoints with single-nucleotide resolution. But ambiguous mappings and breakpoint sequences with further co-occurring mutations hamper split-read alignments against a reference sequence. The trade-off between high sensitivity and low false-positive rate is problematic and often requires a lot of fine-tuning of the analysis method based on knowledge about its algorithm and the characteristics of the data set. We present SoftSV, a method for exact breakpoint detection for small and large deletions, inversions, tandem duplications and inter-chromosomal translocations, which relies solely on the mutual alignment of soft-clipped reads within the neighborhood of discordantly mapped paired-end reads. Unlike other SV detection algorithms, our approach does not require thresholds regarding sequencing coverage or mapping quality. We evaluate SoftSV together with eight approaches (Breakdancer, Clever, CREST, Delly, GASVPro, Pindel, Socrates and SoftSearch) on simulated and real data sets. Our results show that sensitive and reliable SV detection is subject to many different factors like read length, sequence coverage and SV type. While most programs have their individual drawbacks, our greedy approach turns out to be the most robust and sensitive on many experimental setups. Sensitivities above 85% and positive predictive values between 80 and 100% could be achieved consistently for all SV types on simulated data sets starting at relatively short 75 bp reads and low 10-15× sequence coverage. PMID:25998133

  12. BinAligner: a heuristic method to align biological networks.

    PubMed

    Yang, Jialiang; Li, Jun; Grünewald, Stefan; Wan, Xiu-Feng

    2013-01-01

    The advances in high throughput omics technologies have made it possible to characterize molecular interactions within and across various species. Alignments and comparison of molecular networks across species will help detect orthologs and conserved functional modules and provide insights on the evolutionary relationships of the compared species. However, such analyses are not trivial due to the complexity of network and high computational cost. Here we develop a mixture of global and local algorithm, BinAligner, for network alignments. Based on the hypotheses that the similarity between two vertices across networks would be context dependent and that the information from the edges and the structures of subnetworks can be more informative than vertices alone, two scoring schema, 1-neighborhood subnetwork and graphlet, were introduced to derive the scoring matrices between networks, besides the commonly used scoring scheme from vertices. Then the alignment problem is formulated as an assignment problem, which is solved by the combinatorial optimization algorithm, such as the Hungarian method. The proposed algorithm was applied and validated in aligning the protein-protein interaction network of Kaposi's sarcoma associated herpesvirus (KSHV) and that of varicella zoster virus (VZV). Interestingly, we identified several putative functional orthologous proteins with similar functions but very low sequence similarity between the two viruses. For example, KSHV open reading frame 56 (ORF56) and VZV ORF55 are helicase-primase subunits with sequence identity 14.6%, and KSHV ORF75 and VZV ORF44 are tegument proteins with sequence identity 15.3%. These functional pairs can not be identified if one restricts the alignment into orthologous protein pairs. In addition, BinAligner identified a conserved pathway between two viruses, which consists of 7 orthologous protein pairs and these proteins are connected by conserved links. This pathway might be crucial for virus packing and

  13. Graphic arts techniques and equipment: A compilation

    NASA Technical Reports Server (NTRS)

    1974-01-01

    Technology utilization of NASA sponsored projects involving graphic arts techniques and equipment is discussed. The subjects considered are: (1) modification to graphics tools, (1) new graphics tools, (3) visual aids for graphics, and (4) graphic arts shop hints. Photographs and diagrams are included to support the written material.

  14. Graphics Software For VT Terminals

    NASA Technical Reports Server (NTRS)

    Wang, Caroline

    1991-01-01

    VTGRAPH graphics software tool for DEC/VT computer terminal or terminals compatible with it, widely used by government and industry. Callable in FORTRAN or C language, library program enabling user to cope with many computer environments in which VT terminals used for window management and graphic systems. Provides PLOT10-like package plus color or shade capability for VT240, VT241, and VT300 terminals. User can easily design more-friendly user-interface programs and design PLOT10 programs on VT terminals with different computer systems. Requires ReGis graphics set terminal and FORTRAN compiler.

  15. Graphical Planning Of Spacecraft Missions

    NASA Technical Reports Server (NTRS)

    Jeletic, J. F.; Ruley, L. T.

    1991-01-01

    Mission Planning Graphical Tool (MPGT) computer program provides analysts with graphical representations of spacecraft and environmental data used in planning missions. Designed to be generic software tool configured to analyze any specified Earth-orbiting spacecraft mission. Data presented as series of overlays on top of two-dimensional or three-dimensional projection of Earth. Includes spacecraft-orbit tracks, ground-station-antenna masks, solar and lunar ephemerides, and coverage by Tracking Data and Relay Satellite System (TDRSS). From graphical representations, analyst determines such spacecraft-related constraints as communication coverage, infringement upon zones of interference, availability of sunlight, and visibility of targets to instruments.

  16. Shiva automatic pinhole alignment

    SciTech Connect

    Suski, G.J.

    1980-09-05

    This paper describes a computer controlled closed loop alignment subsystem for Shiva, which represents the first use of video sensors for large laser alignment at LLNL. The techniques used on this now operational subsystem are serving as the basis for all closed loop alignment on Nova, the 200 terawatt successor to Shiva.

  17. Fast statistical alignment.

    PubMed

    Bradley, Robert K; Roberts, Adam; Smoot, Michael; Juvekar, Sudeep; Do, Jaeyoung; Dewey, Colin; Holmes, Ian; Pachter, Lior

    2009-05-01

    We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multiple alignments which are accompanied by estimates of the alignment accuracy and uncertainty for every column and character of the alignment--previously available only with alignment programs which use computationally-expensive Markov Chain Monte Carlo approaches--yet can align thousands of long sequences. Moreover, FSA utilizes an unsupervised query-specific learning procedure for parameter estimation which leads to improved accuracy on benchmark reference alignments in comparison to existing programs. The centroid alignment approach taken by FSA, in combination with its learning procedure, drastically reduces the amount of false-positive alignment on biological data in comparison to that given by other methods. The FSA program and a companion visualization tool for exploring uncertainty in alignments can be used via a web interface at http://orangutan.math.berkeley.edu/fsa/, and the source code is available at http://fsa.sourceforge.net/. PMID:19478997

  18. Unrooted unordered homeomorphic subtree alignment of RNA trees.

    PubMed

    Milo, Nimrod; Zakov, Shay; Katzenelson, Erez; Bachmat, Eitan; Dinitz, Yefim; Ziv-Ukelson, Michal

    2013-01-01

    : We generalize some current approaches for RNA tree alignment, which are traditionally confined to ordered rooted mappings, to also consider unordered unrooted mappings. We define the Homeomorphic Subtree Alignment problem (HSA), and present a new algorithm which applies to several modes, combining global or local, ordered or unordered, and rooted or unrooted tree alignments. Our algorithm generalizes previous algorithms that either solved the problem in an asymmetric manner, or were restricted to the rooted and/or ordered cases. Focusing here on the most general unrooted unordered case, we show that for input trees T and S, our algorithm has an O(nTnS + min(dT,dS)LTLS) time complexity, where nT,LT and dT are the number of nodes, the number of leaves, and the maximum node degree in T, respectively (satisfying dT ≤ LT ≤ nT), and similarly for nS,LS and dS with respect to the tree S. This improves the time complexity of previous algorithms for less general variants of the problem.In order to obtain this time bound for HSA, we developed new algorithms for a generalized variant of the Min-Cost Bipartite Matching problem (MCM), as well as to two derivatives of this problem, entitled All-Cavity-MCM and All-Pairs-Cavity-MCM. For two input sets of size n and m, where n ≤ m, MCM and both its cavity derivatives are solved in O(n3 + nm) time, without the usage of priority queues (e.g. Fibonacci heaps) or other complex data structures. This gives the first cubic time algorithm for All-Pairs-Cavity-MCM, and improves the running times of MCM and All-Cavity-MCM problems in the unbalanced case where n ≪ m.We implemented the algorithm (in all modes mentioned above) as a graphical software tool which computes and displays similarities between secondary structures of RNA given as input, and employed it to a preliminary experiment in which we ran all-against-all inter-family pairwise alignments of RNAse P and Hammerhead RNA

  19. Managing facts and concepts: computer graphics and information graphics from a graphic designer's perspective

    SciTech Connect

    Marcus, A.

    1983-01-01

    This book emphasizes the importance of graphic design for an information-oriented society. In an environment in which many new graphic communication technologies are emerging, it raises some issues which graphic designers and managers of graphic design production should consider in using the new technology effectively. In its final sections, it gives an example of the steps taken in designing a visual narrative as a prototype for responsible information-oriented graphic design. The management of complex facts and concepts, of complex systems of ideas and issues, presented in a visual as well as verbal narrative or dialogue and conveyed through new technology will challenge the graphic design community in the coming decades. This shift to visual-verbal communication has repercussions in the educational system and the political/governance systems that go beyond the scope of this book. If there is a single goal for this book, it is to stimulate the reader and then to provide references that will help you learn more about graphic design in an era of communication when know business is show business.

  20. Ichthyophonus parasite phylogeny based on ITS rDNA structure prediction and alignment identifies six clades, with a single dominant marine type

    USGS Publications Warehouse

    Gregg, Jacob; Thompson, Rachel L.; Purcell, Maureen; Friedman, Carolyn S.; Hershberger, Paul

    2016-01-01

    Despite their widespread, global impact in both wild and cultured fishes, little is known of the diversity, transmission patterns, and phylogeography of parasites generally identified as Ichthyophonus. This study constructed a phylogeny based on the structural alignment of internal transcribed spacer (ITS) rDNA sequences to compare Ichthyophonus isolates from fish hosts in the Atlantic and Pacific oceans, and several rivers and aquaculture sites in North America, Europe, and Japan. Structure of the Ichthyophonus ITS1–5.8S–ITS2 transcript exhibited several homologies with other eukaryotes, and 6 distinct clades were identified within Ichthyophonus. A single clade contained a majority (71 of 98) of parasite isolations. This ubiquitous Ichthyophonus type occurred in 13 marine and anadromous hosts and was associated with epizootics in Atlantic herring, Chinook salmon, and American shad. A second clade contained all isolates from aquaculture, despite great geographic separation of the freshwater hosts. Each of the 4 remaining clades contained isolates from single host species. This study is the first to evaluate the genetic relationships among Ichthyophonus species across a significant portion of their host and geographic range. Additionally, parasite infection prevalence is reported in 16 fish species.

  1. Ichthyophonus parasite phylogeny based on ITS rDNA structure prediction and alignment identifies six clades, with a single dominant marine type.

    PubMed

    Gregg, Jacob L; Powers, Rachel L; Purcell, Maureen K; Friedman, Carolyn S; Hershberger, Paul K

    2016-07-01

    Despite their widespread, global impact in both wild and cultured fishes, little is known of the diversity, transmission patterns, and phylogeography of parasites generally identified as Ichthyophonus. This study constructed a phylogeny based on the structural alignment of internal transcribed spacer (ITS) rDNA sequences to compare Ichthyophonus isolates from fish hosts in the Atlantic and Pacific oceans, and several rivers and aquaculture sites in North America, Europe, and Japan. Structure of the Ichthyophonus ITS1-5.8S-ITS2 transcript exhibited several homologies with other eukaryotes, and 6 distinct clades were identified within Ichthyophonus. A single clade contained a majority (71 of 98) of parasite isolations. This ubiquitous Ichthyophonus type occurred in 13 marine and anadromous hosts and was associated with epizootics in Atlantic herring, Chinook salmon, and American shad. A second clade contained all isolates from aquaculture, despite great geographic separation of the freshwater hosts. Each of the 4 remaining clades contained isolates from single host species. This study is the first to evaluate the genetic relationships among Ichthyophonus species across a significant portion of their host and geographic range. Additionally, parasite infection prevalence is reported in 16 fish species. PMID:27409236

  2. Calculators and Computers: Graphical Addition.

    ERIC Educational Resources Information Center

    Spero, Samuel W.

    1978-01-01

    A computer program is presented that generates problem sets involving sketching graphs of trigonometric functions using graphical addition. The students use calculators to sketch the graphs and a computer solution is used to check it. (MP)

  3. XUV ionization of aligned molecules

    SciTech Connect

    Kelkensberg, F.; Siu, W.; Gademann, G.; Rouzee, A.; Vrakking, M. J. J.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.

    2011-11-15

    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  4. Alignment positioning mechanism

    NASA Technical Reports Server (NTRS)

    Fantasia, Peter M. (Inventor)

    1991-01-01

    An alignment positioning mechanism for correcting and compensating for misalignment of structures to be coupled is disclosed. The mechanism comprises a power screw with a base portion and a threaded shank portion. A mounting fixture is provided for rigidly coupling said base portion to the mounting interface of a supporting structure with the axis of the screw perpendicular thereto. A traveling ball nut threaded on the power screw is formed with an external annular arcuate surface configured in the form of a spherical segment and enclosed by a ball nut housing with a conforming arcuate surface for permitting gimballed motion thereon. The ball nut housing is provided with a mounting surface which is positionable in cooperable engagement with the mounting interface of a primary structure to be coupled to the supporting structure. Cooperative means are provided on the ball nut and ball nut housing, respectively, for positioning the ball nut and ball nut housing in relative gimballed position within a predetermined range of relative angular relationship whereby severe structural stresses due to unequal loadings and undesirable bending moments on the mechanism are avoided.

  5. APSRS state-base graphics

    USGS Publications Warehouse

    U.S. Geological Survey

    1981-01-01

    The National Cartographic Information Center (NCIC) is the information branch of the U.S. Geological Survey's National Mapping Division. In order to organize and distribute information about U.S. aerial photography coverage and to help eliminate aerial mapping duplication by tracking individual aerial projects, NCIC developed the Aerial Photography Summary Record System (APSRS). APSRS's principal products are State-Base Graphics (SBG), graphic indexes that show the coverage of conventional aerial photography projects over each State.

  6. Graphic design of pinhole cameras

    NASA Technical Reports Server (NTRS)

    Edwards, H. B.; Chu, W. P.

    1979-01-01

    The paper describes a graphic technique for the analysis and optimization of pinhole size and focal length. The technique is based on the use of the transfer function of optical elements described by Scott (1959) to construct the transfer function of a circular pinhole camera. This transfer function is the response of a component or system to a pattern of lines having a sinusoidally varying radiance at varying spatial frequencies. Some specific examples of graphic design are presented.

  7. Planetary Photojournal Home Page Graphic

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This image is an unannotated version of the Planetary Photojournal Home Page graphic. This digital collage contains a highly stylized rendition of our solar system and points beyond. As this graphic was intended to be used as a navigation aid in searching for data within the Photojournal, certain artistic embellishments have been added (color, location, etc.). Several data sets from various planetary and astronomy missions were combined to create this image.

  8. Photojournal Home Page Graphic 2007

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This image is an unannotated version of the Photojournal Home Page graphic released in October 2007. This digital collage contains a highly stylized rendition of our solar system and points beyond. As this graphic was intended to be used as a navigation aid in searching for data within the Photojournal, certain artistic embellishments have been added (color, location, etc.). Several data sets from various planetary and astronomy missions were combined to create this image.

  9. ggbio: an R package for extending the grammar of graphics for genomic data

    PubMed Central

    2012-01-01

    We introduce ggbio, a new methodology to visualize and explore genomics annotations and high-throughput data. The plots provide detailed views of genomic regions, summary views of sequence alignments and splicing patterns, and genome-wide overviews with karyogram, circular and grand linear layouts. The methods leverage the statistical functionality available in R, the grammar of graphics and the data handling capabilities of the Bioconductor project. The plots are specified within a modular framework that enables users to construct plots in a systematic way, and are generated directly from Bioconductor data structures. The ggbio R package is available at http://www.bioconductor.org/packages/2.11/bioc/html/ggbio.html. PMID:22937822

  10. Girder Alignment Plan

    SciTech Connect

    Wolf, Zackary; Ruland, Robert; LeCocq, Catherine; Lundahl, Eric; Levashov, Yurii; Reese, Ed; Rago, Carl; Poling, Ben; Schafer, Donald; Nuhn, Heinz-Dieter; Wienands, Uli; /SLAC

    2010-11-18

    The girders for the LCLS undulator system contain components which must be aligned with high accuracy relative to each other. The alignment is one of the last steps before the girders go into the tunnel, so the alignment must be done efficiently, on a tight schedule. This note documents the alignment plan which includes efficiency and high accuracy. The motivation for girder alignment involves the following considerations. Using beam based alignment, the girder position will be adjusted until the beam goes through the center of the quadrupole and beam finder wire. For the machine to work properly, the undulator axis must be on this line and the center of the undulator beam pipe must be on this line. The physics reasons for the undulator axis and undulator beam pipe axis to be centered on the beam are different, but the alignment tolerance for both are similar. In addition, the beam position monitor must be centered on the beam to preserve its calibration. Thus, the undulator, undulator beam pipe, quadrupole, beam finder wire, and beam position monitor axes must all be aligned to a common line. All relative alignments are equally important, not just, for example, between quadrupole and undulator. We begin by making the common axis the nominal beam axis in the girder coordinate system. All components will be initially aligned to this axis. A more accurate alignment will then position the components relative to each other, without incorporating the girder itself.

  11. Multiple alignment using hidden Markov models

    SciTech Connect

    Eddy, S.R.

    1995-12-31

    A simulated annealing method is described for training hidden Markov models and producing multiple sequence alignments from initially unaligned protein or DNA sequences. Simulated annealing in turn uses a dynamic programming algorithm for correctly sampling suboptimal multiple alignments according to their probability and a Boltzmann temperature factor. The quality of simulated annealing alignments is evaluated on structural alignments of ten different protein families, and compared to the performance of other HMM training methods and the ClustalW program. Simulated annealing is better able to find near-global optima in the multiple alignment probability landscape than the other tested HMM training methods. Neither ClustalW nor simulated annealing produce consistently better alignments compared to each other. Examination of the specific cases in which ClustalW outperforms simulated annealing, and vice versa, provides insight into the strengths and weaknesses of current hidden Maxkov model approaches.

  12. Systematic Agreement: A Theory of Organizational Alignment.

    ERIC Educational Resources Information Center

    Semler, Steven W.

    1997-01-01

    The theory of organizational alignment considers the extent to which organizational strategy, structure, and culture create an environment that facilitates achievement of organizational objectives and development of high performance work organizations. Well-aligned organizations have systematic agreement among goals, tactics, reward systems, and…

  13. MACSIMS : multiple alignment of complete sequences information management system

    PubMed Central

    Thompson, Julie D; Muller, Arnaud; Waterhouse, Andrew; Procter, Jim; Barton, Geoffrey J; Plewniak, Frédéric; Poch, Olivier

    2006-01-01

    Background In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the vast amount of heterogeneous data available. Multiple alignments of complete sequences provide an ideal environment for the integration of this information in the context of the protein family. Results MACSIMS is a multiple alignment-based information management program that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is retrieved automatically from the public databases. In the multiple alignment, homologous regions are identified and the retrieved data is evaluated and propagated from known to unknown sequences with these reliable regions. In a large-scale evaluation, the specificity of the propagated sequence features is estimated to be >99%, i.e. very few false positive predictions are made. MACSIMS is then used to characterise mutations in a test set of 100 proteins that are known to be involved in human genetic diseases. The number of sequence features associated with these proteins was increased by 60%, compared to the features available in the public databases. An XML format output file allows automatic parsing of the MACSIM results, while a graphical display using the JalView program allows manual analysis. Conclusion MACSIMS is a new information management system that incorporates detailed analyses of protein families at the structural, functional and evolutionary levels. MACSIMS thus provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist. A web server and the source code are available at . PMID:16792820

  14. Improvement of bit error rate and page alignment in the holographic data storage system by using the structural similarity method.

    PubMed

    Chen, Yu-Ta; Ou-Yang, Mang; Lee, Cheng-Chung

    2012-06-01

    Although widely recognized as a promising candidate for the next generation of data storage devices, holographic data storage systems (HDSS) incur adverse effects such as noise, misalignment, and aberration. Therefore, based on the structural similarity (SSIM) concept, this work presents a more accurate locating approach than the gray level weighting method (GLWM). Three case studies demonstrate the effectiveness of the proposed approach. Case 1 focuses on achieving a high performance of a Fourier lens in HDSS, Cases 2 and 3 replace the Fourier lens with a normal lens to decrease the quality of the HDSS, and Case 3 demonstrates the feasibility of a defocus system in the worst-case scenario. Moreover, the bit error rate (BER) is evaluated in several average matrices extended from the located position. Experimental results demonstrate that the proposed SSIM method renders a more accurate centering and a lower BER, lower BER of 2 dB than those of the GLWM in Cases 1 and 2, and BER of 1.5 dB in Case 3. PMID:22695607

  15. Katanin maintains meiotic metaphase chromosome alignment and spindle structure in vivo and has multiple effects on microtubules in vitro.

    PubMed

    McNally, Karen; Berg, Evan; Cortes, Daniel B; Hernandez, Veronica; Mains, Paul E; McNally, Francis J

    2014-04-01

    Assembly of Caenorhabditis elegans female meiotic spindles requires both MEI-1 and MEI-2 subunits of the microtubule-severing ATPase katanin. Strong loss-of-function mutants assemble apolar intersecting microtubule arrays, whereas weaker mutants assemble bipolar meiotic spindles that are longer than wild type. To determine whether katanin is also required for spindle maintenance, we monitored metaphase I spindles after a fast-acting mei-1(ts) mutant was shifted to a nonpermissive temperature. Within 4 min of temperature shift, bivalents moved off the metaphase plate, and microtubule bundles within the spindle lengthened and developed a high degree of curvature. Spindles eventually lost bipolar structure. Immunofluorescence of embryos fixed at increasing temperature indicated that MEI-1 was lost from spindle microtubules before loss of ASPM-1, indicating that MEI-1 and ASPM-1 act independently at spindle poles. We quantified the microtubule-severing activity of purified MEI-1/MEI-2 complexes corresponding to six different point mutations and found a linear relationship between microtubule disassembly rate and meiotic spindle length. Previous work showed that katanin is required for severing at points where two microtubules intersect in vivo. We show that purified MEI-1/MEI-2 complexes preferentially sever at intersections between two microtubules and directly bundle microtubules in vitro. These activities could promote parallel/antiparallel microtubule organization in meiotic spindles. PMID:24501424

  16. Computer graphics in architecture and engineering

    NASA Technical Reports Server (NTRS)

    Greenberg, D. P.

    1975-01-01

    The present status of the application of computer graphics to the building profession or architecture and its relationship to other scientific and technical areas were discussed. It was explained that, due to the fragmented nature of architecture and building activities (in contrast to the aerospace industry), a comprehensive, economic utilization of computer graphics in this area is not practical and its true potential cannot now be realized due to the present inability of architects and structural, mechanical, and site engineers to rely on a common data base. Future emphasis will therefore have to be placed on a vertical integration of the construction process and effective use of a three-dimensional data base, rather than on waiting for any technological breakthrough in interactive computing.

  17. Psychometric Evaluation of the Overexcitability Questionnaire-Two Applying Bayesian Structural Equation Modeling (BSEM) and Multiple-Group BSEM-Based Alignment with Approximate Measurement Invariance

    PubMed Central

    De Bondt, Niki; Van Petegem, Peter

    2015-01-01

    The Overexcitability Questionnaire-Two (OEQ-II) measures the degree and nature of overexcitability, which assists in determining the developmental potential of an individual according to Dabrowski's Theory of Positive Disintegration. Previous validation studies using frequentist confirmatory factor analysis, which postulates exact parameter constraints, led to model rejection and a long series of model modifications. Bayesian structural equation modeling (BSEM) allows the application of zero-mean, small-variance priors for cross-loadings, residual covariances, and differences in measurement parameters across groups, better reflecting substantive theory and leading to better model fit and less overestimation of factor correlations. Our BSEM analysis with a sample of 516 students in higher education yields positive results regarding the factorial validity of the OEQ-II. Likewise, applying BSEM-based alignment with approximate measurement invariance, the absence of non-invariant factor loadings and intercepts across gender is supportive of the psychometric quality of the OEQ-II. Compared to males, females scored significantly higher on emotional and sensual overexcitability, and significantly lower on psychomotor overexcitability. PMID:26733931

  18. Structure and energy level alignment at the dye-electrode interface in p-type DSSCs: new hints on the role of anchoring modes from ab initio calculations.

    PubMed

    Muñoz-García, Ana B; Pavone, Michele

    2015-05-14

    p-type dye-sensitized solar cells (DSSCs) represent the complementary photocathodes to the well-studied n-type DSSCs (Grätzel cells), but their low performances have hindered the development of convenient tandem solar cells based on cost-effective n- and p-type DSSCs. Because of their low efficiencies, experimental investigations highlighted the role of hole-electron transport processes at the dye-electrode interface. However, the effects of the dye anchoring groups on interfacial electronic features are still unclear. We report here a first principles study of a benchmark p-type DSSC model, namely the widely used Coumarin-based dye C343 adsorbed on the p-NiO surface. Together with the original carboxylic acid, we test the alternative phosphonic acid as the anchoring group. We investigate binding energies, structural features and electronic energy level alignments: our results highlight that these properties are highly sensitive to the binding modes. In particular, both the chemical nature of the anchoring group and the binding mode strongly affect the thermodynamic driving force for the dye-electrode hole injection process. From analysis of the electronic densities, we find that favorable driving forces are correlated with small values of the interfacial electrostatic dipole that is formed upon dye adsorption. From our results, we derive new hints for improving open circuit potential and the hole injection process in p-type DSSCs based on NiO electrodes. PMID:25892559

  19. Graphic Somatography: Life Writing, Comics, and the Ethics of Care.

    PubMed

    DeFalco, Amelia

    2016-09-01

    This essay considers the ways in which graphic caregiving memoirs complicate the idealizing tendencies of ethics of care philosophy. The medium's "capacious" layering of words, images, temporalities, and perspectives produces "productive tensions. . . The words and images entwine, but never synthesize" (Chute 2010, 5). In graphic memoirs about care, this "capaciousness" allows for quick oscillation between the rewards and struggles of care work, representing ambiguous, even ambivalent attitudes toward care. Graphic memoirs effectively represent multiple perspectives without synthesis, part of a structural and thematic ambivalence that provides a provocative counterpart to the abstract idealism of ethics of care philosophy. PMID:26435175

  20. Acceleration of Meshfree Radial Point Interpolation Method on Graphics Hardware

    SciTech Connect

    Nakata, Susumu

    2008-09-01

    This article describes a parallel computational technique to accelerate radial point interpolation method (RPIM)-based meshfree method using graphics hardware. RPIM is one of the meshfree partial differential equation solvers that do not require the mesh structure of the analysis targets. In this paper, a technique for accelerating RPIM using graphics hardware is presented. In the method, the computation process is divided into small processes suitable for processing on the parallel architecture of the graphics hardware in a single instruction multiple data manner.

  1. The development of an engineering computer graphics laboratory

    NASA Technical Reports Server (NTRS)

    Anderson, D. C.; Garrett, R. E.

    1975-01-01

    Hardware and software systems developed to further research and education in interactive computer graphics were described, as well as several of the ongoing application-oriented projects, educational graphics programs, and graduate research projects. The software system consists of a FORTRAN 4 subroutine package, in conjunction with a PDP 11/40 minicomputer as the primary computation processor and the Imlac PDS-1 as an intelligent display processor. The package comprises a comprehensive set of graphics routines for dynamic, structured two-dimensional display manipulation, and numerous routines to handle a variety of input devices at the Imlac.

  2. Fabrication and thermoelectric characteristics of [(Bi,Pb)2Ba2O4+/-w]0.5CoO2 bulks with highly aligned grain structure

    NASA Astrophysics Data System (ADS)

    Motohashi, T.; Nonaka, Y.; Sakai, K.; Karppinen, M.; Yamauchi, H.

    2008-02-01

    Here, we report fabrication and thermoelectric characteristics of polycrystalline bulks with aligned grains of the misfit-layered cobalt oxides, [(Bi1-xPbx)2Ba2O4±w]0.5CoO2. High-quality precursor powder was prepared with a spray-drying technique. The precursor was then sintered under a uniaxial pressure to yield dense bulk samples consisting of highly aligned grains. The electrical conductivity of such samples was four times higher than that of conventionally sintered bulks. Accordingly, the thermoelectric characteristics of the grain-aligned specimens were enhanced.

  3. Interfacial band alignment and structural properties of nanoscale TiO{sub 2} thin films for integration with epitaxial crystallographic oriented germanium

    SciTech Connect

    Jain, N.; Zhu, Y.; Hudait, M. K.; Maurya, D.; Varghese, R.; Priya, S.

    2014-01-14

    We have investigated the structural and band alignment properties of nanoscale titanium dioxide (TiO{sub 2}) thin films deposited on epitaxial crystallographic oriented Ge layers grown on (100), (110), and (111)A GaAs substrates by molecular beam epitaxy. The TiO{sub 2} thin films deposited at low temperature by physical vapor deposition were found to be amorphous in nature, and high-resolution transmission electron microscopy confirmed a sharp heterointerface between the TiO{sub 2} thin film and the epitaxially grown Ge with no traceable interfacial layer. A comprehensive assessment on the effect of substrate orientation on the band alignment at the TiO{sub 2}/Ge heterointerface is presented by utilizing x-ray photoelectron spectroscopy and spectroscopic ellipsometry. A band-gap of 3.33 ± 0.02 eV was determined for the amorphous TiO{sub 2} thin film from the Tauc plot. Irrespective of the crystallographic orientation of the epitaxial Ge layer, a sufficient valence band-offset of greater than 2 eV was obtained at the TiO{sub 2}/Ge heterointerface while the corresponding conduction band-offsets for the aforementioned TiO{sub 2}/Ge system were found to be smaller than 1 eV. A comparative assessment on the effect of Ge substrate orientation revealed a valence band-offset relation of ΔE{sub V}(100) > ΔE{sub V}(111) > ΔE{sub V}(110) and a conduction band-offset relation of ΔE{sub C}(110) > ΔE{sub C}(111) > ΔE{sub C}(100). These band-offset parameters are of critical importance and will provide key insight for the design and performance analysis of TiO{sub 2} for potential high-κ dielectric integration and for future metal-insulator-semiconductor contact applications with next generation of Ge based metal-oxide field-effect transistors.

  4. GapBlaster—A Graphical Gap Filler for Prokaryote Genomes

    PubMed Central

    Veras, Adonney; de Melo, Diego Magalhães; Soares, Siomar; Pinheiro, Kenny; Guimarães, Luis; Azevedo, Vasco; Silva, Artur; Ramos, Rommel T. J.

    2016-01-01

    The advent of NGS (Next Generation Sequencing) technologies has resulted in an exponential increase in the number of complete genomes available in biological databases. This advance has allowed the development of several computational tools enabling analyses of large amounts of data in each of the various steps, from processing and quality filtering to gap filling and manual curation. The tools developed for gap closure are very useful as they result in more complete genomes, which will influence downstream analyses of genomic plasticity and comparative genomics. However, the gap filling step remains a challenge for genome assembly, often requiring manual intervention. Here, we present GapBlaster, a graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. The software uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps. GapBlaster program, the user guide and the test datasets are freely available at https://sourceforge.net/projects/gapblaster2015/. It requires Sun JDK 8 and Blast or Mummer. PMID:27171416

  5. GapBlaster-A Graphical Gap Filler for Prokaryote Genomes.

    PubMed

    de Sá, Pablo H C G; Miranda, Fábio; Veras, Adonney; de Melo, Diego Magalhães; Soares, Siomar; Pinheiro, Kenny; Guimarães, Luis; Azevedo, Vasco; Silva, Artur; Ramos, Rommel T J

    2016-01-01

    The advent of NGS (Next Generation Sequencing) technologies has resulted in an exponential increase in the number of complete genomes available in biological databases. This advance has allowed the development of several computational tools enabling analyses of large amounts of data in each of the various steps, from processing and quality filtering to gap filling and manual curation. The tools developed for gap closure are very useful as they result in more complete genomes, which will influence downstream analyses of genomic plasticity and comparative genomics. However, the gap filling step remains a challenge for genome assembly, often requiring manual intervention. Here, we present GapBlaster, a graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. The software uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps. GapBlaster program, the user guide and the test datasets are freely available at https://sourceforge.net/projects/gapblaster2015/. It requires Sun JDK 8 and Blast or Mummer. PMID:27171416

  6. The Overturning Structure of Sodium Layer in Lower-thermospheric Region and Its Relevance to Ionospheric Field Align Irregularity (FAI) and Gravity Waves

    NASA Astrophysics Data System (ADS)

    Xue, X.; Dou, X.

    2014-12-01

    We report a surge-like overturning structure of the sodium layer in the lower thermospheric region (~110-120km) observed by a sodium lidar located at Haikou (20.0N, 110.3E), China. During 15:00UT ~ 15:30UT (Local time +8h), the sodium density shows an abrupt vertical increasing from ~100km to ~120km, and then falls down with a speed of ~2.5km/hr. The adjacent radio observations from COSMIC satellites and two ionosondes located at Fuke (19.5N, 109.1E) and Sanya (18.4N, 109.6E) indicate complicated ionospheric E region structures, i.e., multiple sporadic-E (Es) layers, covering the Hainan island region (18N-21N, 108-111E). Further more, a VHF radar located at Sanya (18.4, 109.6E) observed the field align irregularities (FAIs), which appear almost simultaneously with the surge-like structure of the sodium. The radar receiving SNR and the corresponding Doppler speed show a similar vertical increasing structure extending from ~100km to ~130km and the charged particles moving away (i.e., upward) from radar at the beginning of the FAIs and follows by descend-layer-like FAIs with a downward speed of 2.9km/hr. From these observational evidence, the surge-like structure of sodium layer is linked to the ionospheric E-region FAIs. We propose the possible process related to the formation of the surge-like sodium layer: the preexisted Es might provide a suitable gradient, and the gravity wave could trigger the K-H instability and push the upward moving of the charged particles, which are the source of Na+ and can be converted to Na through the chemical reactions. The investigations using the lidar temperature (35-55km), meteor radar wind (85-95km) and sodium column density and centroid height indicate that the gravity wave with period of ~4 hours and vertical wavelength of ~10km might be potential driver.

  7. Grade-Aligned Math Instruction for Secondary Students with Moderate Intellectual Disability

    ERIC Educational Resources Information Center

    Browder, Diane M.; Jimenez, Bree A.; Trela, Katherine

    2012-01-01

    The purpose of this study was to examine the effects of grade-aligned math instruction on math skill acquisition of four middle schools with moderate intellectual disability. Teachers were trained to follow a task analysis to teach grade-aligned math to middle school students using adapted math problem stories and graphic organizers. The teacher…

  8. Relativistic hydrodynamics on graphic cards

    NASA Astrophysics Data System (ADS)

    Gerhard, Jochen; Lindenstruth, Volker; Bleicher, Marcus

    2013-02-01

    We show how to accelerate relativistic hydrodynamics simulations using graphic cards (graphic processing units, GPUs). These improvements are of highest relevance e.g. to the field of high-energetic nucleus-nucleus collisions at RHIC and LHC where (ideal and dissipative) relativistic hydrodynamics is used to calculate the evolution of hot and dense QCD matter. The results reported here are based on the Sharp And Smooth Transport Algorithm (SHASTA), which is employed in many hydrodynamical models and hybrid simulation packages, e.g. the Ultrarelativistic Quantum Molecular Dynamics model (UrQMD). We have redesigned the SHASTA using the OpenCL computing framework to work on accelerators like graphic processing units (GPUs) as well as on multi-core processors. With the redesign of the algorithm the hydrodynamic calculations have been accelerated by a factor 160 allowing for event-by-event calculations and better statistics in hybrid calculations.

  9. Graphical programming of telerobotic tasks

    SciTech Connect

    Small, D.E.; McDonald, M.J.

    1997-02-01

    With a goal of producing faster, safer, and cheaper technologies for nuclear waste cleanup, Sandia is actively developing and extending intelligent systems technologies. Graphical Programming is a key technology for robotic waste cleanup that Sandia is developing for this goal. This paper describes Sancho, Sandia most advanced Graphical Programming supervisory software. Sancho, now operational on several robot systems, incorporates all of Sandia`s recent advances in supervisory control. Sancho, developed to rapidly apply Graphical Programming on a diverse set of robot systems, uses a general set of tools to implement task and operational behavior. Sancho can be rapidly reconfigured for new tasks and operations without modifying the supervisory code. Other innovations include task-based interfaces, event-based sequencing, and sophisticated GUI design. These innovations have resulted in robot control programs and approaches that are easier and safer to use than teleoperation, off-line programming, or full automation.

  10. Optical design using computer graphics.

    PubMed

    Howard, J M

    2001-07-01

    For decades the computer has been the primary tool used for optical design. Typical tasks include performing numerical calculations for ray tracing and analysis and rendering graphics for system drawings. As machines become faster with each new generation, the time needed for a particular design task has greatly reduced, allowing multiple assignments to be performed with little noticeable delay. This lets the designer modify a system and then immediately see the results rendered in graphics with a single motion. Such visual design methods are discussed here, where graphics of systems and plots relating to their performance are produced in real time, permitting the optical designer to design by pictures. Three examples are given: an educational tutorial for designing a simple microscope objective, an unobstructed reflective telescope composed of three spherical mirrors, and a modified Offner relay with an accessible pupil. PMID:11958264

  11. PHIGS PLUS for scientific graphics

    SciTech Connect

    Crawfis, R.A.

    1991-01-14

    This paper gives a brief overview of the use of computer graphics standards in the scientific community. It particularly details how how PHIGS PLUS meets the needs of users at the Lawrence Livermore National Laboratory. Although standards for computer graphics have improved substantially over the past decade, their acceptance in the scientific community has been slow. As the use and diversity of computers has increased, the scientific graphics libraries have not been able to keep pace with the additional capabilities these new machines offer. Therefore, several organizations have or are now working on converting their scientific libraries to reset upon a portable standard. This paper will address why is transition has been so slow and offer suggestions for future standards work to enhance scientific visualization. This work was performed under the auspices of the US Department of Energy by Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48.

  12. Horizontal carbon nanotube alignment.

    PubMed

    Cole, Matthew T; Cientanni, Vito; Milne, William I

    2016-09-21

    The production of horizontally aligned carbon nanotubes offers a rapid means of realizing a myriad of self-assembled near-atom-scale technologies - from novel photonic crystals to nanoscale transistors. The ability to reproducibly align anisotropic nanostructures has huge technological value. Here we review the present state-of-the-art in horizontal carbon nanotube alignment. For both in and ex situ approaches, we quantitatively assess the reported linear packing densities alongside the degree of alignment possible for each of these core methodologies. PMID:27546174

  13. Orthodontics and Aligners

    MedlinePlus

    ... Repairing Chipped Teeth Teeth Whitening Tooth-Colored Fillings Orthodontics and Aligners Straighten teeth for a healthier smile. Orthodontics When consumers think about orthodontics, braces are the ...

  14. Alignability of Optical Interconnects

    NASA Astrophysics Data System (ADS)

    Beech, Russell Scott

    With the continuing drive towards higher speed, density, and functionality in electronics, electrical interconnects become inadequate. Due to optics' high speed and bandwidth, freedom from capacitive loading effects, and freedom from crosstalk, optical interconnects can meet more stringent interconnect requirements. But, an optical interconnect requires additional components, such as an optical source and detector, lenses, holographic elements, etc. Fabrication and assembly of an optical interconnect requires precise alignment of these components. The successful development and deployment of optical interconnects depend on how easily the interconnect components can be aligned and/or how tolerant the interconnect is to misalignments. In this thesis, a method of quantitatively specifying the relative difficulty of properly aligning an optical interconnect is described. Ways of using this theory of alignment to obtain design and packaging guidelines for optical interconnects are examined. The measure of the ease with which an optical interconnect can be aligned, called the alignability, uses the efficiency of power transfer as a measure of alignment quality. The alignability is related to interconnect package design through the overall cost measure, which depends upon various physical parameters of the interconnect, such as the cost of the components and the time required for fabrication and alignment. Through a mutual dependence on detector size, the relationship between an interconnect's alignability and its bandwidth, signal-to-noise ratio, and bit-error -rate is examined. The results indicate that a range of device sizes exists for which given performance threshold values are satisfied. Next, the alignability of integrated planar-optic backplanes is analyzed in detail. The resulting data show that the alignability can be optimized by varying the substrate thickness or the angle of reflection. By including the effects of crosstalk, in a multi-channel backplane, the

  15. Tidal alignment of galaxies

    NASA Astrophysics Data System (ADS)

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

    2015-08-01

    We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact of smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used "nonlinear alignment model," finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the "GI" term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.

  16. Graphic Journeys: Graphic Novels' Representations of Immigrant Experiences

    ERIC Educational Resources Information Center

    Boatright, Michael D.

    2010-01-01

    This article explores how immigrant experiences are represented in the narratives of three graphic novels published in the last decade: Tan's (2007) "The Arrival," Kiyama's (1931/1999) "The Four Immigrants Manga: A Japanese Experience in San Francisco, 1904-1924," and Yang's (2006) "American Born Chinese." Through a theoretical lens informed by…

  17. New Challenge for Graphic Arts: Modernize Now!

    ERIC Educational Resources Information Center

    Sundeen, Earl I.

    1974-01-01

    The Kodak Graphic Arts Manpower Study obtained information from over 1000 graphic arts companies as to the educational needs of today in graphic arts. Vocational educators may have to stop thinking in terms of graphic arts education and begin working on curriculums for career education in the communication field. (Author/DS)

  18. Graphical Methods of Exploratory Data Analysis

    NASA Astrophysics Data System (ADS)

    Friedman, J. H.; McDonald, J. A.; Stuetzle, W.

    This paper describes briefly Orion I, a graphic system used to study applications of computer graphics - especially interactive motion graphics - in statistics. Orion I is the newest of a family of "Prim" systems whose most striking common feature is the use of real-time motion graphics to display three-dimensional scatterplots.

  19. Antinomies of Semiotics in Graphic Design

    ERIC Educational Resources Information Center

    Storkerson, Peter

    2010-01-01

    The following paper assesses the roles played by semiotics in graphic design and in graphic design education, which both reflects and shapes practice. It identifies a series of factors; graphic design education methods and culture; semiotic theories themselves and their application to graphic design; the two wings of Peircian semiotics and…

  20. Comprehending, Composing, and Celebrating Graphic Poetry

    ERIC Educational Resources Information Center

    Calo, Kristine M.

    2011-01-01

    The use of graphic poetry in classrooms is encouraged as a way to engage students and motivate them to read and write poetry. This article discusses how graphic poetry can help students with their comprehension of poetry while tapping into popular culture. It is organized around three main sections--reading graphic poetry, writing graphic poetry,…

  1. Cartooning History: Canada's Stories in Graphic Novels

    ERIC Educational Resources Information Center

    King, Alyson E.

    2012-01-01

    In recent years, historical events, issues, and characters have been portrayed in an increasing number of non-fiction graphic texts. Similar to comics and graphic novels, graphic texts are defined as fully developed, non-fiction narratives told through panels of sequential art. Such non-fiction graphic texts are being used to teach history in…

  2. Graphic Design Career Guide 2. Revised Edition.

    ERIC Educational Resources Information Center

    Craig, James

    The graphic design field is diverse and includes many areas of specialization. This guide introduces students to career opportunities in graphic design. The guide is organized in four parts. "Part One: Careers in Graphic Design" identifies and discusses the various segments of the graphic design industry, including: Advertising, Audio-Visual, Book…

  3. Galaxy Alignments: Observations and Impact on Cosmology

    NASA Astrophysics Data System (ADS)

    Kirk, Donnacha; Brown, Michael L.; Hoekstra, Henk; Joachimi, Benjamin; Kitching, Thomas D.; Mandelbaum, Rachel; Sifón, Cristóbal; Cacciato, Marcello; Choi, Ami; Kiessling, Alina; Leonard, Adrienne; Rassat, Anais; Schäfer, Björn Malte

    2015-11-01

    Galaxy shapes are not randomly oriented, rather they are statistically aligned in a way that can depend on formation environment, history and galaxy type. Studying the alignment of galaxies can therefore deliver important information about the physics of galaxy formation and evolution as well as the growth of structure in the Universe. In this review paper we summarise key measurements of galaxy alignments, divided by galaxy type, scale and environment. We also cover the statistics and formalism necessary to understand the observations in the literature. With the emergence of weak gravitational lensing as a precision probe of cosmology, galaxy alignments have taken on an added importance because they can mimic cosmic shear, the effect of gravitational lensing by large-scale structure on observed galaxy shapes. This makes galaxy alignments, commonly referred to as intrinsic alignments, an important systematic effect in weak lensing studies. We quantify the impact of intrinsic alignments on cosmic shear surveys and finish by reviewing practical mitigation techniques which attempt to remove contamination by intrinsic alignments.

  4. PROMALS web server for accurate multiple protein sequence alignments.

    PubMed

    Pei, Jimin; Kim, Bong-Hyun; Tang, Ming; Grishin, Nick V

    2007-07-01

    Multiple sequence alignments are essential in homology inference, structure modeling, functional prediction and phylogenetic analysis. We developed a web server that constructs multiple protein sequence alignments using PROMALS, a progressive method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS shows higher alignment accuracy than other advanced methods, such as MUMMALS, ProbCons, MAFFT and SPEM. The PROMALS web server takes FASTA format protein sequences as input. The output includes a colored alignment augmented with information about sequence grouping, predicted secondary structures and positional conservation. The PROMALS web server is available at: http://prodata.swmed.edu/promals/ PMID:17452345

  5. Technology Alignment and Portfolio Prioritization (TAPP)

    NASA Technical Reports Server (NTRS)

    Funaro, Gregory V.; Alexander, Reginald A.

    2015-01-01

    Technology Alignment and Portfolio Prioritization (TAPP) is a method being developed by the Advanced Concepts Office, at NASA Marshall Space Flight Center. The TAPP method expands on current technology assessment methods by incorporating the technological structure underlying technology development, e.g., organizational structures and resources, institutional policy and strategy, and the factors that motivate technological change. This paper discusses the methods ACO is currently developing to better perform technology assessments while taking into consideration Strategic Alignment, Technology Forecasting, and Long Term Planning.

  6. Collection Of Software For Computer Graphics

    NASA Technical Reports Server (NTRS)

    Hibbard, Eric A.; Makatura, George

    1990-01-01

    Ames Research Graphics System (ARCGRAPH) collection of software libraries and software utilities assisting researchers in generating, manipulating, and visualizing graphical data. Defines metafile format containing device-independent graphical data. File format used with various computer-graphics-manipulation and -animation software packages at Ames, including SURF (COSMIC Program ARC-12381) and GAS (COSMIC Program ARC-12379). Consists of two-stage "pipeline" used to put out graphical primitives. ARCGRAPH libraries developed on VAX computer running VMS.

  7. Trend Monitoring System (TMS) graphics software

    NASA Technical Reports Server (NTRS)

    Brown, J. S.

    1979-01-01

    A prototype bus communications systems, which is being used to support the Trend Monitoring System (TMS) and to evaluate the bus concept is considered. A set of FORTRAN-callable graphics subroutines for the host MODCOMP comuter, and an approach to splitting graphics work between the host and the system's intelligent graphics terminals are described. The graphics software in the MODCOMP and the operating software package written for the graphics terminals are included.

  8. Graphic Communications. Career Education Guide.

    ERIC Educational Resources Information Center

    Dependents Schools (DOD), Washington, DC. European Area.

    The curriculum guide is designed to provide students with realistic training in graphic communications theory and practice within the secondary educational framework and to prepare them for entry into an occupation or continuing postsecondary education. The program modules outlined in the guide have been grouped into four areas: printing,…

  9. A Natural Language Graphics System.

    ERIC Educational Resources Information Center

    Brown, David, C.; Kwasny, Stan C.

    This report describes an experimental system for drawing simple pictures on a computer graphics terminal using natural language input. The system is capable of drawing lines, points, and circles on command from the user, as well as answering questions about system capabilities and objects on the screen. Erasures are permitted and language input…

  10. Astronomy Simulation with Computer Graphics.

    ERIC Educational Resources Information Center

    Thomas, William E.

    1982-01-01

    "Planetary Motion Simulations" is a system of programs designed for students to observe motions of a superior planet (one whose orbit lies outside the orbit of the earth). Programs run on the Apple II microcomputer and employ high-resolution graphics to present the motions of Saturn. (Author/JN)

  11. Graphic Novels in the Classroom

    ERIC Educational Resources Information Center

    Martin, Adam

    2009-01-01

    Today many authors and artists adapt works of classic literature into a medium more "user friendly" to the increasingly visual student population. Stefan Petrucha and Kody Chamberlain's version of "Beowulf" is one example. The graphic novel captures the entire epic in arresting images and contrasts the darkness of the setting and characters with…

  12. Graphical fiber shaping control interface

    NASA Astrophysics Data System (ADS)

    Basso, Eric T.; Ninomiya, Yasuyuki

    2016-03-01

    In this paper, we present an improved graphical user interface for defining single-pass novel shaping techniques on glass processing machines that allows for streamlined process development. This approach offers unique modularity and debugging capability to researchers during the process development phase not usually afforded with similar scripting languages.

  13. Revised adage graphics computer system

    NASA Technical Reports Server (NTRS)

    Tulppo, J. S.

    1980-01-01

    Bootstrap loader and mode-control options for Adage Graphics Computer System Significantly simplify operations procedures. Normal load and control functions are performed quickly and easily from control console. Operating characteristics of revised system include greatly increased speed, convenience, and reliability.

  14. Graphic Arts/Offset Lithography.

    ERIC Educational Resources Information Center

    Hoisington, James; Metcalf, Joseph

    This revised curriculum for graphic arts is designed to provide secondary and postsecondary students with entry-level skills and an understanding of current printing technology. It contains lesson plans based on entry-level competencies for offset lithography as identified by educators and industry representatives. The guide is divided into 15…

  15. Recorded Music and Graphic Design.

    ERIC Educational Resources Information Center

    Osterer, Irv

    1998-01-01

    Reviews the history of art as an element of music-recording packaging. Describes a project in which students design a jacket for either cassette or CD using a combination of computerized and traditional rendering techniques. Reports that students have been inspired to look into careers in graphic design. (DSK)

  16. Telidon Graphics and Library Applications.

    ERIC Educational Resources Information Center

    Tenne-Sens, Andrej

    1982-01-01

    Reviews the history of Telidon, the Canadian videotex system; describes Telidon's alphageometric method of graphic-information encoding; discusses some experimental applications of the Telidon system; and describes attempts at developing a North American standard for videotex systems. Five figures are included. (JL)

  17. In Defense of Graphic Novels

    ERIC Educational Resources Information Center

    Hansen, Kathryn Strong

    2012-01-01

    In the 18th century, critics grumbled about a new literary form that supposedly threatened the abilities of youth to distinguish between reality and artificiality. This form was the novel, one of the literary forms that critics now hold dearest. Currently, the graphic novel receives a great deal of criticism. Yet many teachers have shown how…

  18. Multi Platform Graphics Subroutine Library

    1992-02-21

    DIGLIB is a collection of general graphics subroutines. It was designed to be small, reasonably fast, device-independent, and compatible with DEC-supplied operating systems for VAXes, PDP-11s, and LSI-11s, and the DOS operating system for IBM PCs and IBM-compatible machines. The software is readily usable by casual programmers for two-dimensional plotting.

  19. Structural and band alignment properties of Al2O3 on epitaxial Ge grown on (100), (110), and (111)A GaAs substrates by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Hudait, M. K.; Zhu, Y.; Maurya, D.; Priya, S.; Patra, P. K.; Ma, A. W. K.; Aphale, A.; Macwan, I.

    2013-04-01

    Structural and band alignment properties of atomic layer Al2O3 oxide film deposited on crystallographically oriented epitaxial Ge grown in-situ on (100), (110), and (111)A GaAs substrates using two separate molecular beam epitaxy chambers were investigated using cross-sectional transmission microscopy (TEM) and x-ray photoelectron spectroscopy (XPS). High-resolution triple axis x-ray measurement demonstrated pseudomorphic and high-quality Ge epitaxial layer on crystallographically oriented GaAs substrates. The cross-sectional TEM exhibited a sharp interface between the Ge epilayer and each orientation of the GaAs substrate as well as the Al2O3 film and the Ge epilayer. The extracted valence band offset, ΔEv, values of Al2O3 relative to (100), (110), and (111) Ge orientations using XPS measurement were 3.17 eV, 3.34 eV, and 3.10 eV, respectively. Using XPS data, variations in ΔEv related to the crystallographic orientation were ΔEV(110)Ge>ΔEV(100)Ge≥ΔEV(111)Ge and the conduction band offset, ΔEc, related to the crystallographic orientation was ΔEc(111)Ge>ΔEc(110)Ge>ΔEc(100)Ge using the measured ΔEv, bandgap of Al2O3 in each orientation, and well-known Ge bandgap of 0.67 eV. These band offset parameters are important for future application of Ge-based p- and n-channel metal-oxide field-effect transistor design.

  20. SPEAR3 Construction Alignment

    SciTech Connect

    LeCocq, Catherine; Banuelos, Cristobal; Fuss, Brian; Gaudreault, Francis; Gaydosh, Michael; Griffin, Levirt; Imfeld, Hans; McDougal, John; Perry, Michael; Rogers, Michael; /SLAC

    2005-08-17

    An ambitious seven month shutdown of the existing SPEAR2 synchrotron radiation facility was successfully completed in March 2004 when the first synchrotron light was observed in the new SPEAR3 ring, SPEAR3 completely replaced SPEAR2 with new components aligned on a new highly-flat concrete floor. Devices such as magnets and vacuum chambers had to be fiducialized and later aligned on girder rafts that were then placed into the ring over pre-aligned support plates. Key to the success of aligning this new ring was to ensure that the new beam orbit matched the old SPEAR2 orbit so that existing experimental beamlines would not have to be reoriented. In this presentation a pictorial summary of the Alignment Engineering Group's surveying tasks for the construction of the SPEAR3 ring is provided. Details on the networking and analysis of various surveys throughout the project can be found in the accompanying paper.

  1. Advanced computer graphic techniques for laser range finder (LRF) simulation

    NASA Astrophysics Data System (ADS)

    Bedkowski, Janusz; Jankowski, Stanislaw

    2008-11-01

    This paper show an advanced computer graphic techniques for laser range finder (LRF) simulation. The LRF is the common sensor for unmanned ground vehicle, autonomous mobile robot and security applications. The cost of the measurement system is extremely high, therefore the simulation tool is designed. The simulation gives an opportunity to execute algorithm such as the obstacle avoidance[1], slam for robot localization[2], detection of vegetation and water obstacles in surroundings of the robot chassis[3], LRF measurement in crowd of people[1]. The Axis Aligned Bounding Box (AABB) and alternative technique based on CUDA (NVIDIA Compute Unified Device Architecture) is presented.

  2. Der Aufbau mentaler Modelle durch bildliche Darstellungen: Eine experimentalle Studie uber die Bedeutung der Merkmalsdimensionen Elaboriertheit und Strukturierheit im Sachunterricht der Grundschule (The Development of Mental Processes through Graphic Representation with Diverging Degrees of Elaboration and Structurization: An Experimental Study Carried Out in Elementary Science Instruction in Primary School).

    ERIC Educational Resources Information Center

    Martschinke, Sabine

    1996-01-01

    Examines types of graphical representation as to their suitability for knowledge acquisition in primary grades. Uses the concept of mental models to clarify the relationship between external presentation and internal representation of knowledge. Finds that students who learned with highly elaborated and highly structured pictures displayed the…

  3. Computing posterior probabilities for score-based alignments using ppALIGN.

    PubMed

    Wolfsheimer, Stefan; Hartmann, Alexander; Rabus, Ralf; Nuel, Gregory

    2012-01-01

    Score-based pairwise alignments are widely used in bioinformatics in particular with molecular database search tools, such as the BLAST family. Due to sophisticated heuristics, such algorithms are usually fast but the underlying scoring model unfortunately lacks a statistical description of the reliability of the reported alignments. In particular, close to gaps, in low-score or low-complexity regions, a huge number of alternative alignments arise which results in a decrease of the certainty of the alignment. ppALIGN is a software package that uses hidden Markov Model techniques to compute position-wise reliability of score-based pairwise alignments of DNA or protein sequences. The design of the model allows for a direct connection between the scoring function and the parameters of the probabilistic model. For this reason it is suitable to analyze the outcomes of popular score based aligners and search tools without having to choose a complicated set of parameters. By contrast, our program only requires the classical score parameters (the scoring function and gap costs). The package comes along with a library written in C++, a standalone program for user defined alignments (ppALIGN) and another program (ppBLAST) which can process a complete result set of BLAST. The main algorithms essentially exhibit a linear time complexity (in the alignment lengths), and they are hence suitable for on-line computations. We have also included alternative decoding algorithms to provide alternative alignments. ppALIGN is a fast program/library that helps detect and quantify questionable regions in pairwise alignments. Due to its structure, the input/output interface it can to be connected to other post-processing tools. Empirically, we illustrate its usefulness in terms of correctly predicted reliable regions for sequences generated using the ROSE model for sequence evolution, and identify sensor-specific regions in the denitrifying betaproteobacterium Aromatoleum aromaticum. PMID

  4. Space Mirror Alignment System

    NASA Technical Reports Server (NTRS)

    Jau, Bruno M.; McKinney, Colin; Smythe, Robert F.; Palmer, Dean L.

    2011-01-01

    An optical alignment mirror mechanism (AMM) has been developed with angular positioning accuracy of +/-0.2 arcsec. This requires the mirror s linear positioning actuators to have positioning resolutions of +/-112 nm to enable the mirror to meet the angular tip/tilt accuracy requirement. Demonstrated capabilities are 0.1 arc-sec angular mirror positioning accuracy, which translates into linear positioning resolutions at the actuator of 50 nm. The mechanism consists of a structure with sets of cross-directional flexures that enable the mirror s tip and tilt motion, a mirror with its kinematic mount, and two linear actuators. An actuator comprises a brushless DC motor, a linear ball screw, and a piezoelectric brake that holds the mirror s position while the unit is unpowered. An interferometric linear position sensor senses the actuator s position. The AMMs were developed for an Astrometric Beam Combiner (ABC) optical bench, which is part of an interferometer development. Custom electronics were also developed to accommodate the presence of multiple AMMs within the ABC and provide a compact, all-in-one solution to power and control the AMMs.

  5. Hybrid vehicle motor alignment

    DOEpatents

    Levin, Michael Benjamin

    2001-07-03

    A rotor of an electric motor for a motor vehicle is aligned to an axis of rotation for a crankshaft of an internal combustion engine having an internal combustion engine and an electric motor. A locator is provided on the crankshaft, a piloting tool is located radially by the first locator to the crankshaft. A stator of the electric motor is aligned to a second locator provided on the piloting tool. The stator is secured to the engine block. The rotor is aligned to the crankshaft and secured thereto.

  6. Teaching graphics in technical communication classes

    NASA Technical Reports Server (NTRS)

    Spurgeon, K. C.

    1981-01-01

    Graphic aids convey and clarify information more efficiently and accurately than words alone therefore, most technical writing includes the use of graphics. Ways of accumulating and presenting graphics illustrations on a shoestring budget are suggested. These include collecting graphics from companies, annual reports and laminating them for workshop use or putting them on a flip chart for classroom presentation, creating overhead transparencies to demonstrate different levels of effectiveness of graphic aids, and bringing in grahic artists for question/answer periods or in class workshops. Also included are an extensive handout as an introduction to graphics, sample assignments, and a selected and annotated bibliography.

  7. The control data "GIRAFFE" system for interactive graphic finite element analysis

    NASA Technical Reports Server (NTRS)

    Park, S.; Brandon, D. M., Jr.

    1975-01-01

    The Graphical Interface for Finite Elements (GIRAFFE) general purpose interactive graphics application package was described. This system may be used as a pre/post processor for structural analysis computer programs. It facilitates the operations of creating, editing, or reviewing all the structural input/output data on a graphics terminal in a time-sharing mode of operation. An application program for a simple three-dimensional plate problem was illustrated.

  8. Representing Learning With Graphical Models

    NASA Technical Reports Server (NTRS)

    Buntine, Wray L.; Lum, Henry, Jr. (Technical Monitor)

    1994-01-01

    Probabilistic graphical models are being used widely in artificial intelligence, for instance, in diagnosis and expert systems, as a unified qualitative and quantitative framework for representing and reasoning with probabilities and independencies. Their development and use spans several fields including artificial intelligence, decision theory and statistics, and provides an important bridge between these communities. This paper shows by way of example that these models can be extended to machine learning, neural networks and knowledge discovery by representing the notion of a sample on the graphical model. Not only does this allow a flexible variety of learning problems to be represented, it also provides the means for representing the goal of learning and opens the way for the automatic development of learning algorithms from specifications.

  9. Image reproduction with interactive graphics

    NASA Technical Reports Server (NTRS)

    Buckner, J. D.; Council, H. W.; Edwards, T. R.

    1974-01-01

    Software application or development in optical image digital data processing requires a fast, good quality, yet inexpensive hard copy of processed images. To achieve this, a Cambo camera with an f 2.8/150-mm Xenotar lens in a Copal shutter having a Graflok back for 4 x 5 Polaroid type 57 pack-film has been interfaced to an existing Adage, AGT-30/Electro-Mechanical Research, EMR 6050 graphic computer system. Time-lapse photography in conjunction with a log to linear voltage transformation has resulted in an interactive system capable of producing a hard copy in 54 sec. The interactive aspect of the system lies in a Tektronix 4002 graphic computer terminal and its associated hard copy unit.

  10. GnuForPlot Graphics

    2015-11-04

    Gnuforplot Graphics is a Fortran90 program designed to generate two and three dimensional plots of data on a personal computer. The program uses calls to the open source code Gnuplot to generate the plots. Two Fortran90 programs have been written to use the Gnuplot graphics capabilities. The first program, named Plotsetup.f90 reads data from output files created by either the Stadium or LeachXS/Orchestra modeling codes and saves the data in arrays for plotting. This programmore » then calls Gnuforplot which takes the data array along with user specified parameters to set plot specifications and issues Gnuplot commands that generate the screen plots. The user can view the plots and optionally save copies in jpeg format.« less

  11. Blasting, graphical interfaces and Unix

    SciTech Connect

    Knudsen, S.

    1993-11-01

    A discrete element computer program, DMC (Distinct Motion Code) was developed to simulate blast-induced rock motion. To simplify the complex task of entering material and explosive design parameters as well as bench configuration, a full-featured graphical interface has been developed. DMC is currently executed on both Sun SPARCstation 2 and Sun SPARCstation 10 platforms and routinely used to model bench and crater blasting problems. This paper will document the design and development of the full-featured interface to DMC. The development of the interface will be tracked through the various stages, highlighting the adjustments made to allow the necessary parameters to be entered in terms and units that field blasters understand. The paper also discusses a novel way of entering non-integer numbers and the techniques necessary to display blasting parameters in an understandable visual manner. A video presentation will demonstrate the graphics interface and explains its use.

  12. Blasting, graphical interfaces and Unix

    SciTech Connect

    Knudsen, S.

    1994-12-31

    A discrete element computer program, DMC (Distinct Motion Code) was developed to simulate blast-induced rock motion. To simplify the complex task of entering material and explosive design parameters as well as bench configuration, a full-featured graphical interface has been developed. DMC is currently executed on both Sun SPARCstation 2 and Sun SPARCstation 10 platforms and routinely used to model bench and crater blasting problems. This paper will document the design and development of the full-featured interface to DMC. The development of the interface will be tracked through the various stages, highlighting the adjustments made to allow the necessary parameters to be entered in terms and units that field blasters understand. The paper also discusses a novel way of entering non-integer numbers and the techniques necessary to display blasting parameters in an understandable visual manner. A video presentation will demonstrate the graphics interface and explains its use.

  13. GnuForPlot Graphics

    SciTech Connect

    2015-11-04

    Gnuforplot Graphics is a Fortran90 program designed to generate two and three dimensional plots of data on a personal computer. The program uses calls to the open source code Gnuplot to generate the plots. Two Fortran90 programs have been written to use the Gnuplot graphics capabilities. The first program, named Plotsetup.f90 reads data from output files created by either the Stadium or LeachXS/Orchestra modeling codes and saves the data in arrays for plotting. This program then calls Gnuforplot which takes the data array along with user specified parameters to set plot specifications and issues Gnuplot commands that generate the screen plots. The user can view the plots and optionally save copies in jpeg format.

  14. Graphical Models for Ordinal Data

    PubMed Central

    Guo, Jian; Levina, Elizaveta; Michailidis, George; Zhu, Ji

    2014-01-01

    A graphical model for ordinal variables is considered, where it is assumed that the data are generated by discretizing the marginal distributions of a latent multivariate Gaussian distribution. The relationships between these ordinal variables are then described by the underlying Gaussian graphical model and can be inferred by estimating the corresponding concentration matrix. Direct estimation of the model is computationally expensive, but an approximate EM-like algorithm is developed to provide an accurate estimate of the parameters at a fraction of the computational cost. Numerical evidence based on simulation studies shows the strong performance of the algorithm, which is also illustrated on data sets on movie ratings and an educational survey. PMID:26120267

  15. Aligned mesoporous architectures and devices.

    SciTech Connect

    Brinker, C. Jeffrey; Lu, Yunfeng

    2011-03-01

    This is the final report for the Presidential Early Career Award for Science and Engineering - PECASE (LDRD projects 93369 and 118841) awarded to Professor Yunfeng Lu (Tulane University and University of California-Los Angeles). During the last decade, mesoporous materials with tunable periodic pores have been synthesized using surfactant liquid crystalline as templates, opening a new avenue for a wide spectrum of applications. However, the applications are somewhat limited by the unfavorabe pore orientation of these materials. Although substantial effort has been devoted to align the pore channels, fabrication of mesoporous materials with perpendicular pore channels remains challenging. This project focused on fabrication of mesoporous materials with perpendicularly aligned pore channels. We demonstrated structures for use in water purification, separation, sensors, templated synthesis, microelectronics, optics, controlled release, and highly selective catalysts.

  16. Learning Graphical Models With Hubs

    PubMed Central

    Tan, Kean Ming; London, Palma; Mohan, Karthik; Lee, Su-In; Fazel, Maryam; Witten, Daniela

    2014-01-01

    We consider the problem of learning a high-dimensional graphical model in which there are a few hub nodes that are densely-connected to many other nodes. Many authors have studied the use of an ℓ1 penalty in order to learn a sparse graph in the high-dimensional setting. However, the ℓ1 penalty implicitly assumes that each edge is equally likely and independent of all other edges. We propose a general framework to accommodate more realistic networks with hub nodes, using a convex formulation that involves a row-column overlap norm penalty. We apply this general framework to three widely-used probabilistic graphical models: the Gaussian graphical model, the covariance graph model, and the binary Ising model. An alternating direction method of multipliers algorithm is used to solve the corresponding convex optimization problems. On synthetic data, we demonstrate that our proposed framework outperforms competitors that do not explicitly model hub nodes. We illustrate our proposal on a webpage data set and a gene expression data set. PMID:25620891

  17. Debugging software with animated graphics

    NASA Astrophysics Data System (ADS)

    Horn, Dawn; Scrip, Becky; Scrip, Bill

    1997-07-01

    The traditional use of graphics and animation in engineering software development has been to demonstrate the function and utility of individual engineering tools. This paper illustrates the use of graphical rendering and animation for debugging large integrated simulations. The tools presented are part of the THAAD integrated system effectiveness simulation (TISES). TISES has integrated different segment software models to be able to perform analysis of a full THAAD (theater high altitude area defense) battalion. Within each model are implicit coordinates, transformations, reference values (i.e. earth radius) used which may or may not match those of adjacent models. Each interface or integration between the models introduces a source of error. TISES also utilized many different input parameters from a variety of external sources that can be a source of error. The TISES development team has found graphics and animation to be extremely helpful in testing and debugging these interface problems. This paper includes examples of input data verification, model to model interface, and model versus model perceptions that have been utilized in TISES development.

  18. Graphical Language for Data Processing

    NASA Technical Reports Server (NTRS)

    Alphonso, Keith

    2011-01-01

    A graphical language for processing data allows processing elements to be connected with virtual wires that represent data flows between processing modules. The processing of complex data, such as lidar data, requires many different algorithms to be applied. The purpose of this innovation is to automate the processing of complex data, such as LIDAR, without the need for complex scripting and programming languages. The system consists of a set of user-interface components that allow the user to drag and drop various algorithmic and processing components onto a process graph. By working graphically, the user can completely visualize the process flow and create complex diagrams. This innovation supports the nesting of graphs, such that a graph can be included in another graph as a single step for processing. In addition to the user interface components, the system includes a set of .NET classes that represent the graph internally. These classes provide the internal system representation of the graphical user interface. The system includes a graph execution component that reads the internal representation of the graph (as described above) and executes that graph. The execution of the graph follows the interpreted model of execution in that each node is traversed and executed from the original internal representation. In addition, there are components that allow external code elements, such as algorithms, to be easily integrated into the system, thus making the system infinitely expandable.

  19. Antares alignment gimbal positioner

    SciTech Connect

    Day, R.D.; Viswanathan, V.K.; Saxman, A.C.; Lujan, R.E.; Woodfin, G.L.; Sweatt, W.C.

    1981-01-01

    Antares is a 24-beam 40-TW carbon-dioxide (CO/sub 2/) laser fusion system currently under construction at the Los Alamos National Laboratory. The Antares alignment gimbal positioner (AGP) is an optomechanical instrument that will be used for target alignment and alignment of the 24 laser beams, as well as beam quality assessments. The AGP will be capable of providing pointing, focusing, and wavefront optical path difference, as well as aberration information at both helium-neon (He-Ne) and CO/sub 2/ wavelengths. It is designed to allow the laser beams to be aligned to any position within a 1-cm cube to a tolerance of 10 ..mu..m.

  20. Computer Graphics for Multimedia and Hypermedia Development.

    ERIC Educational Resources Information Center

    Mohler, James L.

    1998-01-01

    Discusses several theoretical and technical aspects of computer-graphics development that are useful for creating hypermedia and multimedia materials. Topics addressed include primary bitmap attributes in computer graphics, the jigsaw principle, and raster layering. (MSE)