Science.gov

Sample records for aligned graphic structure

  1. QuickProbs—A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors

    PubMed Central

    Gudyś, Adam; Deorowicz, Sebastian

    2014-01-01

    Multiple sequence alignment is a crucial task in a number of biological analyses like secondary structure prediction, domain searching, phylogeny, etc. MSAProbs is currently the most accurate alignment algorithm, but its effectiveness is obtained at the expense of computational time. In the paper we present QuickProbs, the variant of MSAProbs customised for graphics processors. We selected the two most time consuming stages of MSAProbs to be redesigned for GPU execution: the posterior matrices calculation and the consistency transformation. Experiments on three popular benchmarks (BAliBASE, PREFAB, OXBench-X) on quad-core PC equipped with high-end graphics card show QuickProbs to be 5.7 to 9.7 times faster than original CPU-parallel MSAProbs. Additional tests performed on several protein families from Pfam database give overall speed-up of 6.7. Compared to other algorithms like MAFFT, MUSCLE, or ClustalW, QuickProbs proved to be much more accurate at similar speed. Additionally we introduce a tuned variant of QuickProbs which is significantly more accurate on sets of distantly related sequences than MSAProbs without exceeding its computation time. The GPU part of QuickProbs was implemented in OpenCL, thus the package is suitable for graphics processors produced by all major vendors. PMID:24586435

  2. DINAMO: a coupled sequence alignment editor/molecular graphics tool for interactive homology modeling of proteins.

    PubMed

    Hansen, M; Bentz, J; Baucom, A; Gregoret, L

    1998-01-01

    Gaining functional information about a novel protein is a universal problem in biomedical research. With the explosive growth of the protein sequence and structural databases, it is becoming increasingly common for researchers to attempt to build a three-dimensional model of their protein of interest in order to gain information about its structure and interactions with other molecules. The two most reliable methods for predicting the structure of a protein are homology modeling, in which the novel sequence is modeled on the known three-dimensional structure of a related protein, and fold recognition (threading), where the sequence is scored against a library of fold models, and the highest scoring model is selected. The sequence alignment to a known structure can be ambiguous, and human intervention is often required to optimize the model. We describe an interactive model building and assessment tool in which a sequence alignment editor is dynamically coupled to a molecular graphics display. By means of a set of assessment tools, the user may optimize his or her alignment to satisfy the known heuristics of protein structure. Adjustments to the sequence alignment made by the user are reflected in the displayed model by color and other visual cues. For instance, residues are colored by hydrophobicity in both the three-dimensional model and in the sequence alignment. This aids the user in identifying undesirable buried polar residues. Several different evaluation metrics may be selected including residue conservation, residue properties, and visualization of predicted secondary structure. These characteristics may be mapped to the model both singly and in combination. DINAMO is a Java-based tool that may be run either over the web or installed locally. Its modular architecture also allows Java-literate users to add plug-ins of their own design.

  3. 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.

  4. Protein structure alignment beyond spatial proximity.

    PubMed

    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.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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

  10. HOMSTRAD: a database of protein structure alignments for homologous families.

    PubMed

    Mizuguchi, K; Deane, C M; Blundell, T L; Overington, J P

    1998-11-01

    We describe a database of protein structure alignments for homologous families. The database HOMSTRAD presently contains 130 protein families and 590 aligned structures, which have been selected on the basis of quality of the X-ray analysis and accuracy of the structure. For each family, the database provides a structure-based alignment derived using COMPARER and annotated with JOY in a special format that represents the local structural environment of each amino acid residue. HOMSTRAD also provides a set of superposed atomic coordinates obtained using MNYFIT, which can be viewed with a graphical user interface or used for comparative modeling studies. The database is freely available on the World Wide Web at: http://www-cryst.bioc.cam. ac.uk/-homstrad/, with search facilities and links to other databases.

  11. 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.

  12. 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.

  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. 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.

  18. 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

  19. 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

  20. 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

  1. Approximate protein structural alignment in polynomial time.

    PubMed

    Kolodny, Rachel; Linial, Nathan

    2004-08-17

    Alignment of protein structures is a fundamental task in computational molecular biology. Good structural alignments can help detect distant evolutionary relationships that are hard or impossible to discern from protein sequences alone. Here, we study the structural alignment problem as a family of optimization problems and develop an approximate polynomial-time algorithm to solve them. For a commonly used scoring function, the algorithm runs in O(n(10)/epsilon(6)) time, for globular protein of length n, and it detects alignments that score within an additive error of epsilon from all optima. Thus, we prove that this task is computationally feasible, although the method that we introduce is too slow to be a useful everyday tool. We argue that such approximate solutions are, in fact, of greater interest than exact ones because of the noisy nature of experimentally determined protein coordinates. The measurement of similarity between a pair of protein structures used by our algorithm involves the Euclidean distance between the structures (appropriately rigidly transformed). We show that an alternative approach, which relies on internal distance matrices, must incorporate sophisticated geometric ingredients if it is to guarantee optimality and run in polynomial time. We use these observations to visualize the scoring function for several real instances of the problem. Our investigations yield insights on the computational complexity of protein alignment under various scoring functions. These insights can be used in the design of scoring functions for which the optimum can be approximated efficiently and perhaps in the development of efficient algorithms for the multiple structural alignment problem. PMID:15304646

  2. RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments.

    PubMed

    Schnattinger, Thomas; Schöning, Uwe; Marchfelder, Anita; Kestler, Hans A

    2013-12-01

    Incorporating secondary structure information into the alignment process improves the quality of RNA sequence alignments. Instead of using fixed weighting parameters, sequence and structure components can be treated as different objectives and optimized simultaneously. The result is not a single, but a Pareto-set of equally optimal solutions, which all represent different possible weighting parameters. We now provide the interactive graphical software tool RNA-Pareto, which allows a direct inspection of all feasible results to the pairwise RNA sequence-structure alignment problem and greatly facilitates the exploration of the optimal solution set.

  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. GraSPI (Graphical Structured Packing Interface)

    SciTech Connect

    Almedia, Valmor de

    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. 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.

  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. 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

  7. 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

  8. 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…

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. Fine-tuning structural RNA alignments in the twilight zone

    PubMed Central

    2010-01-01

    Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Results Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Conclusions Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index. PMID:20433706

  14. Web-Beagle: a web server for the alignment of RNA secondary structures

    PubMed Central

    Mattei, Eugenio; Pietrosanto, Marco; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2015-01-01

    Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3′ UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods. PMID:25977293

  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. Genome alignment with graph data structures: a comparison

    PubMed Central

    2014-01-01

    Background Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences. The computational approach of multiple genome alignment allows investigation of evolutionarily related genomes in an integrated fashion, providing a basis for downstream analyses such as rearrangement studies and phylogenetic inference. Graphs have proven to be a powerful tool for coping with the complexity of genome-scale sequence alignments. The potential of graphs to intuitively represent all aspects of genome alignments led to the development of graph-based approaches for genome alignment. These approaches construct a graph from a set of local alignments, and derive a genome alignment through identification and removal of graph substructures that indicate errors in the alignment. Results We compare the structures of commonly used graphs in terms of their abilities to represent alignment information. We describe how the graphs can be transformed into each other, and identify and classify graph substructures common to one or more graphs. Based on previous approaches, we compile a list of modifications that remove these substructures. Conclusion We show that crucial pieces of alignment information, associated with inversions and duplications, are not visible in the structure of all graphs. If we neglect vertex or edge labels, the graphs differ in their information content. Still, many ideas are shared among all graph-based approaches. Based on these findings, we outline a conceptual framework for graph-based genome alignment that can assist in the development of future genome alignment tools. PMID:24712884

  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. GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures

    PubMed Central

    2013-01-01

    Background All sequenced eukaryotic genomes have been shown to possess at least a few introns. This includes those unicellular organisms, which were previously suspected to be intron-less. Therefore, gene splicing must have been present at least in the last common ancestor of the eukaryotes. To explain the evolution of introns, basically two mutually exclusive concepts have been developed. The introns-early hypothesis says that already the very first protein-coding genes contained introns while the introns-late concept asserts that eukaryotic genes gained introns only after the emergence of the eukaryotic lineage. A very important aspect in this respect is the conservation of intron positions within homologous genes of different taxa. Results GenePainter is a standalone application for mapping gene structure information onto protein multiple sequence alignments. Based on the multiple sequence alignments the gene structures are aligned down to single nucleotides. GenePainter accounts for variable lengths in exons and introns, respects split codons at intron junctions and is able to handle sequencing and assembly errors, which are possible reasons for frame-shifts in exons and gaps in genome assemblies. Thus, even gene structures of considerably divergent proteins can properly be compared, as it is needed in phylogenetic analyses. Conserved intron positions can also be mapped to user-provided protein structures. For their visualization GenePainter provides scripts for the molecular graphics system PyMol. Conclusions GenePainter is a tool to analyse gene structure conservation providing various visualization options. A stable version of GenePainter for all operating systems as well as documentation and example data are available at http://www.motorprotein.de/genepainter.html. PMID:23496949

  2. 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

  3. 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.

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

    PubMed Central

    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

    2016-01-01

    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

  5. 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

  6. CLEMAPS: multiple alignment of protein structures based on conformational letters.

    PubMed

    Liu, Xin; Zhao, Ya-Pu; Zheng, Wei-Mou

    2008-05-01

    CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C(alpha) pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.

  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. Protein folds and families: sequence and structure alignments.

    PubMed

    Holm, L; Sander, C

    1999-01-01

    Dali and HSSP are derived databases organizing protein space in the structurally known regions. We use an automatic structure alignment program (Dali) for the classification of all known 3D structures based on all-against-all comparison of 3D structures in the Protein Data Bank. The HSSP database associates 1D sequences with known 3D structures using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). As a result, the HSSP database not only provides aligned sequence families, but also implies secondary and tertiary structures covering 36% of all sequences in Swiss-Prot. The structure classification by Dali and the sequence families in HSSP can be browsed jointly from a web interface providing a rich network of links between neighbours in fold space, between domains and proteins, and between structures and sequences. In particular, this results in a database of explicit multiple alignments of protein families in the twilight zone of sequence similarity. The organization of protein structures and families provides a map of the currently known regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The databases are available from http://www.embl-ebi.ac.uk/dali/

  9. SAS-Pro: simultaneous residue assignment and structure superposition for protein structure alignment.

    PubMed

    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.

  10. 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

  11. A novel approach to structural alignment using realistic structural and environmental information.

    PubMed

    Chen, Yu; Crippen, Gordon M

    2005-12-01

    In the era of structural genomics, it is necessary to generate accurate structural alignments in order to build good templates for homology modeling. Although a great number of structural alignment algorithms have been developed, most of them ignore intermolecular interactions during the alignment procedure. Therefore, structures in different oligomeric states are barely distinguishable, and it is very challenging to find correct alignment in coil regions. Here we present a novel approach to structural alignment using a clique finding algorithm and environmental information (SAUCE). In this approach, we build the alignment based on not only structural coordinate information but also realistic environmental information extracted from biological unit files provided by the Protein Data Bank (PDB). At first, we eliminate all environmentally unfavorable pairings of residues. Then we identify alignments in core regions via a maximal clique finding algorithm. Two extreme value distribution (EVD) form statistics have been developed to evaluate core region alignments. With an optional extension step, global alignment can be derived based on environment-based dynamic programming linking. We show that our method is able to differentiate three-dimensional structures in different oligomeric states, and is able to find flexible alignments between multidomain structures without predetermined hinge regions. The overall performance is also evaluated on a large scale by comparisons to current structural classification databases as well as to other alignment methods. PMID:16260755

  12. Understanding of Relation Structures of Graphical Models by Lower Secondary Students

    ERIC Educational Resources Information Center

    van Buuren, Onne; Heck, André; Ellermeijer, Ton

    2016-01-01

    A learning path has been developed on system dynamical graphical modelling, integrated into the Dutch lower secondary physics curriculum. As part of the developmental research for this learning path, students' understanding of the relation structures shown in the diagrams of graphical system dynamics based models has been investigated. One of our…

  13. 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…

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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…

  19. Aligned two-phase structures in Fe-C alloys

    SciTech Connect

    Shimotomai, Michio; Maruta, Keiichi

    2000-02-14

    One of the goals in the application of magnetic fields to steels has been the alignment of their microstructures along the fields, as this may lead to the control of the textures and mechanical properties. This kind of magnetic alignments has been studied extensively in magneto-rheological fluids and a wealth of experimental data is available. The application of a magnetic field to such fluids induces magnetic dipole and multipole moments on each magnetic particle embedded in a carrier fluid. Anisotropic magnetic forces between pairs of the particles promote the head-to-tail alignment of the moments and draws the particles into proximity. These attractive interparticle forces lead to the formation of chains, columns, or more complicated networks of particles aligned with the direction of the magnetic field. The formation of a similar structure is also known for interacting nonmagnetic polystyrene particles in a magnetized fluid. In this paper, the authors report the first observation of chains or columns of paramagnetic fcc phase nucleated in the ferromagnetic bcc phase of carbon steels during the {alpha}{yields}{gamma} inverse transformation in high magnetic fields.

  20. 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/ .

  1. 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.

  2. NoFold: RNA structure clustering without folding or alignment.

    PubMed

    Middleton, Sarah A; Kim, Junhyong

    2014-11-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures.

  3. Understanding of Relation Structures of Graphical Models by Lower Secondary Students

    NASA Astrophysics Data System (ADS)

    van Buuren, Onne; Heck, André; Ellermeijer, Ton

    2016-10-01

    A learning path has been developed on system dynamical graphical modelling, integrated into the Dutch lower secondary physics curriculum. As part of the developmental research for this learning path, students' understanding of the relation structures shown in the diagrams of graphical system dynamics based models has been investigated. One of our main findings is that only some students understand these structures correctly. Reality-based interpretation of the diagrams can conceal an incorrect understanding of diagram structures. As a result, students seemingly have no problems interpreting the diagrams until they are asked to construct a graphical model. Misconceptions have been identified that are the consequence of the fact that the equations are not clearly communicated by the diagrams or because the icons used in the diagrams mislead novice modellers. Suggestions are made for improvements.

  4. 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.

  5. 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

  6. Automated alignment of serial thoracic scans using bone structure descriptors

    NASA Astrophysics Data System (ADS)

    Gavrielides, Marios A.; Petrick, Nicholas; Myers, Kyle J.

    2007-03-01

    In this manuscript we present an automated algorithm for the alignment of thoracic scans using descriptors of bone structures. Bone structures were utilized because they are expected to be less susceptible to sources of errors such as patient positioning and breath hold. The algorithm employed the positioning of ribs relative to the spinal cord along with a description of the scapula. The spinal cord centroid was detected by extracting local maxima of the distance transform followed by point tracing along consecutive slices. Ribs were segmented using adaptive thresholding followed by the watershed algorithm to detach ribs from the vertebra, and by imposing requirements of rib proximity to the lung border. The angles formed between the spinal cord centroid and segmented rib centroids were used to describe rib positioning. Additionally, the length of the scapula was extracted in each slice. A cost function incorporating the difference of features from rib positioning and scapula length between two slices was derived and used to match slices. The method was evaluated on a set of 12 pairs of full and partial CT scans acquired on the same day. Evaluation was based on whether the slices showing a nodule at its maximum diameter in each scan were matched. Full-to-partial and partial-to-full alignment were performed. Results showed that the proposed metric matched nodule slices within an average distance of 1.08 and 1.17 slices from the target for full-to-partial and partial-to-full alignment respectively. These preliminary results are encouraging for using this method as a first step in an overall process of temporally analyzing CT lung nodules.

  7. 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.

  8. 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

  9. RNAalifold: improved consensus structure prediction for RNA alignments

    PubMed Central

    Bernhart, Stephan H; Hofacker, Ivo L; Will, Sebastian; Gruber, Andreas R; Stadler, Peter F

    2008-01-01

    Background The prediction of a consensus structure for a set of related RNAs is an important first step for subsequent analyses. RNAalifold, which computes the minimum energy structure that is simultaneously formed by a set of aligned sequences, is one of the oldest and most widely used tools for this task. In recent years, several alternative approaches have been advocated, pointing to several shortcomings of the original RNAalifold approach. Results We show that the accuracy of RNAalifold predictions can be improved substantially by introducing a different, more rational handling of alignment gaps, and by replacing the rather simplistic model of covariance scoring with more sophisticated RIBOSUM-like scoring matrices. These improvements are achieved without compromising the computational efficiency of the algorithm. We show here that the new version of RNAalifold not only outperforms the old one, but also several other tools recently developed, on different datasets. Conclusion The new version of RNAalifold not only can replace the old one for almost any application but it is also competitive with other approaches including those based on SCFGs, maximum expected accuracy, or hierarchical nearest neighbor classifiers. PMID:19014431

  10. 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

  11. 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.

  12. Structure alignment of membrane proteins: Accuracy of available tools and a consensus strategy.

    PubMed

    Stamm, Marcus; Forrest, Lucy R

    2015-09-01

    Protein structure alignment methods are used for the detection of evolutionary and functionally related positions in proteins. A wide array of different methods are available, but the choice of the best method is often not apparent to the user. Several studies have assessed the alignment accuracy and consistency of structure alignment methods, but none of these explicitly considered membrane proteins, which are important targets for drug development and have distinct structural features. Here, we compared 13 widely used pairwise structural alignment methods on a test set of homologous membrane protein structures (called HOMEP3). Each pair of structures was aligned and the corresponding sequence alignment was used to construct homology models. The model accuracy compared to the known structures was assessed using scoring functions not incorporated in the tested structural alignment methods. The analysis shows that fragment-based approaches such as FR-TM-align are the most useful for aligning structures of membrane proteins. Moreover, fragment-based approaches are more suitable for comparison of protein structures that have undergone large conformational changes. Nevertheless, no method was clearly superior to all other methods. Additionally, all methods lack a measure to rate the reliability of a position within a structure alignment. To solve both of these problems, we propose a consensus-type approach, combining alignments from four different methods, namely FR-TM-align, DaliLite, MATT, and FATCAT. Agreement between the methods is used to assign confidence values to each position of the alignment. Overall, we conclude that there remains scope for the improvement of structural alignment methods for membrane proteins.

  13. 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.

  14. 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.

  15. 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.

  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. 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

  18. 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

  19. 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

  20. 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.

  1. Large-scale structure and the intrinsic alignment of galaxies

    NASA Astrophysics Data System (ADS)

    Blazek, Jonathan; Seljak, Uroš; Mandelbaum, Rachel

    2016-10-01

    Coherent alignments of galaxy shapes, often called``intrinsic alignments'' (IA), are the most significant source of astrophysical uncertainty in weak lensing measurements. We develop the tidal alignment model of IA and demonstrate its success in describing observational data. We also describe a technique to separate IA from galaxy-galaxy lensing measurements. Applying this technique to luminous red galaxy lenses in the Sloan Digital Sky Survey, we constrain potential IA contamination from associated sources to be below a few percent.

  2. 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.

  3. Effect of Using Suboptimal Alignments in Template-Based Protein Structure Prediction

    PubMed Central

    Chen, Hao; Kihara, Daisuke

    2010-01-01

    Computational protein structure prediction remains a challenging task in protein bioinformatics. In the recent years, the importance of template-based structure prediction is increasing due to the growing number of protein structures solved by the structural genomics projects. To capitalize the significant efforts and investments paid on the structural genomics projects, it is urgent to establish effective ways to use the solved structures as templates by developing methods for exploiting remotely related proteins that cannot be simply identified by homology. In this work, we examine the effect of employing suboptimal alignments in template-based protein structure prediction. We showed that suboptimal alignments are often more accurate than the optimal one, and such accurate suboptimal alignments can occur even at a very low rank of the alignment score. Suboptimal alignments contain a significant number of correct amino acid residue contacts. Moreover, suboptimal alignments can improve template-based models when used as input to Modeller. Finally, we employ suboptimal alignments for handling a contact potential in a probabilistic way in a threading program, SUPRB. The probabilistic contacts strategy outperforms the partly thawed approach which only uses the optimal alignment in defining residue contacts and also the reranking strategy, which uses the contact potential in reranking alignments. The comparison with existing methods in the template-recognition test shows that SUPRB is very competitive and outperform existing methods. PMID:21058297

  4. 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

  5. Nova laser alignment control system

    SciTech Connect

    Van Arsdall, P.J.; Holloway, F.W.; McGuigan, D.L.; Shelton, R.T.

    1984-03-29

    Alignment of the Nova laser requires control of hundreds of optical components in the ten beam paths. Extensive application of computer technology makes daily alignment practical. The control system is designed in a manner which provides both centralized and local manual operator controls integrated with automatic closed loop alignment. Menudriven operator consoles using high resolution color graphics displays overlaid with transport touch panels allow laser personnel to interact efficiently with the computer system. Automatic alignment is accomplished by using image analysis techniques to determine beam references points from video images acquired along the laser chain. A major goal of the design is to contribute substantially to rapid experimental turnaround and consistent alignment results. This paper describes the computer-based control structure and the software methods developed for aligning this large laser system.

  6. Adaptive Smith-Waterman residue match seeding for protein structural alignment.

    PubMed

    Topham, Christopher M; Rouquier, Mickaël; Tarrat, Nathalie; André, Isabelle

    2013-10-01

    The POLYFIT rigid-body algorithm for automated global pairwise and multiple protein structural alignment is presented. Smith-Waterman local alignment is used to establish a set of seed equivalences that are extended using Needleman-Wunsch dynamic programming techniques. Structural and functional interaction constraints provided by evolution are encoded as one-dimensional residue physical environment strings for alignment of highly structurally overlapped protein pairs. Local structure alignment of more distantly related pairs is carried out using rigid-body conformational matching of 15-residue fragments, with allowance made for less stringent conformational matching of metal-ion and small molecule ligand-contact, disulphide bridge, and cis-peptide correspondences. Protein structural plasticity is accommodated through the stepped adjustment of a single empirical distance parameter value in the calculation of the Smith-Waterman dynamic programming matrix. Structural overlap is used both as a measure of similarity and to assess alignment quality. Pairwise alignment accuracy has been benchmarked against that of 10 widely used aligners on the Sippl and Wiederstein set of difficult pairwise structure alignment problems, and more extensively against that of Matt, SALIGN, and MUSTANG in pairwise and multiple structural alignments of protein domains with low shared sequence identity in the SCOP-ASTRAL 40% compendium. The results demonstrate the advantages of POLYFIT over other aligners in the efficient and robust identification of matching seed residue positions in distantly related protein targets and in the generation of longer structurally overlapped alignment lengths. Superposition-based application areas include comparative modeling and protein and ligand design. POLYFIT is available on the Web server at http://polyfit.insa-toulouse.fr.

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

    PubMed

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

    2011-04-01

    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. Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins.

    PubMed Central

    Gerstein, M.; Levitt, M.

    1998-01-01

    We apply a simple method for aligning protein sequences on the basis of a 3D structure, on a large scale, to the proteins in the scop classification of fold families. This allows us to assess, understand, and improve our automatic method against an objective, manually derived standard, a type of comprehensive evaluation that has not yet been possible for other structural alignment algorithms. Our basic approach directly matches the backbones of two structures, using repeated cycles of dynamic programming and least-squares fitting to determine an alignment minimizing coordinate difference. Because of simplicity, our method can be readily modified to take into account additional features of protein structure such as the orientation of side chains or the location-dependent cost of opening a gap. Our basic method, augmented by such modifications, can find reasonable alignments for all but 1.5% of the known structural similarities in scop, i.e., all but 32 of the 2,107 superfamily pairs. We discuss the specific protein structural features that make these 32 pairs so difficult to align and show how our procedure effectively partitions the relationships in scop into different categories, depending on what aspects of protein structure are involved (e.g., depending on whether or not consideration of side-chain orientation is necessary for proper alignment). We also show how our pairwise alignment procedure can be extended to generate a multiple alignment for a group of related structures. We have compared these alignments in detail with corresponding manual ones culled from the literature. We find good agreement (to within 95% for the core regions), and detailed comparison highlights how particular protein structural features (such as certain strands) are problematical to align, giving somewhat ambiguous results. With these improvements and systematic tests, our procedure should be useful for the development of scop and the future classification of protein folds. PMID

  11. Fuzzy Intervals for Designing Structural Signature: An Application to Graphic Symbol Recognition

    NASA Astrophysics Data System (ADS)

    Luqman, Muhammad Muzzamil; Delalandre, Mathieu; Brouard, Thierry; Ramel, Jean-Yves; Lladós, Josep

    The motivation behind our work is to present a new methodology for symbol recognition. The proposed method employs a structural approach for representing visual associations in symbols and a statistical classifier for recognition. We vectorize a graphic symbol, encode its topological and geometrical information by an attributed relational graph and compute a signature from this structural graph. We have addressed the sensitivity of structural representations to noise, by using data adapted fuzzy intervals. The joint probability distribution of signatures is encoded by a Bayesian network, which serves as a mechanism for pruning irrelevant features and choosing a subset of interesting features from structural signatures of underlying symbol set. The Bayesian network is deployed in a supervised learning scenario for recognizing query symbols. The method has been evaluated for robustness against degradations & deformations on pre-segmented 2D linear architectural & electronic symbols from GREC databases, and for its recognition abilities on symbols with context noise i.e. cropped symbols.

  12. 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.

  13. OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures.

    PubMed

    Shih, Edward S C; Gan, Ruei-chi R; Hwang, Ming-Jing

    2006-07-01

    The large number of experimentally determined protein 3D structures is a rich resource for studying protein function and evolution, and protein structure comparison (PSC) is a key method for such studies. When comparing two protein structures, almost all currently available PSC servers report a single and sequential (i.e. topological) alignment, whereas the existence of good alternative alignments, including those involving permutations (i.e. non-sequential or non-topological alignments), is well known. We have recently developed a novel PSC method that can detect alternative alignments of statistical significance (alignment similarity P-value <10(-5)), including structural permutations at all levels of complexity. OPAAS, the server of this PSC method freely accessible at our website (http://opaas.ibms.sinica.edu.tw), provides an easy-to-read hierarchical layout of output to display detailed information on all of the significant alternative alignments detected. Because these alternative alignments can offer a more complete picture on the structural, evolutionary and functional relationship between two proteins, OPAAS can be used in structural bioinformatics research to gain additional insight that is not readily provided by existing PSC servers.

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

    PubMed

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

    2014-07-01

    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.

  15. 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.

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

    PubMed

    Lee, Hui Sun; Im, Wonpil

    2012-10-22

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

  17. 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

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. Computation of the Density Matrix in Electronic Structure Theory in Parallel on Multiple Graphics Processing Units.

    PubMed

    Cawkwell, M J; Wood, M A; Niklasson, Anders M N; Mniszewski, S M

    2014-12-01

    The algorithm developed in Cawkwell, M. J. et al. J. Chem. Theory Comput. 2012 , 8 , 4094 for the computation of the density matrix in electronic structure theory on a graphics processing unit (GPU) using the second-order spectral projection (SP2) method [ Niklasson, A. M. N. Phys. Rev. B 2002 , 66 , 155115 ] has been efficiently parallelized over multiple GPUs on a single compute node. The parallel implementation provides significant speed-ups with respect to the single GPU version with no loss of accuracy. The performance and accuracy of the parallel GPU-based algorithm is compared with the performance of the SP2 algorithm and traditional matrix diagonalization methods on a multicore central processing unit (CPU).

  3. 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

  4. 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

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

    PubMed

    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

  6. 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

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

    PubMed

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

    2013-07-31

    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.

  8. PALI-a database of Phylogeny and ALIgnment of homologous protein structures.

    PubMed

    Balaji, S; Sujatha, S; Kumar, S S; Srinivasan, N

    2001-01-01

    PALI (release 1.2) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of homologous protein domains in various families. The data set of homologous protein structures has been derived by consulting the SCOP database (release 1.50) and the data set comprises 604 families of homologous proteins involving 2739 protein domain structures with each family made up of at least two members. Each member in a family has been structurally aligned with every other member in the same family (pairwise alignment) and all the members in the family are also aligned using simultaneous super-position (multiple alignment). The structural alignments are performed largely automatically, with manual interventions especially in the cases of distantly related proteins, using the program STAMP (version 4.2). Every family is also associated with two dendrograms, calculated using PHYLIP (version 3.5), one based on a structural dissimilarity metric defined for every pairwise alignment and the other based on similarity of topologically equivalent residues. These dendrograms enable easy comparison of sequence and structure-based relationships among the members in a family. Structure-based alignments with the details of structural and sequence similarities, superposed coordinate sets and dendrograms can be accessed conveniently using a web interface. The database can be queried for protein pairs with sequence or structural similarities falling within a specified range. Thus PALI forms a useful resource to help in analysing the relationship between sequence and structure variation at a given level of sequence similarity. PALI also contains over 653 'orphans' (single member families). Using the web interface involving PSI_BLAST and PHYLIP it is possible to associate the sequence of a new protein with one of the families in PALI and generate a phylogenetic tree combining the query sequence and proteins of known 3-D structure. The

  9. 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

  10. 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.

  11. CDD: a database of conserved domain alignments with links to domain three-dimensional structure.

    PubMed

    Marchler-Bauer, Aron; Panchenko, Anna R; Shoemaker, Benjamin A; Thiessen, Paul A; Geer, Lewis Y; Bryant, Stephen H

    2002-01-01

    The Conserved Domain Database (CDD) is a compilation of multiple sequence alignments representing protein domains conserved in molecular evolution. It has been populated with alignment data from the public collections Pfam and SMART, as well as with contributions from colleagues at NCBI. The current version of CDD (v.1.54) contains 3693 such models. CDD alignments are linked to protein sequence and structure data in Entrez. The molecular structure viewer Cn3D serves as a tool to interactively visualize alignments and three-dimensional structure, and to link three-dimensional residue coordinates to descriptions of evolutionary conservation. CDD can be accessed on the World Wide Web at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. Protein query sequences may be compared against databases of position-specific score matrices derived from alignments in CDD, using a service named CD-Search, which can be found at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. CD-Search runs reverse-position-specific BLAST (RPS-BLAST), a variant of the widely used PSI-BLAST algorithm. CD-Search is run by default for protein-protein queries submitted to NCBI's BLAST service at http://www.ncbi.nlm.nih.gov/BLAST.

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

    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.

  13. 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.

  14. 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.

  15. 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

  16. Four-dimensional structural and Doppler optical coherence tomography imaging on graphics processing units

    NASA Astrophysics Data System (ADS)

    Sylwestrzak, Marcin; Szlag, Daniel; Szkulmowski, Maciej; Gorczynska, Iwona; Bukowska, Danuta; Wojtkowski, Maciej; Targowski, Piotr

    2012-10-01

    The authors present the application of graphics processing unit (GPU) programming for real-time three-dimensional (3-D) Fourier domain optical coherence tomography (FdOCT) imaging with implementation of flow visualization algorithms. One of the limitations of FdOCT is data processing time, which is generally longer than data acquisition time. Utilizing additional algorithms, such as Doppler analysis, further increases computation time. The general purpose computing on GPU (GPGPU) has been used successfully for structural OCT imaging, but real-time 3-D imaging of flows has so far not been presented. We have developed software for structural and Doppler OCT processing capable of visualization of two-dimensional (2-D) data (2000 A-scans, 2048 pixels per spectrum) with an image refresh rate higher than 120 Hz. The 3-D imaging of 100×100 A-scans data is performed at a rate of about 9 volumes per second. We describe the software architecture, organization of threads, and optimization. Screen shots recorded during real-time imaging of a flow phantom and the human eye are presented.

  17. Four-dimensional structural and Doppler optical coherence tomography imaging on graphics processing units.

    PubMed

    Sylwestrzak, Marcin; Szlag, Daniel; Szkulmowski, Maciej; Gorczynska, Iwona; Bukowska, Danuta; Wojtkowski, Maciej; Targowski, Piotr

    2012-10-01

    The authors present the application of graphics processing unit (GPU) programming for real-time three-dimensional (3-D) Fourier domain optical coherence tomography (FdOCT) imaging with implementation of flow visualization algorithms. One of the limitations of FdOCT is data processing time, which is generally longer than data acquisition time. Utilizing additional algorithms, such as Doppler analysis, further increases computation time. The general purpose computing on GPU (GPGPU) has been used successfully for structural OCT imaging, but real-time 3-D imaging of flows has so far not been presented. We have developed software for structural and Doppler OCT processing capable of visualization of two-dimensional (2-D) data (2000 A-scans, 2048 pixels per spectrum) with an image refresh rate higher than 120 Hz. The 3-D imaging of 100×100 A-scans data is performed at a rate of about 9 volumes per second. We describe the software architecture, organization of threads, and optimization. Screen shots recorded during real-time imaging of a flow phantom and the human eye are presented.

  18. Introduction of a distance cut-off into structural alignment by the double dynamic programming algorithm.

    PubMed

    Toh, H

    1997-08-01

    Two approximations were introduced into the double dynamic programming algorithm, in order to reduce the computational time for structural alignment. One of them was the so-called distance cut-off, which approximately describes the structural environment of each residue by its local environment. In the approximation, a sphere with a given radius is placed at the center of the side chain of each residue. The local environment of a residue is constituted only by the residues with side chain centers that are present within the sphere, which is expressed by a set of center-to-center distances from the side chain of the residue to those of all the other constituent residues. The residues outside the sphere are neglected from the local environment. Another approximation is associated with the distance cut-off, which is referred to here as the delta N cut-off. If two local environments are similar to each other, the numbers of residues constituting the environments are expected to be similar. The delta N cut-off was introduced based on the idea. If the difference between the numbers of the constituent residues of two local environments is greater than a given threshold value, delta N, the evaluation of the similarity between the local environments is skipped. The introduction of the two approximations dramatically reduced the computational time for structural alignment by the double dynamic programming algorithm. However, the approximations also decreased the accuracy of the alignment. To improve the accuracy with the approximations, a program with a two-step alignment algorithm was constructed. At first, an alignment was roughly constructed with the approximations. Then, the epsilon-suboptimal region for the alignment was determined. Finally, the double dynamic programming algorithm with full structural environments was applied to the residue pairs within the epsilon-suboptimal region to produce an improved alignment.

  19. The alignment of technology and structure through roles and networks.

    PubMed

    Barley, S R

    1990-03-01

    This paper outlines a role-based approach for conceptualizing and investigating the contention in some previous research that technologies change organizational and occupational structures by transforming patterns of action and interaction. Building on Nadel's theory of social structure, the paper argues that the microsocial dynamics occasioned by new technologies reverberate up levels of analysis in an orderly manner. Specifically, a technology's material attributes are said to have an immediate impact on the nonrelational elements of one or more work roles. These changes, in turn, influence the role's relational elements, which eventually affect the structure of an organization's social networks. Consequently, roles and social networks are held to mediate a technology's structural effects. The theory is illustrated by ethnographic and sociometric data drawn from a comparative field study of the use of traditional and computerized imaging devices in two radiology departments. PMID:10106582

  20. SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

    PubMed Central

    Di Tommaso, Paolo; Bussotti, Giovanni; Kemena, Carsten; Capriotti, Emidio; Chatzou, Maria; Prieto, Pablo; Notredame, Cedric

    2014-01-01

    This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve alignment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from http://tcoffee.crg.cat/apps/tcoffee/do:saracoffee. PMID:24972831

  1. SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments.

    PubMed

    Di Tommaso, Paolo; Bussotti, Giovanni; Kemena, Carsten; Capriotti, Emidio; Chatzou, Maria; Prieto, Pablo; Notredame, Cedric

    2014-07-01

    This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve alignment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from http://tcoffee.crg.cat/apps/tcoffee/do:saracoffee.

  2. 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

  3. 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…

  4. 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

  5. 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…

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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.

  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. Aligning USGS senior leadership structure with the USGS science strategy

    USGS Publications Warehouse

    ,

    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.

  13. A Two-Level Structure for Compressing Aligned Bitexts

    NASA Astrophysics Data System (ADS)

    Adiego, Joaquín; Brisaboa, Nieves R.; Martínez-Prieto, Miguel A.; Sánchez-Martínez, Felipe

    A bitext, or bilingual parallel corpus, consists of two texts, each one in a different language, that are mutual translations. Bitexts are very useful in linguistic engineering because they are used as source of knowledge for different purposes. In this paper we propose a strategy to efficiently compress and use bitexts, saving, not only space, but also processing time when exploiting them. Our strategy is based on a two-level structure for the vocabularies, and on the use of biwords, a pair of associated words, one from each language, as basic symbols to be encoded with an ETDC [2] compressor. The resulting compressed bitext needs around 20% of the space and allows more efficient implementations of the different types of searches and operations that linguistic engineerings need to perform on them. In this paper we discuss and provide results for compression, decompression, different types of searches, and bilingual snippets extraction.

  14. 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.…

  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

    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.

  17. 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.

  18. Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment

    PubMed Central

    Sundfeld, Daniel; Havgaard, Jakob H.; de Melo, Alba C. M. A.; Gorodkin, Jan

    2016-01-01

    Motivation: Structured RNAs can be hard to search for as they often are not well conserved in their primary structure and are local in their genomic or transcriptomic context. Thus, the need for tools which in particular can make local structural alignments of RNAs is only increasing. Results: To meet the demand for both large-scale screens and hands on analysis through web servers, we present a new multithreaded version of Foldalign. We substantially improve execution time while maintaining all previous functionalities, including carrying out local structural alignments of sequences with low similarity. Furthermore, the improvements allow for comparing longer RNAs and increasing the sequence length. For example, lengths in the range 2000–6000 nucleotides improve execution up to a factor of five. Availability and implementation: The Foldalign software and the web server are available at http://rth.dk/resources/foldalign Contact: gorodkin@rth.dk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26704597

  19. 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.

  20. Periodic sub-100nm structures fabricated by proximity i-line mask-aligner lithography (and self-aligned double patterning)

    NASA Astrophysics Data System (ADS)

    Bourgin, Yannick; Voigt, Daniel; Käsebier, Thomas; Kley, Ernst-Bernhard; Zeitner, Uwe D.

    2016-03-01

    Diffractive mask-aligner lithography allows printing sub-micrometer resolution structures by using non-contact mode. For such a purpose, binary diffraction gratings are used as masks and are designed to transmit solely the ±1st diffraction orders. The high resolution interferogram is realized by the overlapping and the interference of the propagating beams. By applying the techniques known as Self-Aligned Double Patterning (SADP), it's possible to decrease the period of the fabricated grating (350 nm) by a factor of two, and thus reaching the 90nm structure width. As application, metallic gratings have been fabricated operating as wire grid polarizer (WGP).

  1. Derivation of rules for comparative protein modeling from a database of protein structure alignments.

    PubMed Central

    Sali, A.; Overington, J. P.

    1994-01-01

    We describe a database of protein structure alignments as well as methods and tools that use this database to improve comparative protein modeling. The current version of the database contains 105 alignments of similar proteins or protein segments. The database comprises 416 entries, 78,495 residues, 1,233 equivalent entry pairs, and 230,396 pairs of equivalent alignment positions. At present, the main application of the database is to improve comparative modeling by satisfaction of spatial restraints implemented in the program MODELLER (Sali A, Blundell TL, 1993, J Mol Biol 234:779-815). To illustrate the usefulness of the database, the restraints on the conformation of a disulfide bridge provided by an equivalent disulfide bridge in a related structure are derived from the alignments; the prediction success of the disulfide dihedral angle classes is increased to approximately 80%, compared to approximately 55% for modeling that relies on the stereochemistry of disulfide bridges alone. The second example of the use of the database is the derivation of the probability density function for comparative modeling of the cis/trans isomerism of the proline residues; the prediction success is increased from 0% to 82.9% for cis-proline and from 93.3% to 96.2% for trans-proline. The database is available via electronic mail. PMID:7833817

  2. Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles.

    PubMed

    Gautheret, D; Lambert, A

    2001-11-01

    We present here a new approach to the problem of defining RNA signatures and finding their occurrences in sequence databases. The proposed method is based on "secondary structure profiles". An RNA sequence alignment with secondary structure information is used as an input. Two types of weight matrices/profiles are constructed from this alignment: single strands are represented by a classical lod-scores profile while helical regions are represented by an extended "helical profile" comprising 16 lod-scores per position, one for each of the 16 possible base-pairs. Database searches are then conducted using a simultaneous search for helical profiles and dynamic programming alignment of single strand profiles. The algorithm has been implemented into a new software, ERPIN, that performs both profile construction and database search. Applications are presented for several RNA motifs. The automated use of sequence information in both single-stranded and helical regions yields better sensitivity/specificity ratios than descriptor-based programs. Furthermore, since the translation of alignments into profiles is straightforward with ERPIN, iterative searches can easily be conducted to enrich collections of homologous RNAs.

  3. 3-d structure-based amino acid sequence alignment of esterases, lipases and related proteins

    SciTech Connect

    Gentry, M.K.; Doctor, B.P.; Cygler, M.; Schrag, J.D.; Sussman, J.L.

    1993-05-13

    Acetylcholinesterase and butyrylcholinesterase, enzymes with potential as pretreatment drugs for organophosphate toxicity, are members of a larger family of homologous proteins that includes carboxylesterases, cholesterol esterases, lipases, and several nonhydrolytic proteins. A computer-generated alignment of 18 of the proteins, the acetylcholinesases, butyrylcholinesterases, carboxylesterases, some esterases, and the nonenzymatic proteins has been previously presented. More recently, the three-dimensional structures of two enzymes enzymes in this group, acetylcholinesterase from Torpedo californica and lipase from Geotrichum candidum, have been determined. Based on the x-ray structures and the superposition of these two enzymes, it was possible to obtain an improved amino acid sequence alignment of 32 members of this family of proteins. Examination of this alignment reveals that 24 amino acids are invariant in all of the hydrolytic proteins, and an additional 49 are well conserved. Conserved amino acids include those of the active site, the disulfide bridges, the salt bridges, in the core of the proteins, and at the edges of secondary structural elements. Comparison of the three-dimensional structures makes it possible to find a well-defined structural basis for the conservation of many of these amino acids.

  4. 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.

  5. Graphical and Demographic Synopsis of the Captive Cohort Method for Estimating Population Age Structure in the Wild

    PubMed Central

    Carey, James R.; Müller, Hans-Georg; Wang, Jane-Ling; Papadopoulos, Nikos; Diamantidis, Alexis; Kouloussis, Nikos

    2014-01-01

    The purpose of this paper is to complement the literature concerned with the captive cohort method for estimating age structure including (1) graphic techniques to visualize and thus better understand the underlying life table identity in which the age structure of a stationary population equals the time-to-death distribution of the individuals within it; (2) re-derive the basic model for estimating age structure in non-stationary population in demographic rather than statistical notation; and (3) describe a simplified method for estimating changes in the mean age of a wild population. PMID:22776134

  6. 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.

  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

    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

  11. Assessment of solvent effects: do weak alignment media affect the structure of the solute?

    PubMed

    Shahkhatuni, Astghik A; Shahkhatuni, Aleksan G; Panosyan, Henry A; Sahakyan, Aleksandr B; Byeon, In-Ja L; Gronenborn, Angela M

    2007-07-01

    Alignment media used for measuring residual dipolar couplings, such as solutions of filamentous phages, phospholipid mixtures, polyacrylamide gels and various lyotropic liquid crystalline systems were investigated with respect to solvent effects on molecular structure. Structural parameters of the small rigid model compound 13C-acetonitrile were calculated from dipolar couplings and variations from expectation values were used for assessment of solvent effects. Only minor solvent effects were observed for most of the media employed and the measured structural data are in good agreement with microwave data and theoretical predictions. PMID:17534883

  12. 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.

  13. Graphic Arts.

    ERIC Educational Resources Information Center

    Kempe, Joseph; Kinde, Bruce

    This curriculum guide is intended to assist vocational instructors in preparing students for entry-level employment in the graphic arts field and getting them ready for advanced training in the workplace. The package contains an overview of new and emerging graphic arts technologies, competency/skill and task lists for the occupations of…

  14. 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…

  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. 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.

  17. 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

  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.

  19. Aligned-to-random” nanofiber scaffolds for mimicking the structure of the tendon-to-bone insertion site

    PubMed Central

    Xie, Jingwei; Li, Xiaoran; Lipner, Justin; Manning, Cionne N.; Schwartz, Annie G.; Thomopoulos, Stavros; Xia, Younan

    2013-01-01

    We have demonstrated the fabrication of “aligned-to-random” electrospun nanofiber scaffolds that mimic the structural organization of collagen fibers at the tendon-to-bone insertion site. Tendon fibroblasts cultured on such a scaffold exhibited highly organized and haphazardly oriented morphologies, respectively, on the aligned and random portions. PMID:20648290

  20. 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

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

    DOE PAGES

    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

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

    PubMed

    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

  4. 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

  5. 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

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

    PubMed

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

    2009-07-01

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

  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. Pitch accent alignment in romance: primary and secondary associations with metrical structure.

    PubMed

    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 such facts within the AM model, the article develops the notion of "phonological anchoring" as an extension of the concept of secondary association originally proposed by Pierrehumbert and Beckman (1988), and later adopted by Grice (1995), Grice, Ladd, and Arvaniti (2000), and others to explain the behavior of edge tones. The Romance data represent evidence that not only peripheral edge tones seek secondary associations. We claim that the phonological representation of pitch accents should include two independent mechanisms to encode alignment properties with metrical structure: (1) encoding of the primary phonological association (or affiliation) between the tone and its tone-bearing unit; and (2), for some specific cases, encoding of the secondary phonological anchoring of tones to prosodic edges (moras, syllables, and prosodic words). The Romance data described in the article provide crucial evidence of mora-edge, syllable-edge, and word-edge H tonal associations.

  10. 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.

  11. 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

  12. 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

  13. 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.

  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.

  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. Measuring structural-functional correspondence: spatial variability of specialised brain regions after macro-anatomical alignment.

    PubMed

    Frost, Martin A; Goebel, Rainer

    2012-01-16

    The central question of the relationship between structure and function in the human brain is still not well understood. In order to investigate this fundamental relationship we create functional probabilistic maps from a large set of mapping experiments and compare the location of functionally localised regions across subjects using different whole-brain alignment schemes. To avoid the major problems associated with meta-analysis approaches, all subjects are scanned using the same paradigms, the same scanner and the same analysis pipeline. We show that an advanced, curvature driven cortex based alignment (CBA) scheme largely removes macro-anatomical variability across subjects. Remaining variability in the observed spatial location of functional regions, thus, reflects the "true" functional variability, i.e. the quantified variability is a good estimator of the underlying structural-functional correspondence. After localising 13 widely studied functional areas, we found a large variability in the degree to which functional areas respect macro-anatomical boundaries across the cortex. Some areas, such as the frontal eye fields (FEF) are strongly bound to a macro-anatomical location. Fusiform face area (FFA) on the other hand, varies in its location along the length of the fusiform gyrus even though the gyri themselves are well aligned across subjects. Language areas were found to vary greatly across subjects whilst a high degree of overlap was observed in sensory and motor areas. The observed differences in functional variability for different specialised areas suggest that a more complete estimation of the structure-function relationship across the whole cortex requires further empirical studies with an expanded test battery.

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. Leaf extraction and analysis framework graphical user interface: segmenting and analyzing the structure of leaf veins and areoles.

    PubMed

    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.

  5. 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

  6. 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 for

  7. 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.

  8. 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.

  9. Computing the Density Matrix in Electronic Structure Theory on Graphics Processing Units.

    PubMed

    Cawkwell, M J; Sanville, E J; Mniszewski, S M; Niklasson, Anders M N

    2012-11-13

    The self-consistent solution of a Schrödinger-like equation for the density matrix is a critical and computationally demanding step in quantum-based models of interatomic bonding. This step was tackled historically via the diagonalization of the Hamiltonian. We have investigated the performance and accuracy of the second-order spectral projection (SP2) algorithm for the computation of the density matrix via a recursive expansion of the Fermi operator in a series of generalized matrix-matrix multiplications. We demonstrate that owing to its simplicity, the SP2 algorithm [Niklasson, A. M. N. Phys. Rev. B2002, 66, 155115] is exceptionally well suited to implementation on graphics processing units (GPUs). The performance in double and single precision arithmetic of a hybrid GPU/central processing unit (CPU) and full GPU implementation of the SP2 algorithm exceed those of a CPU-only implementation of the SP2 algorithm and traditional matrix diagonalization when the dimensions of the matrices exceed about 2000 × 2000. Padding schemes for arrays allocated in the GPU memory that optimize the performance of the CUBLAS implementations of the level 3 BLAS DGEMM and SGEMM subroutines for generalized matrix-matrix multiplications are described in detail. The analysis of the relative performance of the hybrid CPU/GPU and full GPU implementations indicate that the transfer of arrays between the GPU and CPU constitutes only a small fraction of the total computation time. The errors measured in the self-consistent density matrices computed using the SP2 algorithm are generally smaller than those measured in matrices computed via diagonalization. Furthermore, the errors in the density matrices computed using the SP2 algorithm do not exhibit any dependence of system size, whereas the errors increase linearly with the number of orbitals when diagonalization is employed.

  10. 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

  11. 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.

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

    DOE PAGES

    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

  13. 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

  14. 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/.

  15. Weak alignment offers new NMR opportunities to study protein structure and dynamics

    PubMed Central

    Bax, Ad

    2003-01-01

    Protein solution nuclear magnetic resonance (NMR) can be conducted in a slightly anisotropic environment, where the orientational distribution of the proteins is no longer random. In such an environment, the large one-bond internuclear dipolar interactions no longer average to zero and report on the average orientation of the corresponding vectors relative to the magnetic field. The desired very weak ordering, on the order of 10−3, can be induced conveniently by the use of aqueous nematic liquid crystalline suspensions or by anisotropically compressed hydrogels. The resulting residual dipolar interactions are scaled down by three orders of magnitude relative to their static values, but nevertheless can be measured at high accuracy. They are very precise reporters on the average orientation of bonds relative to the molecular alignment frame, and they can be used in a variety of ways to enrich our understanding of protein structure and function. Applications to date have focused primarily on validation of structures, determined by NMR, X-ray crystallography, or homology modeling, and on refinement of structures determined by conventional NMR approaches. Although de novo structure determination on the basis of dipolar couplings suffers from a severe multiple minimum problem, related to the degeneracy of dipolar coupling relative to inversion of the internuclear vector, a number of approaches can address this problem and potentially can accelerate the NMR structure determination process considerably. In favorable cases, where large numbers of dipolar couplings can be measured, inconsistency between measured values can report on internal motions. PMID:12493823

  16. RNAMotifScanX: a graph alignment approach for RNA structural motif identification.

    PubMed

    Zhong, Cuncong; Zhang, Shaojie

    2015-03-01

    RNA structural motifs are recurrent three-dimensional (3D) components found in the RNA architecture. These RNA structural motifs play important structural or functional roles and usually exhibit highly conserved 3D geometries and base-interaction patterns. Analysis of the RNA 3D structures and elucidation of their molecular functions heavily rely on efficient and accurate identification of these motifs. However, efficient RNA structural motif search tools are lacking due to the high complexity of these motifs. In this work, we present RNAMotifScanX, a motif search tool based on a base-interaction graph alignment algorithm. This novel algorithm enables automatic identification of both partially and fully matched motif instances. RNAMotifScanX considers noncanonical base-pairing interactions, base-stacking interactions, and sequence conservation of the motifs, which leads to significantly improved sensitivity and specificity as compared with other state-of-the-art search tools. RNAMotifScanX also adopts a carefully designed branch-and-bound technique, which enables ultra-fast search of large kink-turn motifs against a 23S rRNA. The software package RNAMotifScanX is implemented using GNU C++, and is freely available from http://genome.ucf.edu/RNAMotifScanX.

  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.

  18. 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.

  19. 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.

  20. Structural Determination of (Al2O3)(n) (n = 1-15) Clusters Based on Graphic Processing Unit.

    PubMed

    Zhang, Qiyao; Cheng, Longjiu

    2015-05-26

    Global optimization algorithms have been widely used in the field of chemistry to search the global minimum structures of molecular and atomic clusters, which is a nondeterministic polynomial problem with the increasing sizes of clusters. Considering that the computational ability of a graphic processing unit (GPU) is much better than that of a central processing unit (CPU), we developed a GPU-based genetic algorithm for structural prediction of clusters and achieved a high acceleration ratio compared to a CPU. On the one-dimensional (1D) operation of a GPU, taking (Al2O3)n clusters as test cases, the peak acceleration ratio in the GPU is about 220 times that in a CPU in single precision and the value is 103 for double precision in calculation of the analytical interatomic potential. The peak acceleration ratio is about 240 and 107 on the block operation, and it is about 77 and 35 on the 2D operation compared to a CPU in single precision and double precision, respectively. And the peak acceleration ratio of the whole genetic algorithm program is about 35 compared to CPU at double precision. Structures of (Al2O3)n clusters at n = 1-10 reported in previous works are successfully located, and their low-lying structures at n = 11-15 are predicted.

  1. 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.

  2. Optical and structural properties of amorphous SexTe100-x aligned nanorods.

    PubMed

    Al-Agel, Faisal A

    2013-01-01

    In the present work, we report studies on optical and structural phenomenon in as-deposited thin films composed of aligned nanorods of amorphous SexTe100-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.

  3. 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.

  4. 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.

  5. Energy band structure tailoring of vertically aligned InAs/GaAsSb quantum dot structure for intermediate-band solar cell application by thermal annealing process.

    PubMed

    Liu, Wei-Sheng; Chu, Ting-Fu; Huang, Tien-Hao

    2014-12-15

    This study presents an band-alignment tailoring of a vertically aligned InAs/GaAs(Sb) quantum dot (QD) structure and the extension of the carrier lifetime therein by rapid thermal annealing (RTA). Arrhenius analysis indicates a larger activation energy and thermal stability that results from the suppression of In-Ga intermixing and preservation of the QD heterostructure in an annealed vertically aligned InAs/GaAsSb QD structure. Power-dependent and time-resolved photoluminescence were utilized to demonstrate the extended carrier lifetime from 4.7 to 9.4 ns and elucidate the mechanisms of the antimony aggregation resulting in a band-alignment tailoring from straddling to staggered gap after the RTA process. The significant extension in the carrier lifetime of the columnar InAs/GaAsSb dot structure make the great potential in improving QD intermediate-band solar cell application.

  6. An acidic protein aligns magnetosomes along a filamentous structure in magnetotactic bacteria.

    PubMed

    Scheffel, André; Gruska, Manuela; Faivre, Damien; Linaroudis, Alexandros; Plitzko, Jürgen M; Schüler, Dirk

    2006-03-01

    Magnetotactic bacteria are widespread aquatic microorganisms that use unique intracellular organelles to navigate along the Earth's magnetic field. These organelles, called magnetosomes, consist of membrane-enclosed magnetite crystals that are thought to help to direct bacterial swimming towards growth-favouring microoxic zones at the bottom of natural waters. Questions in the study of magnetosome formation include understanding the factors governing the size and redox-controlled synthesis of the nano-sized magnetosomes and their assembly into a regular chain in order to achieve the maximum possible magnetic moment, against the physical tendency of magnetosome agglomeration. A deeper understanding of these mechanisms is expected from studying the genes present in the identified chromosomal 'magnetosome island', for which the connection with magnetosome synthesis has become evident. Here we use gene deletion in Magnetospirillum gryphiswaldense to show that magnetosome alignment is coupled to the presence of the mamJ gene product. MamJ is an acidic protein associated with a novel filamentous structure, as revealed by fluorescence microscopy and cryo-electron tomography. We suggest a mechanism in which MamJ interacts with the magnetosome surface as well as with a cytoskeleton-like structure. According to our hypothesis, magnetosome architecture represents one of the highest structural levels achieved in prokaryotic cells.

  7. 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.

  8. 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

  9. 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.

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

    DOE PAGES

    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

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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

  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. Origin of the energy level alignment at organic/organic interfaces: The role of structural defects

    NASA Astrophysics Data System (ADS)

    Bussolotti, Fabio; Yang, Jinpeng; Hinderhofer, Alexander; Huang, Yuli; Chen, Wei; Kera, Satoshi; Wee, Andrew T. S.; Ueno, Nobuo

    2014-03-01

    In this paper, the electronic properties of as-deposited and N2-exposedCuPc/F16CuPc interface, a prototype system for organic photovoltaic applications, are investigated by using ultralow background, high-sensitivity photoemission spectroscopy. It is found that (i) N2 exposure significantly modifies the energy level alignment (ELA) at the interface between CuPc and F16CuPc layer and (ii) the direction of the N2-induced energy level shift of the CuPc depends on the position of the Fermi level (EF) in the CuPc highest occupied molecular orbital-lowest unoccupied molecular orbital gap of the as-deposited film. These observations are related to the changes in the density of gap states (DOGS) produced by structural imperfections in the molecular packing geometry, as introduced by the N2 penetration into the CuPc layer. This result demonstrates the key role of structure-induced DOGS in controlling the ELA at organic/organic interfaces.

  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. Residue-residue contact substitution probabilities derived from aligned three-dimensional structures and the identification of common folds.

    PubMed Central

    Rodionov, M. A.; Johnson, M. S.

    1994-01-01

    We report the derivation of scores that are based on the analysis of residue-residue contact matrices from 443 3-dimensional structures aligned structurally as 96 families, which can be used to evaluate sequence-structure matches. Residue-residue contacts and the more than 3 x 10(6) amino acid substitutions that take place between pairs of these contacts at aligned positions within each family of structures have been tabulated and segregated according to the solvent accessibility of the residues involved. Contact maps within a family of structures are shown to be highly conserved (approximately 75%) even when the sequence identity is approaching 10%. In a comparison involving a globin structure and the search of a sequence databank (> 21,000 sequences), the contact probability scores are shown to provide a very powerful secondary screen for the top scoring sequence-structure matches, where between 69% and 84% of the unrelated matches are eliminated. The search of an aligned set of 2 globins against a sequence databank and the subsequent residue contact-based evaluation of matches locates all 618 globin sequences before the first non-globin match. From a single bacterial serine proteinase structure, the structural template approach coupled with residue-residue contact substitution data lead to the detection of the mammalian serine proteinase family among the top matches in the search of a sequence databank. PMID:7756991

  3. 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

  4. 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.

  5. Replication of self-centering optical fiber alignment structures using hot embossing

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    With the demand for broadband connectivity on the rise due to various services like video-on-demand and cloud computing becoming more popular, the need for better connectivity infrastructure is high. The only future- proof option to supply this infrastructure is to deploy "fiber to the home" (FTTH) networks. One of the main difficulties with the deployment of FTTH is the vast amount of single-mode fiber (SMF) connections that need to be made. Hence there is a strong need for components which enable high performance, robust and easy-to- use SMF connectors. Since large-scale deployment is the goal, these components should be mass-producible at low cost. We discuss a rapid prototyping process on the basis of hot embossing replication of a self-centering alignment system (SCAS) based on three micro-springs, which can position a SMF independently of its diameter. This is beneficial since there is a fabrication tolerance of up to +/-1 μm on a standard G.652 SMF's diameter that can lead to losses if the outer diameter is used as a reference for alignment. The SCAS is first prototyped with deep proton writing (DPW) in polymethylmethacrylate (PMMA) after which it is glued to a copper substrate with an adhesive. Using an electroforming process, a nickel block is grown over the PMMA prototype followed by mechanical finishing to fabricate a structured nickel mould insert. Even though the mould insert shows non- ideal and rounded features it is used to create PMMA replicas of the SCAS by means of hot embossing. The SCAS possesses a central opening in which a bare SMF can be clamped, which is designed with a diameter of 121 μm. PMMA replicas are dimensionally characterized using a multisensor coordinate measurement machine and show a central opening diameter of 128.3 +/- 2.8 μm. This should be compared to the central opening diameter of the DPW prototype used for mould formation which was measured to be 120.5 μm. This shows that the electroforming and subsequent replication

  6. 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

  7. 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.

  8. PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

    PubMed Central

    Seemann, Stefan E.; Richter, Andreas S.; Gesell, Tanja; Backofen, Rolf; Gorodkin, Jan

    2011-01-01

    Motivation: Predicting RNA–RNA interactions is essential for determining the function of putative non-coding RNAs. Existing methods for the prediction of interactions are all based on single sequences. Since comparative methods have already been useful in RNA structure determination, we assume that conserved RNA–RNA interactions also imply conserved function. Of these, we further assume that a non-negligible amount of the existing RNA–RNA interactions have also acquired compensating base changes throughout evolution. We implement a method, PETcofold, that can take covariance information in intra-molecular and inter-molecular base pairs into account to predict interactions and secondary structures of two multiple alignments of RNA sequences. Results: PETcofold's ability to predict RNA–RNA interactions was evaluated on a carefully curated dataset of 32 bacterial small RNAs and their targets, which was manually extracted from the literature. For evaluation of both RNA–RNA interaction and structure prediction, we were able to extract only a few high-quality examples: one vertebrate small nucleolar RNA and four bacterial small RNAs. For these we show that the prediction can be improved by our comparative approach. Furthermore, PETcofold was evaluated on controlled data with phylogenetically simulated sequences enriched for covariance patterns at the interaction sites. We observed increased performance with increased amounts of covariance. Availability: The program PETcofold is available as source code and can be downloaded from http://rth.dk/resources/petcofold. Contact: gorodkin@rth.dk; backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21088024

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules.

    PubMed

    Boll, Rebecca; Rouzée, Arnaud; Adolph, Marcus; Anielski, Denis; Aquila, Andrew; Bari, Sadia; Bomme, Cédric; Bostedt, Christoph; Bozek, John D; Chapman, Henry N; Christensen, Lauge; Coffee, Ryan; Coppola, Niccola; De, Sankar; Decleva, Piero; Epp, Sascha W; Erk, Benjamin; Filsinger, Frank; Foucar, Lutz; Gorkhover, Tais; Gumprecht, Lars; Hömke, André; Holmegaard, Lotte; Johnsson, Per; Kienitz, Jens S; Kierspel, Thomas; Krasniqi, Faton; Kühnel, Kai-Uwe; Maurer, Jochen; Messerschmidt, Marc; Moshammer, Robert; Müller, Nele L M; Rudek, Benedikt; Savelyev, Evgeny; Schlichting, Ilme; Schmidt, Carlo; Scholz, Frank; Schorb, Sebastian; Schulz, Joachim; Seltmann, Jörn; Stener, Mauro; Stern, Stephan; Techert, Simone; Thøgersen, Jan; Trippel, Sebastian; Viefhaus, Jens; Vrakking, Marc; Stapelfeldt, Henrik; Küpper, Jochen; Ullrich, Joachim; Rudenko, Artem; Rolles, Daniel

    2014-01-01

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C(8)H(5)F) and dissociating, laser-aligned 1,4-dibromobenzene (C(6)H(4)Br(2)) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.

  14. Double-sided structured mask for sub-micron resolution proximity i-line mask-aligner lithography.

    PubMed

    Bourgin, Yannick; Siefke, Thomas; Käsebier, Thomas; Genevée, Pascal; Szeghalmi, Adriana; Kley, Ernst-Bernhard; Zeitner, Uwe D

    2015-06-29

    Diffractive mask-aligner lithography allows printing structures that have a sub-micrometer resolution by using non-contact mode. For such a purpose, masks are often designed to operate with monochromatic linearly polarized light, which is obtained by placing a spectral filter and a polarizer in the beam path. We propose here a mask design that includes a wire-grid polarizer (WGP) on the top side of a photo-mask and a diffractive element on the bottom one to print a 350 nm period grating by using a classical mask-aligner in proximity exposure mode. Linearly polarizing locally an unpolarized incident beam is only possible by using a WGP on the top side of the mask. This configuration opens the possibility to use different linear polarization orientation on a single mask and allows to print high resolution structures with different orientation within one exposure.

  15. 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.

  16. 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

  17. Interstellar Dust Grain Alignment

    NASA Astrophysics Data System (ADS)

    Andersson, B.-G.; Lazarian, A.; Vaillancourt, John E.

    2015-08-01

    Interstellar polarization at optical-to-infrared wavelengths is known to arise from asymmetric dust grains aligned with the magnetic field. This effect provides a potentially powerful probe of magnetic field structure and strength if the details of the grain alignment can be reliably understood. Theory and observations have recently converged on a quantitative, predictive description of interstellar grain alignment based on radiative processes. The development of a general, analytical model for this radiative alignment torque (RAT) theory has allowed specific, testable predictions for realistic interstellar conditions. We outline the theoretical and observational arguments in favor of RAT alignment, as well as reasons the "classical" paramagnetic alignment mechanism is unlikely to work, except possibly for the very smallest grains. With further detailed characterization of the RAT mechanism, grain alignment and polarimetry promise to not only better constrain the interstellar magnetic field but also provide new information on the dust characteristics.

  18. Multiple Radially Aligned Plasmaspheric Structures as Evidence of Standing Hydromagnetic Waves: IMAGE EUV Observations and Forward Modeling

    NASA Technical Reports Server (NTRS)

    Gallagher, D. L.; Adrian, M. L.; Green, J. L.; Sandel, B. R.; Rose, M. Franklin (Technical Monitor)

    2001-01-01

    The IMAGE EUV imager has observed several instances where the outer plasmasphere is populated by multiple radially aligned structures resembling "plasmaspheric fingers". The observation of these plasmaspheric structures suggests the presence of an azimuthal standing hydromagnetic wave mode. Eiganmodes appear to explain finger-like. nearly radial density structures that sometimes divide into two structures with increasing radial distance. The implication is of boundaries at fixed local times, which results in a widening "box" in which standing waves are developed. The structures also suggest a single driving frequency for the source of the waves. We present EUV observations of plasmaspheric fingers observed on August 2000 as well as plasmaspheric modeling of azimuthal wave modes in an effort to quantify the origin of these observed structures

  19. Space Technology 5 Multi-point Observations of Field-aligned Currents: Temporal Variability of Meso-Scale Structures

    NASA Technical Reports Server (NTRS)

    Le, Guan; Wang, Yongli; Slavin, James A.; Strangeway, Robert J.

    2007-01-01

    Space Technology 5 (ST5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from ST5. The data demonstrate that meso-scale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of - 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are approx. 1 min for meso-scale currents and approx. 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.

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

    PubMed

    Hua, Lei; Song, Yang; 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/.

  1. 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

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

    SciTech Connect

    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.

  3. 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.

  4. 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).

  5. Rotational band structures in sup 127 Cs: Shape changes induced by h sub 11/2 neutron alignment

    SciTech Connect

    Liang, Y.; Ma, R.; Paul, E.S.; Xu, N.; Fossan, D.B. ); Wyss, R.A. )

    1990-09-01

    Several rotational bands have been populated to high spin in {sup 127}Cs following the {sup 120}Sn({sup 11}B,4{ital n}) reaction. Rotational bands built on low-lying proton {ital g}{sub 7/2}, {ital d}{sub 5/2}, and {ital g}{sub 9/2} (hole) orbitals, and the unique-parity {ital h}{sub 11/2} orbital were observed and identified. For the {pi}{ital g}{sub 9/2} (hole) case, both signatures were seen in a strongly coupled {Delta}{ital I}=1 band, while for the other cases, decoupled {Delta}{ital I}=2 bands were observed with strong in-band quadrupole transitions. Through comparisons with cranked-shell-model calculations, these band structures are understood to be associated with a prolate ({gamma}{approximately}0{degree}) deformed nuclear shape. At frequencies above {h bar}{omega}=0.3 MeV, the rotational alignment of a pair of {ital h}{sub 11/2} neutrons was observed for each of the {ital h}{sub 11/2}, {ital g}{sub 7/2}, and {ital d}{sub 5/2} bands. This neutron alignment is predicted to drive the nuclear core away from a prolate shape towards the collectively rotating oblate ({gamma}={minus}60{degree}) shape. Changes in the measured signature splittings for the bands below and above the alignment are consistent with the shape changes.

  6. Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques.

    PubMed

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

    2010-10-14

    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 loop

  7. AdoMet radical proteins--from structure to evolution--alignment of divergent protein sequences reveals strong secondary structure element conservation.

    PubMed

    Nicolet, Yvain; Drennan, Catherine L

    2004-01-01

    Eighteen subclasses of S-adenosyl-l-methionine (AdoMet) radical proteins have been aligned in the first bioinformatics study of the AdoMet radical superfamily to utilize crystallographic information. The recently resolved X-ray structure of biotin synthase (BioB) was used to guide the multiple sequence alignment, and the recently resolved X-ray structure of coproporphyrinogen III oxidase (HemN) was used as the control. Despite the low 9% sequence identity between BioB and HemN, the multiple sequence alignment correctly predicted all but one of the core helices in HemN, and correctly predicted the residues in the enzyme active site. This alignment further suggests that the AdoMet radical proteins may have evolved from half-barrel structures (alphabeta)4 to three-quarter-barrel structures (alphabeta)6 to full-barrel structures (alphabeta)8. It predicts that anaerobic ribonucleotide reductase (RNR) activase, an ancient enzyme that, it has been suggested, serves as a link between the RNA and DNA worlds, will have a half-barrel structure, whereas the three-quarter barrel, exemplified by HemN, will be the most common architecture for AdoMet radical enzymes, and fewer members of the superfamily will join BioB in using a complete (alphabeta)8 TIM-barrel fold to perform radical chemistry. These differences in barrel architecture also explain how AdoMet radical enzymes can act on substrates that range in size from 10 atoms to 608 residue proteins.

  8. Alignment of full and partial CT thoracic scans using bony structures

    NASA Astrophysics Data System (ADS)

    Gavrielides, Marios A.; Petrick, Nicholas; Myers, Kyle J.

    2006-03-01

    Diagnostic thoracic procedures using computed tomography (CT) often include comparisons of scans acquired with different slice thicknesses. In this manuscript, we investigated the potential for alignment of different CT scans from the same patient using skeletal knowledge of the thoracic region. Skeletal matching was selected because it is expected to be less susceptible to differences associated with patient breath hold, positioning and cardiac motion. Our method utilized the positioning of the ribs relative to the vertebra for matching. It also included matching the scapula when visible in the scans. Rib positioning was described by the angles formed between the vertebra centroid and combinations of pairs of rib centroids visible on each CT slice; this was used as the primary matching mechanism. Scapula morphology was described using a feature based on the local maxima of the distance transform. Since the scapula is not visible in all slices of a full scan, its description was limited to only defining the potential range of slices. A cost function incorporating the difference of features from rib positioning and scapula morphology between two slices was derived and used to match slices. The method was evaluated on an independent set of 10 pairs of full and partial CT scans. Assessment was based on whether or not slices containing known nodules between each pair of scans were overlapping after the alignment procedure. Results showed that the proposed metric correctly aligned 9 out of 10 scans. The preliminary results are encouraging for using this method as a first step towards temporal analysis of lung nodules.

  9. 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

  10. Hole-Aligning Tool

    NASA Technical Reports Server (NTRS)

    Collins, Frank A.; Saude, Frank; Sep, Martin J.

    1996-01-01

    Tool designed for use in aligning holes in plates or other structural members to be joined by bolt through holes. Holes aligned without exerting forces perpendicular to planes of holes. Tool features screw-driven-wedge design similar to (but simpler than) that of some automotive exhaust-pipe-expanding tools.

  11. 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

  12. 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.

  13. HSX: Engineering Design and Fabrication of the main Magnet Coils, Vacuum Vessel and Support/Alignment Structure

    NASA Astrophysics Data System (ADS)

    Anderson, F. Simon B.; Anderson, D. T.; Almagri, A. F.; Matthews, P. G.; Probert, P. H.; Shohet, J. L.; Talmadge, J. N.

    1996-11-01

    The HSX device, with a magnetic field consisting of a SINGLE dominant HELICAL component, has a set of 48 twisted main magnetic field coils. Engineering analysis (ANSYS) has resulted in a set of construction and alignment constraints and goals for field accuracy and coil structural strength. Close proximity of the main coil set to the magnetic separatrix imposes space restrictions on the vacuum vessel. Fabrication of the vessel using explosive techniques, and the structural analysis for the stresses in the vacuum chamber will be discussed. Crucial to the integrity of the quasihelical magnetic field is the accurate positioning of the magnet coils and maintenance of the position during operation. The design and construct- ion of the completed support structure for HSX coils will also be presented. *** Work supported by U.S Dept. of Energy Grant DE-FG02-93ER54222

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. Indel PDB: A database of structural insertions and deletions derived from sequence alignments of closely related proteins

    PubMed Central

    Hsing, Michael; Cherkasov, Artem

    2008-01-01

    Background Insertions and deletions (indels) represent a common type of sequence variations, which are less studied and pose many important biological questions. Recent research has shown that the presence of sizable indels in protein sequences may be indicative of protein essentiality and their role in protein interaction networks. Examples of utilization of indels for structure-based drug design have also been recently demonstrated. Nonetheless many structural and functional characteristics of indels remain less researched or unknown. Description We have created a web-based resource, Indel PDB, representing a structural database of insertions/deletions identified from the sequence alignments of highly similar proteins found in the Protein Data Bank (PDB). Indel PDB utilized large amounts of available structural information to characterize 1-, 2- and 3-dimensional features of indel sites. Indel PDB contains 117,266 non-redundant indel sites extracted from 11,294 indel-containing proteins. Unlike loop databases, Indel PDB features more indel sequences with secondary structures including alpha-helices and beta-sheets in addition to loops. The insertion fragments have been characterized by their sequences, lengths, locations, secondary structure composition, solvent accessibility, protein domain association and three dimensional structures. Conclusion By utilizing the data available in Indel PDB, we have studied and presented here several sequence and structural features of indels. We anticipate that Indel PDB will not only enable future functional studies of indels, but will also assist protein modeling efforts and identification of indel-directed drug binding sites. PMID:18578882

  20. 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

  1. Grid phenomenon, alignment of formations, ordered structures on planets and satellites

    NASA Astrophysics Data System (ADS)

    Barkin, Yu. V.

    2008-09-01

    Abstract. It is shown, that in a distribution of formations on planets and satellites of terrestrial group it is rather clearly the phenomena of netting (grid) and alignment proves. When, the centers of formations are situated along parallels and meridians or along inclined parallel straight lines (on the plane "longitude - latitude") in this or that system of coordinates connected to a celestial body. Generally, these systems of coordinates are inclined with respect to an axis of planet rotation. This phenomenon already was discussed earlier [1] - [3], and in the given work some new illustrations of the ordered distribution of formations of planets and satellites are given. The presence of similar law in distribution of formations of a celestial body testifies for the benefit of their internal origins, and activity of endogenous processes, their rhythms and orderliness are dictated by gravitational influences of external celestial bodies .

  2. Low-temperature growth of aligned ZnO nanorods: effect of annealing gases on the structural and optical properties.

    PubMed

    Umar, Ahmad; Hahn, Yoon-Bong; Al-Hajry, A; Abaker, M

    2014-06-01

    Aligned ZnO nanorods were grown on ZnO/Si substrate via simple aqueous solution process at low-temperature of - 65 degrees C by using zinc nitrate and hexamethylenetetramine (HMTA). The detailed morphological and structural properties measured by FESEM, XRD, EDS and TEM confirmed that the as-grown nanorods are vertically aligned, well-crystalline possessing wurtzite hexagonal phase and grown along the [0001] direction. The room-temperature photoluminescence spectrum of the grown nanorods exhibited a strong and broad green emission and small ultraviolet emission. The as-prepared ZnO nanorods were post-annealed in nitrogen (N2) and oxygen (O2) environments and further characterized in terms of their morphological, structural and optical properties. After annealing the nanorods exhibit well-crystallinity and wurtzite hexagonal phase. Moreover, by annealing the PL spectra show the enhancement in the UV emission and suppression in the green emission. The presented results demonstrate that simply by post-annealing process, the optical properties of ZnO nanostructures can be controlled.

  3. 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.

  4. 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

  5. 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

  6. 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)

  7. Band alignment in ZnSe/Zn1-x-y Cdx Mny Se quantum-well structures

    NASA Astrophysics Data System (ADS)

    Yu, W. Y.; Salib, M. S.; Petrou, A.; Jonker, B. T.; Warnock, J.

    1997-01-01

    We present a magneto-optical study of ZnSe/Zn1-x-y Cdx Mny Se quantum-well structures in which a suitable choice of the Cd composition leads to a system that is type I at zero magnetic field. When a magnetic field is applied perpendicular to the layers of the structure, the band edges split in such a way as to make the upper σ- (+, +) exciton transition type II, while the ground state σ+ (-, -) exciton component remains type I at all field values. This alignment reduces the probability for carrier relaxation from the higher-energy exciton component and opens the possibility of hole-spin population inversion via optical pumping.

  8. 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.

  9. Graphics and Listening Comprehension.

    ERIC Educational Resources Information Center

    Ruhe, Valerie

    1996-01-01

    Examines the effectiveness of graphics as lecture comprehension supports for low-proficiency English-as-a-Second-Language (ESL) listeners. The study compared the performance of Asian students in Canada listening to an audiotape while viewing an organizational graphic with that of a control group. Findings indicate that the graphics enhanced…

  10. Galaxy Alignments: An Overview

    NASA Astrophysics Data System (ADS)

    Joachimi, Benjamin; Cacciato, Marcello; Kitching, Thomas D.; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Hoekstra, Henk; Kiessling, Alina; Kirk, Donnacha; Rassat, Anais

    2015-11-01

    The alignments between galaxies, their underlying matter structures, and the cosmic web constitute vital ingredients for a comprehensive understanding of gravity, the nature of matter, and structure formation in the Universe. We provide an overview on the state of the art in the study of these alignment processes and their observational signatures, aimed at a non-specialist audience. The development of the field over the past one hundred years is briefly reviewed. We also discuss the impact of galaxy alignments on measurements of weak gravitational lensing, and discuss avenues for making theoretical and observational progress over the coming decade.

  11. 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.

  12. Modifying surface structure to tune surface properties of vertically aligned carbon nanotube films.

    PubMed

    Ci, Lijie; Ajayan, P M

    2010-06-01

    We report a simple etching process to modify surface of vertically aligned carbon nanotube (VACNT) arrays for their applications in superhydrophobic surface, field emission display, and sun energy conversion, etc. At a high temperature (700-800 degrees C), very low concentration water vapor in presence with Ar and hydrogen flow can be a weak oxidant, and mildly etch nanotube tips without damaging their walls. This process can be performed right after the CNT growth process. Surface of nanotube arrays becomes multi-tiered nanotube patterns with open-ended nanotubes standing straightly. Surface morphology of nanotube arrays can be tuned by changing the etching time. Water droplets on a modified nanotube surface show a large contact angle and sliding angle, which make the etched nanotube film suitable for application such as small amount liquid transport. Light absorption measurement indicated that surface roughness has no effect to improve the light absorption, indicating a different mechanism from other black material. The surface modified nanotube arrays have much increased field enhancement factor in our field emission test, showing the better field emission ability of the nanotube arrays with open tips. PMID:20355379

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. Individual Differences in the Alignment of Structural and Functional Markers of the V5/MT Complex in Primates

    PubMed Central

    Large, I.; Bridge, H.; Ahmed, B.; Clare, S.; Kolasinski, J.; Lam, W. W.; Miller, K. L.; Dyrby, T. B.; Parker, A. J.; Smith, J. E. T.; Daubney, G.; Sallet, J.; Bell, A. H.; Krug, K.

    2016-01-01

    Extrastriate visual area V5/MT in primates is defined both structurally by myeloarchitecture and functionally by distinct responses to visual motion. Myelination is directly identifiable from postmortem histology but also indirectly by image contrast with structural magnetic resonance imaging (sMRI). First, we compared the identification of V5/MT using both sMRI and histology in Rhesus macaques. A section-by-section comparison of histological slices with in vivo and postmortem sMRI for the same block of cortical tissue showed precise correspondence in localizing heavy myelination for V5/MT and neighboring MST. Thus, sMRI in macaques accurately locates histologically defined myelin within areas known to be motion selective. Second, we investigated the functionally homologous human motion complex (hMT+) using high-resolution in vivo imaging. Humans showed considerable intersubject variability in hMT+ location, when defined with myelin-weighted sMRI signals to reveal structure. When comparing sMRI markers to functional MRI in response to moving stimuli, a region of high myelin signal was generally located within the hMT+ complex. However, there were considerable differences in the alignment of structural and functional markers between individuals. Our results suggest that variation in area identification for hMT+ based on structural and functional markers reflects individual differences in human regional brain architecture. PMID:27371764

  18. 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

  19. Graphic Design in Educational Television.

    ERIC Educational Resources Information Center

    Clarke, Beverley

    To help educational television (ETV) practitioners achieve maximum clarity, economy and purposiveness, the range of techniques of television graphics is explained. Closed-circuit and broadcast ETV are compared. The design process is discussed in terms of aspect ratio, line structure, cut off, screen size, tone scales, studio apparatus, and…

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. Direct-Write, Self-Aligned Electrospinning on Paper for Controllable Fabrication of Three-Dimensional Structures.

    PubMed

    Luo, Guoxi; Teh, Kwok Siong; Liu, Yumeng; Zang, Xining; Wen, Zhiyu; Lin, Liwei

    2015-12-23

    Electrospinning, a process that converts a solution or melt droplet into an ejected jet under a high electric field, is a well-established technique to produce one-dimensional (1D) fibers or two-dimensional (2D) randomly arranged fibrous meshes. Nevertheless, the direct electrospinning of fibers into controllable three-dimensional (3D) architectures is still a nascent technology. Here, we apply near-field electrospinning (NFES) to directly write arbitrarily shaped 3D structures through consistent and spatially controlled fiber-by-fiber stacking of polyvinylidene fluoride (PVDF) fibers. An element central to the success of this 3D electrospinning is the use of a printing paper placed on the grounded conductive plate and acting as a fiber collector. Once deposited on the paper, residual solvents from near-field electrospun fibers can infiltrate the paper substrate, enhancing the charge transfer between the deposited fibers and the ground plate via the fibrous network within the paper. Such charge transfer grounds the deposited fibers and turns them into locally fabricated electrical poles, which attract subsequent in-flight fibers to deposit in a self-aligned manner on top of each other. This process enables the design and controlled fabrication of electrospun 3D structures such as grids, walls, hollow cylinders, and other 3D logos. As such, this technique has the potential to advance the existing electrospinning technologies in constructing 3D structures for biomedical, microelectronics, and MEMS/NMES applications.

  10. Transformation and Alignment in Similarity

    ERIC Educational Resources Information Center

    Hodgetts, Carl J.; Hahn, Ulrike; Chater, Nick

    2009-01-01

    This paper contrasts two structural accounts of psychological similarity: structural alignment (SA) and Representational Distortion (RD). SA proposes that similarity is determined by how readily the structures of two objects can be brought into alignment; RD measures similarity by the complexity of the transformation that "distorts" one…

  11. 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

  12. Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction.

    PubMed

    Xie, Qiang; Lin, Jinzhong; Qin, Yan; Zhou, Jianfu; Bu, Wenjun

    2011-02-01

    Ribosomal RNAs are important because they catalyze the synthesis of peptides and proteins. Comparative studies of the secondary structure of 18S rRNA have revealed the basic locations of its many length-conserved and length-variable regions. In recent years, many more sequences of 18S rDNA with unusual lengths have been documented in GenBank. These data make it possible to recognize the diversity of the secondary and tertiary structures of 18S rRNAs and to identify the length-conserved parts of 18S rDNAs. The longest 18S rDNA sequences of almost every known eukaryotic phylum were included in this study. We illustrated the bioinformatics-based structure to show that, the regions that are more length-variable, regions that are less length-variable, the splicing sites for introns, and the sites of A-minor interactions are mostly distributed in different parts of the 18S rRNA. Additionally, this study revealed that some length-variable regions or insertion positions could be quite close to the functional part of the 18S rRNA of Foraminifera organisms. The tertiary structure as well as the secondary structure of 18S rRNA can be more diverse than what was previously supposed. Besides revealing how this interesting gene evolves, it can help to remove ambiguity from the alignment of eukaryotic 18S rDNAs and to improve the performance of 18S rDNA in phylogenetic reconstruction. Six nucleotides shared by Archaea and Eukaryota but rarely by Bacteria are also reported here for the first time, which might further support the supposed origin of eukaryote from archaeans.

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

    PubMed

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

    1999-02-15

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

  14. 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.

  15. 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.

  16. Graphics Specialist (AFSC 23151).

    ERIC Educational Resources Information Center

    Air Univ., Gunter AFS, Ala. Extension Course Inst.

    This three-volume set of student texts is intended for use in an extension course to prepare Air Force graphics specialists. The first volume deals with basic equipment, materials, lettering, and drafting (including geometric and graphic construction). Addressed in the second volume are composition and layout techniques and the fundamentals of…

  17. 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…

  18. 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,…

  19. Convergent beam electron diffraction investigation of strain induced by Ti self-aligned silicides in shallow trench Si isolation structures

    NASA Astrophysics Data System (ADS)

    Armigliato, Aldo; Spessot, Alessio; Balboni, Roberto; Benedetti, Alessandro; Carnevale, Gianpietro; Frabboni, Stefano; Mastracchio, Gianfranco; Pavia, Giuseppe

    2006-03-01

    The deformation induced onto silicon by the formation of Ti self-aligned silicides (salicides) in shallow trench isolation structures has been investigated by the convergent beam electron diffraction technique (CBED) in the transmission electron microscope (TEM). The splitting of the high order Laue zone (HOLZ) lines in the CBED patterns taken in TEM cross sections close to the salicide/silicon interface has been explained assuming that the salicide grains induce a local bending of the lattice planes of the underlying matrix. This bending, which affects in opposite sense the silicon areas below adjacent grains, decreases with the distance from the interface, eventually vanishing at a depth of 300-400 nm. The proposed strain field has been implemented into a fully dynamical simulation of the CBED patterns and has proved to be able to reproduce both the asymmetry of the HOLZ line splitting and the associated subsidiary fringes. This model is confirmed by the shift of a Bragg contour observed in large angle CBED patterns, taken in a cross section cut along a perpendicular direction. The whole experimental results cannot be explained by just a strain relaxation of the TEM cross section, induced by the salicide film onto the underlying silicon.

  20. 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.

  1. Biaxial shear of confined colloidal hard spheres: the structure and rheology of the vorticity-aligned string phase.

    PubMed

    Lin, Neil Y C; Cheng, Xiang; Cohen, Itai

    2014-03-28

    Using a novel biaxial confocal rheoscope, we investigate the flow of the shear induced vorticity aligned string phase [X. Cheng et al., Proc. Natl. Acad. Sci. U. S. A., 2011, 109, 63], which has a highly anisotropic microstructure. Using biaxial shear protocols we show that we have excellent control of the string phase anisotropic morphology. We choose a shear protocol that drives the system into the string phase. Subsequently, a biaxial force measurement device is used to determine the suspension rheology along both the flow and vorticity directions. We find no measurable dependence of the suspension stress response along the shear and vorticity directions due to the hydrodynamically induced string morphology. In particular, we find that the suspension's high frequency stress response is nearly identical along the two orthogonal directions. While we do observe an anisotropic stress response at lower shear frequencies associated with shear thinning, we show that this anisotropy is independent of the shear induced string structure. These results suggest that for the range of flows explored, Brownian and hydrodynamic contributions to the stress arising from the anisotropic suspension microstructure are sufficiently weak that they do not significantly contribute to the rheology. Collectively, this study presents a general and powerful approach for using biaxial confocal rheometry to elucidate the relationship between microstructure and rheology in complex fluids driven far-from-equilibrium.

  2. 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.

  3. 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.

  4. Curriculum Alignment.

    ERIC Educational Resources Information Center

    Crowell, Ronald; Tissot, Paula

    Curriculum alignment (CA) refers to the congruence of all the elements of a school's curriculum: curriculum goals; instructional program--what is taught and the materials used; and tests used to judge outcomes. CA can be a very powerful can be a very powerful factor in improving schools. Although further research is needed on CA, there is…

  5. Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and detailed phylogenetic analysis.

    PubMed

    Mallatt, Jon; Craig, Catherine Waggoner; Yoder, Matthew J

    2012-09-01

    This study presents a manually constructed alignment of nearly complete rRNA genes from most animal clades (371 taxa from ~33 of the ~36 metazoan phyla), expanded from the 197 sequences in a previous study. This thorough, taxon-rich alignment, available at http://www.wsu.edu/~jmallatt/research/rRNAalignment.html and in the Dryad Repository (doi: http://dx.doi.org/10.5061/dryad.1v62kr3q), is based rigidly on the secondary structure of the SSU and LSU rRNA molecules, and is annotated in detail, including labeling of the erroneous sequences (contaminants). The alignment can be used for future studies of the molecular evolution of rRNA. Here, we use it to explore if the larger number of sequences produces an improved phylogenetic tree of animal relationships. Disappointingly, the resolution did not improve, neither when the standard maximum-likelihood method was used, nor with more sophisticated methods that partitioned the rRNA into paired and unpaired sites (stem, loop, bulge, junction), or accounted for the evolution of the paired sites. For example, no doublet model of paired-site substitutions (16-state, 16A and 16B, 7A-F, or 6A-C models) corrected the placement of any rogue taxa or increased resolution. The following findings are from the simplest, standard, ML analysis. The 371-taxon tree only imperfectly supported the bilaterian clades of Lophotrochozoa and Ecdysozoa, and this problem remained after 17 taxa with unstably positioned sequences were omitted from the analysis. The problem seems to stem from base-compositional heterogeneity across taxa and from an overrepresentation of highly divergent sequences among the newly added taxa (e.g., sequences from Cephalopoda, Rotifera, Acoela, and Myxozoa). The rogue taxa continue to concentrate in two locations in the rRNA tree: near the base of Arthropoda and of Bilateria. The approximately uncertain (AU) test refuted the monophyly of Mollusca and of Chordata, probably due to long-branch attraction of the highly

  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. 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.

  9. 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

  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. 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

  12. Image alignment

    SciTech Connect

    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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. Magnetically aligned supramolecular hydrogels.

    PubMed

    Wallace, Matthew; Cardoso, Andre Zamith; Frith, William J; Iggo, Jonathan A; Adams, Dave J

    2014-12-01

    The magnetic-field-induced alignment of the fibrillar structures present in an aqueous solution of a dipeptide gelator, and the subsequent retention of this alignment upon transformation to a hydrogel upon the addition of CaCl2 or upon a reduction in solution pH is reported. Utilising the switchable nature of the magnetic field coupled with the slow diffusion of CaCl2 , it is possible to precisely control the extent of anisotropy across a hydrogel, something that is generally very difficult to do using alternative methods. The approach is readily extended to other compounds that form viscous solutions at high pH. It is expected that this work will greatly expand the utility of such low-molecular-weight gelators (LMWG) in areas where alignment is key. PMID:25345918

  18. Vertically aligned nanostructure scanning probe microscope tips

    DOEpatents

    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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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…

  4. 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.

  5. 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…

  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. 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)

  8. Graphically Enhanced Science Notebooks

    ERIC Educational Resources Information Center

    Minogue, James; Wiebe, Eric; Madden, Lauren; Bedward, John; Carter, Mike

    2010-01-01

    A common mode of communication in the elementary classroom is the science notebook. In this article, the authors outline the ways in which "graphically enhanced science notebooks" can help engage students in complete and robust inquiry. Central to this approach is deliberate attention to the efficient and effective use of student-generated…

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. A cholinesterase genes server (ESTHER): a database of cholinesterase-related sequences for multiple alignments, phylogenetic relationships, mutations and structural data retrieval.

    PubMed Central

    Cousin, X; Hotelier, T; Liévin, P; Toutant, J P; Chatonnet, A

    1996-01-01

    We have built a database of sequences phylogenetically related to cholinesterases (ESTHER) for esterases, alpha/beta hydrolase enzymes and relatives). These sequences define a homogeneous group of enzymes (carboxylesterases, lipases and hormone-sensitive lipases) with some related proteins devoid of enzymatic activity. The purpose of ESTHER is to help comparison and alignment of any new sequence appearing in the field, to favour mutation analysis of structure-function relationships and to allow structural data recovery. ESTHER is a World Wide Web server with the URL http://www.montpellier.inra.fr:70/cholinesterase. PMID:8594562

  14. 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).

  15. A cholinesterase genes server (ESTHER): a database of cholinesterase-related sequences for multiple alignments, phylogenetic relationships, mutations and structural data retrieval.

    PubMed

    Cousin, X; Hotelier, T; Liévin, P; Toutant, J P; Chatonnet, A

    1996-01-01

    We have built a database of sequences phylogenetically related to cholinesterases (ESTHER) for esterases, alpha/beta hydrolase enzymes and relatives). These sequences define a homogeneous group of enzymes (carboxylesterases, lipases and hormone-sensitive lipases) with some related proteins devoid of enzymatic activity. The purpose of ESTHER is to help comparison and alignment of any new sequence appearing in the field, to favour mutation analysis of structure-function relationships and to allow structural data recovery. ESTHER is a World Wide Web server with the URL http://www.montpellier.inra.fr:70/cholinesterase.

  16. Mixed scale joint graphical lasso.

    PubMed

    Pircalabelu, Eugen; Claeskens, Gerda; Waldorp, Lourens J

    2016-10-01

    SummaryWe have developed a method for estimating brain networks from fMRI datasets that have not all been measured using the same set of brain regions. Some of the coarse scale regions have been split in smaller subregions. The proposed penalized estimation procedure selects undirected graphical models with similar structures that combine information from several subjects and several coarseness scales. Both within-scale edges and between-scale edges that identify possible connections between a large region and its subregions are estimated. PMID:27324414

  17. 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.

  18. Global alignment: Finding rearrangements during alignment

    SciTech Connect

    Brudno, Michael; Malde, Sanket; Poliakov, Alexander; Do, Chuong B.; Couronne, Olivier; Dubchak, Inna; Batzoglou, Serafim

    2003-01-06

    Motivation: To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the conserved biological features between distant species. The two main classes of pairwise alignments are global alignment, where one string is transformed into the other, and local alignment, where all locations of similarity between the two strings are returned. Global alignments are less prone to demonstrating false homology as each letter of one sequence is constrained to being aligned to only one letter of the other. Local alignments, on the other hand, can cope with rearrangements between non-syntenic, orthologous sequences by identifying similar regions in sequences; this, however, comes at the expense of a higher false positive rate due to the inability of local aligners to take into account overall conservation maps.

  19. Magnetic alignment of nickel-coated carbon fibers

    SciTech Connect

    Hao, Chuncheng; 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.

  20. 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.

  1. 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.

  2. 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…

  3. 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.

  4. 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)

  5. 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

  6. 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

  7. Highly-ordered nitrogen doped carbon nanotube novel structures of aligned carpet for enhanced field emission properties

    NASA Astrophysics Data System (ADS)

    Padya, Balaji; Jain, P. K.; Padmanabham, G.; Ravi, M.; Bhat, K. S.

    2013-06-01

    Substitutional nitrogen doped aligned carbon nanotubes (NACNTs) with uniform height and high packing density of arrays was synthesized by using the liquid injection CVD process. Transmission electron micrographs indicated that the NACNTs are having nano-bell morphology of graphene layers with series of internal compartments. Field emission study of NACNTs showed that they are good emitters with low turn-on and threshold field. The maximum current density was observed to be 18.8 mA/cm2 at electric field of 1.89 V/μm.

  8. Activated Schwann Cell-Like Cells on Aligned Fibrin-Poly(Lactic-Co-Glycolic Acid) Structures: A Novel Construct for Application in Peripheral Nerve Regeneration.

    PubMed

    Schuh, Christina M A P; Morton, Tatjana J; Banerjee, Asmita; Grasl, Christian; Schima, Heinrich; Schmidhammer, Robert; Redl, Heinz; Ruenzler, Dominik

    2015-01-01

    Tissue engineering approaches in nerve regeneration search for ways to support gold standard therapy (autologous nerve grafts) and to improve results by bridging nerve defects with different kinds of conduits. In this study, we describe electrospinning of aligned fibrin-poly(lactic-co-glycolic acid) (PLGA) fibers in an attempt to create a biomimicking tissue-like material seeded with Schwann cell-like cells (SCLs) in vitro for potential use as an in vivo scaffold. Rat adipose-derived stem cells (rASCs) were differentiated into SCLs and evaluated with flow cytometry concerning their differentiation and activation status [S100b, P75, myelin-associated glycoprotein (MAG), and protein 0 (P0)]. After receiving the proliferation stimulus forskolin, SCLs expressed S100b and P75; comparable to native, activated Schwann cells, while cultured without forskolin, cells switched to a promyelinating phenotype and expressed S100b, MAG, and P0. Human fibrinogen and thrombin, blended with PLGA, were electrospun and the alignment and homogeneity of the fibers were proven by scanning electron microscopy. Electrospun scaffolds were seeded with SCLs and the formation of Büngner-like structures in SCLs was evaluated with phalloidin/propidium iodide staining. Carrier fibrin gels containing rASCs acted as a self-shaping matrix to form a tubular structure. In this study, we could show that rASCs can be differentiated into activated, proliferating SCLs and that these cells react to minimal changes in stimulus, switching to a promyelinating phenotype. Aligned electrospun fibrin-PLGA fibers promoted the formation of Büngner-like structures in SCLs, which also rolled the fibrin-PLGA matrix into a tubular scaffold. These in vitro findings favor further in vivo testing. PMID:26372904

  9. Graphical environment for DAQ simulations

    NASA Astrophysics Data System (ADS)

    Wang, Chung-Ching; Booth, Alexander W.; Chen, Yen-Min; Botlo, Michael

    1994-02-01

    At the Superconducting Super Collider Laboratory (SSCL) a tool called DAQSIM has been developed to study the behavior of data acquisition (DAQ) systems. This paper reports and discusses the graphics use in DAQSIM. DAQSIM graphics includes graphical user interface (GUI), animation debugging, and control facilities. DAQSIM graphics not only provides a convenient DAQ simulation environment, it also serves as an efficient manager in simulation development and verification.

  10. 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…

  11. 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.

  12. 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…

  13. 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.

  14. 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.

  15. 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.

  16. Aligned PVDF-TrFE nanofibers with high-density PVDF nanofibers and PVDF core–shell structures for endovascular pressure sensing.

    PubMed

    Sharma, Tushar; Naik, Sahil; Langevine, Jewel; Gill, Brijesh; Zhang, John X J

    2015-01-01

    Nanostructures of polyvinyledenedifluoride-tetrafluoroethylene (PVDF-TrFE), a semicrystalline polymer with high piezoelectricity, results in significant enhancement of crystallinity and better device performance as sensors, actuators, and energy harvesters. Using electrospinning of PVDF to manufacture nanofibers, we demonstrate a new method to pattern high-density, highly aligned nanofibers. To further boost the charge transfer from such a bundle of nanofibers, we fabricated novel core-shell structures. Finally, we developed pressure sensors utilizing these fiber structures for endovascular applications. The sensors were tested in vitro under simulated physiological conditions. We observed significant improvements using core-shell electrospun fibers (4.5 times gain in signal intensity, 4000 μV/mmHg sensitivity) over PVDF nanofibers (280 μV/mmHg). The preliminary results showed that core-shell fiber-based devices exhibit nearly 40-fold higher sensitivity, compared to the thin-film structures demonstrated earlier. PMID:25095247

  17. 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.

  18. Simultaneous Alignment and Folding of Protein Sequences

    PubMed Central

    Waldispühl, Jérôme; O'Donnell, Charles W.; Will, Sebastian; Devadas, Srinivas; Backofen, Rolf

    2014-01-01

    Abstract Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We present partiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm's complexity is polynomial in time and space. Algorithmically, partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We demonstrate the efficacy of these techniques on transmembrane β-barrel proteins, an important yet difficult class of proteins with few known three-dimensional structures. Testing against structurally derived sequence alignments, partiFold-Align significantly outperforms state-of-the-art pairwise and multiple sequence alignment tools in the most difficult low-sequence homology case. It also improves secondary structure prediction where current approaches fail. Importantly, partiFold-Align requires no prior training. These general techniques are widely applicable to many more protein families (partiFold-Align is available at http://partifold.csail.mit.edu/). PMID:24766258

  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. Synthetic approach to designing optical alignment systems.

    PubMed

    Whang, A J; Gallagher, N C

    1988-08-15

    The objective of this study is twofold: to design reticle patterns with desirable alignment properties; to build an automatic alignment system using these patterns. We design such reticle patterns via a synthetic approach; the resultant patterns, so-called pseudonoise arrays, are binary and their autocorrelation functions are bilevel. Both properties are desirable in optical alignment. Besides, these arrays have attractive signal-to-noise ratio performance when employed in alignment. We implement the pseudonoise array as a 2-D cross-grating structure of which the grating period is much less than the wavelength of impinging light used for alignment. The short grating period feature, together with the use of polarized light, enables us to perform essentially 2-D optical alignment in one dimension. This alignment separability allows us to build a system that performs alignment automatically according to a simple 1-D algorithm. PMID:20539412

  1. 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.

  2. 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

  3. 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.

  4. 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…

  5. 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

  6. 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

  7. Galaxy Alignments: Theory, Modelling & Simulations

    NASA Astrophysics Data System (ADS)

    Kiessling, Alina; Cacciato, Marcello; Joachimi, Benjamin; Kirk, Donnacha; Kitching, Thomas D.; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Brown, Michael L.; Rassat, Anais

    2015-11-01

    The shapes of galaxies are not randomly oriented on the sky. During the galaxy formation and evolution process, environment has a strong influence, as tidal gravitational fields in the large-scale structure tend to align nearby galaxies. Additionally, events such as galaxy mergers affect the relative alignments of both the shapes and angular momenta of galaxies throughout their history. These "intrinsic galaxy alignments" are known to exist, but are still poorly understood. This review will offer a pedagogical introduction to the current theories that describe intrinsic galaxy alignments, including the apparent difference in intrinsic alignment between early- and late-type galaxies and the latest efforts to model them analytically. It will then describe the ongoing efforts to simulate intrinsic alignments using both N-body and hydrodynamic simulations. Due to the relative youth of this field, there is still much to be done to understand intrinsic galaxy alignments and this review summarises the current state of the field, providing a solid basis for future work.

  8. 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.

  9. 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

  10. 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.

  11. 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…

  12. 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,…

  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. 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.

  17. High-voltage electric-field-induced growth of aligned ``cow-nipple-like'' submicro-nano carbon isomeric structure via chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Liao, Chengwei; Zhang, Yupeng; Pan, Chunxu

    2012-12-01

    In this study, a novel vertically aligned carbon material, named "cow-nipple-like" submicro-nano carbon isomeric structure, was synthesized by the thermal decomposition of C2H2 in a chemical-vapor deposition system with a high-voltage external electric field. The microstructures were characterized by using scanning electron microscopy, high-resolution transmission electron microscopy, and Raman spectroscopy, respectively. The results revealed that (1) the total height of the carbon isomeric structure was in a rang of 90-250 nm; (2) the carbon isomeric structure consisted of a submicro- or nano-sized hemisphere carbon ball with 30-120 nm in diameter at the bottom and a vertically grown carbon nanotube with 10-40 nm in diameter upon the carbon ball; (3) there was a sudden change in diameter at the junction of the carbon ball and carbon nanotube. In addition, the carbon isomeric structure showed an excellent controllability, that is, the density, height, and diameter could be controlled effectively by adjusting the precursor ferrocene concentration in the catalytic solution and C2H2 ventilation time. A possible growth model was proposed to describe the formation mechanism, and a theoretic calculation was carried out to discuss the effect of high-voltage electric field upon the growth of the carbon isomeric structure.

  18. 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.

  19. 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

  20. Transformation and alignment in similarity.

    PubMed

    Hodgetts, Carl J; Hahn, Ulrike; Chater, Nick

    2009-10-01

    This paper contrasts two structural accounts of psychological similarity: structural alignment (SA) and Representational Distortion (RD). SA proposes that similarity is determined by how readily the structures of two objects can be brought into alignment; RD measures similarity by the complexity of the transformation that "distorts" one representation into the other. We assess RD by defining a simple coding scheme of psychological transformations for the experimental materials. In two experiments, this "concrete" version of RD provides compelling fits of the data and compares favourably with SA. Finally, stepping back from particular models, we argue that perceptual theory suggests that transformations and alignment processes should generally be viewed as complementary, in contrast to the current distinction in the literature. PMID:19720370

  1. Graphically Speaking: Graphics Software for Non-Artists.

    ERIC Educational Resources Information Center

    Crawford, Walt

    1994-01-01

    Discusses microcomputer-based graphics and describes software for Windows and other operating systems. Highlights include file formats for painting and drawing; sources of artwork, including clip art, scanning, and public domain images; examples; and graphics toolkits. A review of 26 recent articles on personal computers, other hardware, and…

  2. 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…

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. Graphics Display of Foreign Scripts.

    ERIC Educational Resources Information Center

    Abercrombie, John R.

    1987-01-01

    Describes Graphics Project for Foreign Language Learning at the University of Pennsylvania, which has developed ways of displaying foreign scripts on microcomputers. Character design on computer screens is explained; software for graphics, printing, and language instruction is discussed; and a text editor is described that corrects optically…

  8. 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.…

  9. 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…

  10. Low-Budget Graphic Databases.

    ERIC Educational Resources Information Center

    Mahoney, Dan

    1994-01-01

    Explains the use of a standard text-based database program (i.e., dBase III) to run external programs that display graphic files during a database session and reduces costs normally encountered when preparing a computer to run a graphical database. An example is given of a simple database with two fields. (LRW)

  11. Use a spreadsheet for turbomachinery alignment

    SciTech Connect

    Cassolato, B.M. , Sarnia, Ontario )

    1995-01-01

    Turbomachinery shaft alignment has an impact on plant profitability and safety. A simple sign error in the alignment process may incur days of production loss to correct, or worse if the mistake is undetected. Positioning large machinery, such as a centrifugal gas compressor weighing many tons to within thousandths of an inch, is laborious time-consuming work. Overhaul plans should specify the exact techniques, tools, desired results and quality assurance checks to be used in the alignment stages. The methods must be established by proven experience and best practices. The reverse indicator method is the most common precision alignment technique. The paper presents an instructional step-by-step development of a typical spreadsheet program for the reverse indicator method. The screen interface comprised of a cell range combining formulae and graphics provides the context for spreadsheet entries described in the following discussion. The worksheet is protected to disallow over-writing formulae and graphics, except in cell ranges reserved for input data. The program is designed to be user-friendly and comply with industry accepted practices. Special programming experience is not required of the operator.

  12. 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

  13. 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.

  14. 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.

  15. Computer graphics and graphic artists: a rocky courtship

    SciTech Connect

    Clark, B.A.

    1982-01-01

    A presentation- and publication-quality computer-graphics system has been implemented at Union Carbide Corporation Nuclear Division over the past four years. Success of the implementation required close interaction between programmers and illustrators. This paper discusses the problems involved in establishing a computer-graphics capability in a conventional graphic arts department. The problems dealt with fall into three areas: identifying and acquiring appropriate hardware, acquiring user-friendly software that could meet stringent quality standards, and overcoming the prejudices and misconceptions of all the people involved.

  16. 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.

  17. Alignment algorithm for homology modeling and threading.

    PubMed Central

    Alexandrov, N. N.; Luethy, R.

    1998-01-01

    A DNA/protein sequence comparison is a popular computational tool for molecular biologists. Finding a good alignment implies an evolutionary and/or functional relationship between proteins or genomic loci. Sequential similarity between two proteins indicates their structural resemblance, providing a practical approach for structural modeling, when structure of one of these proteins is known. The first step in the homology modeling is a construction of an accurate sequence alignment. The commonly used alignment algorithms do not provide an adequate treatment of the structurally mismatched residues in locally dissimilar regions. We propose a simple modification of the existing alignment algorithm which treats these regions properly and demonstrate how this modification improves sequence alignments in real proteins. PMID:9521100

  18. MAVID multiple alignment server.

    PubMed

    Bray, Nicolas; Pachter, Lior

    2003-07-01

    MAVID is a multiple alignment program suitable for many large genomic regions. The MAVID web server allows biomedical researchers to quickly obtain multiple alignments for genomic sequences and to subsequently analyse the alignments for conserved regions. MAVID has been successfully used for the alignment of closely related species such as primates and also for the alignment of more distant organisms such as human and fugu. The server is fast, capable of aligning hundreds of kilobases in less than a minute. The multiple alignment is used to build a phylogenetic tree for the sequences, which is subsequently used as a basis for identifying conserved regions in the alignment. The server can be accessed at http://baboon.math.berkeley.edu/mavid/.

  19. 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.

  20. BinAligner: a heuristic method to align biological networks

    PubMed Central

    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

  1. 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.

  2. 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

  3. The twilight zone of cis element alignments.

    PubMed

    Sebastian, Alvaro; Contreras-Moreira, Bruno

    2013-02-01

    Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein-DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein-DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments.

  4. 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

  5. A general graphical user interface for automatic reliability modeling

    NASA Technical Reports Server (NTRS)

    Liceaga, Carlos A.; Siewiorek, Daniel P.

    1991-01-01

    Reported here is a general Graphical User Interface (GUI) for automatic reliability modeling of Processor Memory Switch (PMS) structures using a Markov model. This GUI is based on a hierarchy of windows. One window has graphical editing capabilities for specifying the system's communication structure, hierarchy, reconfiguration capabilities, and requirements. Other windows have field texts, popup menus, and buttons for specifying parameters and selecting actions. An example application of the GUI is given.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. XUV ionization of aligned molecules

    NASA Astrophysics Data System (ADS)

    Kelkensberg, F.; Rouzée, A.; Siu, W.; Gademann, G.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.; Vrakking, M. J. J.

    2011-11-01

    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 CO2 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.

  11. 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.

  12. 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

  13. 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.

  14. Raster graphics extensions to the core system

    NASA Technical Reports Server (NTRS)

    Foley, J. D.

    1984-01-01

    A conceptual model of raster graphics systems was developed. The model integrates core-like graphics package concepts with contemporary raster display architectures. The conceptual model of raster graphics introduces multiple pixel matrices with associated index tables.

  15. 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.

  16. 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.

  17. Alignment Nashville. Complementary Learning in Action

    ERIC Educational Resources Information Center

    Bouffard, Suzanne; Malone, Helen

    2007-01-01

    This profile illustrates how Alignment Nashville brings together diverse community members and organizations to leverage existing resources in support of Nashville's youth and the Metro Nashville Public Schools. In addition to a diversified funding structure, Alignment leaders point to three factors that have helped them get the effort off the…

  18. 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

  19. 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.

  20. 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.

  1. APSRS state-base graphics

    USGS Publications Warehouse

    ,

    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.

  2. 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.

  3. Statistical graphics: mapping the pathways of science.

    PubMed

    Wainer, H; Velleman, P F

    2001-01-01

    This chapter traces the evolution of statistical graphics starting with its departure from the common noun structure of Cartesian determinism, through William Playfair's revolutionary grammatical shift to graphs as proper nouns, and alights on the modern conception of graph as an active participant in the scientific process of discovery. The ubiquitous availability of data, software, and cheap, high-powered, computing when coupled with the broad acceptance of the ideas in Tukey's 1977 treatise on exploratory data analysis has yielded a fundamental change in the way that the role of statistical graphics is thought of within science-as a dynamic partner and guide to the future rather than as a static monument to the discoveries of the past. We commemorate and illustrate this development while pointing readers to the new tools available and providing some indications of their potential.

  4. 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.

  5. HMI conventions for process control graphics.

    PubMed

    Pikaar, Ruud N

    2012-01-01

    Process operators supervise and control complex processes. To enable the operator to do an adequate job, instrumentation and process control engineers need to address several related topics, such as console design, information design, navigation, and alarm management. In process control upgrade projects, usually a 1:1 conversion of existing graphics is proposed. This paper suggests another approach, efficiently leading to a reduced number of new powerful process graphics, supported by a permanent process overview displays. In addition a road map for structuring content (process information) and conventions for the presentation of objects, symbols, and so on, has been developed. The impact of the human factors engineering approach on process control upgrade projects is illustrated by several cases.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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…

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. Computer graphic modeling in drug design--conformational analysis of antifolate binding to avian dihydrofolate reductase: crystal and molecular structures of 2,4-diamino-5-cyclohexyl-6-methylpyrimidine and 5-cyclohexyl-6-methyluracil.

    PubMed

    Cody, V; Ciszak, E

    1991-05-01

    The results of crystal structure determinations of the antifolate 2,4-diamino-5-cyclohexyl-6-methylprimidine (I), and its uracil derivative (II), show that the 5-cyclohexyl ring is gauche to the planar pyrimidine ring with torsion angles 82.4 (3) degrees and 63.7 (3) degrees for (I) and (II), respectively. Hydrogen bond patterns observed for these free base pyrimidines indicate a preference for N...N or N...O dimer formation around inversion centers, as observed in other antifolate structures. Computer graphic modeling studies were carried out comparing the avian dihydrofolate reductase active site interactions of the cyclohexyl antifolate (I) with the more potent 5-adamantyl analog and the less potent 5-hexyl and 5-heptyl antifolates. These data showed that although the cyclohexyl ring fits into the same conformational space as adamantyl, it makes fewer hydrophobic contacts. Similarly, cyclohexyl fills the active site better than either the 5-n-hexyl or heptyl side chains. These data are consistent with the increased potency of the adamantyl and cyclohexyl antifolates compared to n-alkyl analogs with similar hydrophobicities. These data indicate that the rigid structure of these ring systems increases their hydrophobic interactions, thus enhancing their biochemical activity.

  16. 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

  17. 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.

  18. 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 ...

  19. 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.

  20. 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

  1. Graphical inference for Infovis.

    PubMed

    Wickham, Hadley; Cook, Dianne; Hofmann, Heike; Buja, Andreas

    2010-01-01

    How do we know if what we see is really there? When visualizing data, how do we avoid falling into the trap of apophenia where we see patterns in random noise? Traditionally, infovis has been concerned with discovering new relationships, and statistics with preventing spurious relationships from being reported. We pull these opposing poles closer with two new techniques for rigorous statistical inference of visual discoveries. The "Rorschach" helps the analyst calibrate their understanding of uncertainty and "line-up" provides a protocol for assessing the significance of visual discoveries, protecting against the discovery of spurious structure.

  2. Training manual on optical alignment instruments

    NASA Technical Reports Server (NTRS)

    1968-01-01

    Training Manual RQA/M5 provides a basic course of instruction in the use of optical instruments for precise dimensional control and alignment of structural elements and assemblies, such as associated with space vehicles, aircraft, ships, and buildings.

  3. Graphics-System Color-Code Interface

    NASA Technical Reports Server (NTRS)

    Tulppo, J. S.

    1982-01-01

    Circuit originally developed for a flight simulator interfaces a computer graphics system with color monitor. Subsystem is intended for particular display computer (AGT-130, ADAGE Graphics Terminal) and specific color monitor (beam penetration tube--Penetron). Store-and-transmit channel is one of five in graphics/color-monitor interface. Adding 5-bit color code to existing graphics programs requires minimal programing effort.

  4. 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…

  5. 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,…

  6. 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…

  7. Computer Graphics. Curriculum Guide for Technology Education.

    ERIC Educational Resources Information Center

    Craft, Clyde O.

    This curriculum guide for a 1-quarter or 1-semester course in computer graphics is designed to be used with Apple II computers. Some of the topics covered include the following: computer graphics terminology and applications, operating Apple computers, graphics programming in BASIC using various programs and commands, computer graphics painting,…

  8. 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

  9. 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.

  10. The Systems Biology Graphical Notation.

    PubMed

    Le Novère, Nicolas; Hucka, Michael; Mi, Huaiyu; Moodie, Stuart; Schreiber, Falk; Sorokin, Anatoly; Demir, Emek; Wegner, Katja; Aladjem, Mirit I; Wimalaratne, Sarala M; Bergman, Frank T; Gauges, Ralph; Ghazal, Peter; Kawaji, Hideya; Li, Lu; Matsuoka, Yukiko; Villéger, Alice; Boyd, Sarah E; Calzone, Laurence; Courtot, Melanie; Dogrusoz, Ugur; Freeman, Tom C; Funahashi, Akira; Ghosh, Samik; Jouraku, Akiya; Kim, Sohyoung; Kolpakov, Fedor; Luna, Augustin; Sahle, Sven; Schmidt, Esther; Watterson, Steven; Wu, Guanming; Goryanin, Igor; Kell, Douglas B; Sander, Chris; Sauro, Herbert; Snoep, Jacky L; Kohn, Kurt; Kitano, Hiroaki

    2009-08-01

    Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.

  11. 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.

  12. VAX Professional Workstation goes graphic

    SciTech Connect

    Downward, J.G.

    1984-01-01

    The VAX Professional Workstation (VPW) is a collection of programs and procedures designed to provide an integrated work-station environment for the staff at KMS Fusion's research laboratories. During the past year numerous capabilities have been added to VPW, including support for VT125/VT240/4014 graphic workstations, editing windows, and additional desk utilities. Graphics workstation support allows users to create, edit, and modify graph data files, enter the data via a graphic tablet, create simple plots with DATATRIEVE or DECgraph on ReGIS terminals, or elaborate plots with TEKGRAPH on ReGIS or Tektronix terminals. Users may assign display error bars to the data and interactively plot it in a variety of ways. Users also can create and display viewgraphs. Hard copy output for a large network of office terminals is obtained by multiplexing each terminal's video output into a recently developed video multiplexer front ending a single channel video hard copy unit.

  13. 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…

  14. 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.

  15. 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.

  16. 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.

  17. Color graphics, interactive processing, and the supercomputer

    NASA Technical Reports Server (NTRS)

    Smith-Taylor, Rudeen

    1987-01-01

    The development of a common graphics environment for the NASA Langley Research Center user community and the integration of a supercomputer into this environment is examined. The initial computer hardware, the software graphics packages, and their configurations are described. The addition of improved computer graphics capability to the supercomputer, and the utilization of the graphic software and hardware are discussed. Consideration is given to the interactive processing system which supports the computer in an interactive debugging, processing, and graphics environment.

  18. Graphics Design Technology Curriculum Guide.

    ERIC Educational Resources Information Center

    Idaho State Dept. of Education, Boise. Div. of Vocational Education.

    This Idaho secondary education curriculum guide provides lists of tasks, performance objectives, and enabling objectives for instruction intended to impart entry-level employment skills in graphics design technology. The first list states all tasks for 11 areas; separate lists for each area follow. Each task on the lists is accompanied by a…

  19. 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)

  20. 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.

  1. 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…

  2. 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,…

  3. 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)

  4. LONGLIB Graphics-Library Program

    NASA Technical Reports Server (NTRS)

    Long, David G.

    1988-01-01

    LONGLIB computer program is set of subroutines designed for plotting vectors of cathode-ray tubes, plotting machines, and dot-matrix and laser printers. Contains extensive set of routines to enable viewport clipping, extended character sets, graphic input shading, polar plots, and three-dimensional plotting with or without removal of hidden lines. Written in FORTRAN 77.

  5. 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…

  6. 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.

  7. 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…

  8. 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…

  9. 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.

  10. Formation and Structural Characteristic of Perpendicularly Aligned Boron Nitride Nanosheet Bridges in Polymer/Boron Nitride Composite Film and Its Thermal Conductivity

    NASA Astrophysics Data System (ADS)

    Cho, Hong-Baek; Nakayama, Tadachika; Suzuki, Tsuneo; Tanaka, Satoshi; Jiang, Weihua; Suematsu, Hisayuki; Niihara, Koichi

    2011-01-01

    The anisotropic alignment of boron nitride (BN) nanosheets was performed in polysiloxane/BN nanosheet composite film under a DC electric field with a change in polarity. The hexagonal BN nanosheets were dispersed by sonication in a prepolymer mixture of polysiloxane followed by high-speed mixing. The homogeneous suspension was cast onto a spacer of microscale thickness and applied to a high DC electric field while changing polarity before the mixture became cross-linked. Analysis revealed that linearly aligned BN nanosheet (LABN) bridges were fabricated in the composite film while connecting the film planes as bridges. This is for first report on the fabrication of linearly aligned nanosheet bridges inside organic-inorganic hybrid films. The fabricated LABN bridges were attributed to the enhancement in the thermal conductivity of the composite film, and the mechanisms underlying the formation of LABN bridges and heat conduction were discussed.

  11. 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

  12. 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.

  13. 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.

  14. Radiative Grain Alignment

    NASA Astrophysics Data System (ADS)

    Andersson, B. G.

    2015-12-01

    Polarization due to aligned dust grains was discovered in the interstellar medium more than 60 years ago. A quantitative, observationally well tested theory of the phenomenon has finally emerged in the last decade, promising not only an improved understanding of interstellar magnetic fields, but new tools for studying the dust environments and grain characteristics. This Radiative Alignment Torque (RAT) theory also has many potential applications in solar system physics, including for comet dust characteristics. I will review the main aspects of the theory and the observational tests performed to date, as well as some of the new possibilities for using polarization as a tool to study dust and its environment, with RAT alignment.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. Graphics applications utilizing parallel processing

    NASA Technical Reports Server (NTRS)

    Rice, John R.

    1990-01-01

    The results are presented of research conducted to develop a parallel graphic application algorithm to depict the numerical solution of the 1-D wave equation, the vibrating string. The research was conducted on a Flexible Flex/32 multiprocessor and a Sequent Balance 21000 multiprocessor. The wave equation is implemented using the finite difference method. The synchronization issues that arose from the parallel implementation and the strategies used to alleviate the effects of the synchronization overhead are discussed.

  4. 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.

  5. Freedom System Text and Graphics System (TAGS)

    NASA Technical Reports Server (NTRS)

    1989-01-01

    The Text and Graphics System (TAGS) is a high-resolution facsimile system that scans text or graphics material and converts the analog SCAN data into serial digital data. This video shows the TAGS in operation.

  6. Computer Graphics and Administrative Decision-Making.

    ERIC Educational Resources Information Center

    Yost, Michael

    1984-01-01

    Reduction in prices now makes it possible for almost any institution to use computer graphics for administrative decision making and research. Current and potential uses of computer graphics in these two areas are discussed. (JN)

  7. PDV Probe Alignment Technique

    SciTech Connect

    Whitworth, T L; May, C M; Strand, O T

    2007-10-26

    This alignment technique was developed while performing heterodyne velocimetry measurements at LLNL. There are a few minor items needed, such as a white card with aperture in center, visible alignment laser, IR back reflection meter, and a microscope to view the bridge surface. The work was performed on KCP flyers that were 6 and 8 mils wide. The probes used were Oz Optics manufactured with focal distances of 42mm and 26mm. Both probes provide a spot size of approximately 80?m at 1550nm. The 42mm probes were specified to provide an internal back reflection of -35 to -40dB, and the probe back reflections were measured to be -37dB and -33dB. The 26mm probes were specified as -30dB and both measured -30.5dB. The probe is initially aligned normal to the flyer/bridge surface. This provides a very high return signal, up to -2dB, due to the bridge reflectivity. A white card with a hole in the center as an aperture can be used to check the reflected beam position relative to the probe and launch beam, and the alignment laser spot centered on the bridge, see Figure 1 and Figure 2. The IR back reflection meter is used to measure the dB return from the probe and surface, and a white card or similar object is inserted between the probe and surface to block surface reflection. It may take several iterations between the visible alignment laser and the IR back reflection meter to complete this alignment procedure. Once aligned normal to the surface, the probe should be tilted to position the visible alignment beam as shown in Figure 3, and the flyer should be translated in the X and Y axis to reposition the alignment beam onto the flyer as shown in Figure 4. This tilting of the probe minimizes the amount of light from the bridge reflection into the fiber within the probe while maintaining the alignment as near normal to the flyer surface as possible. When the back reflection is measured after the tilt adjustment, the level should be about -3dB to -6dB higher than the probes

  8. Curriculum Alignment Research Suggests that Alignment Can Improve Student Achievement

    ERIC Educational Resources Information Center

    Squires, David

    2012-01-01

    Curriculum alignment research has developed showing the relationship among three alignment categories: the taught curriculum, the tested curriculum and the written curriculum. Each pair (for example, the taught and the written curriculum) shows a positive impact for aligning those results. Following this, alignment results from the Third…

  9. Corrective optics space telescope axial replacement alignment system

    NASA Astrophysics Data System (ADS)

    Slusher, Robert B.; Satter, Michael J.; Kaplan, Michael L.; Martella, Mark A.; Freymiller, Ed D.; Buzzetta, Victor

    1993-10-01

    To facilitate the accurate placement and alignment of the corrective optics space telescope axial replacement (COSTAR) structure, mechanisms, and optics, the COSTAR Alignment System (CAS) has been designed and assembled. It consists of a 20-foot optical bench, support structures for holding and aligning the COSTAR instrument at various stages of assembly, a focal plane target fixture (FPTF) providing an accurate reference to the as-built Hubble Space Telescope (HST) focal plane, two alignment translation stages with interchangeable alignment telescopes and alignment lasers, and a Zygo Mark IV interferometer with a reference sphere custom designed to allow accurate double-pass operation of the COSTAR correction optics. The system is used to align the fixed optical bench (FOB), the track, the deployable optical bench (DOB), the mechanisms, and the optics to ensure that the correction mirrors are all located in the required positions and orientations on-orbit after deployment. In this paper, the layout of the CAS is presented and the various alignment operations are listed along with the relevant alignment requirements. In addition, calibration of the necessary support structure elements and alignment aids is described, including the two-axis translation stages, the latch positions, the FPTF, and the COSTAR-mounted alignment cubes.

  10. Building Regression Models: The Importance of Graphics.

    ERIC Educational Resources Information Center

    Dunn, Richard

    1989-01-01

    Points out reasons for using graphical methods to teach simple and multiple regression analysis. Argues that a graphically oriented approach has considerable pedagogic advantages in the exposition of simple and multiple regression. Shows that graphical methods may play a central role in the process of building regression models. (Author/LS)

  11. The Evolution of Graphics in CAL.

    ERIC Educational Resources Information Center

    Skyrme, David J.

    1982-01-01

    Traces the evolution of graphics in computer assisted learning (CAL), discusses different classes of graphics terminals as they relate to the desirable requirements of a student terminal, and draws conclusions about the growth of graphics in CAL. A bibliography of 13 items is included. (CHC)

  12. Information Graphic Classification, Decomposition and Alternative Representation

    ERIC Educational Resources Information Center

    Gao, Jinglun

    2012-01-01

    This thesis work is mainly focused on two problems related to improving accessibility of information graphics for visually impaired users. The first problem is automated analysis of information graphics for information extraction and the second problem is multi-modal representations for accessibility. Information graphics are graphical…

  13. Mathematical Creative Activity and the Graphic Calculator

    ERIC Educational Resources Information Center

    Duda, Janina

    2011-01-01

    Teaching mathematics using graphic calculators has been an issue of didactic discussions for years. Finding ways in which graphic calculators can enrich the development process of creative activity in mathematically gifted students between the ages of 16-17 is the focus of this article. Research was conducted using graphic calculators with…

  14. Narrative Problems of Graphic Design History.

    ERIC Educational Resources Information Center

    Margolin, Victor

    1994-01-01

    Discusses three major accounts (by Philip Meggs, Enric Satue and Richard Hollis) of graphic design history. Notes that these texts address the history of graphic design, but each raises questions about what material to include, as well as how graphic design is both related to and distinct from other visual practices such as typography, art…

  15. Graphic Novels in Your School Library

    ERIC Educational Resources Information Center

    Karp, Jesse

    2011-01-01

    Many educators now agree that graphic novels inform as well as entertain, and to dismiss the educational potential of the graphic novel is to throw away a golden opportunity to reach out to young readers. This dynamic book takes a look at the term "graphic novel," how the format has become entwined in our culture, and the ways in which graphic…

  16. Minard's Graphic of Napoleon in Russia.

    ERIC Educational Resources Information Center

    Hardy, Charles

    1992-01-01

    Describes the use of Charles Minard's graphic of Napoleon's 1812 Russian Campaign as an instructional tool in history classes. Maintains that the graphic, created in 1861, can be analyzed by students to determine six historical and geographical factors involved in Napoleon's defeat. Includes a copy of Minard's graphic. (CFR)

  17. Graphics: A Catalyst to Institutional Identity

    ERIC Educational Resources Information Center

    Lahti, Robert E.

    1971-01-01

    Graphic impressions (stationery, publications, bookstore items, displays, campus signage) is one of four communication mechanisms available to a college. Harper College in Illinois offers an example of a uniform graphics approach. A graphics designer has the role of publicizing a college to its community. (CA)

  18. Creating Graphics Files for SGML Documents.

    ERIC Educational Resources Information Center

    Lunemann, Rhonda S.

    1995-01-01

    Suggests that, when creating graphics files for documents in a Standard Generalized Markup Language (SGML) environment, technical writers should consider the differences between bitmapped and vector file formats; be familiar with available file formats; determine which graphics format best meets the needs; and incorporate the graphic into the SGML…

  19. Graphic Design Is Not a Medium.

    ERIC Educational Resources Information Center

    Gruber, John Edward, Jr.

    2001-01-01

    Discusses graphic design and reviews its development from analog processes to a digital tool with the use of computers. Topics include graphical user interfaces; the need for visual communication concepts; transmedia as opposed to repurposing; and graphic design instruction in higher education. (LRW)

  20. Computer graphics: Programmers's Hierarchical Interactive Graphics System (PHIGS). Language bindings (Part 3. Ada). Category: Software standard. Subcategory: Graphics. Final report

    SciTech Connect

    Benigni, D.R.

    1990-01-01

    The publication announces the adoption of the American National Standard Programmer's Hierarchical Interactive Graphics System, ANSI X3.144-1988, as a Federal Information Processing Standard (FIPS). The standard specifies the control and data interchange between an application program and its graphic support system. It provides a set of functions and programming language bindings, (or toolbox package) for the definition, display and modification of two-dimensional (2D) or three-dimensional (3D) graphical data. In addition, the standard supports highly interactive processing and geometric articulation, multi-level or hierarchical graphics data, and rapid modification of both the graphics data and the relationships between the graphical data. The purpose of the standard is to promote portability of graphics application programs between different installations.