Science.gov

Sample records for 3d structural information

  1. The RCSB protein data bank: integrative view of protein, gene and 3D structural information.

    PubMed

    Rose, Peter W; Prlić, Andreas; Altunkaya, Ali; Bi, Chunxiao; Bradley, Anthony R; Christie, Cole H; Costanzo, Luigi Di; Duarte, Jose M; Dutta, Shuchismita; Feng, Zukang; Green, Rachel Kramer; Goodsell, David S; Hudson, Brian; Kalro, Tara; Lowe, Robert; Peisach, Ezra; Randle, Christopher; Rose, Alexander S; Shao, Chenghua; Tao, Yi-Ping; Valasatava, Yana; Voigt, Maria; Westbrook, John D; Woo, Jesse; Yang, Huangwang; Young, Jasmine Y; Zardecki, Christine; Berman, Helen M; Burley, Stephen K

    2017-01-04

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.' Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive.

  2. The RCSB protein data bank: integrative view of protein, gene and 3D structural information

    PubMed Central

    Rose, Peter W.; Prlić, Andreas; Altunkaya, Ali; Bi, Chunxiao; Bradley, Anthony R.; Christie, Cole H.; Costanzo, Luigi Di; Duarte, Jose M.; Dutta, Shuchismita; Feng, Zukang; Green, Rachel Kramer; Goodsell, David S.; Hudson, Brian; Kalro, Tara; Lowe, Robert; Peisach, Ezra; Randle, Christopher; Rose, Alexander S.; Shao, Chenghua; Tao, Yi-Ping; Valasatava, Yana; Voigt, Maria; Westbrook, John D.; Woo, Jesse; Yang, Huangwang; Young, Jasmine Y.; Zardecki, Christine; Berman, Helen M.; Burley, Stephen K.

    2017-01-01

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a ‘Structural View of Biology.’ Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive. PMID:27794042

  3. Disulfide Connectivity Prediction Based on Modelled Protein 3D Structural Information and Random Forest Regression.

    PubMed

    Yu, Dong-Jun; Li, Yang; Hu, Jun; Yang, Xibei; Yang, Jing-Yu; Shen, Hong-Bin

    2015-01-01

    Disulfide connectivity is an important protein structural characteristic. Accurately predicting disulfide connectivity solely from protein sequence helps to improve the intrinsic understanding of protein structure and function, especially in the post-genome era where large volume of sequenced proteins without being functional annotated is quickly accumulated. In this study, a new feature extracted from the predicted protein 3D structural information is proposed and integrated with traditional features to form discriminative features. Based on the extracted features, a random forest regression model is performed to predict protein disulfide connectivity. We compare the proposed method with popular existing predictors by performing both cross-validation and independent validation tests on benchmark datasets. The experimental results demonstrate the superiority of the proposed method over existing predictors. We believe the superiority of the proposed method benefits from both the good discriminative capability of the newly developed features and the powerful modelling capability of the random forest. The web server implementation, called TargetDisulfide, and the benchmark datasets are freely available at: http://csbio.njust.edu.cn/bioinf/TargetDisulfide for academic use.

  4. Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank.

    PubMed

    Prlić, Andreas; Kalro, Tara; Bhattacharya, Roshni; Christie, Cole; Burley, Stephen K; Rose, Peter W

    2016-12-15

    The Protein Data Bank (PDB) now contains more than 120,000 three-dimensional (3D) structures of biological macromolecules. To allow an interpretation of how PDB data relates to other publicly available annotations, we developed a novel data integration platform that maps 3D structural information across various datasets. This integration bridges from the human genome across protein sequence to 3D structure space. We developed novel software solutions for data management and visualization, while incorporating new libraries for web-based visualization using SVG graphics.

  5. The role of perspective information in the recovery of 3D structure-from-motion.

    PubMed

    Eagle, R A; Hogervorst, M A

    1999-05-01

    When investigating the recovery of three-dimensional structure-from-motion (SFM), vision scientists often assume that scaled-orthographic projection, which removes effects due to depth variations across the object, is an adequate approximation to full perspective projection. This is so even though SFM judgements can, in principle, be improved by exploiting perspective projection of scenes on to the retina. In an experiment, pairs of rotating hinged planes (open books) were simulated on a computer monitor, under either perspective or orthographic projection, and human observers were asked to indicate which they perceived had the larger dihedral angle. For small displays (4.6 x 6.0 degrees) discrimination thresholds were found to be similar under the two conditions, but diverged for all larger stimuli. In particular, as stimulus size was increased, performance under orthographic projection declined and by a stimulus size of 32 x 41 degrees performance was at chance for all subjects. In contrast, thresholds decreased under perspective projection as stimulus size was increased. These results show that human observers can use the information gained from perspective projection to recover SFM and that scaled-orthographic projection becomes an unacceptable approximation even at quite modest stimulus sizes. A model of SFM that incorporates measurement errors on the retinal motions accounts for performance under both projection systems, suggesting that this early noise forms the primary limitation on 3D discrimination performance.

  6. Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank

    PubMed Central

    Prlić, Andreas; Kalro, Tara; Bhattacharya, Roshni; Christie, Cole; Burley, Stephen K.; Rose, Peter W.

    2016-01-01

    Summary: The Protein Data Bank (PDB) now contains more than 120,000 three-dimensional (3D) structures of biological macromolecules. To allow an interpretation of how PDB data relates to other publicly available annotations, we developed a novel data integration platform that maps 3D structural information across various datasets. This integration bridges from the human genome across protein sequence to 3D structure space. We developed novel software solutions for data management and visualization, while incorporating new libraries for web-based visualization using SVG graphics. Availability and Implementation: The new views are available from http://www.rcsb.org and software is available from https://github.com/rcsb/. Contact: andreas.prlic@rcsb.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27551105

  7. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    ERIC Educational Resources Information Center

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  8. 3D-graphite structure

    SciTech Connect

    Belenkov, E. A. Ali-Pasha, V. A.

    2011-01-15

    The structure of clusters of some new carbon 3D-graphite phases have been calculated using the molecular-mechanics methods. It is established that 3D-graphite polytypes {alpha}{sub 1,1}, {alpha}{sub 1,3}, {alpha}{sub 1,5}, {alpha}{sub 2,1}, {alpha}{sub 2,3}, {alpha}{sub 3,1}, {beta}{sub 1,2}, {beta}{sub 1,4}, {beta}{sub 1,6}, {beta}{sub 2,1}, and {beta}{sub 3,2} consist of sp{sup 2}-hybridized atoms, have hexagonal unit cells, and differ in regards to the structure of layers and order of their alternation. A possible way to experimentally synthesize new carbon phases is proposed: the polymerization and carbonization of hydrocarbon molecules.

  9. 3D structured illumination microscopy

    NASA Astrophysics Data System (ADS)

    Dougherty, William M.; Goodwin, Paul C.

    2011-03-01

    Three-dimensional structured illumination microscopy achieves double the lateral and axial resolution of wide-field microscopy, using conventional fluorescent dyes, proteins and sample preparation techniques. A three-dimensional interference-fringe pattern excites the fluorescence, filling in the "missing cone" of the wide field optical transfer function, thereby enabling axial (z) discrimination. The pattern acts as a spatial carrier frequency that mixes with the higher spatial frequency components of the image, which usually succumb to the diffraction limit. The fluorescence image encodes the high frequency content as a down-mixed, moiré-like pattern. A series of images is required, wherein the 3D pattern is shifted and rotated, providing down-mixed data for a system of linear equations. Super-resolution is obtained by solving these equations. The speed with which the image series can be obtained can be a problem for the microscopy of living cells. Challenges include pattern-switching speeds, optical efficiency, wavefront quality and fringe contrast, fringe pitch optimization, and polarization issues. We will review some recent developments in 3D-SIM hardware with the goal of super-resolved z-stacks of motile cells.

  10. Quon 3D language for quantum information

    PubMed Central

    Liu, Zhengwei; Wozniakowski, Alex; Jaffe, Arthur M.

    2017-01-01

    We present a 3D topological picture-language for quantum information. Our approach combines charged excitations carried by strings, with topological properties that arise from embedding the strings in the interior of a 3D manifold with boundary. A quon is a composite that acts as a particle. Specifically, a quon is a hemisphere containing a neutral pair of open strings with opposite charge. We interpret multiquons and their transformations in a natural way. We obtain a type of relation, a string–genus “joint relation,” involving both a string and the 3D manifold. We use the joint relation to obtain a topological interpretation of the C∗-Hopf algebra relations, which are widely used in tensor networks. We obtain a 3D representation of the controlled NOT (CNOT) gate that is considerably simpler than earlier work, and a 3D topological protocol for teleportation. PMID:28167790

  11. 3D Structured Grid Adaptation

    NASA Technical Reports Server (NTRS)

    Banks, D. W.; Hafez, M. M.

    1996-01-01

    Grid adaptation for structured meshes is the art of using information from an existing, but poorly resolved, solution to automatically redistribute the grid points in such a way as to improve the resolution in regions of high error, and thus the quality of the solution. This involves: (1) generate a grid vis some standard algorithm, (2) calculate a solution on this grid, (3) adapt the grid to this solution, (4) recalculate the solution on this adapted grid, and (5) repeat steps 3 and 4 to satisfaction. Steps 3 and 4 can be repeated until some 'optimal' grid is converged to but typically this is not worth the effort and just two or three repeat calculations are necessary. They also may be repeated every 5-10 time steps for unsteady calculations.

  12. 3D Structures of Responsive Nanocompartmentalized Microgels.

    PubMed

    Gelissen, Arjan P H; Oppermann, Alex; Caumanns, Tobias; Hebbeker, Pascal; Turnhoff, Sarah K; Tiwari, Rahul; Eisold, Sabine; Simon, Ulrich; Lu, Yan; Mayer, Joachim; Richtering, Walter; Walther, Andreas; Wöll, Dominik

    2016-11-09

    Compartmentalization in soft matter is important for segregating and coordinating chemical reactions, sequestering (re)active components, and integrating multifunctionality. Advances depend crucially on quantitative 3D visualization in situ with high spatiotemporal resolution. Here, we show the direct visualization of different compartments within adaptive microgels using a combination of in situ electron and super-resolved fluorescence microscopy. We unravel new levels of structural details and address the challenge of reconstructing 3D information from 2D projections for nonuniform soft matter as opposed to monodisperse proteins. Moreover, we visualize the thermally induced shrinkage of responsive core-shell microgels live in water. This strategy opens doors for systematic in situ studies of soft matter systems and their application as smart materials.

  13. Inferential modeling of 3D chromatin structure.

    PubMed

    Wang, Siyu; Xu, Jinbo; Zeng, Jianyang

    2015-04-30

    For eukaryotic cells, the biological processes involving regulatory DNA elements play an important role in cell cycle. Understanding 3D spatial arrangements of chromosomes and revealing long-range chromatin interactions are critical to decipher these biological processes. In recent years, chromosome conformation capture (3C) related techniques have been developed to measure the interaction frequencies between long-range genome loci, which have provided a great opportunity to decode the 3D organization of the genome. In this paper, we develop a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data. By modeling each chromosome as a polymer chain, we define the conformational energy based on our current knowledge on polymer physics and use it as prior information in the Bayesian framework. We also propose an expectation-maximization (EM) based algorithm to estimate the unknown parameters of the Bayesian model and infer an ensemble of chromatin structures based on interaction frequency data. We have validated our Bayesian inference approach through cross-validation and verified the computed chromatin conformations using the geometric constraints derived from fluorescence in situ hybridization (FISH) experiments. We have further confirmed the inferred chromatin structures using the known genetic interactions derived from other studies in the literature. Our test results have indicated that our Bayesian framework can compute an accurate ensemble of 3D chromatin conformations that best interpret the distance constraints derived from 3C-based data and also agree with other sources of geometric constraints derived from experimental evidence in the previous studies. The source code of our approach can be found in https://github.com/wangsy11/InfMod3DGen.

  14. Computational modeling of RNA 3D structures and interactions.

    PubMed

    Dawson, Wayne K; Bujnicki, Janusz M

    2016-04-01

    RNA molecules have key functions in cellular processes beyond being carriers of protein-coding information. These functions are often dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is difficult, which has prompted the development of computational methods for structure prediction from sequence. Recent progress in 3D structure modeling of RNA and emerging approaches for predicting RNA interactions with ions, ligands and proteins have been stimulated by successes in protein 3D structure modeling.

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

    PubMed

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

    2015-07-01

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

  17. Self assembled structures for 3D integration

    NASA Astrophysics Data System (ADS)

    Rao, Madhav

    Three dimensional (3D) micro-scale structures attached to a silicon substrate have various applications in microelectronics. However, formation of 3D structures using conventional micro-fabrication techniques are not efficient and require precise control of processing parameters. Self assembly is a method for creating 3D structures that takes advantage of surface area minimization phenomena. Solder based self assembly (SBSA), the subject of this dissertation, uses solder as a facilitator in the formation of 3D structures from 2D patterns. Etching a sacrificial layer underneath a portion of the 2D pattern allows the solder reflow step to pull those areas out of the substrate plane resulting in a folded 3D structure. Initial studies using the SBSA method demonstrated low yields in the formation of five different polyhedra. The failures in folding were primarily attributed to nonuniform solder deposition on the underlying metal pads. The dip soldering method was analyzed and subsequently refined. A modified dip soldering process provided improved yield among the polyhedra. Solder bridging referred as joining of solder deposited on different metal patterns in an entity influenced the folding mechanism. In general, design parameters such as small gap-spacings and thick metal pads were found to favor solder bridging for all patterns studied. Two types of soldering: face and edge soldering were analyzed. Face soldering refers to the application of solder on the entire metal face. Edge soldering indicates application of solder only on the edges of the metal face. Mechanical grinding showed that face soldered SBSA structures were void free and robust in nature. In addition, the face soldered 3D structures provide a consistent heat resistant solder standoff height that serve as attachments in the integration of dissimilar electronic technologies. Face soldered 3D structures were developed on the underlying conducting channel to determine the thermo-electric reliability of

  18. 3D Structure of Tillage Soils

    NASA Astrophysics Data System (ADS)

    González-Torre, Iván; Losada, Juan Carlos; Falconer, Ruth; Hapca, Simona; Tarquis, Ana M.

    2015-04-01

    Soil structure may be defined as the spatial arrangement of soil particles, aggregates and pores. The geometry of each one of these elements, as well as their spatial arrangement, has a great influence on the transport of fluids and solutes through the soil. Fractal/Multifractal methods have been increasingly applied to quantify soil structure thanks to the advances in computer technology (Tarquis et al., 2003). There is no doubt that computed tomography (CT) has provided an alternative for observing intact soil structure. These CT techniques reduce the physical impact to sampling, providing three-dimensional (3D) information and allowing rapid scanning to study sample dynamics in near real-time (Houston et al., 2013a). However, several authors have dedicated attention to the appropriate pore-solid CT threshold (Elliot and Heck, 2007; Houston et al., 2013b) and the better method to estimate the multifractal parameters (Grau et al., 2006; Tarquis et al., 2009). The aim of the present study is to evaluate the effect of the algorithm applied in the multifractal method (box counting and box gliding) and the cube size on the calculation of generalized fractal dimensions (Dq) in grey images without applying any threshold. To this end, soil samples were extracted from different areas plowed with three tools (moldboard, chissel and plow). Soil samples for each of the tillage treatment were packed into polypropylene cylinders of 8 cm diameter and 10 cm high. These were imaged using an mSIMCT at 155keV and 25 mA. An aluminium filter (0.25 mm) was applied to reduce beam hardening and later several corrections where applied during reconstruction. References Elliot, T.R. and Heck, R.J. 2007. A comparison of 2D and 3D thresholding of CT imagery. Can. J. Soil Sci., 87(4), 405-412. Grau, J, Médez, V.; Tarquis, A.M., Saa, A. and Díaz, M.C.. 2006. Comparison of gliding box and box-counting methods in soil image analysis. Geoderma, 134, 349-359. González-Torres, Iván. Theory and

  19. MSV3d: database of human MisSense Variants mapped to 3D protein structure.

    PubMed

    Luu, Tien-Dao; Rusu, Alin-Mihai; Walter, Vincent; Ripp, Raymond; Moulinier, Luc; Muller, Jean; Toursel, Thierry; Thompson, Julie D; Poch, Olivier; Nguyen, Hoan

    2012-01-01

    The elucidation of the complex relationships linking genotypic and phenotypic variations to protein structure is a major challenge in the post-genomic era. We present MSV3d (Database of human MisSense Variants mapped to 3D protein structure), a new database that contains detailed annotation of missense variants of all human proteins (20 199 proteins). The multi-level characterization includes details of the physico-chemical changes induced by amino acid modification, as well as information related to the conservation of the mutated residue and its position relative to functional features in the available or predicted 3D model. Major releases of the database are automatically generated and updated regularly in line with the dbSNP (database of Single Nucleotide Polymorphism) and SwissVar releases, by exploiting the extensive Décrypthon computational grid resources. The database (http://decrypthon.igbmc.fr/msv3d) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in XML or flat file formats. Database URL: http://decrypthon.igbmc.fr/msv3d.

  20. Formal representation of 3D structural geological models

    NASA Astrophysics Data System (ADS)

    Wang, Zhangang; Qu, Honggang; Wu, Zixing; Yang, Hongjun; Du, Qunle

    2016-05-01

    The development and widespread application of geological modeling methods has increased demands for the integration and sharing services of three dimensional (3D) geological data. However, theoretical research in the field of geological information sciences is limited despite the widespread use of Geographic Information Systems (GIS) in geology. In particular, fundamental research on the formal representations and standardized spatial descriptions of 3D structural models is required. This is necessary for accurate understanding and further applications of geological data in 3D space. In this paper, we propose a formal representation method for 3D structural models using the theory of point set topology, which produces a mathematical definition for the major types of geological objects. The spatial relationships between geologic boundaries, structures, and units are explained in detail using the 9-intersection model. Reasonable conditions for describing the topological space of 3D structural models are also provided. The results from this study can be used as potential support for the standardized representation and spatial quality evaluation of 3D structural models, as well as for specific needs related to model-based management, query, and analysis.

  1. Automated modeling of RNA 3D structure.

    PubMed

    Rother, Kristian; Rother, Magdalena; Skiba, Pawel; Bujnicki, Janusz M

    2014-01-01

    This chapter gives an overview over the current methods for automated modeling of RNA structures, with emphasis on template-based methods. The currently used approaches to RNA modeling are presented with a side view on the protein world, where many similar ideas have been used. Two main programs for automated template-based modeling are presented: ModeRNA assembling structures from fragments and MacroMoleculeBuilder performing a simulation to satisfy spatial restraints. Both approaches have in common that they require an alignment of the target sequence to a known RNA structure that is used as a modeling template. As a way to find promising template structures and to align the target and template sequences, we propose a pipeline combining the ParAlign and Infernal programs on RNA family data from Rfam. We also briefly summarize template-free methods for RNA 3D structure prediction. Typically, RNA structures generated by automated modeling methods require local or global optimization. Thus, we also discuss methods that can be used for local or global refinement of RNA structures.

  2. Discovering Structural Regularity in 3D Geometry

    PubMed Central

    Pauly, Mark; Mitra, Niloy J.; Wallner, Johannes; Pottmann, Helmut; Guibas, Leonidas J.

    2010-01-01

    We introduce a computational framework for discovering regular or repeated geometric structures in 3D shapes. We describe and classify possible regular structures and present an effective algorithm for detecting such repeated geometric patterns in point- or mesh-based models. Our method assumes no prior knowledge of the geometry or spatial location of the individual elements that define the pattern. Structure discovery is made possible by a careful analysis of pairwise similarity transformations that reveals prominent lattice structures in a suitable model of transformation space. We introduce an optimization method for detecting such uniform grids specifically designed to deal with outliers and missing elements. This yields a robust algorithm that successfully discovers complex regular structures amidst clutter, noise, and missing geometry. The accuracy of the extracted generating transformations is further improved using a novel simultaneous registration method in the spatial domain. We demonstrate the effectiveness of our algorithm on a variety of examples and show applications to compression, model repair, and geometry synthesis. PMID:21170292

  3. Effective 3-D surface modeling for geographic information systems

    NASA Astrophysics Data System (ADS)

    Yüksek, K.; Alparslan, M.; Mendi, E.

    2016-01-01

    In this work, we propose a dynamic, flexible and interactive urban digital terrain platform with spatial data and query processing capabilities of geographic information systems, multimedia database functionality and graphical modeling infrastructure. A new data element, called Geo-Node, which stores image, spatial data and 3-D CAD objects is developed using an efficient data structure. The system effectively handles data transfer of Geo-Nodes between main memory and secondary storage with an optimized directional replacement policy (DRP) based buffer management scheme. Polyhedron structures are used in digital surface modeling and smoothing process is performed by interpolation. The experimental results show that our framework achieves high performance and works effectively with urban scenes independent from the amount of spatial data and image size. The proposed platform may contribute to the development of various applications such as Web GIS systems based on 3-D graphics standards (e.g., X3-D and VRML) and services which integrate multi-dimensional spatial information and satellite/aerial imagery.

  4. 3D Printing: 3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures.

    PubMed

    Hong, Sungmin; Sycks, Dalton; Chan, Hon Fai; Lin, Shaoting; Lopez, Gabriel P; Guilak, Farshid; Leong, Kam W; Zhao, Xuanhe

    2015-07-15

    X. Zhao and co-workers develop on page 4035 a new biocompatible hydrogel system that is extremely tough and stretchable and can be 3D printed into complex structures, such as the multilayer mesh shown. Cells encapsulated in the tough and printable hydrogel maintain high viability. 3D-printed structures of the tough hydrogel can sustain high mechanical loads and deformations.

  5. 3D annotation and manipulation of medical anatomical structures

    NASA Astrophysics Data System (ADS)

    Vitanovski, Dime; Schaller, Christian; Hahn, Dieter; Daum, Volker; Hornegger, Joachim

    2009-02-01

    Although the medical scanners are rapidly moving towards a three-dimensional paradigm, the manipulation and annotation/labeling of the acquired data is still performed in a standard 2D environment. Editing and annotation of three-dimensional medical structures is currently a complex task and rather time-consuming, as it is carried out in 2D projections of the original object. A major problem in 2D annotation is the depth ambiguity, which requires 3D landmarks to be identified and localized in at least two of the cutting planes. Operating directly in a three-dimensional space enables the implicit consideration of the full 3D local context, which significantly increases accuracy and speed. A three-dimensional environment is as well more natural optimizing the user's comfort and acceptance. The 3D annotation environment requires the three-dimensional manipulation device and display. By means of two novel and advanced technologies, Wii Nintendo Controller and Philips 3D WoWvx display, we define an appropriate 3D annotation tool and a suitable 3D visualization monitor. We define non-coplanar setting of four Infrared LEDs with a known and exact position, which are tracked by the Wii and from which we compute the pose of the device by applying a standard pose estimation algorithm. The novel 3D renderer developed by Philips uses either the Z-value of a 3D volume, or it computes the depth information out of a 2D image, to provide a real 3D experience without having some special glasses. Within this paper we present a new framework for manipulation and annotation of medical landmarks directly in three-dimensional volume.

  6. Coarse-grained modeling of RNA 3D structure.

    PubMed

    Dawson, Wayne K; Maciejczyk, Maciej; Jankowska, Elzbieta J; Bujnicki, Janusz M

    2016-07-01

    Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.

  7. Microfabricating 3D Structures by Laser Origami

    DTIC Science & Technology

    2011-11-09

    technique generates 3D microstructures by controlled out-of- plane folding of 2D patterns through a variety of laser-based digital fabrication...processes. Digital microfabrication techniques such as laser direct-write (LDW) offer a viable alternative for generating 3D self-folding designs. These...folding at the microscale where manual or mechanized actuation of the smaller struc- tures is not practical. LDW techniques allow micromachining and

  8. Extending 3D city models with legal information

    NASA Astrophysics Data System (ADS)

    Frank, A. U.; Fuhrmann, T.; Navratil, G.

    2012-10-01

    3D city models represent existing physical objects and their topological and functional relations. In everyday life the rights and responsibilities connected to these objects, primarily legally defined rights and obligations but also other socially and culturally established rights, are of importance. The rights and obligations are defined in various laws and it is often difficult to identify the rules applicable for a certain case. The existing 2D cadastres show civil law rights and obligations and plans to extend them to provide information about public law restrictions for land use are in several countries under way. It is tempting to design extensions to the 3D city models to provide information about legal rights in 3D. The paper analyses the different types of information that are needed to reduce conflicts and to facilitate decisions about land use. We identify the role 3D city models augmented with planning information in 3D can play, but do not advocate a general conversion from 2D to 3D for the legal cadastre. Space is not anisotropic and the up/down dimension is practically very different from the two dimensional plane - this difference must be respected when designing spatial information systems. The conclusions are: (1) continue the current regime for ownership of apartments, which is not ownership of a 3D volume, but co-ownership of a building with exclusive use of some rooms; such exclusive use rights could be shown in a 3D city model; (2) ownership of 3D volumes for complex and unusual building situations can be reported in a 3D city model, but are not required everywhere; (3) indicate restrictions for land use and building in 3D city models, with links to the legal sources.

  9. 3D-GNOME: an integrated web service for structural modeling of the 3D genome.

    PubMed

    Szalaj, Przemyslaw; Michalski, Paul J; Wróblewski, Przemysław; Tang, Zhonghui; Kadlof, Michal; Mazzocco, Giovanni; Ruan, Yijun; Plewczynski, Dariusz

    2016-07-08

    Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/.

  10. 3D-GNOME: an integrated web service for structural modeling of the 3D genome

    PubMed Central

    Szalaj, Przemyslaw; Michalski, Paul J.; Wróblewski, Przemysław; Tang, Zhonghui; Kadlof, Michal; Mazzocco, Giovanni; Ruan, Yijun; Plewczynski, Dariusz

    2016-01-01

    Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/. PMID:27185892

  11. Three-dimensional (3D) printing of mouse primary hepatocytes to generate 3D hepatic structure

    PubMed Central

    Kim, Yohan; Kang, Kyojin; Jeong, Jaemin; Paik, Seung Sam; Kim, Ji Sook; Park, Su A; Kim, Wan Doo; Park, Jisun

    2017-01-01

    Purpose The major problem in producing artificial livers is that primary hepatocytes cannot be cultured for many days. Recently, 3-dimensional (3D) printing technology draws attention and this technology regarded as a useful tool for current cell biology. By using the 3D bio-printing, these problems can be resolved. Methods To generate 3D bio-printed structures (25 mm × 25 mm), cells-alginate constructs were fabricated by 3D bio-printing system. Mouse primary hepatocytes were isolated from the livers of 6–8 weeks old mice by a 2-step collagenase method. Samples of 4 × 107 hepatocytes with 80%–90% viability were printed with 3% alginate solution, and cultured with well-defined culture medium for primary hepatocytes. To confirm functional ability of hepatocytes cultured on 3D alginate scaffold, we conducted quantitative real-time polymerase chain reaction and immunofluorescence with hepatic marker genes. Results Isolated primary hepatocytes were printed with alginate. The 3D printed hepatocytes remained alive for 14 days. Gene expression levels of Albumin, HNF-4α and Foxa3 were gradually increased in the 3D structures. Immunofluorescence analysis showed that the primary hepatocytes produced hepatic-specific proteins over the same period of time. Conclusion Our research indicates that 3D bio-printing technique can be used for long-term culture of primary hepatocytes. It can therefore be used for drug screening and as a potential method of producing artificial livers. PMID:28203553

  12. Estimating a structural bottle neck for eye-brain transfer of visual information from 3D-volumes of the optic nerve head from a commercial OCT device

    NASA Astrophysics Data System (ADS)

    Malmberg, Filip; Sandberg-Melin, Camilla; Söderberg, Per G.

    2016-03-01

    The aim of this project was to investigate the possibility of using OCT optic nerve head 3D information captured with a Topcon OCT 2000 device for detection of the shortest distance between the inner limit of the retina and the central limit of the pigment epithelium around the circumference of the optic nerve head. The shortest distance between these boundaries reflects the nerve fiber layer thickness and measurement of this distance is interesting for follow-up of glaucoma.

  13. RNA Structure: Advances and Assessment of 3D Structure Prediction.

    PubMed

    Miao, Zhichao; Westhof, Eric

    2017-03-30

    Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of RNA structure is frequently based on 2D structures, which describe only the Watson-Crick (WC) base pairs. Here, we hierarchically review the structural elements of RNA and how they contribute to RNA 3D structure. We focus our analysis on the non-WC base pairs and on RNA modules. Several computer programs have now been designed to predict RNA modules. We describe the RNA-Puzzles initiative, which is a community-wide, blind assessment of RNA 3D structure prediction programs to determine the capabilities and bottlenecks of current predictions. The assessment metrics used in RNA-Puzzles are briefly described. The detection of RNA 3D modules from sequence data and their automatic implementation belong to the current challenges in RNA 3D structure prediction. Expected final online publication date for the Annual Review of Biophysics Volume 46 is May 20, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  14. 3D Image Display Courses for Information Media Students.

    PubMed

    Yanaka, Kazuhisa; Yamanouchi, Toshiaki

    2016-01-01

    Three-dimensional displays are used extensively in movies and games. These displays are also essential in mixed reality, where virtual and real spaces overlap. Therefore, engineers and creators should be trained to master 3D display technologies. For this reason, the Department of Information Media at the Kanagawa Institute of Technology has launched two 3D image display courses specifically designed for students who aim to become information media engineers and creators.

  15. Strategies to reconstruct 3D Coffea arabica L. plant structure.

    PubMed

    Matsunaga, Fabio Takeshi; Tosti, Jonas Barbosa; Androcioli-Filho, Armando; Brancher, Jacques Duílio; Costes, Evelyne; Rakocevic, Miroslava

    2016-01-01

    Accurate model of structural elements is necessary to model the foliage and fruit distributions in cultivated plants, both of them being key parameters for yield prediction. However, the level of details in architectural data collection could vary, simplifying the data collection when plants get older and because of the high time cost required. In the present study, we aimed at reconstructing and analyzing plant structure, berry distributions and yield in Coffea arabica (Arabica coffee), by using both detailed or partial morphological information and probabilistic functions. Different datasets of coffee plant architectures were available with different levels of detail depending on the tree age. Three scales of decomposition-plant, axes and metamers were used reconstruct the plant architectures. CoffePlant3D, a software which integrates a series of mathematical, computational and statistical methods organized in three newly developed modules, AmostraCafe3D, VirtualCafe3D and Cafe3D, was developed to accurately reconstruct coffee plants in 3D, whatever the level of details available. The number of metamers of the 2nd order axes was shown to be linearly proportional to that of the orthotropic trunk, and the number of berries per metamer was modeled as a Gaussian function within a specific zone along the plagiotropic axes. This ratio of metamer emission rhythm between the orthotropic trunk and plagiotropic axes represents the pillar of botanical events in the C. arabica development and was central in our modeling approach, especially to reconstruct missing data. The methodology proposed for reconstructing coffee plants under the CoffePlant3D was satisfactorily validated across dataset available and could be performed for any other Arabica coffee variety.

  16. CH5M3D: an HTML5 program for creating 3D molecular structures

    PubMed Central

    2013-01-01

    Background While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Results Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user’s computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. Conclusions A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/. PMID:24246004

  17. Quantitative 3D structured illumination microscopy of nuclear structures.

    PubMed

    Kraus, Felix; Miron, Ezequiel; Demmerle, Justin; Chitiashvili, Tsotne; Budco, Alexei; Alle, Quentin; Matsuda, Atsushi; Leonhardt, Heinrich; Schermelleh, Lothar; Markaki, Yolanda

    2017-05-01

    3D structured illumination microscopy (3D-SIM) is the super-resolution technique of choice for multicolor volumetric imaging. Here we provide a validated sample preparation protocol for labeling nuclei of cultured mammalian cells, image acquisition and registration practices, and downstream image analysis of nuclear structures and epigenetic marks. Using immunostaining and replication labeling combined with image segmentation, centroid mapping and nearest-neighbor analyses in open-source environments, 3D maps of nuclear structures are analyzed in individual cells and normalized to fluorescence standards on the nanometer scale. This protocol fills an unmet need for the application of 3D-SIM to the technically challenging nuclear environment, and subsequent quantitative analysis of 3D nuclear structures and epigenetic modifications. In addition, it establishes practical guidelines and open-source solutions using ImageJ/Fiji and the TANGO plugin for high-quality and routinely comparable data generation in immunostaining experiments that apply across model systems. From sample preparation through image analysis, the protocol can be executed within one week.

  18. The 3D Structure of the Proton

    NASA Astrophysics Data System (ADS)

    Kaiser, Ralf

    2012-09-01

    When Rutherford, Geiger and Marsden discovered the atomic nucleus in 1909 in Manchester, they at the same time also laid the foundations for the most successful method to study the structure of nuclei and nucleons. They found a point-like scattering centre inside the atom and identified it with the atomic nucleus and the theoretical description of this process has been known as Rutherford scattering ever since. The deviation between the theoretical description for a point-like scattering centre and experimental data has since been used to reveal information about the structure of the nucleus as well as the nucleon. There has been a continuous development from Hofstadters experiments in the 1950s, over the SLAC experiments in the 60s and 70s to the the HERA experiments at DESY and the experimental programme at Jeffersonlab. In this paper I am presenting the most recent results in Deeply Virtual Compton Scattering from the Hermes experiment at DESY, taken with a high density unpolarised target and a recoil detector in 2006/7.

  19. 3D Modeling from Photos Given Topological Information.

    PubMed

    Kim, Young Min; Cho, Junghyun; Ahn, Sang Chul

    2016-09-01

    Reconstructing 3D models given a single-view 2D information is inherently an ill-posed problem and requires additional information such as shape prior or user input.We introduce a method to generate multiple 3D models of a particular category given corresponding photographs when the topological information is known. While there is a wide range of shapes for an object of a particular category, the basic topology usually remains constant.In consequence, the topological prior needs to be provided only once for each category and can be easily acquired by consulting an existing database of 3D models or by user input. The input of topological description is only connectivity information between parts; this is in contrast to previous approaches that have required users to interactively mark individual parts. Given the silhouette of an object and the topology, our system automatically finds a skeleton and generates a textured 3D model by jointly fitting multiple parts. The proposed method, therefore, opens the possibility of generating a large number of 3D models by consulting a massive number of photographs. We demonstrate examples of the topological prior and reconstructed 3D models using photos.

  20. [3D visualization and information interaction in biomedical applications].

    PubMed

    Pu, F; Fan, Y; Jiang, W; Zhang, M; Mak, A F; Chen, J

    2001-06-01

    3D visualization and virtual reality are important trend in the development of modern science and technology, and as well in the studies on biomedical engineering. This paper presents a computer procedure developed for 3D visualization in biomedical applications. The biomedical models are constructed in slice sequences based on polygon cells and information interaction is realized on the basis of OpenGL selection mode in particular consideration of the specialties in this field such as irregularity in geometry and complexity in material etc. The software developed has functions of 3D model construction and visualization, real-time modeling transformation, information interaction and so on. It could serve as useful platform for 3D visualization in biomedical engineering research.

  1. Topological Quantum Information in a 3D Neutral Atom Array

    DTIC Science & Technology

    2015-01-02

    AFRL-OSR-VA-TR-2015-0051 TOPOLOGICAL QUANTUM INFORMATION IN A 3D NEUTRAL ATOM ARRAY David Weiss PENNSYLVANIA STATE UNIVERSITY Final Report 01/02/2015...v Prescribed by ANSI Std. Z39.18 12-23-2014 Final 12-01-2008-9-30-2014 (DARPA) TOPOLOGICAL QUANTUM INFORMATION IN A 3D NEUTRAL ATOM ARRAY FA9550-09...using neutral atoms in an optical lattice, with the ultimate end to execute a version of the Kitaev toric code Hamiltonian model . Toward that end we

  2. 3D Geo-Information in Urban Climate Studies

    NASA Astrophysics Data System (ADS)

    Petrescu, F.; Aldea, M.; Luca, O.; Iacoboaea, C.; Gaman, F.; Parlow, E.

    2016-10-01

    3D geo-information is essential for urban climate studies. It is obvious that both natural environment and built-up environment play the fundamental role in defining the climatic conditions for urban areas, which affect the quality of human life and human comfort. The paper presents the main categories of 3D geo-information used in urban climate studies and roles in creating and operating the numerical models specially designed to simulate urban planning scenarios and improvement of the urban climate situation.

  3. 3D Imaging with Structured Illumination for Advanced Security Applications

    SciTech Connect

    Birch, Gabriel Carisle; Dagel, Amber Lynn; Kast, Brian A.; Smith, Collin S.

    2015-09-01

    Three-dimensional (3D) information in a physical security system is a highly useful dis- criminator. The two-dimensional data from an imaging systems fails to provide target dis- tance and three-dimensional motion vector, which can be used to reduce nuisance alarm rates and increase system effectiveness. However, 3D imaging devices designed primarily for use in physical security systems are uncommon. This report discusses an architecture favorable to physical security systems; an inexpensive snapshot 3D imaging system utilizing a simple illumination system. The method of acquiring 3D data, tests to understand illumination de- sign, and software modifications possible to maximize information gathering capability are discussed.

  4. Unit cell geometry of 3-D braided structures

    NASA Technical Reports Server (NTRS)

    Du, Guang-Wu; Ko, Frank K.

    1993-01-01

    The traditional approach used in modeling of composites reinforced by three-dimensional (3-D) braids is to assume a simple unit cell geometry of a 3-D braided structure with known fiber volume fraction and orientation. In this article, we first examine 3-D braiding methods in the light of braid structures, followed by the development of geometric models for 3-D braids using a unit cell approach. The unit cell geometry of 3-D braids is identified and the relationship of structural parameters such as yarn orientation angle and fiber volume fraction with the key processing parameters established. The limiting geometry has been computed by establishing the point at which yarns jam against each other. Using this factor makes it possible to identify the complete range of allowable geometric arrangements for 3-D braided preforms. This identified unit cell geometry can be translated to mechanical models which relate the geometrical properties of fabric preforms to the mechanical responses of composite systems.

  5. Dynactin 3D structure: implications for assembly and dynein binding.

    PubMed

    Imai, Hiroshi; Narita, Akihiro; Maéda, Yuichiro; Schroer, Trina A

    2014-09-23

    The multisubunit protein complex, dynactin, is an essential component of the cytoplasmic dynein motor. High-resolution structural work on dynactin and the dynein/dynactin supercomplex has been limited to small subunits and recombinant fragments that do not report fully on either ≈1MDa assembly. In the present study, we used negative-stain electron microscopy and image analysis based on random conical tilt reconstruction to obtain a three-dimensional (3D) structure of native vertebrate dynactin. The 35-nm-long dynactin molecule has a V-shaped shoulder at one end and a flattened tip at the other end, both offset relative to the long axis of the actin-related protein (Arp) backbone. The shoulder projects dramatically away from the Arp filament core in a way that cannot be appreciated in two-dimensional images, which has implications for the mechanism of dynein binding. The 3D structure allows the helical parameters of the entire Arp filament core, which includes the actin capping protein, CP, to be determined for the first time. This structure exhibits near identity to F-actin and can be well fitted into the dynactin envelope. Molecular fitting of modeled CP-Arp polymers into the envelope shows that the filament contains between 7 and 9 Arp protomers and is capped at both ends. In the 7 Arp model, which agrees best with measured Arp stoichiometry and other structural information, actin capping protein (CP) is not present at the distal tip of the structure, unlike what is seen in the other models. The 3D structure suggests a mechanism for dynactin assembly and length specification.

  6. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  7. Advancements in 3D Structural Analysis of Geothermal Systems

    SciTech Connect

    Siler, Drew L; Faulds, James E; Mayhew, Brett; McNamara, David

    2013-06-23

    . Analysis of fault intersection density indicates that the highest density of structurally controlled permeability within the field lies in a narrow (10-to-10s of m) zone plunging moderately (~35°) to the NNW beneath Pleistocene tufa deposits. This zone of increased fracture density, which we interpret as the primary upflow zone, is controlled by the intersection of N-to-NNW striking normal faults and a WNW striking dextral fault zone and represents the most promising target for future drilling. Construction of a 3D geologic model involves integration of a variety of data into an internally consistent framework. A robust model allows for spatial comparison between the various types of data (structural, stratigraphic, geophysical, temperature, etc.) that are commonly used independently to site geothermal wells. Furthermore, highly detailed 3D geologic models provide the basis for additional quantitative analysis, including 3D fault slip and dilation tendency analysis and the precise location of structurally controlled permeability pathways. These analyses provide detailed information relating to the internal dynamics of geothermal systems and can mitigate the costs and risks of geothermal exploration and development by contributing to better well targeting and more accurate evaluations of resource potential.

  8. Automatic structural matching of 3D image data

    NASA Astrophysics Data System (ADS)

    Ponomarev, Svjatoslav; Lutsiv, Vadim; Malyshev, Igor

    2015-10-01

    A new image matching technique is described. It is implemented as an object-independent hierarchical structural juxtaposition algorithm based on an alphabet of simple object-independent contour structural elements. The structural matching applied implements an optimized method of walking through a truncated tree of all possible juxtapositions of two sets of structural elements. The algorithm was initially developed for dealing with 2D images such as the aerospace photographs, and it turned out to be sufficiently robust and reliable for matching successfully the pictures of natural landscapes taken in differing seasons from differing aspect angles by differing sensors (the visible optical, IR, and SAR pictures, as well as the depth maps and geographical vector-type maps). At present (in the reported version), the algorithm is enhanced based on additional use of information on third spatial coordinates of observed points of object surfaces. Thus, it is now capable of matching the images of 3D scenes in the tasks of automatic navigation of extremely low flying unmanned vehicles or autonomous terrestrial robots. The basic principles of 3D structural description and matching of images are described, and the examples of image matching are presented.

  9. 3D Animations for Exploring Nucleon Structure

    NASA Astrophysics Data System (ADS)

    Gorman, Waverly; Burkardt, Matthias

    2016-09-01

    Over the last few years many intuitive pictures have been developed for the interpretation of electron hadron scattering experiments, such as a mechanism for transverse single-spin asymmetries in semi-inclusive deep-inelastic scattering experiments. While Dr. Burkardt's pictures have been helpful for many researchers in the field, they are still difficult to visualize for broader audiences since they rely mostly on 2-dimensional static images. In order to make more accessible for a broader audience what can be learned from Jefferson Lab experiments, we have started to work on developing 3-dimensional animations for these processes. The goal is to enable the viewer to repeatedly look at the same microscopic mechanism for a specific reaction, with the viewpoint of the observer changing. This should help an audience that is not so familiar with these reactions to better understand what can be learned from various experiments at Jefferson Lab aimed at exploring the nucleon structure. Jefferson Lab Minority/Female Undergraduate Research Assistantship.

  10. Preliminary investigations on 3D PIC simulation of DPHC structure using NEPTUNE3D code

    NASA Astrophysics Data System (ADS)

    Zhao, Hailong; Dong, Ye; Zhou, Haijing; Zou, Wenkang; Wang, Qiang

    2016-10-01

    Cubic region (34cm × 34cm × 18cm) including the double post-hole convolute (DPHC) structure was chosen to perform a series of fully 3D PIC simulations using NEPTUNE3D codes, massive data ( 200GB) could be acquired and solved in less than 5 hours. Cold-chamber tests were performed during which only cathode electron emission was considered without temperature rise or ion emission, current loss efficiency was estimated by comparisons between output magnetic field profiles with or without electron emission. PIC simulation results showed three stages of current transforming process with election emission in DPHC structure, the maximum ( 20%) current loss was 437kA at 15ns, while only 0.46% 0.48% was lost when driving current reached its peak. DPHC structure proved valuable functions during energy transform process in PTS facility, and NEPTUNE3D provided tools to explore this sophisticated physics. Project supported by the National Natural Science Foundation of China, Grant No. 11571293, 11505172.

  11. Complete Tem-Tomography: 3D Structure of Gems Cluster

    NASA Technical Reports Server (NTRS)

    Matsuno, J.; Miyake, A.; Tsuchiyama, A.; Messenger, S.; Nakamura-Messenger, K.

    2015-01-01

    GEMS (glass with embedded metal and sulfide) grains in interplanetary dust particles (IDPs) are considered to be one of the ubiquitous and fundamental building blocks of solids in the Solar System. They have been considered to be interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk but the elemental and isotopic composition measurements suggest that most of them have been formed in the protoplanetary disk as condensates from high temperature gas. This formation model is also supported by the formation of GEMS-like grains with respect to the size, mineral assemblage, texture and infrared spectrum by condensation experiments from mean GEMS composition materials. Previous GEMS studies were performed only with 2D observation by transmission electron microscopy (TEM) or scanning TEM (STEM). However, the 3D shape and structure of GEMS grains and the spatial distribution of Fe/FeS's has critical information about their formation and origin. Recently, the 3D structure of GEMS grains in ultrathin sections of cluster IDPs was revealed by electron tomography using a TEM/STEM (JEM-2100F, JEOL). However, CT images of thin sections mounted on Cu grids acquired by conventional TEM-tomography are limited to low tilt angles (e. g., less than absolute value of 75 deg. In fact, previous 3D TEM observations of GEMS were affected by some artifacts related to the limited tilt range in the TEM used. Complete tomographic images should be acquired by rotating the sample tilt angle over a range of more than absolute value of 80 deg otherwise the CT images lose their correct structures. In order to constrain the origin and formation process of GEMS grains more clearly, we performed complete electron tomography for GEMS grains. Here we report the sample preparation method we have developed for this study, and the preliminary results.

  12. Characterizing 3D Vegetation Structure from Space: Mission Requirements

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G.; Bergen, Kathleen; Blair, James B.; Dubayah, Ralph; Houghton, Richard; Hurtt, George; Kellndorfer, Josef; Lefsky, Michael; Ranson, Jon; Saatchi, Sasan; Shugart, H. H.; Wickland, Diane

    2012-01-01

    Human and natural forces are rapidly modifying the global distribution and structure of terrestrial ecosystems on which all of life depends, altering the global carbon cycle, affecting our climate now and for the foreseeable future, causing steep reductions in species diversity, and endangering Earth s sustainability. To understand changes and trends in terrestrial ecosystems and their functioning as carbon sources and sinks, and to characterize the impact of their changes on climate, habitat and biodiversity, new space assets are urgently needed to produce high spatial resolution global maps of the three-dimensional (3D) structure of vegetation, its biomass above ground, the carbon stored within and the implications for atmospheric green house gas concentrations and climate. These needs were articulated in a 2007 National Research Council (NRC) report (NRC, 2007) recommending a new satellite mission, DESDynI, carrying an L-band Polarized Synthetic Aperture Radar (Pol-SAR) and a multi-beam lidar (Light RAnging And Detection) operating at 1064 nm. The objectives of this paper are to articulate the importance of these new, multi-year, 3D vegetation structure and biomass measurements, to briefly review the feasibility of radar and lidar remote sensing technology to meet these requirements, to define the data products and measurement requirements, and to consider implications of mission durations. The paper addresses these objectives by synthesizing research results and other input from a broad community of terrestrial ecology, carbon cycle, and remote sensing scientists and working groups. We conclude that: (1) current global biomass and 3-D vegetation structure information is unsuitable for both science and management and policy. The only existing global datasets of biomass are approximations based on combining land cover type and representative carbon values, instead of measurements of actual biomass. Current measurement attempts based on radar and multispectral

  13. 3-D visualization of geologic structures and processes

    NASA Astrophysics Data System (ADS)

    Pflug, R.; Klein, H.; Ramshorn, Ch.; Genter, M.; Stärk, A.

    Interactive 3-D computer graphics techniques are used to visualize geologic structures and simulated geologic processes. Geometric models that serve as input to 3-D viewing programs are generated from contour maps, from serial sections, or directly from simulation program output. Choice of viewing parameters strongly affects the perception of irregular surfaces. An interactive 3-D rendering program and its graphical user interface provide visualization tools for structural geology, seismic interpretation, and visual post-processing of simulations. Dynamic display of transient ground-water simulations and sedimentary process simulations can visualize processes developing through time.

  14. Finding Organized Structures in 3-D LADAR Data

    DTIC Science & Technology

    2004-12-01

    work exists also on how to extract planar and linear objects from scattered 3-D point clouds , see for example [5], [6]. Methods were even proposed to...of structure detection and segmentation from 3-D point clouds collected from a single sensor location or integrated from multiple locations. In [2...primitives to point clouds are difficult to use practically for large data sets containing multiple complex structures, in opposition to multiple planar

  15. Evaluation of 3D Printer Accuracy in Producing Fractal Structure.

    PubMed

    Kikegawa, Kana; Takamatsu, Kyuuichirou; Kawakami, Masaru; Furukawa, Hidemitsu; Mayama, Hiroyuki; Nonomura, Yoshimune

    2017-01-01

    Hierarchical structures, also known as fractal structures, exhibit advantageous material properties, such as water- and oil-repellency as well as other useful optical characteristics, owing to its self-similarity. Various methods have been developed for producing hierarchical geometrical structures. Recently, fractal structures have been manufactured using a 3D printing technique that involves computer-aided design data. In this study, we confirmed the accuracy of geometrical structures when Koch curve-like fractal structures with zero to three generations were printed using a 3D printer. The fractal dimension was analyzed using a box-counting method. This analysis indicated that the fractal dimension of the third generation hierarchical structure was approximately the same as that of the ideal Koch curve. These findings demonstrate that the design and production of fractal structures can be controlled using a 3D printer. Although the interior angle deviated from the ideal value, the side length could be precisely controlled.

  16. Direct-Write 3D Nanoprinting of Plasmonic Structures

    DOE PAGES

    Winkler, Robert; Schmidt, Franz-Philipp; Karl-Franzens Univ.; ...

    2016-11-23

    During the past decade, significant progress has been made in the field of resonant optics ranging from fundamental aspects to concrete applications. And while several techniques have been introduced for the fabrication of highly defined metallic nanostructures, the synthesis of complex, free-standing three-dimensional (3D) structures is still an intriguing, but so far intractable, challenge. Here, we demonstrate a 3D direct-write synthesis approach that addresses this challenge. Specifically, we succeeded in the direct-write fabrication of 3D nanoarchitectures via electron-stimulated reactions, which are applicable on virtually any material and surface morphology. Furthermore, by that, complex 3D nanostructures composed of highly compact, puremore » gold can be fabricated, which reveal strong plasmonic activity and pave the way for a new generation of 3D nanoplasmonic architectures that can be printed on-demand.« less

  17. Direct-Write 3D Nanoprinting of Plasmonic Structures.

    PubMed

    Winkler, Robert; Schmidt, Franz-Philipp; Haselmann, Ulrich; Fowlkes, Jason D; Lewis, Brett B; Kothleitner, Gerald; Rack, Philip D; Plank, Harald

    2017-03-08

    During the past decade, significant progress has been made in the field of resonant optics ranging from fundamental aspects to concrete applications. While several techniques have been introduced for the fabrication of highly defined metallic nanostructures, the synthesis of complex, free-standing three-dimensional (3D) structures is still an intriguing, but so far intractable, challenge. In this study, we demonstrate a 3D direct-write synthesis approach that addresses this challenge. Specifically, we succeeded in the direct-write fabrication of 3D nanoarchitectures via electron-stimulated reactions, which are applicable on virtually any material and surface morphology. By that, complex 3D nanostructures composed of highly compact, pure gold can be fabricated, which reveal strong plasmonic activity and pave the way for a new generation of 3D nanoplasmonic architectures that can be printed on-demand.

  18. Direct-Write 3D Nanoprinting of Plasmonic Structures

    SciTech Connect

    Winkler, Robert; Schmidt, Franz-Philipp; Haselmann, Ulrich; Fowlkes, Jason D.; Lewis, Brett B.; Kothleitner, Gerald; Rack, Philip D.; Plank, Harald

    2016-11-23

    During the past decade, significant progress has been made in the field of resonant optics ranging from fundamental aspects to concrete applications. And while several techniques have been introduced for the fabrication of highly defined metallic nanostructures, the synthesis of complex, free-standing three-dimensional (3D) structures is still an intriguing, but so far intractable, challenge. Here, we demonstrate a 3D direct-write synthesis approach that addresses this challenge. Specifically, we succeeded in the direct-write fabrication of 3D nanoarchitectures via electron-stimulated reactions, which are applicable on virtually any material and surface morphology. Furthermore, by that, complex 3D nanostructures composed of highly compact, pure gold can be fabricated, which reveal strong plasmonic activity and pave the way for a new generation of 3D nanoplasmonic architectures that can be printed on-demand.

  19. 3D-Fun: predicting enzyme function from structure.

    PubMed

    von Grotthuss, Marcin; Plewczynski, Dariusz; Vriend, Gert; Rychlewski, Leszek

    2008-07-01

    The 'omics' revolution is causing a flurry of data that all needs to be annotated for it to become useful. Sequences of proteins of unknown function can be annotated with a putative function by comparing them with proteins of known function. This form of annotation is typically performed with BLAST or similar software. Structural genomics is nowadays also bringing us three dimensional structures of proteins with unknown function. We present here software that can be used when sequence comparisons fail to determine the function of a protein with known structure but unknown function. The software, called 3D-Fun, is implemented as a server that runs at several European institutes and is freely available for everybody at all these sites. The 3D-Fun servers accept protein coordinates in the standard PDB format and compare them with all known protein structures by 3D structural superposition using the 3D-Hit software. If structural hits are found with proteins with known function, these are listed together with their function and some vital comparison statistics. This is conceptually very similar in 3D to what BLAST does in 1D. Additionally, the superposition results are displayed using interactive graphics facilities. Currently, the 3D-Fun system only predicts enzyme function but an expanded version with Gene Ontology predictions will be available soon. The server can be accessed at http://3dfun.bioinfo.pl/ or at http://3dfun.cmbi.ru.nl/.

  20. Protein 3D structure computed from evolutionary sequence variation.

    PubMed

    Marks, Debora S; Colwell, Lucy J; Sheridan, Robert; Hopf, Thomas A; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

    2011-01-01

    The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing.In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy.We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues, including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7-4.8 Å C(α)-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein structures

  1. Extensible 3D (X3D) Graphics Clouds for Geographic Information Systems

    DTIC Science & Technology

    2008-03-01

    browser such as Microsoft Internet Explorer or Netscape using an X3D or VRML supporting plug-in. The benefits of diverse support can cause...typing model output with a particular method of 3D cloud production. Data-driven adaptation and production of cloud models for web -based delivery...and production of cloud models for web -based delivery is an achievable capability given continued research and development. vi THIS PAGE

  2. Semiautomatic approaches to account for 3-D distortion of the electric field from local, near-surface structures in 3-D resistivity inversions of 3-D regional magnetotelluric data

    USGS Publications Warehouse

    Rodriguez, Brian D.

    2017-03-31

    This report summarizes the results of three-dimensional (3-D) resistivity inversion simulations that were performed to account for local 3-D distortion of the electric field in the presence of 3-D regional structure, without any a priori information on the actual 3-D distribution of the known subsurface geology. The methodology used a 3-D geologic model to create a 3-D resistivity forward (“known”) model that depicted the subsurface resistivity structure expected for the input geologic configuration. The calculated magnetotelluric response of the modeled resistivity structure was assumed to represent observed magnetotelluric data and was subsequently used as input into a 3-D resistivity inverse model that used an iterative 3-D algorithm to estimate 3-D distortions without any a priori geologic information. A publicly available inversion code, WSINV3DMT, was used for all of the simulated inversions, initially using the default parameters, and subsequently using adjusted inversion parameters. A semiautomatic approach of accounting for the static shift using various selections of the highest frequencies and initial models was also tested. The resulting 3-D resistivity inversion simulation was compared to the “known” model and the results evaluated. The inversion approach that produced the lowest misfit to the various local 3-D distortions was an inversion that employed an initial model volume resistivity that was nearest to the maximum resistivities in the near-surface layer.

  3. Dual multispectral and 3D structured light laparoscope

    NASA Astrophysics Data System (ADS)

    Clancy, Neil T.; Lin, Jianyu; Arya, Shobhit; Hanna, George B.; Elson, Daniel S.

    2015-03-01

    Intraoperative feedback on tissue function, such as blood volume and oxygenation would be useful to the surgeon in cases where current clinical practice relies on subjective measures, such as identification of ischaemic bowel or tissue viability during anastomosis formation. Also, tissue surface profiling may be used to detect and identify certain pathologies, as well as diagnosing aspects of tissue health such as gut motility. In this paper a dual modality laparoscopic system is presented that combines multispectral reflectance and 3D surface imaging. White light illumination from a xenon source is detected by a laparoscope-mounted fast filter wheel camera to assemble a multispectral image (MSI) cube. Surface shape is then calculated using a spectrally-encoded structured light (SL) pattern detected by the same camera and triangulated using an active stereo technique. Images of porcine small bowel were acquired during open surgery. Tissue reflectance spectra were acquired and blood volume was calculated at each spatial pixel across the bowel wall and mesentery. SL features were segmented and identified using a `normalised cut' algoritm and the colour vector of each spot. Using the 3D geometry defined by the camera coordinate system the multispectral data could be overlaid onto the surface mesh. Dual MSI and SL imaging has the potential to provide augmented views to the surgeon supplying diagnostic information related to blood supply health and organ function. Future work on this system will include filter optimisation to reduce noise in tissue optical property measurement, and minimise spot identification errors in the SL pattern.

  4. Toward mobile 3D visualization for structural biologists.

    PubMed

    Tanramluk, Duangrudee; Akavipat, Ruj; Charoensawan, Varodom

    2013-12-01

    Technological advances in crystallography have led to the ever-rapidly increasing number of biomolecular structures deposited in public repertoires. This undoubtedly shifts the bottleneck of structural biology research from obtaining high-quality structures to data analysis and interpretation. The recently available glasses-free autostereoscopic laptop offers an unprecedented opportunity to visualize and study 3D structures using a much more affordable, and for the first time, portable device. Together with a gamepad re-programmed for 3D structure controlling, we describe how the gaming technologies can deliver the output 3D images for high-quality viewing, comparable to that of a passive stereoscopic system, and can give the user more control and flexibility than the conventional controlling setup using only a mouse and a keyboard.

  5. 3D Ultrasonic Wave Simulations for Structural Health Monitoring

    NASA Technical Reports Server (NTRS)

    Campbell, Leckey Cara A/; Miler, Corey A.; Hinders, Mark K.

    2011-01-01

    Structural health monitoring (SHM) for the detection of damage in aerospace materials is an important area of research at NASA. Ultrasonic guided Lamb waves are a promising SHM damage detection technique since the waves can propagate long distances. For complicated flaw geometries experimental signals can be difficult to interpret. High performance computing can now handle full 3-dimensional (3D) simulations of elastic wave propagation in materials. We have developed and implemented parallel 3D elastodynamic finite integration technique (3D EFIT) code to investigate ultrasound scattering from flaws in materials. EFIT results have been compared to experimental data and the simulations provide unique insight into details of the wave behavior. This type of insight is useful for developing optimized experimental SHM techniques. 3D EFIT can also be expanded to model wave propagation and scattering in anisotropic composite materials.

  6. Proposed traceable structural resolution protocols for 3D imaging systems

    NASA Astrophysics Data System (ADS)

    MacKinnon, David; Beraldin, J.-Angelo; Cournoyer, Luc; Carrier, Benjamin; Blais, François

    2009-08-01

    A protocol for determining structural resolution using a potentially-traceable reference material is proposed. Where possible, terminology was selected to conform to those published in ISO JCGM 200:2008 (VIM) and ASTM E 2544-08 documents. The concepts of resolvability and edge width are introduced to more completely describe the ability of an optical non-contact 3D imaging system to resolve small features. A distinction is made between 3D range cameras, that obtain spatial data from the total field of view at once, and 3D range scanners, that accumulate spatial data for the total field of view over time. The protocol is presented through the evaluation of a 3D laser line range scanner.

  7. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

    The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.

  8. 3D WHOLE-PROMINENCE FINE STRUCTURE MODELING

    SciTech Connect

    Gunár, Stanislav; Mackay, Duncan H.

    2015-04-20

    We present the first 3D whole-prominence fine structure model. The model combines a 3D magnetic field configuration of an entire prominence obtained from nonlinear force-free field simulations, with a detailed description of the prominence plasma. The plasma is located in magnetic dips in hydrostatic equilibrium and is distributed along multiple fine structures within the 3D magnetic model. Through the use of a novel radiative transfer visualization technique for the Hα line such plasma-loaded magnetic field model produces synthetic images of the modeled prominence comparable with high-resolution observations. This allows us for the first time to use a single technique to consistently study, in both emission on the limb and absorption against the solar disk, the fine structures of prominences/filaments produced by a magnetic field model.

  9. Automated 3D structure composition for large RNAs

    PubMed Central

    Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J.; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W.

    2012-01-01

    Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues. PMID:22539264

  10. Automated 3D structure composition for large RNAs.

    PubMed

    Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W

    2012-08-01

    Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.

  11. Designing 3D Structure by 5-7 Kirigami

    NASA Astrophysics Data System (ADS)

    Gong, Xingting; Cho, Yigil; Castle, Toen; Sussman, Daniel; Kamien, Randall

    2015-03-01

    The purpose of this talk is to explore how one can create 3D structures from 2D materials through the art of kirigami. Kirigami expands upon origami by allowing not only folds, but also cuts, into materials. If we take an incompressible material such as paper and remove a hole from it, the paper will buckle into the third dimension once that hole is sealed in order to relieve strain. Thus, orienting cuts and folds in certain places throughout a sheet of paper can influence its ``pop-up,'' 3D structure. To narrow down the inverse design problem, we confined ourselves to making only one kind of cut (which we call the ``5-7 cut'') on a honeycomb grid, and we show how this single cut can give rise to arbitrarily complex three dimensional structures. A simple set of rules exists: (a) one 5-7 cut divides the material into 2 sections which can choose to pop-up or down independently of each other, (b) rows of uniform cuts must pop up or down in unison, giving (nearly) arbitrary 2D structure, and (c) the 5-7 cuts can be arranged in various ways to create 6 basic pop-up ``modes,'' which can then be arranged to give (nearly) arbitrary 3D structure. These simple rules allow a framework for designing targeted 3D structure from an initial 2D sheet of material. This work was supported by NSF EFRI-ODISSEI Grant EFRI 13-31583.

  12. Coherent structures in 3D viscous time-periodic flow

    NASA Astrophysics Data System (ADS)

    Znaien, J. G.; Speetjens, M. F. M.; Trieling, R. R.; Clercx, H. J. H.

    2010-11-01

    Periodically driven laminar flows occur in many industrial processes from food-mixing devices to micro-mixer in lab-on-a-chip systems. The present study is motivated by better understanding fundamental transport phenomena in three-dimensional viscous time-periodic flows. Both numerical simulation and three-dimensional Particle Tracking Velocimetry measurements are performed to investigate the 3D advection of a passive scalar in a lid-driven cylindrical cavity flow. The flow is forced by a time-periodic in-plane motion of one endwall via a given forcing protocol. We concentrate on the formation and interaction of coherent structures due to fluid inertia, which play an important role in 3D mixing by geometrically determining the tracer transport. The disintegration of these structures by fluid inertia reflects an essentially 3D route to chaos. Data from tracking experiments of small particles will be compared with predictions from numerical simulations on transport of passive tracers.

  13. 3D Seismic Imaging over a Potential Collapse Structure

    NASA Astrophysics Data System (ADS)

    Gritto, Roland; O'Connell, Daniel; Elobaid Elnaiem, Ali; Mohamed, Fathelrahman; Sadooni, Fadhil

    2016-04-01

    The Middle-East has seen a recent boom in construction including the planning and development of complete new sub-sections of metropolitan areas. Before planning and construction can commence, however, the development areas need to be investigated to determine their suitability for the planned project. Subsurface parameters such as the type of material (soil/rock), thickness of top soil or rock layers, depth and elastic parameters of basement, for example, comprise important information needed before a decision concerning the suitability of the site for construction can be made. A similar problem arises in environmental impact studies, when subsurface parameters are needed to assess the geological heterogeneity of the subsurface. Environmental impact studies are typically required for each construction project, particularly for the scale of the aforementioned building boom in the Middle East. The current study was conducted in Qatar at the location of a future highway interchange to evaluate a suite of 3D seismic techniques in their effectiveness to interrogate the subsurface for the presence of karst-like collapse structures. The survey comprised an area of approximately 10,000 m2 and consisted of 550 source- and 192 receiver locations. The seismic source was an accelerated weight drop while the geophones consisted of 3-component 10 Hz velocity sensors. At present, we analyzed over 100,000 P-wave phase arrivals and performed high-resolution 3-D tomographic imaging of the shallow subsurface. Furthermore, dispersion analysis of recorded surface waves will be performed to obtain S-wave velocity profiles of the subsurface. Both results, in conjunction with density estimates, will be utilized to determine the elastic moduli of the subsurface rock layers.

  14. 3D printing of nano- and micro-structures

    NASA Astrophysics Data System (ADS)

    Ramasamy, Mouli; Varadan, Vijay K.

    2016-04-01

    Additive manufacturing or 3D printing techniques are being vigorously investigated as a replacement to the traditional and conventional methods in fabrication to bring forth cost and time effective approaches. Introduction of 3D printing has led to printing micro and nanoscale structures including tissues and organelles, bioelectric sensors and devices, artificial bones and transplants, microfluidic devices, batteries and various other biomaterials. Various microfabrication processes have been developed to fabricate micro components and assemblies at lab scale. 3D Fabrication processes that can accommodate the functional and geometrical requirements to realize complicated structures are becoming feasible through advances in additive manufacturing. This advancement could lead to simpler development mechanisms of novel components and devices exhibiting complex features. For instance, development of microstructure electrodes that can penetrate the epidermis of the skin to collect the bio potential signal may prove very effective than the electrodes that measure signal from the skin's surface. The micro and nanostructures will have to possess extraordinary material and mechanical properties for its dexterity in the applications. A substantial amount of research being pursued on stretchable and flexible devices based on PDMA, textiles, and organic electronics. Despite the numerous advantages these substrates and techniques could solely offer, 3D printing enables a multi-dimensional approach towards finer and complex applications. This review emphasizes the use of 3D printing to fabricate micro and nanostructures for that can be applied for human healthcare.

  15. 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

  16. 3D structures of membrane proteins from genomic sequencing

    PubMed Central

    Hopf, Thomas A.; Colwell, Lucy J.; Sheridan, Robert; Rost, Burkhard; Sander, Chris; Marks, Debora S.

    2012-01-01

    Summary We show that amino acid co-variation in proteins, extracted from the evolutionary sequence record, can be used to fold transmembrane proteins. We use this technique to predict previously unknown, 3D structures for 11 transmembrane proteins (with up to 14 helices) from their sequences alone. The prediction method (EVfold_membrane), applies a maximum entropy approach to infer evolutionary co-variation in pairs of sequence positions within a protein family and then generates all-atom models with the derived pairwise distance constraints. We benchmark the approach with blinded, de novo computation of known transmembrane protein structures from 23 families, demonstrating unprecedented accuracy of the method for large transmembrane proteins. We show how the method can predict oligomerization, functional sites, and conformational changes in transmembrane proteins. With the rapid rise in large-scale sequencing, more accurate and more comprehensive information on evolutionary constraints can be decoded from genetic variation, greatly expanding the repertoire of transmembrane proteins amenable to modelling by this method. PMID:22579045

  17. 3D genome structure modeling by Lorentzian objective function.

    PubMed

    Trieu, Tuan; Cheng, Jianlin

    2016-11-29

    The 3D structure of the genome plays a vital role in biological processes such as gene interaction, gene regulation, DNA replication and genome methylation. Advanced chromosomal conformation capture techniques, such as Hi-C and tethered conformation capture, can generate chromosomal contact data that can be used to computationally reconstruct 3D structures of the genome. We developed a novel restraint-based method that is capable of reconstructing 3D genome structures utilizing both intra-and inter-chromosomal contact data. Our method was robust to noise and performed well in comparison with a panel of existing methods on a controlled simulated data set. On a real Hi-C data set of the human genome, our method produced chromosome and genome structures that are consistent with 3D FISH data and known knowledge about the human chromosome and genome, such as, chromosome territories and the cluster of small chromosomes in the nucleus center with the exception of the chromosome 18. The tool and experimental data are available at https://missouri.box.com/v/LorDG.

  18. RNA and protein 3D structure modeling: similarities and differences.

    PubMed

    Rother, Kristian; Rother, Magdalena; Boniecki, Michał; Puton, Tomasz; Bujnicki, Janusz M

    2011-09-01

    In analogy to proteins, the function of RNA depends on its structure and dynamics, which are encoded in the linear sequence. While there are numerous methods for computational prediction of protein 3D structure from sequence, there have been very few such methods for RNA. This review discusses template-based and template-free approaches for macromolecular structure prediction, with special emphasis on comparison between the already tried-and-tested methods for protein structure modeling and the very recently developed "protein-like" modeling methods for RNA. We highlight analogies between many successful methods for modeling of these two types of biological macromolecules and argue that RNA 3D structure can be modeled using "protein-like" methodology. We also highlight the areas where the differences between RNA and proteins require the development of RNA-specific solutions.

  19. Using 3D visualization and seismic attributes to improve structural and stratigraphic resolution of reservoirs

    SciTech Connect

    Kerr, J. ); Jones, G.L. )

    1996-01-01

    Recent advances in hardware and software have given the interpreter and engineer new ways to view 3D seismic data and well bore information. Recent papers have also highlighted the use of various statistics and seismic attributes. By combining new 3D rendering technologies with recent trends in seismic analysis, the interpreter can improve the structural and stratigraphic resolution of hydrocarbon reservoirs. This paper gives several examples using 3D visualization to better define both the structural and stratigraphic aspects of several different structural types from around the world. Statistics, 3D visualization techniques and rapid animation are used to show complex faulting and detailed channel systems. These systems would be difficult to map using either 2D or 3D data with conventional interpretation techniques.

  20. Using 3D visualization and seismic attributes to improve structural and stratigraphic resolution of reservoirs

    SciTech Connect

    Kerr, J.; Jones, G.L.

    1996-12-31

    Recent advances in hardware and software have given the interpreter and engineer new ways to view 3D seismic data and well bore information. Recent papers have also highlighted the use of various statistics and seismic attributes. By combining new 3D rendering technologies with recent trends in seismic analysis, the interpreter can improve the structural and stratigraphic resolution of hydrocarbon reservoirs. This paper gives several examples using 3D visualization to better define both the structural and stratigraphic aspects of several different structural types from around the world. Statistics, 3D visualization techniques and rapid animation are used to show complex faulting and detailed channel systems. These systems would be difficult to map using either 2D or 3D data with conventional interpretation techniques.

  1. Instability and Wave Propagation in Structured 3D Composites

    NASA Astrophysics Data System (ADS)

    Kaynia, Narges; Fang, Nicholas X.; Boyce, Mary C.

    2014-03-01

    Many structured composites found in nature possess undulating and wrinkled interfacial layers that regulate mechanical, chemical, acoustic, adhesive, thermal, electrical and optical functions of the material. This research focused on the complex instability and wrinkling pattern arising in 3D structured composites and the effect of the buckling pattern on the overall structural response. The 3D structured composites consisted of stiffer plates supported by soft matrix on both sides. Compression beyond the critical strain led to complex buckling patterns in the initially straight plates. The motivation of our work is to elaborate the formation of a system of prescribed periodic scatterers (metamaterials) due to buckling, and their effect to interfere wave propagation through the metamaterial structures. Such metamaterials made from elastomers enable large reversible deformation and, as a result, significant changes of the wave propagation properties. We developed analytical and finite element models to capture various aspects of the instability mechanism. Mechanical experiments were designed to further explore the modeling results. The ability to actively alter the 3D composite structure can enable on-demand tunability of many different functions, such as active control of wave propagation to create band-gaps and waveguides.

  2. A framework for querying a database for structural information on 3D images of macromolecules: A web-based query-by-content prototype on the BioImage macromolecular server.

    PubMed

    de Alarcón, P A; Gupta, A; Carazo, J M

    1999-01-01

    Nowadays we are experiencing a remarkable growth in the number of databases that have become accessible over the Web. However, in a certain number of cases, for example, in the case of BioImage, this information is not of a textual nature, thus posing new challenges in the design of tools to handle these data. In this work, we concentrate on the development of new mechanisms aimed at "querying" these databases of complex data sets by their intrinsic content, rather than by their textual annotations only. We concentrate our efforts on a subset of BioImage containing 3D images (volumes) of biological macromolecules, implementing a first prototype of a "query-by-content" system. In the context of databases of complex data types the term query-by-content makes reference to those data modeling techniques in which user-defined functions aim at "understanding" (to some extent) the informational content of the data sets. In these systems the matching criteria introduced by the user are related to intrinsic features concerning the 3D images themselves, hence, complementing traditional queries by textual key words only. Efficient computational algorithms are required in order to "extract" structural information of the 3D images prior to storing them in the database. Also, easy-to-use interfaces should be implemented in order to obtain feedback from the expert. Our query-by-content prototype is used to construct a concrete query, making use of basic structural features, which are then evaluated over a set of three-dimensional images of biological macromolecules. This experimental implementation can be accessed via the Web at the BioImage server in Madrid, at http://www.bioimage.org/qbc/index.html.

  3. Structured Light-Based 3D Reconstruction System for Plants.

    PubMed

    Nguyen, Thuy Tuong; Slaughter, David C; Max, Nelson; Maloof, Julin N; Sinha, Neelima

    2015-07-29

    Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants. This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance.

  4. Structured Light-Based 3D Reconstruction System for Plants

    PubMed Central

    Nguyen, Thuy Tuong; Slaughter, David C.; Max, Nelson; Maloof, Julin N.; Sinha, Neelima

    2015-01-01

    Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants.This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance. PMID:26230701

  5. 3D lidar imaging for detecting and understanding plant responses and canopy structure.

    PubMed

    Omasa, Kenji; Hosoi, Fumiki; Konishi, Atsumi

    2007-01-01

    Understanding and diagnosing plant responses to stress will benefit greatly from three-dimensional (3D) measurement and analysis of plant properties because plant responses are strongly related to their 3D structures. Light detection and ranging (lidar) has recently emerged as a powerful tool for direct 3D measurement of plant structure. Here the use of 3D lidar imaging to estimate plant properties such as canopy height, canopy structure, carbon stock, and species is demonstrated, and plant growth and shape responses are assessed by reviewing the development of lidar systems and their applications from the leaf level to canopy remote sensing. In addition, the recent creation of accurate 3D lidar images combined with natural colour, chlorophyll fluorescence, photochemical reflectance index, and leaf temperature images is demonstrated, thereby providing information on responses of pigments, photosynthesis, transpiration, stomatal opening, and shape to environmental stresses; these data can be integrated with 3D images of the plants using computer graphics techniques. Future lidar applications that provide more accurate dynamic estimation of various plant properties should improve our understanding of plant responses to stress and of interactions between plants and their environment. Moreover, combining 3D lidar with other passive and active imaging techniques will potentially improve the accuracy of airborne and satellite remote sensing, and make it possible to analyse 3D information on ecophysiological responses and levels of various substances in agricultural and ecological applications and in observations of the global biosphere.

  6. Designing stereoscopic information visualization for 3D-TV: What can we can learn from S3D gaming?

    NASA Astrophysics Data System (ADS)

    Schild, Jonas; Masuch, Maic

    2012-03-01

    This paper explores graphical design and spatial alignment of visual information and graphical elements into stereoscopically filmed content, e.g. captions, subtitles, and especially more complex elements in 3D-TV productions. The method used is a descriptive analysis of existing computer- and video games that have been adapted for stereoscopic display using semi-automatic rendering techniques (e.g. Nvidia 3D Vision) or games which have been specifically designed for stereoscopic vision. Digital games often feature compelling visual interfaces that combine high usability with creative visual design. We explore selected examples of game interfaces in stereoscopic vision regarding their stereoscopic characteristics, how they draw attention, how we judge effect and comfort and where the interfaces fail. As a result, we propose a list of five aspects which should be considered when designing stereoscopic visual information: explicit information, implicit information, spatial reference, drawing attention, and vertical alignment. We discuss possible consequences, opportunities and challenges for integrating visual information elements into 3D-TV content. This work shall further help to improve current editing systems and identifies a need for future editing systems for 3DTV, e.g., live editing and real-time alignment of visual information into 3D footage.

  7. 3D printed components with ultrasonically arranged microscale structure

    NASA Astrophysics Data System (ADS)

    Llewellyn-Jones, Thomas M.; Drinkwater, Bruce W.; Trask, Richard S.

    2016-02-01

    This paper shows the first application of in situ manipulation of discontinuous fibrous structure mid-print, within a 3D printed polymeric composite architecture. Currently, rapid prototyping methods (fused filament fabrication, stereolithography) are gaining increasing popularity within the engineering commnity to build structural components. Unfortunately, the full potential of these components is limited by the mechanical properties of the materials used. The aim of this study is to create and demonstrate a novel method to instantaneously orient micro-scale glass fibres within a selectively cured photocurable resin system, using ultrasonic forces to align the fibres in the desired 3D architecture. To achieve this we have mounted a switchable, focused laser module on the carriage of a three-axis 3D printing stage, above an in-house ultrasonic alignment rig containing a mixture of photocurable resin and discontinuous 14 μm diameter glass fibre reinforcement(50 μm length). In our study, a suitable print speed of 20 mm s-1 was used, which is comparable to conventional additive layer techniques. We show the ability to construct in-plane orthogonally aligned sections printed side by side, where the precise orientation of the configurations is controlled by switching the ultrasonic standing wave profile mid-print. This approach permits the realisation of complex fibrous architectures within a 3D printed landscape. The versatile nature of the ultrasonic manipulation technique also permits a wide range of particle types (diameters, aspect ratios and functions) and architectures (in-plane, and out-plane) to be patterned, leading to the creation of a new generation of fibrous reinforced composites for 3D printing.

  8. The 3-D inelastic analyses for computational structural mechanics

    NASA Technical Reports Server (NTRS)

    Hopkins, D. A.; Chamis, C. C.

    1989-01-01

    The 3-D inelastic analysis method is a focused program with the objective to develop computationally effective analysis methods and attendant computer codes for three-dimensional, nonlinear time and temperature dependent problems present in the hot section of turbojet engine structures. Development of these methods was a major part of the Hot Section Technology (HOST) program over the past five years at Lewis Research Center.

  9. 3D reconstruction methods of coronal structures by radio observations

    NASA Technical Reports Server (NTRS)

    Aschwanden, Markus J.; Bastian, T. S.; White, Stephen M.

    1992-01-01

    The ability to carry out the three dimensional (3D) reconstruction of structures in the solar corona would represent a major advance in the study of the physical properties in active regions and in flares. Methods which allow a geometric reconstruction of quasistationary coronal structures (for example active region loops) or dynamic structures (for example flaring loops) are described: stereoscopy of multi-day imaging observations by the VLA (Very Large Array); tomography of optically thin emission (in radio or soft x-rays); multifrequency band imaging by the VLA; and tracing of magnetic field lines by propagating electron beams.

  10. Cancer3D: understanding cancer mutations through protein structures.

    PubMed

    Porta-Pardo, Eduard; Hrabe, Thomas; Godzik, Adam

    2015-01-01

    The new era of cancer genomics is providing us with extensive knowledge of mutations and other alterations in cancer. The Cancer3D database at http://www.cancer3d.org gives an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins in which they are found. The database also helps users analyze the distribution patterns of the mutations as well as their relationship to changes in drug activity through two algorithms: e-Driver and e-Drug. These algorithms use knowledge of modular structure of genes and proteins to separately study each region. This approach allows users to find novel candidate driver regions or drug biomarkers that cannot be found when similar analyses are done on the whole-gene level. The Cancer3D database provides access to the results of such analyses based on data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE). In addition, it displays mutations from over 14,700 proteins mapped to more than 24,300 structures from PDB. This helps users visualize the distribution of mutations and identify novel three-dimensional patterns in their distribution.

  11. The 3D lightweight structural characteristics of the beetle forewing.

    PubMed

    Chen, Jinxiang; Tuo, Wanyong; Guo, Zhensheng; Yan, Lili

    2017-02-01

    The present paper renewedly expounds upon the characteristics of the 3D lightweight structure of beetle forewings and notes that two biomimetic structures (models) that have appeared in recent years do not comply with these characteristics based on a comparison of the structures of the biological prototypes. The first model features transverse tubules based on observations of circular holes in cross-sectional figures of the Cybister forewing. The second is a biomimetic spherical cavity model with hollow trabeculae that reportedly exhibits superior mechanical properties because its structures are most similar to the biological prototype. Finally, a false biomimetic proposition that the mechanical properties of biomimetic structures with "fiber winding" patterns are superior to those of structures constructed of pure "epoxy" is also noted. Hopefully, the present study can serve to improve the state of research on biomimetic applications of beetle forewing structures.

  12. Myosin filament 3D structure in mammalian cardiac muscle☆

    PubMed Central

    AL-Khayat, Hind A.; Morris, Edward P.; Kensler, Robert W.; Squire, John M.

    2008-01-01

    A number of cardiac myopathies (e.g. familial hypertrophic cardiomyopathy and dilated cardiomyopathy) are linked to mutations in cardiac muscle myosin filament proteins, including myosin and myosin binding protein C (MyBP-C). To understand the myopathies it is necessary to know the normal 3D structure of these filaments. We have carried out 3D single particle analysis of electron micrograph images of negatively stained isolated myosin filaments from rabbit cardiac muscle. Single filament images were aligned and divided into segments about 2 × 430 Å long, each of which was treated as an independent ‘particle’. The resulting 40 Å resolution 3D reconstruction showed both axial and azimuthal (no radial) myosin head perturbations within the 430 Å repeat, with successive crown rotations of approximately 60°, 60° and 0°, rather than the regular 40° for an unperturbed helix. However, it is shown that the projecting density peaks appear to start at low radius from origins closer to those expected for an unperturbed helical filament, and that the azimuthal perturbation especially increases with radius. The head arrangements in rabbit cardiac myosin filaments are very similar to those in fish skeletal muscle myosin filaments, suggesting a possible general structural theme for myosin filaments in all vertebrate striated muscles (skeletal and cardiac). PMID:18472277

  13. Manufacturing of a 3D complex hyperstable Cesic structure

    NASA Astrophysics Data System (ADS)

    Kroedel, Matthias; Courteau, Pascal; Poupinet, Anne; Sarri, Giuseppe

    2007-09-01

    Global astrometry requires extremely stable materials for instrument structures, such as optical benches. Cesic®, developed by ECM and Thales Alenia Space for mirrors and high stability structures, offers an excellent compromise in terms of structural strength, stability and very high lightweight capability, with a coefficient of thermal expansion that is virtually zero at cryogenic T°. The High-Stability Optical Bench (HSOB) GAIA study, realized by Thales Alenia Space under ESA contract, aimed to design, develop and test a full-scale representative of the HSOB bench, made entirely of Cesic®. The bench has been equipped with SAGEIS-CSO laser metrology system MOUSE1, a Michelson interferometer composed of integrated optics with nm-resolution. The HSOB bench has been submitted to a homogeneous T° step under vacuum to characterize 3-D expansion behavior of its two arms. The quite negligible interarm differential, measured with a nm-range reproducibility, demonstrates that a complete 3-D structure made of Cesic® has the same CTE homogeneity as do characterization samples, fully in line with the stringent GAIA requirements (1ppm at 120K). This demonstrates that Cesic® properties at cryogenic temperatures are fully appropriate to the manufacturing of complex highly stable optical structures. This successful study confirms ECM's and Thales Alenia Space's ability to design and manufacture monolithic lightweight highly stable optical structures, based on inner-cell triangular design made possible by the unique Cesic® manufacturing process.

  14. Multivoxel pattern analysis reveals 3D place information in the human hippocampus.

    PubMed

    Kim, Misun; Jeffery, Kate J; Maguire, Eleanor A

    2017-03-20

    The spatial world is three-dimensional (3D), and humans and other animals move both horizontally and vertically within it. Extant neuroscientific studies have typically investigated spatial navigation on a horizontal two-dimensional plane, leaving much unknown about how 3D spatial information is represented in the brain. Specifically, horizontal and vertical information may be encoded in the same or different neural structures with equal or unequal sensitivity. Here, we investigated these possibilities using functional MRI (fMRI) while participants were passively moved within a 3D lattice structure as if riding a rollercoaster. Multivoxel pattern analysis was used to test for the existence of information relating to where and in which direction participants were heading in this virtual environment. Behaviorally, participants had similarly accurate memory for vertical and horizontal locations, and the right anterior hippocampus expressed place information that was sensitive to changes along both horizontal and vertical axes. This is suggestive of isotropic 3D place encoding. By contrast, participants indicated their heading direction faster and more accurately when they were heading in a tilted-up or tilted-down direction. This direction information was expressed in the right retrosplenial cortex and posterior hippocampus, and was only sensitive to vertical pitch, which could reflect the importance of the vertical (gravity) axis as a reference frame. Overall, our findings extend previous knowledge of how we represent the spatial world and navigate within it, by taking into account the important third dimension.SIGNIFICANCE STATEMENTThe spatial world is three-dimensional (3D) -- we can move horizontally across surfaces, but also vertically, going up slopes or stairs. Little is known about how the brain supports representations of 3D space. A key question is whether or not horizontal and vertical information is equally well represented. Here we measured functional MRI

  15. An endoscopic 3D scanner based on structured light.

    PubMed

    Schmalz, Christoph; Forster, Frank; Schick, Anton; Angelopoulou, Elli

    2012-07-01

    We present a new endoscopic 3D scanning system based on Single Shot Structured Light. The proposed design makes it possible to build an extremely small scanner. The sensor head contains a catadioptric camera and a pattern projection unit. The paper describes the working principle and calibration procedure of the sensor. The prototype sensor head has a diameter of only 3.6mm and a length of 14mm. It is mounted on a flexible shaft. The scanner is designed for tubular cavities and has a cylindrical working volume of about 30mm length and 30mm diameter. It acquires 3D video at 30 frames per second and typically generates approximately 5000 3D points per frame. By design, the resolution varies over the working volume, but is generally better than 200μm. A prototype scanner has been built and is evaluated in experiments with phantoms and biological samples. The recorded average error on a known test object was 92μm.

  16. 3D and 4D atlas system of living human body structure.

    PubMed

    Suzuki, N; Takatsu, A; Hattori, A; Ezumi, T; Oda, S; Yanai, T; Tominaga, H

    1998-01-01

    A reference system for accessing anatomical information from a complete 3D structure of the whole body "living human", including 4D cardiac dynamics, was reconstructed with 3D and 4D data sets obtained from normal volunteers. With this system, we were able to produce a human atlas in which sectional images can be accessed from any part of the human body interactively by real-time image generation.

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

    PubMed

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

    2017-02-01

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

  18. 3-D Attenuation Structure around the SAFOD site, Parkfield, California

    NASA Astrophysics Data System (ADS)

    Harrington, N. L.; Thurber, C. H.; Zhang, H.; Roecker, S.

    2006-12-01

    We are developing models of the 3-D attenuation structure, both Qp and Qs, for a region about 15 km square centered on SAFOD. We are analyzing local earthquake data collected in 2001 and 2002 from the UW/RPI PASO array, the UC-Berkeley HRSN, and USGS seismic network stations around Parkfield. We determine the P- or S-wave t* values for an individual local earthquake for each of the observing stations by fitting observed spectra using a joint inversion for a common corner frequency, low-frequency amplitude, and t*. Within our initial data set, we examine 575 events recorded at up to 111 stations and obtain over 19000 P- wave t* values. We use these t* values in simul2000 and tomoDD to perform the inversion to obtain a 3-D, frequency-independent Qp model of the attenuation structure, using an existing 3-D Vp model and associated event locations. We will use this same procedure to obtain the Qs structure. In our preliminary Qp structure results, we observe a high Qp feature (about 250) at 0-8 km depth on the southwest side of the fault. We associate this feature with the high density, high velocity Salinian basement rocks. We also see a moderate Qp feature (about 150) in the fault zone that encompasses the hypocenters of our events. On the northeast side of the fault, we observe Qp values generally increasing with depth, from 125 at the surface to 200 at 8 km. We will present our final Qp and Qs models, identify major features within the two, and discuss how these features relate to the findings of other geophysical studies in the area (seismic velocity, electrical resistivity, anisotropy). We will discuss how these features relate to the nature of the crust in that area, including the local geology, presence of fluids, fracturing, etc.

  19. Gene3D: modelling protein structure, function and evolution.

    PubMed

    Yeats, Corin; Maibaum, Michael; Marsden, Russell; Dibley, Mark; Lee, David; Addou, Sarah; Orengo, Christine A

    2006-01-01

    The Gene3D release 4 database and web portal (http://cathwww.biochem.ucl.ac.uk:8080/Gene3D) provide a combined structural, functional and evolutionary view of the protein world. It is focussed on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species. The protein sequences have also been clustered into whole-chain families so as to aid functional prediction. The structural annotation is generated using HMM models based on the CATH domain families; CATH is a repository for manually deduced protein domains. Amongst the changes from the last publication are: the addition of over 100 genomes and the UniProt sequence database, domain data from Pfam, metabolic pathway and functional data from COGs, KEGG and GO, and protein-protein interaction data from MINT and BIND. The website has been rebuilt to allow more sophisticated querying and the data returned is presented in a clearer format with greater functionality. Furthermore, all data can be downloaded in a simple XML format, allowing users to carry out complex investigations at their own computers.

  20. Water linked 3D coordination polymers: Syntheses, structures and applications

    NASA Astrophysics Data System (ADS)

    Singh, Suryabhan; Bhim, Anupam

    2016-12-01

    Three new coordination polymers (CPs) based on Cd and Pb, [Cd(OBA)(μ-H2O)(H2O)]n1, [Pb(OBA)(μ-H2O)]n2 [where OBA=4,4'-Oxybis(benzoate)] and [Pb(SDBA)(H2O)]n.1/4DMF 3 (SDBA=4,4'-Sulfonyldibenzoate), have been synthesized and characterized. The single crystal structural studies reveal that CPs 1 and 2 have three dimensional structure. A water molecule bridges two metal centres which appears to the responsible for the dimensionality increase from 2D to 3D. Compound 3 has a supramolecular 3D structure involving water molecule and hydrogen bonds. A structural transformation is observed when 3 was heated at 100 °C or kept in methanol, forming [Pb(SDBA)]n4. Compound 4 is used as supporting matrix for palladium nanoparticles, PdNPs@4. The PdNPs@4 exhibits good catalytic activity toward the reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) in the presence of NaBH4 at room temperature. Luminescence studies revealed that all CPs could be an effective sensor for nitroaromatic explosives.

  1. Structural analysis of tropical cyclone using INSAT-3D observations

    NASA Astrophysics Data System (ADS)

    Jaiswal, Neeru; Kishtawal, C. M.

    2016-05-01

    The continuous observations from visible and thermal infrared (TIR) channels of geostationary satellites are highly useful for obtaining the features associated with the shape and dynamics of cloud structures within the tropical cyclones (TCs). As TC develops from an unstructured cloud cluster and intensifies, the cloud structures become more axisymmetric around the centre of the TC. To better understand the structure of TC during different stages of its evolution i.e. from its cyclogenesis to maturity and dissipation, the continuous satellite observations plays a key role. The high spatial and temporal resolution observations from geostationary satellites are very useful in order to analyze the cloud organization during the cyclogenesis. The gradient of the brightness temperatures measures the level of symmetry of each structure, which characterizes the degree of cloud organization of the TC. In the present work, the structural analysis of TC during its life period using the observations from Indian geostationary satellite INSAT-3D has been discussed. The visible and TIR observations from INSAT-3D satellite were used to fix the center position of the cyclone which is an input for the cyclone track and intensity prediction models. This data is also used to estimate the intensity of cyclone in the advanced Dvorak technique (ADT), and in the estimation of radius of maximum winds (Rmax) of TC which is an essential input parameter for the prediction of storm surge associated to the cyclones. The different patterns of cloud structure during the intensification stage, eye-wall formation and dissipation have been discussed. The early identification of these features helps in predicting the rapid intensification of TC which in turn improves the intensity predictions.

  2. 3D Printing of Hierarchical Silk Fibroin Structures.

    PubMed

    Sommer, Marianne R; Schaffner, Manuel; Carnelli, Davide; Studart, André R

    2016-12-21

    Like many other natural materials, silk is hierarchically structured from the amino acid level up to the cocoon or spider web macroscopic structures. Despite being used industrially in a number of applications, hierarchically structured silk fibroin objects with a similar degree of architectural control as in natural structures have not been produced yet due to limitations in fabrication processes. In a combined top-down and bottom-up approach, we exploit the freedom in macroscopic design offered by 3D printing and the template-guided assembly of ink building blocks at the meso- and nanolevel to fabricate hierarchical silk porous materials with unprecedented structural control. Pores with tunable sizes in the range 40-350 μm are generated by adding sacrificial organic microparticles as templates to a silk fibroin-based ink. Commercially available wax particles or monodisperse polycaprolactone made by microfluidics can be used as microparticle templates. Since closed pores are generated after template removal, an ultrasonication treatment can optionally be used to achieve open porosity. Such pore templating particles can be further modified with nanoparticles to create a hierarchical template that results in porous structures with a defined nanotopography on the pore walls. The hierarchically porous silk structures obtained with this processing technique can potentially be utilized in various application fields from structural materials to thermal insulation to tissue engineering scaffolds.

  3. Diagnosis and control of 3D elastic mechanical structures

    NASA Astrophysics Data System (ADS)

    Krajcin, Idriz; Soeffker, Dirk

    2005-05-01

    In this paper, a model-based approach for fault detection and vibration control of flexible structures is proposed and applied to 3D-structures. Faults like cracks or impacts acting on a flexible structure are considered as unknown inputs acting on the structure. The Proportional-Integral-Observer (PI-Observer) is used to estimate the system states as well as unknown inputs acting on a system. Also the effects of structural changes are understood as external effects (related to the unchanged structure) and are considered as fictitious external forces or moments. The paper deals with the design of the PI-Observer for practical applications when measurement noise and model uncertainties are present and shows its performance in experimental results. As examples, impacts acting upon a one side clamped elastic beam and on a thin plate structure are estimated using displacement or strain measurements. To control the vibration of the flexible plate, two piezoelectric patches bonded on the structure are used as actuators. The control algorithm introduced in this contribution contains a state feedback control and additionally a disturbance rejection. The disturbances are estimated using the PI-Observer. Experimental results show the performance and the robustness properties of the control strategy for the vibration control of a very thin plate.

  4. Protein-protein interaction networks studies and importance of 3D structure knowledge.

    PubMed

    Lu, Hui-Chun; Fornili, Arianna; Fraternali, Franca

    2013-12-01

    Protein-protein interaction networks (PPINs) are a powerful tool to study biological processes in living cells. In this review, we present the progress of PPIN studies from abstract to more detailed representations. We will focus on 3D interactome networks, which offer detailed information at the atomic level. This information can be exploited in understanding not only the underlying cellular mechanisms, but also how human variants and disease-causing mutations affect protein functions and complexes' stability. Recent studies have used structural information on PPINs to also understand the molecular mechanisms of binding partner selection. We will address the challenges in generating 3D PPINs due to the restricted number of solved protein structures. Finally, some of the current use of 3D PPINs will be discussed, highlighting their contribution to the studies in genotype-phenotype relationships and in the optimization of targeted studies to design novel chemical compounds for medical treatments.

  5. Recovering physical property information from subduction plate boundaries using 3D full-waveform seismic inversion

    NASA Astrophysics Data System (ADS)

    Bell, R. E.; Morgan, J. V.; Warner, M.

    2013-12-01

    Our understanding of subduction margin seismogenesis has been revolutionised in the last couple of decades with the discovery that the size of the seismogenic zone may not be controlled simply by temperature and a broad spectrum of seismic behaviour exists from stick-slip to stable sliding. Laboratory and numerical experiments suggest that physical properties, particularly fluid pressure may play an important role in controlling the seismic behaviour of subduction margins. Although drilling can provide information on physical properties along subduction thrust faults at point locations at relatively shallow depths, correlations between physical properties and seismic velocity using rock physics relationships are required to resolve physical properties along the margin and down-dip. Therefore, high resolution seismic velocity models are key to recovering physical property information at subduction plate boundaries away from drill sites. 3D Full waveform inversion (FWI) is a technique pioneered by the oil industry to obtain high-resolution high-fidelity models of physical properties in the sub-surface. 3D FWI involves the inversion of low-frequency (>2 to <7 Hz), early arriving (principally transmitted) seismic data, to recover the macro (intermediate to long-wavelength) velocity structure. Although 2D FWI has been used to improve velocity models of subduction plate boundaries before, 3D FWI has not yet been attempted. 3D inversions have superior convergence and accuracy, as they sample the subsurface with multi-azimuth multiply-crossing wavefields. In this contribution we perform a suite of synthetic tests to investigate if 3D FWI could be used to better resolve physical property information along subduction margin plate boundaries using conventionally collected 3D seismic data. We base our analysis on the Muroto Basin area of the Nankai margin and investigate if the acquisition parameters and geometry of the subduction margin render 3D seismic data collected across

  6. Vascular Structure Identification in Intraoperative 3D Contrast-Enhanced Ultrasound Data

    PubMed Central

    Ilunga-Mbuyamba, Elisee; Avina-Cervantes, Juan Gabriel; Lindner, Dirk; Cruz-Aceves, Ivan; Arlt, Felix; Chalopin, Claire

    2016-01-01

    In this paper, a method of vascular structure identification in intraoperative 3D Contrast-Enhanced Ultrasound (CEUS) data is presented. Ultrasound imaging is commonly used in brain tumor surgery to investigate in real time the current status of cerebral structures. The use of an ultrasound contrast agent enables to highlight tumor tissue, but also surrounding blood vessels. However, these structures can be used as landmarks to estimate and correct the brain shift. This work proposes an alternative method for extracting small vascular segments close to the tumor as landmark. The patient image dataset involved in brain tumor operations includes preoperative contrast T1MR (cT1MR) data and 3D intraoperative contrast enhanced ultrasound data acquired before (3D-iCEUSstart) and after (3D-iCEUSend) tumor resection. Based on rigid registration techniques, a preselected vascular segment in cT1MR is searched in 3D-iCEUSstart and 3D-iCEUSend data. The method was validated by using three similarity measures (Normalized Gradient Field, Normalized Mutual Information and Normalized Cross Correlation). Tests were performed on data obtained from ten patients overcoming a brain tumor operation and it succeeded in nine cases. Despite the small size of the vascular structures, the artifacts in the ultrasound images and the brain tissue deformations, blood vessels were successfully identified. PMID:27070610

  7. 3D-printing and mechanics of bio-inspired articulated and multi-material structures.

    PubMed

    Porter, Michael M; Ravikumar, Nakul; Barthelat, Francois; Martini, Roberto

    2016-12-21

    3D-printing technologies allow researchers to build simplified physical models of complex biological systems to more easily investigate their mechanics. In recent years, a number of 3D-printed structures inspired by the dermal armors of various fishes have been developed to study their multiple mechanical functionalities, including flexible protection, improved hydrodynamics, body support, or tail prehensility. Natural fish armors are generally classified according to their shape, material and structural properties as elasmoid scales, ganoid scales, placoid scales, carapace scutes, or bony plates. Each type of dermal armor forms distinct articulation patterns that facilitate different functional advantages. In this paper, we highlight recent studies that developed 3D-printed structures not only to inform the design and application of some articulated and multi-material structures, but also to explain the mechanics of the natural biological systems they mimic.

  8. SU-E-T-801: Verification of Dose Information Passed Through 3D-Printed Products

    SciTech Connect

    Jeong, S; Yoon, M; Kim, D; Chung, W; Chung, M; Shin, D

    2015-06-15

    Purpose: When quality assurance (QA) of patient treatment beam is performed, homogeneous water equivalent phantom which has different structure from patient’s internal structure is normally used. In these days, it is possible to make structures which have same shapes of human organs with commercialization of 3D-printer. As a Result, structures with same shape of human organs made by 3D-printer could be used to test qualification of treatment beam with greater accuracy than homogeneous water phantom. In this study, we estimated the dose response of 3D-printer materials to test the probability as a humanoid phantom or new generation of compensator tool. Methods: The rectangular products with variety densities (50%, 75% and 100%) were made to verify their characteristics. The products for experiment group and solid water phantom and air for control group with 125 cubic centimeters were put on solid water phantom with enough thickness. CT image of two products were acquired to know their HU values and to know about their radiologic characteristics. 6MV beams with 500MU were exposed for each experiment. Doses were measured behind the 3D-printed products. These measured doses were compared to the results taken by TPS. Results: Absorbed dose penetrated from empty air is normalized to 100%. Doses measured from 6MV photon beams penetrated from 50%, 75% and 100% products were 99%, 96% and 84%, respectively. HU values of 50%, 75% and 100% products are about −910, −860 and −10. Conclusion: 3D-printer can produce structures which have similar characteristics with human organ. These results would be used to make similar phantoms with patient information. This work was supported by the Nuclear Safety Research Program (Grant No. 1305033 and 1403019) of the Korea Radiation Safety Foundation and the Nuclear Safety and Security Commission and Radiation Technology Development Program (2013M2A2A4027117) of the Republic of Korea.

  9. Single cell detection using 3D magnetic rolled-up structures.

    PubMed

    Ger, Tzong-Rong; Huang, Hao-Ting; Huang, Chen-Yu; Lai, Mei-Feng

    2013-11-07

    A 3D rolled-up structure made of a SiO2 layer and a fishbone-like magnetic thin film was proposed here as a biosensor. The magnetoresistance (MR) measurement results of the sensor suggest that the presence of the stray field, which is induced by the magnetic nanoparticles, significantly increased the switching field. Comparing the performance of the 2D sensor and 3D sensor designed in this study, the response in switching field variation was 12.14% in the 2D sensor and 62.55% in the 3D sensor. The response in MR ratio variation was 4.55% in the 2D sensor and 82.32% in the 3D sensor. In addition, the design of the 3D sensor structure also helped to attract and trap a single magnetic cell due to its stronger stray field compared with the 2D structure. The 3D magnetic biosensor designed here can provide important information for future biochip research and applications.

  10. POISs3: A 3D poisson smoother of structured grids

    NASA Astrophysics Data System (ADS)

    Lehtimaeki, R.

    Flow solvers based on solving Navier-Stokes or Euler equations generally need a computational grid to represent the domain of the flow. A structured computational grid can be efficiently produced by algebraic methods like transfinite interpolation. Unfortunately, algebraic methods propagate all kinds of unsmoothness of the boundary into the field. Unsmoothness of the grid, in turn, can result in inaccuracy in the flow solver. In the present work a 3D elliptic grid smoother was developed. The smoother is based on solving three Poisson equations, one for each curvilinear direction. The Poisson equations formed in the physical region are first transformed to the computational (rectilinear) region. The resulting equations form a system of three coupled elliptic quasi-linear partial differential equations in the computational domain. A short review of the Poisson method is presented. The regularity of a grid cell is studied and a skewness value is developed.

  11. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine.

    PubMed

    McGuire, Ross; Verhoeven, Stefan; Vass, Márton; Vriend, Gerrit; de Esch, Iwan J P; Lusher, Scott J; Leurs, Rob; Ridder, Lars; Kooistra, Albert J; Ritschel, Tina; de Graaf, Chris

    2017-02-27

    3D-e-Chem-VM is an open source, freely available Virtual Machine ( http://3d-e-chem.github.io/3D-e-Chem-VM/ ) that integrates cheminformatics and bioinformatics tools for the analysis of protein-ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein-ligand interaction data from proteomewide databases (e.g., ChEMBLdb and PDB), as well as customized information systems focused on, e.g., G protein-coupled receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb).

  12. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

    PubMed Central

    2017-01-01

    3D-e-Chem-VM is an open source, freely available Virtual Machine (http://3d-e-chem.github.io/3D-e-Chem-VM/) that integrates cheminformatics and bioinformatics tools for the analysis of protein–ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein–ligand interaction data from proteomewide databases (e.g., ChEMBLdb and PDB), as well as customized information systems focused on, e.g., G protein-coupled receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb). PMID:28125221

  13. Multifunctional 3D printing of heterogeneous hydrogel structures.

    PubMed

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-09-15

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing.

  14. Multifunctional 3D printing of heterogeneous hydrogel structures

    NASA Astrophysics Data System (ADS)

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-09-01

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing.

  15. Multifunctional 3D printing of heterogeneous hydrogel structures

    PubMed Central

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-01-01

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing. PMID:27630079

  16. 3D Wilson cycle: structural inheritance and subduction polarity reversals

    NASA Astrophysics Data System (ADS)

    Beaussier, Stephane; Gerya, Taras; Burg, Jean-Pierre

    2016-04-01

    Many orogenies display along-strike variations in their orogenic wedge geometry. For instance, the Alps is an example of lateral changes in the subducting lithosphere polarity. High resolution tomography has shown that the southeast dipping European lithosphere is separated from the northeast dipping Adriatic lithosphere by a narrow transition zone at about the "Judicarian" line (Kissling et al. 2006). The formation of such 3D variations remains conjectural. We investigate the conditions that can spontaneously induce such lithospheric structures, and intend to identify the main parameters controlling their formation and geometry. Using the 3D thermo-mechanical code, I3ELVIS (Gerya and Yuen 2007) we modelled a Wilson cycle starting from a continental lithosphere in an extensional setting resulting in continental breakup and oceanic spreading. At a later stage, divergence is gradually reversed to convergence, which induce subduction of the oceanic lithosphere formed during oceanic spreading. In this model, all lateral and longitudinal structures of the lithospheres are generated self-consistently, and are consequences of the initial continental structure, tectono-magmatic inheritance, and material rheology. Our numerical simulations point out the control of rheological parameters defining the brittle/plastic yielding conditions for the lithosphere. Formation of several opposing domains of opposing subduction polarity is facilitated by wide and weak oceanic lithospheres. Furthermore, contrasts of strength between the continental and oceanic lithosphere, as well as the angle between the plate suture and the shortening direction have a second order effect on the lateral geometry of the subduction zone. In our numerical experiments systematic lateral changes in the subduction lithosphere polarity during subduction initiation form spontaneously suggesting intrinsic physical origin of this phenomenon. Further studies are necessary to understand why this feature, observed

  17. 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.

  18. 3D printing technology using high viscous materials - Synthesis of functional materials and fabrication of 3D metal structure

    NASA Astrophysics Data System (ADS)

    Hong, Seongik

    In the 3D printing technology, the research for using various materials has been performing. In this research work, 3D printable high viscous materials are suggested as one of the solutions for problems in the traditional 3D printing technology. First, Cu-Ag coreshell was synthesized as a functional material. In terms of the reaction rate, reaction rate limiting step was defined as a fundamental research, and then prepared Cu-Ag coreshell was printed and analyzed. Second, the high viscous Cu paste was prepared and then metal 3D printed structure was fabricated by using new printing method. In the synthesis of Cu-Ag coreshell, different sizes of Cu particle, 2μm and 100nm were used, and when 2μm Cu was applied, the reaction rate was limited by film diffusion control. However, when 100nm Cu was applied, reaction rate was controlled by CuO film and the rate of the reaction, which includes removing CuO film in the solution, is limited by chemical reaction control. The shape of Cu-Ag particle is spherical in the 2μm Cu condition and dendrite shape in the 100nm Cu condition respectively. The conductivity of Cu-Ag coreshell paste increased as increasing content of coreshell particle in the paste and sintering temperature. In order to print high viscous metal paste, the high viscous Cu paste was printed by using screw extruder, and the viscosity of Cu paste was measured as a fundamental research. As increasing wt.% of Cu in the paste, the viscosity also increased. In addition, the shrinkage factor was reduced by increasing wt.% of Cu in the paste. An optimized printing condition for the high viscous material was obtained, and by using this condition, 3D metal structure was fabricated. The final product was heat treated and polished. Through these processes, a fine quality of metal 3D structure was printed.

  19. Parameterization of 3D brain structures for statistical shape analysis

    NASA Astrophysics Data System (ADS)

    Zhu, Litao; Jiang, Tianzi

    2004-05-01

    Statistical Shape Analysis (SSA) is a powerful tool for noninvasive studies of pathophysiology and diagnosis of brain diseases. It also provides a shape constraint for the segmentation of brain structures. There are two key problems in SSA: the representation of shapes and their alignments. The widely used parameterized representations are obtained by preserving angles or areas and the alignments of shapes are achieved by rotating parameter net. However, representations preserving angles or areas do not really guarantee the anatomical correspondence of brain structures. In this paper, we incorporate shape-based landmarks into parameterization of banana-like 3D brain structures to address this problem. Firstly, we get the triangulated surface of the object and extract two landmarks from the mesh, i.e. the ends of the banana-like object. Then the surface is parameterized by creating a continuous and bijective mapping from the surface to a spherical surface based on a heat conduction model. The correspondence of shapes is achieved by mapping the two landmarks to the north and south poles of the sphere and using an extracted origin orientation to select the dateline during parameterization. We apply our approach to the parameterization of lateral ventricle and a multi-resolution shape representation is obtained by using the Discrete Fourier Transform.

  20. The 3D structure of Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

    Patsourakos, Spiros

    2016-07-01

    Coronal Mass Ejections (CMEs) represent one of the most powerful energy release phenomena in the entire solar system and are a major driver of space weather. Prior to 2006, our observational access to CMEs was limited to single viewpoint remote sensing observations in the inner/outer corona, and in-situ observations further away, e.g. at 1 AU. Taking all these factors together, turned out to be a major obstacle in our understanding and characterizing of the 3D structure and evolution of CMEs. The situation improved dramatically with the availability of multi-viewpoint imaging observations of CMEs, all way through from the Sun to 1 AU, from the STEREO mission since 2006, combined with observations from other missions (SOHO, Hinode, SDO, IRIS). With this talk we will discuss several key recent results in CME science resulting from the analysis of multi-viewpoint observations. This includes: (1) shape and structure; (2) kinematics and energetics; (3) trajectories, deflections and rotations; (4) arrival times and velocities at 1 AU; (5) magnetic field structure; (6) relationships with coronal and interplanetary shocks and solar energetic particles. The implications of these results in terms of CME theories and models will be also addressed. We will conclude with a discussion of important open issues in our understanding of CMEs and how these could be addressed with upcoming (Solar Orbiter, Solar Probe Plus) and under-study missions (e.g., L5).

  1. Improved hybrid optimization algorithm for 3D protein structure prediction.

    PubMed

    Zhou, Changjun; Hou, Caixia; Wei, Xiaopeng; Zhang, Qiang

    2014-07-01

    A new improved hybrid optimization algorithm - PGATS algorithm, which is based on toy off-lattice model, is presented for dealing with three-dimensional protein structure prediction problems. The algorithm combines the particle swarm optimization (PSO), genetic algorithm (GA), and tabu search (TS) algorithms. Otherwise, we also take some different improved strategies. The factor of stochastic disturbance is joined in the particle swarm optimization to improve the search ability; the operations of crossover and mutation that are in the genetic algorithm are changed to a kind of random liner method; at last tabu search algorithm is improved by appending a mutation operator. Through the combination of a variety of strategies and algorithms, the protein structure prediction (PSP) in a 3D off-lattice model is achieved. The PSP problem is an NP-hard problem, but the problem can be attributed to a global optimization problem of multi-extremum and multi-parameters. This is the theoretical principle of the hybrid optimization algorithm that is proposed in this paper. The algorithm combines local search and global search, which overcomes the shortcoming of a single algorithm, giving full play to the advantage of each algorithm. In the current universal standard sequences, Fibonacci sequences and real protein sequences are certified. Experiments show that the proposed new method outperforms single algorithms on the accuracy of calculating the protein sequence energy value, which is proved to be an effective way to predict the structure of proteins.

  2. 3D topography of biologic tissue by multiview imaging and structured light illumination

    NASA Astrophysics Data System (ADS)

    Liu, Peng; Zhang, Shiwu; Xu, Ronald

    2014-02-01

    Obtaining three-dimensional (3D) information of biologic tissue is important in many medical applications. This paper presents two methods for reconstructing 3D topography of biologic tissue: multiview imaging and structured light illumination. For each method, the working principle is introduced, followed by experimental validation on a diabetic foot model. To compare the performance characteristics of these two imaging methods, a coordinate measuring machine (CMM) is used as a standard control. The wound surface topography of the diabetic foot model is measured by multiview imaging and structured light illumination methods respectively and compared with the CMM measurements. The comparison results show that the structured light illumination method is a promising technique for 3D topographic imaging of biologic tissue.

  3. Structure-From-Motion in 3D Space Using 2D Lidars

    PubMed Central

    Choi, Dong-Geol; Bok, Yunsu; Kim, Jun-Sik; Shim, Inwook; Kweon, In So

    2017-01-01

    This paper presents a novel structure-from-motion methodology using 2D lidars (Light Detection And Ranging). In 3D space, 2D lidars do not provide sufficient information for pose estimation. For this reason, additional sensors have been used along with the lidar measurement. In this paper, we use a sensor system that consists of only 2D lidars, without any additional sensors. We propose a new method of estimating both the 6D pose of the system and the surrounding 3D structures. We compute the pose of the system using line segments of scan data and their corresponding planes. After discarding the outliers, both the pose and the 3D structures are refined via nonlinear optimization. Experiments with both synthetic and real data show the accuracy and robustness of the proposed method. PMID:28165372

  4. CARd-3D: Carbon Distribution in 3D Structure Program for Globular Proteins.

    PubMed

    Ekambaram, Rajasekaran; Kannaiyan, Akila; Marimuthu, Vijayasarathy; Swaminathan, Vinobha Chinnaiah; Renganathan, Senthil; Perumal, Ananda Gopu

    2014-01-01

    Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein's atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structure has better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxin protein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broad spectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. The carbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help in understanding the protein folding and function.

  5. The 3D Attenuation Structure of Deception Island (Antarctica)

    NASA Astrophysics Data System (ADS)

    Prudencio, J.; De Siena, L.; Ibáñez, J. M.; Del Pezzo, E.; García-Yeguas, A.; Díaz-Moreno, A.

    2015-05-01

    The seismic and volcanological structure of Deception Island (Antarctica) is an intense focus topic in Volcano Geophysics. The interpretations given by scientists on the origin, nature, and location of the structures buried under the island strongly diverge. We present a high-resolution 3D P-wave attenuation tomography model obtained by using the coda normalization method on 20,293 high-quality waveforms produced by active sources. The checkerboard and synthetic anomaly tests guarantee the reproduction of the input anomalies under the island down to a depth of 4 km. The results, once compared with our current knowledge on the geological, geochemical, and geophysical structure of the region, depict Deception as a piecemeal caldera structure coming out of the Bransfield Trough. High-attenuation anomalies contouring the northeastern emerged caldera rim correlate with the locations of sediments. In our interpretation, the main attenuation contrast, which appears under the collapsed southeastern caldera rim, is related to the deeper feeding systems. A unique P-wave high-attenuation spherical-like anomaly in the inner bay extends between depths of 1 and 3 km. The northern contour of the anomaly coincides with the calderic rim both at 1 and 2 km, while smaller anomalies connect it with deeper structures below 3 km, dipping toward the Bransfield Trough. In our interpretation, the large upper anomaly is caused by a high-temperature shallow (1-3 km deep) geothermal system, located beneath the sediment-filled bay in the collapsed blocks and heated by smaller, deeper contributions of molten materials (magma) rising from southeast.

  6. a 3d Information System for the Documentation of Archaeologica L Excavations

    NASA Astrophysics Data System (ADS)

    Ardissone, P.; Bornaz, L.; Degattis, G.; Domaine, R.

    2013-07-01

    Documentation of archaeological and cultural heritage sites is at the heart of the archaeological process and an important component in cultural heritage research, presentation and restorations. In 2012 the Superintendence of Cultural Heritage of Aosta Valley - IT (Soprintendenza per i Beni e le Attività Culturali della Region e Autonoma Valle d'Aosta) carried out a complex archaeological excavation in a composite archaeological context, situated an urban background: the Aosta city centre. This archaeological excavation has been characterized by the classical urban archaeological issues: little space, short time, complex stratigraphy. Moreover the investigations have come out several structures and walls that required safety and conservation measures. Ad hoc 3D solutions carried out a complete 3D survey of the area in 10 different time/situations of the Archaeological digs, chosen in collaborations with the archaeological staff. In this way a multi temporal 3D description of the site has been provided for the archaeological analysis and for the project of the restorations activities. The 3D surveys has been carried out integrating GPS, laser scanner technology and photogrammetry. In order to meet the needs of the site, and its complex logistics and to obtain products that guarantee the high quality and detail required for archaeological analysis, we have developed different procedures and methodologies: hdr imaging for 3D model with correct, consistent and uniform colours, noise filtering and people filtering, for the removal of interference between laser instrument and object of the survey, Advanced laser scanner triangulation, in order to consider both artificial and natural tie points, for a correct registration of a huge amount of scans. Single image orientation on 3D data, in order to integrate the laser data with data coming from digital photogrammetry (faster on the field than the laser scanner survey, than used in certain situations). The results of all

  7. Pack Aluminization Synthesis of Superalloy 3D Woven and 3D Braided Structures

    NASA Astrophysics Data System (ADS)

    Erdeniz, Dinc; Levinson, Amanda J.; Sharp, Keith W.; Rowenhorst, David J.; Fonda, Richard W.; Dunand, David C.

    2015-01-01

    Micro-architectured, precipitation-strengthened structures were created in a new process combining weaving, gas-phase alloying, diffusion, and precipitation. First, high-ductility Ni-20 wt pct Cr wires with 202 μm diameter were braided, or non-crimp orthogonal woven, into three-dimensional structures. Second, these structures were vapor-phase alloyed with Al at 1273 K (1000 °C) by pack cementation, creating uniform NiAl coatings on the wires when using a retort. Also, solid-state bonding was achieved at wire intersections, where two wires were sufficiently close to each other, as determined via optical and X-ray tomographic microscopy. Third, the NiAl-coated wires were fully homogenized and aged to form γ' precipitates distributed in a γ matrix phase, the same microstructure providing strength in nickel-based superalloys. The resulting structures—consisting of wires (i) woven in a controlled three-dimensional architecture, (ii) bonded at contact points and (iii) strengthened by γ' precipitates—are expected to show high strength at ambient and elevated temperatures, low density, and high permeability which is useful for active cooling.

  8. Computational methods for constructing protein structure models from 3D electron microscopy maps.

    PubMed

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-10-01

    Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided.

  9. Searching protein 3-D structures for optimal structure alignment using intelligent algorithms and data structures.

    PubMed

    Novosád, Tomáš; Snášel, Václav; Abraham, Ajith; Yang, Jack Y

    2010-11-01

    In this paper, we present a novel algorithm for measuring protein similarity based on their 3-D structure (protein tertiary structure). The algorithm used a suffix tree for discovering common parts of main chains of all proteins appearing in the current research collaboratory for structural bioinformatics protein data bank (PDB). By identifying these common parts, we build a vector model and use some classical information retrieval (IR) algorithms based on the vector model to measure the similarity between proteins--all to all protein similarity. For the calculation of protein similarity, we use term frequency × inverse document frequency ( tf × idf ) term weighing schema and cosine similarity measure. The goal of this paper is to introduce new protein similarity metric based on suffix trees and IR methods. Whole current PDB database was used to demonstrate very good time complexity of the algorithm as well as high precision. We have chosen the structural classification of proteins (SCOP) database for verification of the precision of our algorithm because it is maintained primarily by humans. The next success of this paper would be the ability to determine SCOP categories of proteins not included in the latest version of the SCOP database (v. 1.75) with nearly 100% precision.

  10. Innovative 3D information system for the restoration and preventive maintenance plan of the Milan Cathedral

    NASA Astrophysics Data System (ADS)

    Giunta, Giuseppe G.; Di Paola, Eleonora; Morlin Visconti Castiglione, Benigno

    2004-02-01

    The restoration and maintenance of architecturally complex monuments need advanced tools for helping the definition of the working plan and for storing analysing and updating all the data produced. In the case of the Gothic Milan Cathedral a three-dimensional metric support has been developed. It comprises several oriented and connected stereoscopic models which makes it possible, through the stereoscopic vision, to navigate through several photograms, to accurately measure the dimension of architectural details, to draw structures with a millimeter precision. In this way a 3D-CAD model of the facade and of the internal walls of the Milan Cathedral have been created. On those vectorial models, it is possible to insert photos, documents, characterisation data and even to draw thematic maps. For instance, the load bearing structures maps have been realised after a GPR (Ground Penetrating Radar) structural survey. These maps provide structural information (e.g. fractures, block thickness and status, lessons, etc.) extremely useful for planning the restoration and maintenance work. The photogrammetric survey has been proceeded by a 3D laser scanning survey, necessary for providing a preliminary model for planning the work until the complete elaboration of the stereoscopic model. All the data have been updated in the georeferenced and integrated 3D data base of the Cathedral, which now constitutes the necessary support for defining the specific operations.

  11. Voxel-coding method for quantification of vascular structure from 3D images

    NASA Astrophysics Data System (ADS)

    Soltanian-Zadeh, Hamid; Shahrokni, Ali; Zoroofi, Reza A.

    2001-05-01

    This paper presents an image processing method for information extraction from 3D images of vasculature. It automates the study of vascular structures by extracting quantitative information such as skeleton, length, diameter, and vessel-to- tissue ratio for different vessels as well as their branches. Furthermore, it generates 3D visualization of vessels based on desired anatomical characteristics such as vessel diameter or 3D connectivity. Steps of the proposed approach are as follows. (1) Preprocessing, in which intensity adjustment, optimal thresholding, and median filtering are done. (2) 3D thinning, in which medial axis and skeleton of the vessels are found. (3) Branch labeling, in which different branches are identified and each voxel is assigned to the corresponding branch. (4) Quantitation, in which length of each branch is estimated, based on the number of voxels assigned to it, and its diameter is calculated using the medial axis direction. (5) Visualization, in which vascular structure is shown in 3D, using color coding and surface rendering methods. We have tested and evaluated the proposed algorithms using simulated images of multi-branch vessels and real confocal microscopic images of the vessels in rat brains. Experimental results illustrate performance of the methods and usefulness of the results for medical image analysis applications.

  12. Freehand photoacoustic tomography for 3D angiography using local gradient information

    NASA Astrophysics Data System (ADS)

    Kirchner, Thomas; Wild, Esther; Maier-Hein, Klaus H.; Maier-Hein, Lena

    2016-03-01

    Photo-acoustic tomography (PAT) is capable of imaging optical absorption in depths beyond the diffusion limit. As blood is one of the main absorbers in tissue, one important application is the visualization of vasculature, which can provide important clues for diagnosing diseases like cancer. While the state-of-the-art work in photo-acoustic 3D angiography has focused on computed tomography systems involving complex setups, we propose an approach based on optically tracking a freehand linear ultrasound probe that can be smoothly integrated into the clinical workflow. To this end, we present a method for calibration of a PAT system using an N-wire phantom specifically designed for PAT and show how to use local gradient information in the 3D reconstructed volume to significantly enhance the signal. According to experiments performed with a tissue mimicking intra-lipid phantom, the signal-to-noise ratio, contrast and contrast-to-noise ratio measured in the full field of view of the linear probe can be improved by factors of 1.7+/-0.7, 14.6+/-5.8 and 2.8+/-1.2 respectively, when comparing the post envelope detection reconstructed 3D volume with the processed one. Qualitative validation performed in tissue mimicking gelatin phantoms further showed good agreement of the reconstructed vasculature with corresponding structures extracted from X-ray computed tomographies. As our method provides high contrast 3D images of the vasculature despite a low hardware complexity its potential for clinical application is high.

  13. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

    PubMed Central

    Hayat, Sikander; Sander, Chris; Marks, Debora S.

    2015-01-01

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand–strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases. PMID:25858953

  14. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.

    PubMed

    Hayat, Sikander; Sander, Chris; Marks, Debora S; Elofsson, Arne

    2015-04-28

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand-strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases.

  15. 3D Soil Images Structure Quantification using Relative Entropy

    NASA Astrophysics Data System (ADS)

    Tarquis, A. M.; Gonzalez-Nieto, P. L.; Bird, N. R. A.

    2012-04-01

    Soil voids manifest the cumulative effect of local pedogenic processes and ultimately influence soil behavior - especially as it pertains to aeration and hydrophysical properties. Because of the relatively weak attenuation of X-rays by air, compared with liquids or solids, non-disruptive CT scanning has become a very attractive tool for generating three-dimensional imagery of soil voids. One of the main steps involved in this analysis is the thresholding required to transform the original (greyscale) images into the type of binary representation (e.g., pores in white, solids in black) needed for fractal analysis or simulation with Lattice-Boltzmann models (Baveye et al., 2010). The objective of the current work is to apply an innovative approach to quantifying soil voids and pore networks in original X-ray CT imagery using Relative Entropy (Bird et al., 2006; Tarquis et al., 2008). These will be illustrated using typical imagery representing contrasting soil structures. Particular attention will be given to the need to consider the full 3D context of the CT imagery, as well as scaling issues, in the application and interpretation of this index.

  16. Slat Cove Unsteadiness Effect of 3D Flow Structures

    NASA Technical Reports Server (NTRS)

    Choudhari, Meelan M.; Khorrami, Mehdi R.

    2006-01-01

    Previous studies have indicated that 2D, time accurate computations based on a pseudo-laminar zonal model of the slat cove region (within the framework of the Reynolds-Averaged Navier-Stokes equations) are inadequate for predicting the full unsteady dynamics of the slat cove flow field. Even though such computations could capture the large-scale, unsteady vorticity structures in the slat cove region without requiring any external forcing, the simulated vortices were excessively strong and the recirculation zone was unduly energetic in comparison with the PIV measurements for a generic high-lift configuration. To resolve this discrepancy and to help enable physics based predictions of slat aeroacoustics, the present paper is focused on 3D simulations of the slat cove flow over a computational domain of limited spanwise extent. Maintaining the pseudo-laminar approach, current results indicate that accounting for the three-dimensionality of flow fluctuations leads to considerable improvement in the accuracy of the unsteady, nearfield solution. Analysis of simulation data points to the likely significance of turbulent fluctuations near the reattachment region toward the generation of broadband slat noise. The computed acoustic characteristics (in terms of the frequency spectrum and spatial distribution) within short distances from the slat resemble the previously reported, subscale measurements of slat noise.

  17. Voxel-Based 3-D Tree Modeling from Lidar Images for Extracting Tree Structual Information

    NASA Astrophysics Data System (ADS)

    Hosoi, F.

    2014-12-01

    Recently, lidar (light detection and ranging) has been used to extracting tree structural information. Portable scanning lidar systems can capture the complex shape of individual trees as a 3-D point-cloud image. 3-D tree models reproduced from the lidar-derived 3-D image can be used to estimate tree structural parameters. We have proposed the voxel-based 3-D modeling for extracting tree structural parameters. One of the tree parameters derived from the voxel modeling is leaf area density (LAD). We refer to the method as the voxel-based canopy profiling (VCP) method. In this method, several measurement points surrounding the canopy and optimally inclined laser beams are adopted for full laser beam illumination of whole canopy up to the internal. From obtained lidar image, the 3-D information is reproduced as the voxel attributes in the 3-D voxel array. Based on the voxel attributes, contact frequency of laser beams on leaves is computed and LAD in each horizontal layer is obtained. This method offered accurate LAD estimation for individual trees and woody canopy trees. For more accurate LAD estimation, the voxel model was constructed by combining airborne and portable ground-based lidar data. The profiles obtained by the two types of lidar complemented each other, thus eliminating blind regions and yielding more accurate LAD profiles than could be obtained by using each type of lidar alone. Based on the estimation results, we proposed an index named laser beam coverage index, Ω, which relates to the lidar's laser beam settings and a laser beam attenuation factor. It was shown that this index can be used for adjusting measurement set-up of lidar systems and also used for explaining the LAD estimation error using different types of lidar systems. Moreover, we proposed a method to estimate woody material volume as another application of the voxel tree modeling. In this method, voxel solid model of a target tree was produced from the lidar image, which is composed of

  18. 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures

    PubMed Central

    Wang, Jian; Zhao, Yunjie; Zhu, Chunyan; Xiao, Yi

    2015-01-01

    Model evaluation is a necessary step for better prediction and design of 3D RNA structures. For proteins, this has been widely studied and the knowledge-based statistical potential has been proved to be one of effective ways to solve this problem. Currently, a few knowledge-based statistical potentials have also been proposed to evaluate predicted models of RNA tertiary structures. The benchmark tests showed that they can identify the native structures effectively but further improvements are needed to identify near-native structures and those with non-canonical base pairs. Here, we present a novel knowledge-based potential, 3dRNAscore, which combines distance-dependent and dihedral-dependent energies. The benchmarks on different testing datasets all show that 3dRNAscore are more efficient than existing evaluation methods in recognizing native state from a pool of near-native states of RNAs as well as in ranking near-native states of RNA models. PMID:25712091

  19. Multi-scale modelling of strongly heterogeneous 3D composite structures using spatial Voronoi tessellation

    NASA Astrophysics Data System (ADS)

    El Said, Bassam; Ivanov, Dmitry; Long, Andrew C.; Hallett, Stephen R.

    2016-03-01

    3D composite materials are characterized by complex internal yarn architectures, leading to complex deformation and failure development mechanisms. Net-shaped preforms, which are originally periodic in nature, lose their periodicity when the fabric is draped, deformed on a tool, and consolidated to create geometrically complex composite components. As a result, the internal yarn architecture, which dominates the mechanical behaviour, becomes dependent on the structural geometry. Hence, predicting the mechanical behaviour of 3D composites requires an accurate representation of the yarn architecture within structural scale models. When applied to 3D composites, conventional finite element modelling techniques are limited to either homogenised properties at the structural scale, or the unit cell scale for a more detailed material property definition. Consequently, these models fail to capture the complex phenomena occurring across multiple length scales and their effects on a 3D composite's mechanical response. Here a multi-scale modelling approach based on a 3D spatial Voronoi tessellation is proposed. The model creates an intermediate length scale suitable for homogenisation to deal with the non-periodic nature of the final material. Information is passed between the different length scales to allow for the effect of the structural geometry to be taken into account on the smaller scales. The stiffness and surface strain predictions from the proposed model have been found to be in good agreement with experimental results. The proposed modelling framework has been used to gain important insight into the behaviour of this category of materials. It has been observed that the strain and stress distributions are strongly dependent on the internal yarn architecture and consequently on the final component geometry. Even for simple coupon tests, the internal architecture and geometric effects dominate the mechanical response. Consequently, the behaviour of 3D woven

  20. Study on the Construction and Application of 3D Geographic Information Services for the Smart City

    NASA Astrophysics Data System (ADS)

    Mao, W.-Q.

    2014-04-01

    Smart City, whose main characteristics are intelligence and interconnection capability, has become an important goal of some cities' development. This paper, based on urban three-dimensional geographic information characteristics, analyses 3D geographic information requirements in the Smart City construction and development process, proposes construction and management methods for 3D geographic information. Furthermore, this paper takes Shanghai Geographic Information Public Service Platform as an example, discusses 3D geographic information application in multiple fields, and proves that it is an effective ways to promote Intelligent City construction.

  1. The National 3-D Geospatial Information Web-Based Service of Korea

    NASA Astrophysics Data System (ADS)

    Lee, D. T.; Kim, C. W.; Kang, I. G.

    2013-09-01

    3D geospatial information systems should provide efficient spatial analysis tools and able to use all capabilities of the third dimension, and a visualization. Currently, many human activities make steps toward the third dimension like land use, urban and landscape planning, cadastre, environmental monitoring, transportation monitoring, real estate market, military applications, etc. To reflect this trend, the Korean government has been started to construct the 3D geospatial data and service platform. Since the geospatial information was introduced in Korea, the construction of geospatial information (3D geospatial information, digital maps, aerial photographs, ortho photographs, etc.) has been led by the central government. The purpose of this study is to introduce the Korean government-lead 3D geospatial information web-based service for the people who interested in this industry and we would like to introduce not only the present conditions of constructed 3D geospatial data but methodologies and applications of 3D geospatial information. About 15% (about 3,278.74 km2) of the total urban area's 3D geospatial data have been constructed by the national geographic information institute (NGII) of Korea from 2005 to 2012. Especially in six metropolitan cities and Dokdo (island belongs to Korea) on level of detail (LOD) 4 which is photo-realistic textured 3D models including corresponding ortho photographs were constructed in 2012. In this paper, we represented web-based 3D map service system composition and infrastructure and comparison of V-world with Google Earth service will be presented. We also represented Open API based service cases and discussed about the protection of location privacy when we construct 3D indoor building models. In order to prevent an invasion of privacy, we processed image blurring, elimination and camouflage. The importance of public-private cooperation and advanced geospatial information policy is emphasized in Korea. Thus, the progress of

  2. Person re-identification employing 3D scene information

    NASA Astrophysics Data System (ADS)

    Bak, Sławomir; Brémond, François

    2015-09-01

    The person reidentification task applied in a real-world scenario is addressed. Finding people in a network of cameras is challenging due to significant variations in lighting conditions, different color responses, and different camera viewpoints. State-of-the-art algorithms are likely to fail due to serious perspective and pose changes. Most of the existing approaches try to cope with all these changes by applying metric learning tools to find a transfer function between a camera pair while ignoring the body alignment issue. Additionally, this transfer function usually depends on the camera pair and requires labeled training data for each camera. This might be unattainable in a large camera network. We employ three-dimensional scene information for minimizing perspective distortions and estimating the target pose. The estimated pose is further used for splitting a target trajectory into reliable chunks, each one with a uniform pose. These chunks are matched through a network of cameras using a previously learned metric pool. However, instead of learning transfer functions that cope with all appearance variations, we propose to learn a generic metric pool that only focuses on pose changes. This pool consists of metrics, each one learned to match a specific pair of poses and not being limited to a specific camera pair. Automatically estimated poses determine the proper metric, thus improving matching. We show that metrics learned using only a single camera can significantly improve the matching across the whole camera network, providing a scalable solution. We validated our approach on publicly available datasets, demonstrating increase in the reidentification performance.

  3. Computerized 3-D reconstruction of complicated anatomical structure

    NASA Astrophysics Data System (ADS)

    Andreasen, Arne; Drewes, Asbjorn M.; Assentoft, Joergen E.

    1992-06-01

    In the study of the rabbit hippocampal region, images of 430 serial sections were aligned by a `parameter-shift' algorithm. The resulting 3-D matrix represents a fixed and stained but `whole' rabbit brain. From this virtual object the slice procedure, displacement, and re- alignment could be computer simulated and the artifacts associated with these procedures estimated.

  4. Postprocessing techniques for 3D non-linear structures

    NASA Technical Reports Server (NTRS)

    Gallagher, Richard S.

    1987-01-01

    How graphics postprocessing techniques are currently used to examine the results of 3-D nonlinear analyses, some new techniques which take advantage of recent technology, and how these results relate to both the finite element model and its geometric parent are reviewed.

  5. Combination of Virtual Tours, 3d Model and Digital Data in a 3d Archaeological Knowledge and Information System

    NASA Astrophysics Data System (ADS)

    Koehl, M.; Brigand, N.

    2012-08-01

    The site of the Engelbourg ruined castle in Thann, Alsace, France, has been for some years the object of all the attention of the city, which is the owner, and also of partners like historians and archaeologists who are in charge of its study. The valuation of the site is one of the main objective, as well as its conservation and its knowledge. The aim of this project is to use the environment of the virtual tour viewer as new base for an Archaeological Knowledge and Information System (AKIS). With available development tools we add functionalities in particular through diverse scripts that convert the viewer into a real 3D interface. By beginning with a first virtual tour that contains about fifteen panoramic images, the site of about 150 times 150 meters can be completely documented by offering the user a real interactivity and that makes visualization very concrete, almost lively. After the choice of pertinent points of view, panoramic images were realized. For the documentation, other sets of images were acquired at various seasons and climate conditions, which allow documenting the site in different environments and states of vegetation. The final virtual tour was deducted from them. The initial 3D model of the castle, which is virtual too, was also joined in the form of panoramic images for completing the understanding of the site. A variety of types of hotspots were used to connect the whole digital documentation to the site, including videos (as reports during the acquisition phases, during the restoration works, during the excavations, etc.), digital georeferenced documents (archaeological reports on the various constituent elements of the castle, interpretation of the excavations and the searches, description of the sets of collected objects, etc.). The completely personalized interface of the system allows either to switch from a panoramic image to another one, which is the classic case of the virtual tours, or to go from a panoramic photographic image

  6. Small-angle scattering and 3D structure interpretation.

    PubMed

    Trewhella, Jill

    2016-10-01

    This review focuses on advances in the application of solution small-angle scattering (SAS) in structural analysis of biomolecules and the complexes they form. Examples highlighted illustrate the unique contribution of SAS, using both X-rays and neutrons, in hybrid or integrative modelling methods. The increased information content when neutron scattering with contrast variation is used is a particular focus. Finally, progress toward an agreed reporting framework, the development of open data and model archives, and the importance of these initiatives is covered.

  7. Real-time structured light intraoral 3D measurement pipeline

    NASA Astrophysics Data System (ADS)

    Gheorghe, Radu; Tchouprakov, Andrei; Sokolov, Roman

    2013-02-01

    Computer aided design and manufacturing (CAD/CAM) is increasingly becoming a standard feature and service provided to patients in dentist offices and denture manufacturing laboratories. Although the quality of the tools and data has slowly improved in the last years, due to various surface measurement challenges, practical, accurate, invivo, real-time 3D high quality data acquisition and processing still needs improving. Advances in GPU computational power have allowed for achieving near real-time 3D intraoral in-vivo scanning of patient's teeth. We explore in this paper, from a real-time perspective, a hardware-software-GPU solution that addresses all the requirements mentioned before. Moreover we exemplify and quantify the hard and soft deadlines required by such a system and illustrate how they are supported in our implementation.

  8. Learning the 3-D structure of objects from 2-D views depends on shape, not format

    PubMed Central

    Tian, Moqian; Yamins, Daniel; Grill-Spector, Kalanit

    2016-01-01

    Humans can learn to recognize new objects just from observing example views. However, it is unknown what structural information enables this learning. To address this question, we manipulated the amount of structural information given to subjects during unsupervised learning by varying the format of the trained views. We then tested how format affected participants' ability to discriminate similar objects across views that were rotated 90° apart. We found that, after training, participants' performance increased and generalized to new views in the same format. Surprisingly, the improvement was similar across line drawings, shape from shading, and shape from shading + stereo even though the latter two formats provide richer depth information compared to line drawings. In contrast, participants' improvement was significantly lower when training used silhouettes, suggesting that silhouettes do not have enough information to generate a robust 3-D structure. To test whether the learned object representations were format-specific or format-invariant, we examined if learning novel objects from example views transfers across formats. We found that learning objects from example line drawings transferred to shape from shading and vice versa. These results have important implications for theories of object recognition because they suggest that (a) learning the 3-D structure of objects does not require rich structural cues during training as long as shape information of internal and external features is provided and (b) learning generates shape-based object representations independent of the training format. PMID:27153196

  9. Binary 3D image interpolation algorithm based global information and adaptive curves fitting

    NASA Astrophysics Data System (ADS)

    Zhang, Tian-yi; Zhang, Jin-hao; Guan, Xiang-chen; Li, Qiu-ping; He, Meng

    2013-08-01

    Interpolation is a necessary processing step in 3-D reconstruction because of the non-uniform resolution. Conventional interpolation methods simply use two slices to obtain the missing slices between the two slices .when the key slice is missing, those methods may fail to recover it only employing the local information .And the surface of 3D object especially for the medical tissues may be highly complicated, so a single interpolation can hardly get high-quality 3D image. We propose a novel binary 3D image interpolation algorithm. The proposed algorithm takes advantages of the global information. It chooses the best curve adaptively from lots of curves based on the complexity of the surface of 3D object. The results of this algorithm are compared with other interpolation methods on artificial objects and real breast cancer tumor to demonstrate the excellent performance.

  10. Development of the Improving Process for the 3D Printed Structure

    NASA Astrophysics Data System (ADS)

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-01

    The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics.

  11. Development of the Improving Process for the 3D Printed Structure

    PubMed Central

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-01

    The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics. PMID:28054558

  12. Development of the Improving Process for the 3D Printed Structure.

    PubMed

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-05

    The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics.

  13. Fragment-based strategy for structural optimization in combination with 3D-QSAR.

    PubMed

    Yuan, Haoliang; Tai, Wenting; Hu, Shihe; Liu, Haichun; Zhang, Yanmin; Yao, Sihui; Ran, Ting; Lu, Shuai; Ke, Zhipeng; Xiong, Xiao; Xu, Jinxing; Chen, Yadong; Lu, Tao

    2013-10-01

    Fragment-based drug design has emerged as an important methodology for lead discovery and drug design. Different with other studies focused on fragment library design and active fragment identification, a fragment-based strategy was developed in combination with three-dimensional quantitative structure-activity relationship (3D-QSAR) for structural optimization in this study. Based on a validated scaffold or fragment hit, a series of structural optimization was conducted to convert it to lead compounds, including 3D-QSAR modelling, active site analysis, fragment-based structural optimization and evaluation of new molecules. 3D-QSAR models and active site analysis provided sufficient information for confirming the SAR and pharmacophoric features for fragments. This strategy was evaluated through the structural optimization on a c-Met inhibitor scaffold 5H-benzo[4,5]cyclohepta[1,2-b]pyridin-5-one, which resulted in an c-Met inhibitor with high inhibitory activity. Our study suggested the effectiveness of this fragment-based strategy and the druggability of our newly explored active region. The reliability of this strategy indicated it could also be applied to facilitate lead optimization of other targets.

  14. Fragment-based strategy for structural optimization in combination with 3D-QSAR

    NASA Astrophysics Data System (ADS)

    Yuan, Haoliang; Tai, Wenting; Hu, Shihe; Liu, Haichun; Zhang, Yanmin; Yao, Sihui; Ran, Ting; Lu, Shuai; Ke, Zhipeng; Xiong, Xiao; Xu, Jinxing; Chen, Yadong; Lu, Tao

    2013-10-01

    Fragment-based drug design has emerged as an important methodology for lead discovery and drug design. Different with other studies focused on fragment library design and active fragment identification, a fragment-based strategy was developed in combination with three-dimensional quantitative structure-activity relationship (3D-QSAR) for structural optimization in this study. Based on a validated scaffold or fragment hit, a series of structural optimization was conducted to convert it to lead compounds, including 3D-QSAR modelling, active site analysis, fragment-based structural optimization and evaluation of new molecules. 3D-QSAR models and active site analysis provided sufficient information for confirming the SAR and pharmacophoric features for fragments. This strategy was evaluated through the structural optimization on a c-Met inhibitor scaffold 5H-benzo[4,5]cyclohepta[1,2-b]pyridin-5-one, which resulted in an c-Met inhibitor with high inhibitory activity. Our study suggested the effectiveness of this fragment-based strategy and the druggability of our newly explored active region. The reliability of this strategy indicated it could also be applied to facilitate lead optimization of other targets.

  15. Segmentation of bone structures in 3D CT images based on continuous max-flow optimization

    NASA Astrophysics Data System (ADS)

    Pérez-Carrasco, J. A.; Acha-Piñero, B.; Serrano, C.

    2015-03-01

    In this paper an algorithm to carry out the automatic segmentation of bone structures in 3D CT images has been implemented. Automatic segmentation of bone structures is of special interest for radiologists and surgeons to analyze bone diseases or to plan some surgical interventions. This task is very complicated as bones usually present intensities overlapping with those of surrounding tissues. This overlapping is mainly due to the composition of bones and to the presence of some diseases such as Osteoarthritis, Osteoporosis, etc. Moreover, segmentation of bone structures is a very time-consuming task due to the 3D essence of the bones. Usually, this segmentation is implemented manually or with algorithms using simple techniques such as thresholding and thus providing bad results. In this paper gray information and 3D statistical information have been combined to be used as input to a continuous max-flow algorithm. Twenty CT images have been tested and different coefficients have been computed to assess the performance of our implementation. Dice and Sensitivity values above 0.91 and 0.97 respectively were obtained. A comparison with Level Sets and thresholding techniques has been carried out and our results outperformed them in terms of accuracy.

  16. Analysis of the 3D Structure and Velocity of a CME on 2 January 2008

    NASA Astrophysics Data System (ADS)

    López, F. M.; Cremades, H.

    We perform an analysis of the 3D structure and velocity of a CME (coronal mass ejection) ejected on 2 January 2008. The event was imaged by both STEREO A and B spacecraft (mutual separation of ˜44°), providing polarized images of the event from two different points of view. To obtain information on the 3D structure of the CME from polarized images, a polarization technique (Moran & Davila, Science 305, 66, 2003) is applied. Aided by this method, we have constructed topographical maps which show the height of the various event features from the plane of the sky (i.e. toward or away from the observer) and have dinamically analyzed and compared the real and projected on the plane of the sky velocities.

  17. Building a 3D Virtual Liver: Methods for Simulating Blood Flow and Hepatic Clearance on 3D Structures

    PubMed Central

    Rezania, Vahid; Tuszynski, Jack

    2016-01-01

    In this paper, we develop a spatio-temporal modeling approach to describe blood and drug flow, as well as drug uptake and elimination, on an approximation of the liver. Extending on previously developed computational approaches, we generate an approximation of a liver, which consists of a portal and hepatic vein vasculature structure, embedded in the surrounding liver tissue. The vasculature is generated via constrained constructive optimization, and then converted to a spatial grid of a selected grid size. Estimates for surrounding upscaled lobule tissue properties are then presented appropriate to the same grid size. Simulation of fluid flow and drug metabolism (hepatic clearance) are completed using discretized forms of the relevant convective-diffusive-reactive partial differential equations for these processes. This results in a single stage, uniformly consistent method to simulate equations for blood and drug flow, as well as drug metabolism, on a 3D structure representative of a liver. PMID:27649537

  18. Comparison of low cost 3D structured light scanners for face modeling.

    PubMed

    Bakirman, Tolga; Gumusay, Mustafa Umit; Reis, Hatice Catal; Selbesoglu, Mahmut Oguz; Yosmaoglu, Serra; Yaras, Mehmet Cem; Seker, Dursun Zafer; Bayram, Bulent

    2017-02-01

    This study aims to compare three different structured light scanner systems to generate accurate 3D human face models. Among these systems, the most dense and expensive one was denoted as the reference and the other two that were low cost and low resolution were compared according to the reference system. One female face and one male face were scanned with three light scanner systems. Point-cloud filtering, mesh generation, and hole-filling steps were carried out using a trial version of commercial software; moreover, the data evaluation process was realized using CloudCompare open-source software. Various filtering and mesh smoothing levels were applied on reference data to compare with other low-cost systems. Thus, the optimum reduction level of reference data was evaluated to continue further processes. The outcome of the presented study shows that low-cost structured light scanners have a great potential for 3D object modeling, including the human face. A considerable cheap structured light system has been used due to its capacity to obtain spatial and morphological information in the case study of 3D human face modeling. This study also discusses the benefits and accuracy of low-cost structured light systems.

  19. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.

    PubMed

    Miao, Zhichao; Adamiak, Ryszard W; Antczak, Maciej; Batey, Robert T; Becka, Alexander J; Biesiada, Marcin; Boniecki, Michał J; Bujnicki, Janusz; Chen, Shi-Jie; Cheng, Clarence Yu; Chou, Fang-Chieh; Ferré-D'Amaré, Adrian R; Das, Rhiju; Dawson, Wayne K; Feng, Ding; Dokholyan, Nikolay V; Dunin-Horkawicz, Stanisław; Geniesse, Caleb; Kappel, Kalli; Kladwang, Wipapat; Krokhotin, Andrey; Łach, Grzegorz E; Major, François; Mann, Thomas H; Magnus, Marcin; Pachulska-Wieczorek, Katarzyna; Patel, Dinshaw J; Piccirilli, Joseph A; Popenda, Mariusz; Purzycka, Katarzyna J; Ren, Aiming; Rice, Greggory M; Santalucia, John; Sarzynska, Joanna; Szachniuk, Marta; Tandon, Arpit; Trausch, Jeremiah J; Tian, Siqi; Wang, Jian; Weeks, Kevin M; Williams, Benfeard; Xiao, Yi; Xu, Xiaojun; Zhang, Dong; Zok, Tomasz; Westhof, Eric

    2017-01-30

    RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF) and one set describes large conformational changes between ligand-free and ligand-bound states; the Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All the puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homology-derived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal notable need for algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.

  20. Face recognition using 3D facial shape and color map information: comparison and combination

    NASA Astrophysics Data System (ADS)

    Godil, Afzal; Ressler, Sandy; Grother, Patrick

    2004-08-01

    In this paper, we investigate the use of 3D surface geometry for face recognition and compare it to one based on color map information. The 3D surface and color map data are from the CAESAR anthropometric database. We find that the recognition performance is not very different between 3D surface and color map information using a principal component analysis algorithm. We also discuss the different techniques for the combination of the 3D surface and color map information for multi-modal recognition by using different fusion approaches and show that there is significant improvement in results. The effectiveness of various techniques is compared and evaluated on a dataset with 200 subjects in two different positions.

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

    PubMed Central

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

    2010-01-01

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

  2. A method for 3D scene recognition using shadow information and a single fixed viewpoint

    NASA Astrophysics Data System (ADS)

    Bamber, David C.; Rogers, Jeremy D.; Page, Scott F.

    2012-05-01

    The ability to passively reconstruct a scene in 3D provides significant benefit to Situational Awareness systems employed in security and surveillance applications. Traditionally, passive 3D scene modelling techniques, such as Shape from Silhouette, require images from multiple sensor viewpoints, acquired either through the motion of a single sensor or from multiple sensors. As a result, the application of these techniques often attracts high costs, and presents numerous practical challenges. This paper presents a 3D scene reconstruction approach based on exploiting scene shadows, which only requires information from a single static sensor. This paper demonstrates that a large amount of 3D information about a scene can be interpreted from shadows; shadows reveal the shape of objects as viewed from a solar perspective and additional perspectives are gained as the sun arcs across the sky. The approach has been tested on synthetic and real data and is shown to be capable of reconstructing 3D scene objects where traditional 3D imaging methods fail. Providing the shadows within a scene are discernible, the proposed technique is able to reconstruct 3D objects that are camouflaged, obscured or even outside of the sensor's Field of View. The proposed approach can be applied in a range of applications, for example urban surveillance, checkpoint and border control, critical infrastructure protection and for identifying concealed or suspicious objects or persons which would normally be hidden from the sensor viewpoint.

  3. Synthesis, structure and properties of a 3D acentric coordination polymer with noninterpenetrated (10,3)-d topology

    NASA Astrophysics Data System (ADS)

    Lun, Huijie; Li, Xuefei; Wang, Xiao; Li, Haiyan; Li, Yamin; Bai, Yan

    2017-01-01

    A new coordination polymer, {[Mn(HPIDC)(H2O)]·2H2O}n (1) (H3PIDC = 2-(pyridin-4-yl)-1H-imidazole-4,5-dicarboxylic acid), has been obtained by hydrothermal method and structurally characterized by X-ray single crystal diffraction, elemental analysis and thermogravimetric analysis (TGA). X-ray single crystal diffraction reveals that compound 1 crystallizing in acentric Pna21 space group, exhibits an ultimate racemic three-dimension framework with rare noninterpenetrated (10,3)-d (or utp) topology due to the alternate array of left- and right-handed helixes. Moreover, compound 1 also features ferroelectric, nonlinear optical (NLO) and antiferromagnetic behaviors.

  4. Genome3D: exploiting structure to help users understand their sequences

    PubMed Central

    Lewis, Tony E.; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L.; Buchan, Daniel W.A.; Chothia, Cyrus; Cozzetto, Domenico; Dana, José M.; Filippis, Ioannis; Gough, Julian; Jones, David T.; Kelley, Lawrence A.; Kleywegt, Gerard J.; Minneci, Federico; Mistry, Jaina; Murzin, Alexey G.; Ochoa-Montaño, Bernardo; Oates, Matt E.; Punta, Marco; Rackham, Owen J.L.; Stahlhacke, Jonathan; Sternberg, Michael J.E.; Velankar, Sameer; Orengo, Christine

    2015-01-01

    Genome3D (http://www.genome3d.eu) is a collaborative resource that provides predicted domain annotations and structural models for key sequences. Since introducing Genome3D in a previous NAR paper, we have substantially extended and improved the resource. We have annotated representatives from Pfam families to improve coverage of diverse sequences and added a fast sequence search to the website to allow users to find Genome3D-annotated sequences similar to their own. We have improved and extended the Genome3D data, enlarging the source data set from three model organisms to 10, and adding VIVACE, a resource new to Genome3D. We have analysed and updated Genome3D's SCOP/CATH mapping. Finally, we have improved the superposition tools, which now give users a more powerful interface for investigating similarities and differences between structural models. PMID:25348407

  5. A 3-D fluorescence imaging system incorporating structured illumination technology

    NASA Astrophysics Data System (ADS)

    Antos, L.; Emord, P.; Luquette, B.; McGee, B.; Nguyen, D.; Phipps, A.; Phillips, D.; Helguera, M.

    2010-02-01

    A currently available 2-D high-resolution, optical molecular imaging system was modified by the addition of a structured illumination source, OptigridTM, to investigate the feasibility of providing depth resolution along the optical axis. The modification involved the insertion of the OptigridTM and a lens in the path between the light source and the image plane, as well as control and signal processing software. Projection of the OptigridTM onto the imaging surface at an angle, was resolved applying the Scheimpflug principle. The illumination system implements modulation of the light source and provides a framework for capturing depth resolved mages. The system is capable of in-focus projection of the OptigridTM at different spatial frequencies, and supports the use of different lenses. A calibration process was developed for the system to achieve consistent phase shifts of the OptigridTM. Post-processing extracted depth information using depth modulation analysis using a phantom block with fluorescent sheets at different depths. An important aspect of this effort was that it was carried out by a multidisciplinary team of engineering and science students as part of a capstone senior design program. The disciplines represented are mechanical engineering, electrical engineering and imaging science. The project was sponsored by a financial grant from New York State with equipment support from two industrial concerns. The students were provided with a basic imaging concept and charged with developing, implementing, testing and validating a feasible proof-of-concept prototype system that was returned to the originator of the concept for further evaluation and characterization.

  6. [MOLECULAR EVOLUTION OF ION CHANNELS: AMINO ACID SEQUENCES AND 3D STRUCTURES].

    PubMed

    Korkosh, V S; Zhorov, B S; Tikhonov, D B

    2016-01-01

    An integral part of modern evolutionary biology is comparative analysis of structure and function of macromolecules such as proteins. The first and critical step to understand evolution of homologous proteins is their amino acid sequence alignment. However, standard algorithms fop not provide unambiguous sequence alignments for proteins of poor homology. More reliable results can be obtained by comparing experimental 3D structures obtained at atomic resolution, for instance, with the aid of X-ray structural analysis. If such structures are lacking, homology modeling is used, which may take into account indirect experimental data on functional roles of individual amino-acid residues. An important problem is that the sequence alignment, which reflects genetic modifications, does not necessarily correspond to the functional homology. The latter depends on three-dimensional structures which are critical for natural selection. Since alignment techniques relying only on the analysis of primary structures carry no information on the functional properties of proteins, including 3D structures into consideration is very important. Here we consider several examples involving ion channels and demonstrate that alignment of their three-dimensional structures can significantly improve sequence alignments obtained by traditional methods.

  7. Histo-anatomic 3D printing of dental structures.

    PubMed

    Schweiger, J; Beuer, F; Stimmelmayr, M; Edelhoff, D; Magne, P; Güth, J F

    2016-11-04

    The creation of dental restorations with natural appearance and biomechanics represents a major challenge for the restorative team. The manufacturing-process of high-aesthetic restorations from tooth-coloured restorative materials is currently dominated by manual manufacturing procedures and the outcome is highly dependent on the knowledge and skills of the performing dental technician. On the other hand, due to the simplicity of the manufacturing process, CAD/CAM restorations from different material classes gain more and more acceptance in the daily routine. Multi-layered restorations show significant aesthetic advantages versus monolithic ones, but are difficult to fabricate using digital technologies. The key element for the successful automated digital fabrication of aesthetic anterior restorations seems to be the form of the individual dentine core as defined by dentine enamel junction (DEJ) covered by a more transparent layer of material imitating the enamel layer to create the outer enamel surface (OES). This article describes the possibilities and technologies available for so-called '4D-printing'. It introduces the digital manufacturing process of multilayered anterior teeth using 3D multipart printing, taking the example of manufacturing replicas of extracted intact natural teeth.

  8. Air-structured optical fiber drawn from a 3D-printed preform.

    PubMed

    Cook, Kevin; Canning, John; Leon-Saval, Sergio; Reid, Zane; Hossain, Md Arafat; Comatti, Jade-Edouard; Luo, Yanhua; Peng, Gang-Ding

    2015-09-01

    A structured optical fiber is drawn from a 3D-printed structured preform. Preforms containing a single ring of holes around the core are fabricated using filament made from a modified butadiene polymer. More broadly, 3D printers capable of processing soft glasses, silica, and other materials are likely to come on line in the not-so-distant future. 3D printing of optical preforms signals a new milestone in optical fiber manufacture.

  9. Multi Length Scale Imaging of Flocculated Estuarine Sediments; Insights into their Complex 3D Structure

    NASA Astrophysics Data System (ADS)

    Wheatland, Jonathan; Bushby, Andy; Droppo, Ian; Carr, Simon; Spencer, Kate

    2015-04-01

    Suspended estuarine sediments form flocs that are compositionally complex, fragile and irregularly shaped. The fate and transport of suspended particulate matter (SPM) is determined by the size, shape, density, porosity and stability of these flocs and prediction of SPM transport requires accurate measurements of these three-dimensional (3D) physical properties. However, the multi-scaled nature of flocs in addition to their fragility makes their characterisation in 3D problematic. Correlative microscopy is a strategy involving the spatial registration of information collected at different scales using several imaging modalities. Previously, conventional optical microscopy (COM) and transmission electron microscopy (TEM) have enabled 2-dimensional (2D) floc characterisation at the gross (> 1 µm) and sub-micron scales respectively. Whilst this has proven insightful there remains a critical spatial and dimensional gap preventing the accurate measurement of geometric properties and an understanding of how structures at different scales are related. Within life sciences volumetric imaging techniques such as 3D micro-computed tomography (3D µCT) and focused ion beam scanning electron microscopy [FIB-SEM (or FIB-tomography)] have been combined to characterise materials at the centimetre to micron scale. Combining these techniques with TEM enables an advanced correlative study, allowing material properties across multiple spatial and dimensional scales to be visualised. The aims of this study are; 1) to formulate an advanced correlative imaging strategy combining 3D µCT, FIB-tomography and TEM; 2) to acquire 3D datasets; 3) to produce a model allowing their co-visualisation; 4) to interpret 3D floc structure. To reduce the chance of structural alterations during analysis samples were first 'fixed' in 2.5% glutaraldehyde/2% formaldehyde before being embedding in Durcupan resin. Intermediate steps were implemented to improve contrast and remove pore water, achieved by the

  10. Using "click-e-bricks" to make 3D elastomeric structures.

    PubMed

    Morin, Stephen A; Shevchenko, Yanina; Lessing, Joshua; Kwok, Sen Wai; Shepherd, Robert F; Stokes, Adam A; Whitesides, George M

    2014-09-10

    Soft, 3D elastomeric structures and composite structures are easy to fabricate using click-e-bricks, and the internal architecture of these structures together with the capabilities built into the bricks themselves provide mechanical, optical, electrical, and fluidic functions.

  11. 3D Geo-Structures Visualization Education Project (3dgeostructuresvis.ucdavis.edu)

    NASA Astrophysics Data System (ADS)

    Billen, M. I.

    2014-12-01

    Students of field-based geology must master a suite of challenging skills from recognizing rocks, to measuring orientations of features in the field, to finding oneself (and the outcrop) on a map and placing structural information on maps. Students must then synthesize this information to derive meaning from the observations and ultimately to determine the three-dimensional (3D) shape of the deformed structures and their kinematic history. Synthesizing this kind of information requires sophisticated visualizations skills in order to extrapolate observations into the subsurface or missing (eroded) material. The good news is that students can learn 3D visualization skills through practice, and virtual tools can help provide some of that practice. Here I present a suite of learning modules focused at developing students' ability to imagine (visualize) complex 3D structures and their exposure through digital topographic surfaces. Using the software 3DVisualizer, developed by KeckCAVES (keckcaves.org) we have developed visualizations of common geologic structures (e.g., syncline, dipping fold) in which the rock is represented by originally flat-lying layers of sediment, each with a different color, which have been subsequently deformed. The exercises build up in complexity, first focusing on understanding the structure in 3D (penetrative understanding), and then moving to the exposure of the structure at a topographic surface. Individual layers can be rendered as a transparent feature to explore how the layer extends above and below the topographic surface (e.g., to follow an eroded fold limb across a valley). The exercises are provided using either movies of the visualization (which can also be used for examples during lectures), or the data and software can be downloaded to allow for more self-driven exploration and learning. These virtual field models and exercises can be used as "practice runs" before going into the field, as make-up assignments, as a field

  12. Integration of 3D structure from disparity into biological motion perception independent of depth awareness.

    PubMed

    Wang, Ying; Jiang, Yi

    2014-01-01

    Images projected onto the retinas of our two eyes come from slightly different directions in the real world, constituting binocular disparity that serves as an important source for depth perception - the ability to see the world in three dimensions. It remains unclear whether the integration of disparity cues into visual perception depends on the conscious representation of stereoscopic depth. Here we report evidence that, even without inducing discernible perceptual representations, the disparity-defined depth information could still modulate the visual processing of 3D objects in depth-irrelevant aspects. Specifically, observers who could not discriminate disparity-defined in-depth facing orientations of biological motions (i.e., approaching vs. receding) due to an excessive perceptual bias nevertheless exhibited a robust perceptual asymmetry in response to the indistinguishable facing orientations, similar to those who could consciously discriminate such 3D information. These results clearly demonstrate that the visual processing of biological motion engages the disparity cues independent of observers' depth awareness. The extraction and utilization of binocular depth signals thus can be dissociable from the conscious representation of 3D structure in high-level visual perception.

  13. Characterizing 3D RNA structure by single molecule FRET.

    PubMed

    Stephenson, James D; Kenyon, Julia C; Symmons, Martyn F; Lever, Andrew M L

    2016-07-01

    The importance of elucidating the three dimensional structures of RNA molecules is becoming increasingly clear. However, traditional protein structural techniques such as NMR and X-ray crystallography have several important drawbacks when probing long RNA molecules. Single molecule Förster resonance energy transfer (smFRET) has emerged as a useful alternative as it allows native sequences to be probed in physiological conditions and allows multiple conformations to be probed simultaneously. This review serves to describe the method of generating a three dimensional RNA structure from smFRET data from the biochemical probing of the secondary structure to the computational refinement of the final model.

  14. The use of 2D and 3D information in a perceptual-cognitive judgement task.

    PubMed

    Put, Koen; Wagemans, Johan; Spitz, Jochim; Gallardo, Manuel Armenteros; Williams, A Mark; Helsen, Werner F

    2014-01-01

    We examined whether the use of three-dimensional (3D) simulations in an off-field offside decision-making task is beneficial compared to the more widely available two-dimensional (2D) simulations. Thirty-three assistant referees, who were all involved in professional football, participated in the experiment. They assessed 40 offside situations in both 2D and 3D formats using a counterbalanced design. A distinction was made between offside situations near (i.e., 15 m) and far (i.e., 30 m) from the touchline. Subsequently, a frame recognition task was performed in which assistant referees were asked to indicate which of the five pictures represented the previous video scene. A higher response accuracy score was observed under 3D (80.0%) compared to 2D (75.0%) conditions, in particular for the situations near the touchline (3D: 81.8%; 2D: 72.7%). No differences were reported between 2D and 3D in the frame recognition task. Findings suggest that in highly dynamic and complex situations, the visual system can benefit from the availability of 3D information, especially for relatively fine, metric position judgements. In the memory task, in which a mental abstraction had to be made from a dynamic situation to a static snapshot, 3D stereo disparities do not add anything over and beyond 2D simulations. The specific task demands should be taken into account when considering the most appropriate format for testing and training.

  15. SAFAS: Unifying Form and Structure through Interactive 3D Simulation

    ERIC Educational Resources Information Center

    Polys, Nicholas F.; Bacim, Felipe; Setareh, Mehdi; Jones, Brett D.

    2015-01-01

    There has been a significant gap between the tools used for the design of a building's architectural form and those that evaluate the structural physics of that form. Seeking to bring the perspectives of visual design and structural engineering closer together, we developed and evaluated a design tool for students and practitioners to explore the…

  16. The 3D Structure of the Galactic Bulge

    NASA Astrophysics Data System (ADS)

    Zoccali, Manuela; Valenti, Elena

    2016-06-01

    We review the observational evidences concerning the three-dimensional structure of the Galactic bulge. Although the inner few kpc of our Galaxy are normally referred to as the bulge, all the observations demonstrate that this region is dominated by a bar, i.e., the bulge is a bar. The bar has a boxy/peanut (X-shaped) structure in its outer regions, while it seems to become less and less elongated in its innermost region. A thinner and longer structure departing from the main bar has also been found, although the observational evidences that support the scenario of two separate structures has been recently challenged. Metal-poor stars ([Fe/H] ≲ -0.5 dex) trace a different structure, and also have different kinematics.

  17. Gene3D: Structural Assignment for Whole Genes and Genomes Using the CATH Domain Structure Database

    PubMed Central

    Buchan, Daniel W.A.; Shepherd, Adrian J.; Lee, David; Pearl, Frances M.G.; Rison, Stuart C.G.; Thornton, Janet M.; Orengo, Christine A.

    2002-01-01

    We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. Currently Gene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30% and 40% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies. PMID:11875040

  18. Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

    NASA Astrophysics Data System (ADS)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

    NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

  19. Interactive 3D visualization of structural changes in the brain of a person with corticobasal syndrome.

    PubMed

    Hänel, Claudia; Pieperhoff, Peter; Hentschel, Bernd; Amunts, Katrin; Kuhlen, Torsten

    2014-01-01

    The visualization of the progression of brain tissue loss in neurodegenerative diseases like corticobasal syndrome (CBS) can provide not only information about the localization and distribution of the volume loss, but also helps to understand the course and the causes of this neurodegenerative disorder. The visualization of such medical imaging data is often based on 2D sections, because they show both internal and external structures in one image. Spatial information, however, is lost. 3D visualization of imaging data is capable to solve this problem, but it faces the difficulty that more internally located structures may be occluded by structures near the surface. Here, we present an application with two designs for the 3D visualization of the human brain to address these challenges. In the first design, brain anatomy is displayed semi-transparently; it is supplemented by an anatomical section and cortical areas for spatial orientation, and the volumetric data of volume loss. The second design is guided by the principle of importance-driven volume rendering: A direct line-of-sight to the relevant structures in the deeper parts of the brain is provided by cutting out a frustum-like piece of brain tissue. The application was developed to run in both, standard desktop environments and in immersive virtual reality environments with stereoscopic viewing for improving the depth perception. We conclude, that the presented application facilitates the perception of the extent of brain degeneration with respect to its localization and affected regions.

  20. Refining 3D Earth models by unifying geological and geophysical information on unstructured meshes

    NASA Astrophysics Data System (ADS)

    Lelièvre, P. G.; Carter-McAuslan, A.; Tycholiz, C.; Farquharson, C. G.; Hurich, C. A.

    2012-04-01

    Earth models used for mineral exploration or other subsurface investigations should be consistent with all available geological and geophysical information. Geophysical inversion provides the means to integrate geological information, geophysical survey data, and physical property measurements taken on rock samples. Incorporation of geological information into inversions is always an iterative process. One begins with the geologists' best guess about the Earth (i.e. the geological model) and the models recovered from geophysical inversion may indicate that the geological model should be changed slightly prior to the next iteration of the procedure. In this way, geological and geophysical data can be combined through inversion and we can move towards the creation of a common Earth model consistent with all the available data. As more information is incorporated, the inherent non-uniqueness of the inverse problem is reduced, yielding a higher potential to resolve deeper features that are less well-constrained by the geophysical data alone. Geological ore deposit models are commonly created during delineation drilling. The accuracy of these models is crucial when used to determine if a deposit is economic. 3D geological Earth models typically comprise wireframe surfaces that represent the geological contacts between different rock units. The contacts may be known at points from down-hole intersections and surface mapping, and can be interpolated between boreholes and extrapolated outwards. Contacts may also be interpreted from seismic traces. Wireframe surfaces, comprising tessellated triangular facets, are sufficiently flexible to allow the representation of arbitrarily complicated geological structures. These surfaces can be honoured exactly within fully unstructured 3D volumetric tetrahedral meshes. In contrast, geophysical forward modelling and inversion algorithms typically work with rectilinear meshes when parameterizing the subsurface because this simplifies

  1. Structured light 3D depth map enhancement and gesture recognition using image content adaptive filtering

    NASA Astrophysics Data System (ADS)

    Ramachandra, Vikas; Nash, James; Atanassov, Kalin; Goma, Sergio

    2013-03-01

    A structured-light system for depth estimation is a type of 3D active sensor that consists of a structured-light projector that projects an illumination pattern on the scene (e.g. mask with vertical stripes) and a camera which captures the illuminated scene. Based on the received patterns, depths of different regions in the scene can be inferred. In this paper, we use side information in the form of image structure to enhance the depth map. This side information is obtained from the received light pattern image reflected by the scene itself. The processing steps run real time. This post-processing stage in the form of depth map enhancement can be used for better hand gesture recognition, as is illustrated in this paper.

  2. The 3D structures of VDAC represent a native conformation

    PubMed Central

    Hiller, Sebastian; Abramson, Jeff; Mannella, Carmen; Wagner, Gerhard; Zeth, Kornelius

    2010-01-01

    The most abundant protein of the mitochondrial outer membrane is the voltage-dependent anion channel (VDAC), which facilitates the exchange of ions and molecules between mitochondria and cytosol and is regulated by interactions with other proteins and small molecules. VDAC has been extensively studied for more than three decades, and last year three independent investigations revealed a structure of VDAC-1 exhibiting 19 transmembrane β-strands, constituting a unique structural class of β-barrel membrane proteins. Here, we provide a historical perspective on VDAC research and give an overview of the experimental design used to obtain these structures. Furthermore, we validate the protein refolding approach and summarize biochemical and biophysical evidence that links the 19-stranded structure to the native form of VDAC. PMID:20708406

  3. MUFOLD: A new solution for protein 3D structure prediction.

    PubMed

    Zhang, Jingfen; Wang, Qingguo; Barz, Bogdan; He, Zhiquan; Kosztin, Ioan; Shang, Yi; Xu, Dong

    2010-04-01

    There have been steady improvements in protein structure prediction during the past 2 decades. However, current methods are still far from consistently predicting structural models accurately with computing power accessible to common users. Toward achieving more accurate and efficient structure prediction, we developed a number of novel methods and integrated them into a software package, MUFOLD. First, a systematic protocol was developed to identify useful templates and fragments from Protein Data Bank for a given target protein. Then, an efficient process was applied for iterative coarse-grain model generation and evaluation at the Calpha or backbone level. In this process, we construct models using interresidue spatial restraints derived from alignments by multidimensional scaling, evaluate and select models through clustering and static scoring functions, and iteratively improve the selected models by integrating spatial restraints and previous models. Finally, the full-atom models were evaluated using molecular dynamics simulations based on structural changes under simulated heating. We have continuously improved the performance of MUFOLD by using a benchmark of 200 proteins from the Astral database, where no template with >25% sequence identity to any target protein is included. The average root-mean-square deviation of the best models from the native structures is 4.28 A, which shows significant and systematic improvement over our previous methods. The computing time of MUFOLD is much shorter than many other tools, such as Rosetta. MUFOLD demonstrated some success in the 2008 community-wide experiment for protein structure prediction CASP8.

  4. Structured light imaging system for structural and optical characterization of 3D tissue-simulating phantoms

    NASA Astrophysics Data System (ADS)

    Liu, Songde; Smith, Zach; Xu, Ronald X.

    2016-10-01

    There is a pressing need for a phantom standard to calibrate medical optical devices. However, 3D printing of tissue-simulating phantom standard is challenged by lacking of appropriate methods to characterize and reproduce surface topography and optical properties accurately. We have developed a structured light imaging system to characterize surface topography and optical properties (absorption coefficient and reduced scattering coefficient) of 3D tissue-simulating phantoms. The system consisted of a hyperspectral light source, a digital light projector (DLP), a CMOS camera, two polarizers, a rotational stage, a translation stage, a motion controller, and a personal computer. Tissue-simulating phantoms with different structural and optical properties were characterized by the proposed imaging system and validated by a standard integrating sphere system. The experimental results showed that the proposed system was able to achieve pixel-level optical properties with a percentage error of less than 11% for absorption coefficient and less than 7% for reduced scattering coefficient for phantoms without surface curvature. In the meanwhile, 3D topographic profile of the phantom can be effectively reconstructed with an accuracy of less than 1% deviation error. Our study demonstrated that the proposed structured light imaging system has the potential to characterize structural profile and optical properties of 3D tissue-simulating phantoms.

  5. Subtractive 3D Printing of Optically Active Diamond Structures

    NASA Astrophysics Data System (ADS)

    Martin, Aiden A.; Toth, Milos; Aharonovich, Igor

    2014-05-01

    Controlled fabrication of semiconductor nanostructures is an essential step in engineering of high performance photonic and optoelectronic devices. Diamond in particular has recently attracted considerable attention as a promising platform for quantum technologies, photonics and high resolution sensing applications. Here we demonstrate the fabrication of optically active, functional diamond structures using gas-mediated electron beam induced etching (EBIE). The technique achieves dry chemical etching at room temperature through the dissociation of surface-adsorbed H2O molecules by energetic electrons in a water vapor environment. Parallel processing is possible by electron flood exposure and the use of an etch mask, while high resolution, mask-free, iterative editing is demonstrated by direct write etching of inclined facets of diamond microparticles. The realized structures demonstrate the potential of EBIE for the fabrication of optically active structures in diamond.

  6. Study on embedding fiber Bragg grating sensor into the 3D printing structure for health monitoring

    NASA Astrophysics Data System (ADS)

    Li, Ruiya; Tan, Yuegang; Zhou, Zude; Fang, Liang; Chen, Yiyang

    2016-10-01

    3D printing technology is a rapidly developing manufacturing technology, which is known as a core technology in the third industrial revolution. With the continuous improvement of the application of 3D printing products, the health monitoring of the 3D printing structure is particularly important. Fiber Bragg grating (FBG) sensing technology is a new type of optical sensing technology with unique advantages comparing to traditional sensing technology, and it has great application prospects in structural health monitoring. In this paper, the FBG sensors embedded in the internal structure of the 3D printing were used to monitor the static and dynamic strain variation of 3D printing structure during loading process. The theoretical result and experimental result has good consistency and the characteristic frequency detected by FBG sensor is consistent with the testing results of traditional accelerator in the dynamic experiment. The results of this paper preliminary validate that FBG embedded in the 3D printing structure can effectively detecting the static and dynamic stain change of the 3D printing structure, which provide some guidance for the health monitoring of 3D printing structure.

  7. Evaluation of the 3d Urban Modelling Capabilities in Geographical Information Systems

    NASA Astrophysics Data System (ADS)

    Dogru, A. O.; Seker, D. Z.

    2010-12-01

    Geographical Information System (GIS) Technology, which provides successful solutions to basic spatial problems, is currently widely used in 3 dimensional (3D) modeling of physical reality with its developing visualization tools. The modeling of large and complicated phenomenon is a challenging problem in terms of computer graphics currently in use. However, it is possible to visualize that phenomenon in 3D by using computer systems. 3D models are used in developing computer games, military training, urban planning, tourism and etc. The use of 3D models for planning and management of urban areas is very popular issue of city administrations. In this context, 3D City models are produced and used for various purposes. However the requirements of the models vary depending on the type and scope of the application. While a high level visualization, where photorealistic visualization techniques are widely used, is required for touristy and recreational purposes, an abstract visualization of the physical reality is generally sufficient for the communication of the thematic information. The visual variables, which are the principle components of cartographic visualization, such as: color, shape, pattern, orientation, size, position, and saturation are used for communicating the thematic information. These kinds of 3D city models are called as abstract models. Standardization of technologies used for 3D modeling is now available by the use of CityGML. CityGML implements several novel concepts to support interoperability, consistency and functionality. For example it supports different Levels-of-Detail (LoD), which may arise from independent data collection processes and are used for efficient visualization and efficient data analysis. In one CityGML data set, the same object may be represented in different LoD simultaneously, enabling the analysis and visualization of the same object with regard to different degrees of resolution. Furthermore, two CityGML data sets

  8. Combination of photogrammetric and geoelectric methods to assess 3d structures associated to natural hazards

    NASA Astrophysics Data System (ADS)

    Fargier, Yannick; Dore, Ludovic; Antoine, Raphael; Palma Lopes, Sérgio; Fauchard, Cyrille

    2016-04-01

    The extraction of subsurface materials is a key element for the economy of a nation. However, natural degradation of underground quarries is a major issue from an economic and public safety point of view. Consequently, the quarries stakeholders require relevant tools to define hazards associated to these structures. Safety assessment methods of underground quarries are recent and mainly based on rock physical properties. This kind of method leads to a certain homogeneity assumption of pillar internal properties that can cause an underestimation of the risk. Electrical Resistivity Imaging (ERI) is a widely used method that possesses two advantages to overcome this limitation. The first is to provide a qualitative understanding for the detection and monitoring of anomalies in the pillar body (e.g. faults). The second is to provide a quantitative description of the electrical resistivity distribution inside the pillar. This quantitative description can be interpreted with constitutive laws to help decision support (water content decreases the mechanical resistance of a chalk). However, conventional 2D and 3D Imaging techniques are usually applied to flat surface surveys or to surfaces with moderate topography. A 3D inversion of more complex media (case of the pillar) requires a full consideration of the geometry that was never taken into account before. The Photogrammetric technique presents a cost effective solution to obtain an accurate description of the external geometry of a complex media. However, this method has never been fully coupled with a geophysical method to enhance/improve the inversion process. Consequently we developed a complete procedure showing that photogrammetric and ERI tools can be efficiently combined to assess a complex 3D structure. This procedure includes in a first part a photogrammetric survey, a processing stage with an open source software and a post-processing stage finalizing a 3D surface model. The second part necessitates the

  9. Delineation of nuclear structures in 3D multicellular systems

    SciTech Connect

    2013-09-13

    A pipeline, implemented within the Insight Segmentation and Registration Toolkit (ITK) and The Visualization Toolkit (VTK) framework, to delineate each nucleus and to profile morphometric and colony organization. At an abstract level, our approach is an extension of a previously developed method for monolayer call structure models.

  10. Imaging solar coronal magnetic structures in 3D

    NASA Astrophysics Data System (ADS)

    Cartledge, N. P.

    The study of solar coronal structures and, in particular prominences, is a key part of understanding the highly complex physical mechanisms occurring in the Sun's atmosphere. Solar prominences are important in their own right and some of the most puzzling questions in solar theory have arisen through their study. For example, how do they form and how is their mass continuously replenished? How can the magnetic field provide their continuous support against gravity over time periods of several months? How can such cool, dense material exist in thermal equilibrium in the surrounding coronal environment? Why do they erupt? A study of their structure and that of the surrounding medium is important in determining the nature of the coronal plasma and magnetic field. Also, prominences are closely associated with other key phenomena such as coronal mass ejections and eruptive solar flares which occur as a prominence loses equilibrium and rises from the solar surface. Our current understanding of these fascinating structures is extremely limited and we know very little about their basic global structure. In fact, recent prominence observations have caused our basic paradigms to be challenged (Priest, 1996) and so we must set up new models in order to gain even a fundamental understanding. Prominences are highly nonlinear, three-dimensional structures. Large feet (or barbs) reach out from the main body of a prominence and reach down to the photosphere where the dense material continuously drains away. These provide a real clue to the three-dimensional nature of the coronal field and its relation to the photospheric field. It is important, therefore, to make stereographic observations of prominences in order to gain a basic understanding of their essentially three-dimensional nature and attempt to formulate new paradigms for their structure and evolution. There is no doubt that the study of prominences in three dimensions is a crucial exercise if we are to develop a better

  11. ProSAT+: visualizing sequence annotations on 3D structure.

    PubMed

    Stank, Antonia; Richter, Stefan; Wade, Rebecca C

    2016-08-01

    PRO: tein S: tructure A: nnotation T: ool-plus (ProSAT(+)) is a new web server for mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure. ProSAT(+) incorporates many of the features of the preceding ProSAT and ProSAT2 tools but also provides new options for the visualization and sharing of protein annotations. Data are extracted from the UniProt KnowledgeBase, the RCSB PDB and the PDBe SIFTS resource, and visualization is performed using JSmol. User-defined sequence annotations can be added directly to the URL, thus enabling visualization and easy data sharing. ProSAT(+) is available at http://prosat.h-its.org.

  12. Rapid Prototyping across the Spectrum: RF to Optical 3D Electromagnetic Structures

    DTIC Science & Technology

    2015-11-17

    fabricated using 3D printer . The fill factor decreases radially outwards and the voids are visible in the unit cells as you approach the periphery of the...with thin walls) [29]. Figure 6: Examples of lenses fabricated with AM (a) GRIN lens fabricated using 3D printer . The fill factor decreases...AFRL-RW-EG-TP-2015-002 Rapid Prototyping across the Spectrum: RF to Optical 3D Electromagnetic Structures Jeffery W. Allen Monica S. Allen Brett

  13. 3D Printing for Spacecraft Multi-Functional Structures

    NASA Astrophysics Data System (ADS)

    Roddy, P. A.; Huang, C. Y.; Lyke, J.; Baur, J.; Durstock, M.; MacDonald, E.

    2013-12-01

    Three-dimensional printing, more formally Additive Manufacturing (AM), is being explored by groups worldwide for use in space missions, but we recognize the amazing potential of this emerging technology to produce space weather environmental sensors at costs commensurate with declining research budgets. We present here a plan to go substantially beyond the novelty stage of this technology by developing a foundation for using AM in high-assurance space system missions. Our two-pronged approach involves (1) a disciplined investigation of material properties and reliability (electrical, mechanical, radiation) of AM and (2) the extension of this knowledge to make complex structures that can exploit the advantages of AM. We address the design, manufacture, and optimization of multifunctional space structures using multi-physics design methods, integrated computational models, and AM. Integrated multifunctional structures have significant advantage in flexibility, size, weight, and power in comparison to formally attached elements, but their design and fabrication can be complex. The complexity and range in element shape, processing method, material properties and vehicle integration make this an ideal problem to advance the current state of the art methods for multiphysics mechanism design and strengthening AM processing science.

  14. Code System for Analysis of 3-D Reinforced Concrete Structures.

    SciTech Connect

    ANDERSON, C. A.

    1999-11-22

    Version 00 NONSAP-C is a finite element program for determining the static and dynamic response of three-dimensional reinforced concrete structures. Long-term, or creep, behavior of concrete structures can also be analyzed. Nonlinear constitutive relations for concrete under short-term loads are incorporated in two time-independent models, a variable-modulus approach with orthotropic behavior induced in the concrete due to the development of different tangent moduli in different directions and an elastic-plastic model in which the concrete is assumed to be a continuous, isotropic, and linearly elastic-plastic strain-hardening-fracture material. A viscoelastic constitutive model for long-term thermal creep of concrete is included. Three-dimensional finite elements available in NONSAP-C include a truss element, a multinode tendon element for prestressed and post tensioned concrete structures, an elastic-plastic membrane element to represent the behavior of cavity liners, and a general isoparametric element with a variable number of nodes for analysis of solids and thick shells.

  15. Using flow information to support 3D vessel reconstruction from rotational angiography

    SciTech Connect

    Waechter, Irina; Bredno, Joerg; Weese, Juergen; Barratt, Dean C.; Hawkes, David J.

    2008-07-15

    For the assessment of cerebrovascular diseases, it is beneficial to obtain three-dimensional (3D) morphologic and hemodynamic information about the vessel system. Rotational angiography is routinely used to image the 3D vascular geometry and we have shown previously that rotational subtraction angiography has the potential to also give quantitative information about blood flow. Flow information can be determined when the angiographic sequence shows inflow and possibly outflow of contrast agent. However, a standard volume reconstruction assumes that the vessel tree is uniformly filled with contrast agent during the whole acquisition. If this is not the case, the reconstruction exhibits artifacts. Here, we show how flow information can be used to support the reconstruction of the 3D vessel centerline and radii in this case. Our method uses the fast marching algorithm to determine the order in which voxels are analyzed. For every voxel, the rotational time intensity curve (R-TIC) is determined from the image intensities at the projection points of the current voxel. Next, the bolus arrival time of the contrast agent at the voxel is estimated from the R-TIC. Then, a measure of the intensity and duration of the enhancement is determined, from which a speed value is calculated that steers the propagation of the fast marching algorithm. The results of the fast marching algorithm are used to determine the 3D centerline by backtracking. The 3D radius is reconstructed from 2D radius estimates on the projection images. The proposed method was tested on computer simulated rotational angiography sequences with systematically varied x-ray acquisition, blood flow, and contrast agent injection parameters and on datasets from an experimental setup using an anthropomorphic cerebrovascular phantom. For the computer simulation, the mean absolute error of the 3D centerline and 3D radius estimation was 0.42 and 0.25 mm, respectively. For the experimental datasets, the mean absolute

  16. Using flow information to support 3D vessel reconstruction from rotational angiography.

    PubMed

    Waechter, Irina; Bredno, Joerg; Weese, Juergen; Barratt, Dean C; Hawkes, David J

    2008-07-01

    For the assessment of cerebrovascular diseases, it is beneficial to obtain three-dimensional (3D) morphologic and hemodynamic information about the vessel system. Rotational angiography is routinely used to image the 3D vascular geometry and we have shown previously that rotational subtraction angiography has the potential to also give quantitative information about blood flow. Flow information can be determined when the angiographic sequence shows inflow and possibly outflow of contrast agent. However, a standard volume reconstruction assumes that the vessel tree is uniformly filled with contrast agent during the whole acquisition. If this is not the case, the reconstruction exhibits artifacts. Here, we show how flow information can be used to support the reconstruction of the 3D vessel centerline and radii in this case. Our method uses the fast marching algorithm to determine the order in which voxels are analyzed. For every voxel, the rotational time intensity curve (R-TIC) is determined from the image intensities at the projection points of the current voxel. Next, the bolus arrival time of the contrast agent at the voxel is estimated from the R-TIC. Then, a measure of the intensity and duration of the enhancement is determined, from which a speed value is calculated that steers the propagation of the fast marching algorithm. The results of the fast marching algorithm are used to determine the 3D centerline by backtracking. The 3D radius is reconstructed from 2D radius estimates on the projection images. The proposed method was tested on computer simulated rotational angiography sequences with systematically varied x-ray acquisition, blood flow, and contrast agent injection parameters and on datasets from an experimental setup using an anthropomorphic cerebrovascular phantom. For the computer simulation, the mean absolute error of the 3D centerline and 3D radius estimation was 0.42 and 0.25 mm, respectively. For the experimental datasets, the mean absolute

  17. Topologic connection between 2-D layered structures and 3-D diamond structures for conventional semiconductors

    PubMed Central

    Wang, Jianwei; Zhang, Yong

    2016-01-01

    When coming to identify new 2D materials, our intuition would suggest us to look from layered instead of 3D materials. However, since graphite can be hypothetically derived from diamond by stretching it along its [111] axis, many 3D materials can also potentially be explored as new candidates for 2D materials. Using a density functional theory, we perform a systematic study over the common Group IV, III–V, and II–VI semiconductors along different deformation paths to reveal new structures that are topologically connected to but distinctly different from the 3D parent structure. Specifically, we explore two major phase transition paths, originating respectively from wurtzite and NiAs structure, by applying compressive and tensile strain along the symmetry axis, and calculating the total energy changes to search for potential metastable states, as well as phonon spectra to examine the structural stability. Each path is found to further split into two branches under tensile strain–low buckled and high buckled structures, which respectively lead to a low and high buckled monolayer structure. Most promising new layered or planar structures identified include BeO, GaN, and ZnO on the tensile strain side, Ge, Si, and GaP on the compressive strain side. PMID:27090430

  18. Structural 3d Monitoring Using a New Sinusoidal Fitting Adjustment

    NASA Astrophysics Data System (ADS)

    Detchev, I.; Habib, A.; Lichti, D.; El-Badry, M.

    2016-06-01

    Digital photogrammetric systems combined with image processing techniques have been used for structural monitoring purposes for more than a decade. For applications requiring sub-millimetre level precision, the use of off-the-shelf DSLR cameras is a suitable choice, especially when the low cost of the involved sensors is a priority. The disadvantage in the use of entry level DSLRs is that there is a trade-off between frame rate and burst rate - a high frame rate is either not available or it cannot be sustained long enough. This problem must be overcome when monitoring a structural element undergoing a dynamic test, where a range of loads are cycled through multiple times a second. In order to estimate deflections during such a scenario, this paper proposes a new least-squares adjustment for sinusoidal fitting. The new technique is capable of processing multiple back-to-back bursts of data within the same adjustment, which synthetically increases the de-facto temporal resolution of the system. The paper describes a beam deformation test done in a structures laboratory. The experimental results were assessed in terms of both their precision and accuracy. The new method increased the effective sampling frequency three-fold, which improved the standard deviations of the estimated parameters with up to two orders of magnitude. A residual RMSE as low as 30 μm was attained, and likewise the RMSE of the computed amplitudes between the photogrammetric system and the control laser transducers was as small as 34 μm.

  19. Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

    PubMed Central

    Lewis, Tony E.; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L.; Buchan, Daniel W.A.; Chothia, Cyrus; Cuff, Alison; Dana, Jose M.; Filippis, Ioannis; Gough, Julian; Hunter, Sarah; Jones, David T.; Kelley, Lawrence A.; Kleywegt, Gerard J.; Minneci, Federico; Mitchell, Alex; Murzin, Alexey G.; Ochoa-Montaño, Bernardo; Rackham, Owen J. L.; Smith, James; Sternberg, Michael J. E.; Velankar, Sameer; Yeats, Corin; Orengo, Christine

    2013-01-01

    Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence–structure–function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker’s yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs). PMID:23203986

  20. Model-based segmentation and quantification of subcellular structures in 2D and 3D fluorescent microscopy images

    NASA Astrophysics Data System (ADS)

    Wörz, Stefan; Heinzer, Stephan; Weiss, Matthias; Rohr, Karl

    2008-03-01

    We introduce a model-based approach for segmenting and quantifying GFP-tagged subcellular structures of the Golgi apparatus in 2D and 3D microscopy images. The approach is based on 2D and 3D intensity models, which are directly fitted to an image within 2D circular or 3D spherical regions-of-interest (ROIs). We also propose automatic approaches for the detection of candidates, for the initialization of the model parameters, and for adapting the size of the ROI used for model fitting. Based on the fitting results, we determine statistical information about the spatial distribution and the total amount of intensity (fluorescence) of the subcellular structures. We demonstrate the applicability of our new approach based on 2D and 3D microscopy images.

  1. 3D nano-structures for laser nano-manipulation

    PubMed Central

    Seniutinas, Gediminas; Gervinskas, Gediminas; Brasselet, Etienne; Juodkazis, Saulius

    2013-01-01

    Summary The resputtering of gold films from nano-holes defined in a sacrificial PMMA mask, which was made by electron beam lithography, was carried out with a dry plasma etching tool in order to form well-like structures with a high aspect ratio (height/width ≈ 3–4) at the rims of the nano-holes. The extraordinary transmission through the patterns of such nano-wells was investigated experimentally and numerically. By doing numerical simulations of 50-nm and 100-nm diameter polystyrene beads in water and air, we show the potential of such patterns for self-induced back-action (SIBA) trapping. The best trapping conditions were found to be a trapping force of 2 pN/W/μm2 (numerical result) exerted on a 50-nm diameter bead in water. The simulations were based on the analytical Lorentz force model. PMID:24062979

  2. 3-D Structure of Sunspots using Imaging Spectroscopy

    NASA Technical Reports Server (NTRS)

    Balasubramaniam, K. S.; Gary, G. Allen; Reardon, K.

    2006-01-01

    We use the Interferometric BIdimensional Spectrometer (IBIS) of the INAF/Arcetri Astrophysical Observatory and installed at the National Solar Observatory (NSO) Dunn Solar Telescope, to understand the structure of sunspots. Using the spectral lines FeI 6301.5 A, FeII 7224.4 A, and CaII 8542.6 A, we examine the spectroscopic variation of sunspot penumbral and umbral structures at the heights of formation of these lines. These high resolution observations were acquired on 2004 July 30-31, of active region NOAA 10654, using the high order NSO adaptive optics system. We map the spatio-temporal variation of Doppler signatures in these spectral lines, from the photosphere to the chromosphere. From a 70-minute temporal average of individual 32-second cadence Doppler observations we find that the averaged velocities decrease with height, about 3.5 times larger in the deeper photosphere (FeII 7224.4 A; height-of-formation approx. 50 km) than in the upper photosphere FeI 6301.5 A; height-of-formation approx. 350 km), There is a remarkable coherence of Doppler signals over the height difference of 300 km. From a high-speed animation of the Doppler sequence we find evidence for what appears to be ejection of high speed gas concentrations from edges of penumbral filaments into the surrounding granular photosphere. The Evershed flow persists a few arcseconds beyond the traditionally demarcated penumbra-granulation boundary. We present these and other results and discuss the implications of these measurements for sunspot models.

  3. Acquiring 3-D information about thick objects from differential interference contrast images using texture extraction.

    PubMed

    Sierra, Heidy; Brooks, Dana; DiMarzio, Charles

    2010-01-01

    The extraction of 3-D morphological information about thick objects is explored in this work. We extract this information from 3-D differential interference contrast (DIC) images by applying a texture detection method. Texture extraction methods have been successfully used in different applications to study biological samples. A 3-D texture image is obtained by applying a local entropy-based texture extraction method. The use of this method to detect regions of blastocyst mouse embryos that are used in assisted reproduction techniques such as in vitro fertilization is presented as an example. Results demonstrate the potential of using texture detection methods to improve morphological analysis of thick samples, which is relevant to many biomedical and biological studies. Fluorescence and optical quadrature microscope phase images are used for validation.

  4. Acquiring 3-D information about thick objects from differential interference contrast images using texture extraction

    NASA Astrophysics Data System (ADS)

    Sierra, Heidy; Brooks, Dana; Dimarzio, Charles

    2010-07-01

    The extraction of 3-D morphological information about thick objects is explored in this work. We extract this information from 3-D differential interference contrast (DIC) images by applying a texture detection method. Texture extraction methods have been successfully used in different applications to study biological samples. A 3-D texture image is obtained by applying a local entropy-based texture extraction method. The use of this method to detect regions of blastocyst mouse embryos that are used in assisted reproduction techniques such as in vitro fertilization is presented as an example. Results demonstrate the potential of using texture detection methods to improve morphological analysis of thick samples, which is relevant to many biomedical and biological studies. Fluorescence and optical quadrature microscope phase images are used for validation.

  5. Sequence co-evolution gives 3D contacts and structures of protein complexes

    PubMed Central

    Hopf, Thomas A; Schärfe, Charlotta P I; Rodrigues, João P G L M; Green, Anna G; Kohlbacher, Oliver; Sander, Chris; Bonvin, Alexandre M J J; Marks, Debora S

    2014-01-01

    Protein–protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein–protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein–protein interaction networks and used for interaction predictions at residue resolution. DOI: http://dx.doi.org/10.7554/eLife.03430.001 PMID:25255213

  6. Fabrication of 2D and 3D photonic structures using laser lithography

    NASA Astrophysics Data System (ADS)

    Gaso, P.; Jandura, D.; Pudis, D.

    2016-12-01

    In this paper we demonstrate possibilities of three-dimensional (3D) printing technology based on two photon polymerization. We used three-dimensional dip-in direct-laser-writing (DLW) optical lithography to fabricate 2D and 3D optical structures for optoelectronics and for optical sensing applications. DLW lithography allows us use a non conventional way how to couple light into the waveguide structure. We prepared ring resonator and we investigated its transmission spectral characteristic. We present 3D inverse opal structure from its design to printing and scanning electron microscope (SEM) imaging. Finally, SEM images of some prepared photonic crystal structures were performed.

  7. Stress Recovery and Error Estimation for 3-D Shell Structures

    NASA Technical Reports Server (NTRS)

    Riggs, H. R.

    2000-01-01

    The C1-continuous stress fields obtained from finite element analyses are in general lower- order accurate than are the corresponding displacement fields. Much effort has focussed on increasing their accuracy and/or their continuity, both for improved stress prediction and especially error estimation. A previous project developed a penalized, discrete least squares variational procedure that increases the accuracy and continuity of the stress field. The variational problem is solved by a post-processing, 'finite-element-type' analysis to recover a smooth, more accurate, C1-continuous stress field given the 'raw' finite element stresses. This analysis has been named the SEA/PDLS. The recovered stress field can be used in a posteriori error estimators, such as the Zienkiewicz-Zhu error estimator or equilibrium error estimators. The procedure was well-developed for the two-dimensional (plane) case involving low-order finite elements. It has been demonstrated that, if optimal finite element stresses are used for the post-processing, the recovered stress field is globally superconvergent. Extension of this work to three dimensional solids is straightforward. Attachment: Stress recovery and error estimation for shell structure (abstract only). A 4-node, shear-deformable flat shell element developed via explicit Kirchhoff constraints (abstract only). A novel four-node quadrilateral smoothing element for stress enhancement and error estimation (abstract only).

  8. The 3D velocity structure beneath Iceland: Identifying melt pathways

    NASA Astrophysics Data System (ADS)

    Allen, R.

    2003-04-01

    The integration of various seismic datasets, recorded by the broadband HOTSPOT network deployed across Iceland, provides one of the highest resolution studies of the crust and mantle structure associated with a plume-ridge system. The mantle P- and S-velocity models (ICEMAN), derived from teleseismic body-wave and surface wave analysis, show a vertical, cylindrical low velocity anomaly ˜200 km in diameter extending from ˜400 km, the maximum depth of resolution, up to ˜200 km above which low velocity material is present beneath all of Iceland. The maximum P- and S-velocity anomalies of -2% and -4% respectively are found beneath the northwestern edge of Vatnajokull. The crustal S-velocity model (ICECRTb) is constrained by local surface waves, refraction experiments and receiver functions, and shows significant variation in crustal thickness. The thinnest, ˜15 km, crust is found around coastal regions, the thickest crust is beneath northwestern Vatnajokull where it reaches a thickness of 45 km. Within this thick crustal root is a vertical low velocity anomaly connecting the core of the mantle anomaly to horizontal low velocity regions that extend along the western and eastern volcanic zones but not the northern volcanic zone. These crustal low velocity zones are interpreted as regions through which melt is fed from the mantle to shallow magma chambers beneath the rift zones, where crustal formation occurs. The pipework between the core of the mantle anomaly and the southern rift zones is responsible for ˜30 km thick crust. Its absence to the north results in relatively thin, ˜20 km thick, crust.

  9. Electrodeposition-based 3D Printing of Metallic Microarchitectures with Controlled Internal Structures.

    PubMed

    Seol, Seung Kwon; Kim, Daeho; Lee, Sanghyeon; Kim, Jung Hyun; Chang, Won Suk; Kim, Ji Tae

    2015-08-26

    3D printing of metallic microarchitectures with controlled internal structures is realized at room temperature in ambient air conditions by the manipulation of metal ion concentration and pulsed electric potentials in the electrolyte meniscus during the meniscus-guided electrodeposition. Precise control of the printing nozzle enables the drawing of complex 3D microarchitectures with well-defined geometries and positions.

  10. Locally adaptive 2D-3D registration using vascular structure model for liver catheterization.

    PubMed

    Kim, Jihye; Lee, Jeongjin; Chung, Jin Wook; Shin, Yeong-Gil

    2016-03-01

    Two-dimensional-three-dimensional (2D-3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which makes it difficult to obtain the correct solution of 2D-3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34±1.94mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets.

  11. Predicting RNA 3D structure using a coarse-grain helix-centered model.

    PubMed

    Kerpedjiev, Peter; Höner Zu Siederdissen, Christian; Hofacker, Ivo L

    2015-06-01

    A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sample tertiary structures given a secondary structure. It strikes a balance between the precision of an all-atom tertiary structure model and the simplicity and effectiveness of a secondary structure representation. It provides a simplified tool for exploring global arrangements of helices and loops within RNA structures. We provide an example of a novel energy function relying only on the positions of stems and loops. We show that coupling our model to this energy function produces predictions as good as or better than the current state of the art tools. We propose that given the wide range of conformational space that needs to be explored, a coarse-grain approach can explore more conformations in less iterations than an all-atom model coupled to a fine-grain energy function. Finally, we emphasize the overarching theme of providing an ensemble of predicted structures, something which our tool excels at, rather than providing a handful of the lowest energy structures.

  12. Traversing and labeling interconnected vascular tree structures from 3D medical images

    NASA Astrophysics Data System (ADS)

    O'Dell, Walter G.; Govindarajan, Sindhuja Tirumalai; Salgia, Ankit; Hegde, Satyanarayan; Prabhakaran, Sreekala; Finol, Ender A.; White, R. James

    2014-03-01

    Purpose: Detailed characterization of pulmonary vascular anatomy has important applications for the diagnosis and management of a variety of vascular diseases. Prior efforts have emphasized using vessel segmentation to gather information on the number or branches, number of bifurcations, and branch length and volume, but accurate traversal of the vessel tree to identify and repair erroneous interconnections between adjacent branches and neighboring tree structures has not been carefully considered. In this study, we endeavor to develop and implement a successful approach to distinguishing and characterizing individual vascular trees from among a complex intermingling of trees. Methods: We developed strategies and parameters in which the algorithm identifies and repairs false branch inter-tree and intra-tree connections to traverse complicated vessel trees. A series of two-dimensional (2D) virtual datasets with a variety of interconnections were constructed for development, testing, and validation. To demonstrate the approach, a series of real 3D computed tomography (CT) lung datasets were obtained, including that of an anthropomorphic chest phantom; an adult human chest CT; a pediatric patient chest CT; and a micro-CT of an excised rat lung preparation. Results: Our method was correct in all 2D virtual test datasets. For each real 3D CT dataset, the resulting simulated vessel tree structures faithfully depicted the vessel tree structures that were originally extracted from the corresponding lung CT scans. Conclusion: We have developed a comprehensive strategy for traversing and labeling interconnected vascular trees and successfully implemented its application to pulmonary vessels observed using 3D CT images of the chest.

  13. Spectrally encoded fiber-based structured lighting probe for intraoperative 3D imaging

    PubMed Central

    Clancy, Neil T.; Stoyanov, Danail; Maier-Hein, Lena; Groch, Anja; Yang, Guang-Zhong; Elson, Daniel S.

    2011-01-01

    Three dimensional quantification of organ shape and structure during minimally invasive surgery (MIS) could enhance precision by allowing the registration of multi-modal or pre-operative image data (US/MRI/CT) with the live optical image. Structured illumination is one technique to obtain 3D information through the projection of a known pattern onto the tissue, although currently these systems tend to be used only for macroscopic imaging or open procedures rather than in endoscopy. To account for occlusions, where a projected feature may be hidden from view and/or confused with a neighboring point, a flexible multispectral structured illumination probe has been developed that labels each projected point with a specific wavelength using a supercontinuum laser. When imaged by a standard endoscope camera they can then be segmented using their RGB values, and their 3D coordinates calculated after camera calibration. The probe itself is sufficiently small (1.7 mm diameter) to allow it to be used in the biopsy channel of commonly used medical endoscopes. Surgical robots could therefore also employ this technology to solve navigation and visualization problems in MIS, and help to develop advanced surgical procedures such as natural orifice translumenal endoscopic surgery. PMID:22076272

  14. Complex Crustal Structure Beneath Western Turkey Revealed by 3D Seismic Full Waveform Inversion (FWI)

    NASA Astrophysics Data System (ADS)

    Cubuk-Sabuncu, Yesim; Taymaz, Tuncay; Fichtner, Andreas

    2016-04-01

    We present a 3D radially anisotropic velocity model of the crust and uppermost mantle structure beneath the Sea of Marmara and surroundings based on the full waveform inversion method. The intense seismic activity and crustal deformation are observed in the Northwest Turkey due to transition tectonics between the strike-slip North Anatolian Fault (NAF) and the extensional Aegean region. We have selected and simulated complete waveforms of 62 earthquakes (Mw > 4.0) occurred during 2007-2015, and recorded at (Δ < 10°) distances. Three component earthquake data is obtained from broadband seismic stations of Kandilli Observatory and Earthquake Research Center (KOERI, Turkey), Hellenic Unified Seismic Network (HUSN, Greece) and Earthquake Research Center of Turkey (AFAD-DAD). The spectral-element solver of the wave equation, SES3D algorithm, is used to simulate seismic wave propagation in 3D spherical coordinates (Fichtner, 2009). The Large Scale Seismic Inversion Framework (LASIF) workflow tool is also used to perform full seismic waveform inversion (Krischer et al., 2015). The initial 3D Earth model is implemented from the multi-scale seismic tomography study of Fichtner et al. (2013). Discrepancies between the observed and simulated synthetic waveforms are determined using the time-frequency misfits which allows a separation between phase and amplitude information (Fichtner et al., 2008). The conjugate gradient optimization method is used to iteratively update the initial Earth model when minimizing the misfit. The inversion is terminated after 19 iterations since no further advances are observed in updated models. Our analysis revealed shear wave velocity variations of the shallow and deeper crustal structure beneath western Turkey down to depths of ~35-40 km. Low shear wave velocity anomalies are observed in the upper and mid crustal depths beneath major fault zones located in the study region. Low velocity zones also tend to mark the outline of young volcanic

  15. Direct ambient noise tomography for 3-D near surface shear velocity structure: methodology and applications

    NASA Astrophysics Data System (ADS)

    Yao, H.; Fang, H.; Li, C.; Liu, Y.; Zhang, H.; van der Hilst, R. D.; Huang, Y. C.

    2014-12-01

    Ambient noise tomography has provided essential constraints on crustal and uppermost mantle shear velocity structure in global seismology. Recent studies demonstrate that high frequency (e.g., ~ 1 Hz) surface waves between receivers at short distances can be successfully retrieved from ambient noise cross-correlation and then be used for imaging near surface or shallow crustal shear velocity structures. This approach provides important information for strong ground motion prediction in seismically active area and overburden structure characterization in oil and gas fields. Here we propose a new tomographic method to invert all surface wave dispersion data for 3-D variations of shear wavespeed without the intermediate step of phase or group velocity maps.The method uses frequency-dependent propagation paths and a wavelet-based sparsity-constrained tomographic inversion. A fast marching method is used to compute, at each period, surface wave traveltimes and ray paths between sources and receivers. This avoids the assumption of great-circle propagation that is used in most surface wave tomographic studies, but which is not appropriate in complex media. The wavelet coefficients of the velocity model are estimated with an iteratively reweighted least squares (IRLS) algorithm, and upon iterations the surface wave ray paths and the data sensitivity matrix are updated from the newly obtained velocity model. We apply this new method to determine the 3-D near surface wavespeed variations in the Taipei basin of Taiwan, Hefei urban area and a shale and gas production field in China using the high-frequency interstation Rayleigh wave dispersion data extracted from ambient noisecross-correlation. The results reveal strong effects of off-great-circle propagation of high-frequency surface waves in these regions with above 30% shear wavespeed variations. The proposed approach is more efficient and robust than the traditional two-step surface wave tomography for imaging complex

  16. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction

    PubMed Central

    Boniecki, Michal J.; Lach, Grzegorz; Dawson, Wayne K.; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M.; Bujnicki, Janusz M.

    2016-01-01

    RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures. PMID:26687716

  17. Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information

    PubMed Central

    Blouin, Christian; Boucher, Yan; Roger, Andrew J.

    2003-01-01

    Comparative sequence analysis has been used to study specific questions about the structure and function of proteins for many years. Here we propose a knowledge-based framework in which the maximum likelihood rate of evolution is used to quantify the level of constraint on the identity of a site. We demonstrate that site-rate mapping on 3D structures using datasets of rhodopsin-like G-protein receptors and α- and β-tubulins provides an excellent tool for pinpointing the functional features shared between orthologous and paralogous proteins. In addition, functional divergence within protein families can be inferred by examining the differences in the site rates, the differences in the chemical properties of the side chains or amino acid usage between aligned sites. Two novel analytical methods are introduced to characterize rate- independent functional divergence. These are tested using a dataset of two classes of HMG-CoA reductases for which only one class can perform both the forward and reverse reaction. We show that functionally divergent sites occur in a cluster of sites interacting with the catalytic residues and that this information should facilitate the design of experimental strategies to directly test functional properties of residues. PMID:12527789

  18. Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information.

    PubMed

    Blouin, Christian; Boucher, Yan; Roger, Andrew J

    2003-01-15

    Comparative sequence analysis has been used to study specific questions about the structure and function of proteins for many years. Here we propose a knowledge-based framework in which the maximum likelihood rate of evolution is used to quantify the level of constraint on the identity of a site. We demonstrate that site-rate mapping on 3D structures using datasets of rhodopsin-like G-protein receptors and alpha- and beta-tubulins provides an excellent tool for pinpointing the functional features shared between orthologous and paralogous proteins. In addition, functional divergence within protein families can be inferred by examining the differences in the site rates, the differences in the chemical properties of the side chains or amino acid usage between aligned sites. Two novel analytical methods are introduced to characterize rate- independent functional divergence. These are tested using a dataset of two classes of HMG-CoA reductases for which only one class can perform both the forward and reverse reaction. We show that functionally divergent sites occur in a cluster of sites interacting with the catalytic residues and that this information should facilitate the design of experimental strategies to directly test functional properties of residues.

  19. Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images

    NASA Astrophysics Data System (ADS)

    Babu, Sabarish; Liao, Pao-Chuan; Shin, Min C.; Tsap, Leonid V.

    2006-12-01

    The objectives of this work include automatic recovery and visualization of a 3D chromosome structure from a sequence of 2D tomographic reconstruction images taken through the nucleus of a cell. Structure is very important for biologists as it affects chromosome functions, behavior of the cell, and its state. Analysis of chromosome structure is significant in the detection of diseases, identification of chromosomal abnormalities, study of DNA structural conformation, in-depth study of chromosomal surface morphology, observation of in vivo behavior of the chromosomes over time, and in monitoring environmental gene mutations. The methodology incorporates thresholding based on a histogram analysis with a polyline splitting algorithm, contour extraction via active contours, and detection of the 3D chromosome structure by establishing corresponding regions throughout the slices. Visualization using point cloud meshing generates a 3D surface. The 3D triangular mesh of the chromosomes provides surface detail and allows a user to interactively analyze chromosomes using visualization software.

  20. 3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

    NASA Astrophysics Data System (ADS)

    Madura, T. I.; Clementel, N.; Gull, T. R.; Kruip, C. J. H.; Paardekooper, J.-P.

    2015-06-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (≳120 M⊙), highly eccentric (e ˜ 0.9) binary star system η Carinae. We demonstrate the methodology used to incorporate 3D interactive figures into a PDF (Portable Document Format) journal publication and the benefits of using 3D visualization and 3D printing as tools to analyse data from multidimensional numerical simulations. Using a consumer-grade 3D printer (MakerBot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of η Carinae's inner (r ˜ 110 au) wind-wind collision interface at multiple orbital phases. The 3D prints and visualizations reveal important, previously unknown `finger-like' structures at orbital phases shortly after periastron (φ ˜ 1.045) that protrude radially outwards from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. thin-shell, Rayleigh-Taylor) that arise at the interface between the radiatively cooled layer of dense post-shock primary-star wind and the fast (3000 km s-1), adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unrecognized physical features highlight the important role 3D printing and interactive graphics can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

  1. Emerging Technologies in the Built Environment: Geographic Information Science (GIS), 3D Printing, and Additive Manufacturing

    SciTech Connect

    New, Joshua Ryan

    2014-01-01

    Abstract 1: Geographic information systems emerged as a computer application in the late 1960s, led in part by projects at ORNL. The concept of a GIS has shifted through time in response to new applications and new technologies, and is now part of a much larger world of geospatial technology. This presentation discusses the relationship of GIS and estimating hourly and seasonal energy consumption profiles in the building sector at spatial scales down to the individual parcel. The method combines annual building energy simulations for city-specific prototypical buildings and commonly available geospatial data in a GIS framework. Abstract 2: This presentation focuses on 3D printing technologies and how they have rapidly evolved over the past couple of years. At a basic level, 3D printing produces physical models quickly and easily from 3D CAD, BIM (Building Information Models), and other digital data. Many AEC firms have adopted 3D printing as part of commercial building design development and project delivery. This presentation includes an overview of 3D printing, discusses its current use in building design, and talks about its future in relation to the HVAC industry. Abstract 3: This presentation discusses additive manufacturing and how it is revolutionizing the design of commercial and residential facilities. Additive manufacturing utilizes a broad range of direct manufacturing technologies, including electron beam melting, ultrasonic, extrusion, and laser metal deposition for rapid prototyping. While there is some overlap with the 3D printing talk, this presentation focuses on the materials aspect of additive manufacturing and also some of the more advanced technologies involved with rapid prototyping. These technologies include design of carbon fiber composites, lightweight metals processing, transient field processing, and more.

  2. Laser direct writing 3D structures for microfluidic channels: flow meter and mixer

    NASA Astrophysics Data System (ADS)

    Lin, Chih-Lang; Liu, Yi-Jui; Lin, Zheng-Da; Wu, Bo-Long; Lee, Yi-Hsiung; Shin, Chow-Shing; Baldeck, Patrice L.

    2015-03-01

    The 3D laser direct-writing technology is aimed at the modeling of arbitrary three-dimensional (3D) complex microstructures by scanning a laser-focusing point along predetermined trajectories. Through the perspective technique, the details of designed 3D structures can be properly fabricated in a microchannel. This study introduces a direct reading flow meter and a 3D passive mixer fabricated by laser direct writing for microfluidic applications. The flow meter consists of two rod-shaped springs, a pillar, an anchor, and a wedge-shaped indicator, installed inside a microfluidic channel. The indicator is deflected by the flowing fluid while restrained by the spring to establish an equilibrium indication according to the flow rate. The measurement is readily carried out by optical microscopy observation. The 3D passive Archimedes-screw-shaped mixer is designed to disturb the laminar flow 3D direction for enhancing the mixing efficiency. The simulation results indicate that the screw provides 3D disturbance of streamlines in the microchannel. The mixing demonstration for fluids flowing in the micrchannel approximately agrees with the simulation result. Thanks to the advantage of the laser direct writing technology, this study performs the ingenious applications of 3D structures for microchannels.

  3. Fluorescence in situ hybridization applications for super-resolution 3D structured illumination microscopy.

    PubMed

    Markaki, Yolanda; Smeets, Daniel; Cremer, Marion; Schermelleh, Lothar

    2013-01-01

    Fluorescence in situ hybridization on three-dimensionally preserved cells (3D-FISH) is an efficient tool to analyze the subcellular localization and spatial arrangement of targeted DNA sequences and RNA transcripts at the single cell level. 3D reconstructions from serial optical sections obtained by confocal laser scanning microscopy (CLSM) have long been considered the gold standard for 3D-FISH analyses. Recent super-resolution techniques circumvent the diffraction-limit of optical resolution and have defined a new state-of-the-art in bioimaging. Three-dimensional structured illumination microscopy (3D-SIM) represents one of these technologies. Notably, 3D-SIM renders an eightfold improved volumetric resolution over conventional imaging, and allows the simultaneous visualization of differently labeled target structures. These features make this approach highly attractive for the analysis of spatial relations and substructures of nuclear targets that escape detection by conventional light microscopy. Here, we focus on the application of 3D-SIM for the visualization of subnuclear 3D-FISH preparations. In comparison with conventional fluorescence microscopy, the quality of 3D-SIM data is dependent to a much greater extent on the optimal sample preparation, labeling and acquisition conditions. We describe typical problems encountered with super-resolution imaging of in situ hybridizations in mammalian tissue culture cells and provide optimized DNA-/(RNA)-FISH protocols including combinations with immunofluorescence staining (Immuno-FISH) and DNA replication labeling using click chemistry.

  4. 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography

    PubMed Central

    Nicastro, Daniela; McIntosh, J. Richard; Baumeister, Wolfgang

    2005-01-01

    We have used cryo-electron tomography to investigate the 3D structure and macromolecular organization of intact, frozen-hydrated sea urchin sperm flagella in a quiescent state. The tomographic reconstructions provide information at a resolution better than 6 nm about the in situ arrangements of macromolecules that are key for flagellar motility. We have visualized the heptameric rings of the motor domains in the outer dynein arm complex and determined that they lie parallel to the plane that contains the axes of neighboring flagellar microtubules. Both the material associated with the central pair of microtubules and the radial spokes display a plane of symmetry that helps to explain the planar beat pattern of these flagella. Cryo-electron tomography has proven to be a powerful technique for helping us understand the relationships between flagellar structure and function and the design of macromolecular machines in situ. PMID:16246999

  5. 3D building reconstruction from ALS data using unambiguous decomposition into elementary structures

    NASA Astrophysics Data System (ADS)

    Jarząbek-Rychard, M.; Borkowski, A.

    2016-08-01

    The objective of the paper is to develop an automated method that enables for the recognition and semantic interpretation of topological building structures. The novelty of the proposed modeling approach is an unambiguous decomposition of complex objects into predefined simple parametric structures, resulting in the reconstruction of one topological unit without independent overlapping elements. The aim of a data processing chain is to generate complete polyhedral models at LOD2 with an explicit topological structure and semantic information. The algorithms are performed on 3D point clouds acquired by airborne laser scanning. The presented methodology combines data-based information reflected in an attributed roof topology graph with common knowledge about buildings stored in a library of elementary structures. In order to achieve an appropriate balance between reconstruction precision and visualization aspects, the implemented library contains a set of structure-depended soft modeling rules instead of strictly defined geometric primitives. The proposed modeling algorithm starts with roof plane extraction performed by the segmentation of building point clouds, followed by topology identification and recognition of predefined structures. We evaluate the performance of the novel procedure by the analysis of the modeling accuracy and the degree of modeling detail. The assessment according to the validation methods standardized by the International Society for Photogrammetry and Remote Sensing shows that the completeness of the algorithm is above 80%, whereas the correctness exceeds 98%.

  6. 3D Printers Can Provide an Added Dimension for Teaching Structure-Energy Relationships

    ERIC Educational Resources Information Center

    Blauch, David N.; Carroll, Felix A.

    2014-01-01

    A 3D printer is used to prepare a variety of models representing potential energy as a function of two geometric coordinates. These models facilitate the teaching of structure-energy relationships in molecular conformations and in chemical reactions.

  7. A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures

    PubMed Central

    Li, Haotian; Huang, Yangyu

    2017-01-01

    Computational prediction of RNA-protein complex 3D structures includes two basic steps: one is sampling possible structures and another is scoring the sampled structures to pick out the correct one. At present, constructing accurate scoring functions is still not well solved and the performances of the scoring functions usually depend on used benchmarks. Here we propose a pair-conformation-dependent scoring function, 3dRPC-Score, for 3D RNA-protein complex structure prediction by considering the nucleotide-residue pairs having the same energy if their conformations are similar, instead of the distance-only dependence of the most existing scoring functions. Benchmarking shows that 3dRPC-Score has a consistent performance in three test sets. PMID:28358834

  8. A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures.

    PubMed

    Li, Haotian; Huang, Yangyu; Xiao, Yi

    2017-01-01

    Computational prediction of RNA-protein complex 3D structures includes two basic steps: one is sampling possible structures and another is scoring the sampled structures to pick out the correct one. At present, constructing accurate scoring functions is still not well solved and the performances of the scoring functions usually depend on used benchmarks. Here we propose a pair-conformation-dependent scoring function, 3dRPC-Score, for 3D RNA-protein complex structure prediction by considering the nucleotide-residue pairs having the same energy if their conformations are similar, instead of the distance-only dependence of the most existing scoring functions. Benchmarking shows that 3dRPC-Score has a consistent performance in three test sets.

  9. A 3D acquisition system combination of structured-light scanning and shape from silhouette

    NASA Astrophysics Data System (ADS)

    Sun, Changku; Tao, Li; Wang, Peng; He, Li

    2006-05-01

    A robust and accurate three dimensional (3D) acquisition system is presented, which is a combination of structured-light scanning and shape from silhouette. Using common world coordinate system, two groups of point data can be integrated into the final complete 3D model without any integration and registration algorithm. The mathematics model of structured-light scanning is described in detail, and the shape from silhouette algorithm is introduced as well. The complete 3D model of a cup with a handle is obtained successfully by the proposed technique. At last the measurement on a ball bearing is performed, with the measurement precision better than 0.15 mm.

  10. Robust volumetric change detection using mutual information with 3D fractals

    NASA Astrophysics Data System (ADS)

    Rahmes, Mark; Akbari, Morris; Henning, Ronda; Pokorny, John

    2014-06-01

    We discuss a robust method for quantifying change of multi-temporal remote sensing point data in the presence of affine registration errors. Three dimensional image processing algorithms can be used to extract and model an electronic module, consisting of a self-contained assembly of electronic components and circuitry, using an ultrasound scanning sensor. Mutual information (MI) is an effective measure of change. We propose a multi-resolution 3D fractal algorithm which is a novel extension to MI or regional mutual information (RMI). Our method is called fractal mutual information (FMI). This extension efficiently takes neighborhood fractal patterns of corresponding voxels (3D pixels) into account. The goal of this system is to quantify the change in a module due to tampering and provide a method for quantitative and qualitative change detection and analysis.

  11. Structure-based 3D QSAR and design of novel acetylcholinesterase inhibitors

    NASA Astrophysics Data System (ADS)

    Sippl, Wolfgang; Contreras, Jean-Marie; Parrot, Isabelle; Rival, Yveline M.; Wermuth, Camille G.

    2001-05-01

    The paper describes the construction, validation and application of a structure-based 3D QSAR model of novel acetylcholinesterase (AChE) inhibitors. Initial use was made of four X-ray structures of AChE complexed with small, non-specific inhibitors to create a model of the binding of recently developed aminopyridazine derivatives. Combined automated and manual docking methods were applied to dock the co-crystallized inhibitors into the binding pocket. Validation of the modelling process was achieved by comparing the predicted enzyme-bound conformation with the known conformation in the X-ray structure. The successful prediction of the binding conformation of the known inhibitors gave confidence that we could use our model to evaluate the binding conformation of the aminopyridazine compounds. The alignment of 42 aminopyridazine compounds derived by the docking procedure was taken as the basis for a 3D QSAR analysis applying the GRID/GOLPE method. A model of high quality was obtained using the GRID water probe, as confirmed by the cross-validation method (q2 LOO=0.937, q2 L50% O=0.910). The validated model, together with the information obtained from the calculated AChE-inhibitor complexes, were considered for the design of novel compounds. Seven designed inhibitors which were synthesized and tested were shown to be highly active. After performing our modelling study the X-ray structure of AChE complexed with donepezil, an inhibitor structurally related to the developed aminopyirdazines, has been made available. The good agreement found between the predicted binding conformation of the aminopyridazines and the one observed for donepezil in the crystal structure further supports our developed model.

  12. FlySanDiego: a web-aware 3D interactive regional information system

    NASA Astrophysics Data System (ADS)

    Lukas, David S.; Bailey, Michael J.

    2002-03-01

    Communication of regional geographic information to the population as a whole should be a municipal priority, but sadly it is not. From traffic patterns to weather information to emergency information to proposed highways, a city or county has, in electronic form, all of this useful information and more. With the ubiquity of web browsers and the arrival of online 3D graphics technologies such as VRML and Java 3D,this information could and should be made available. By using Java andJava3D, the rendering power of an OpenGL-type application can be combined with multithreading, allowing a program to invisibly access data sets from Internet sites with dedicated threads while processing user interaction with another. Any type of relevant data can be transformed into a three-dimensional interpretation and mapped over the terrain that the user is analyzing. This prototype is designed to be extremely extensible and expandable in order to accommodate future revisions and/or portability. This paper discusses the issues surrounding the creation of such a model, along with challenges, problems, and solutions.

  13. Effect of 3d doping on the electronic structure of BaFe2As2

    SciTech Connect

    McLeod, John A.; Buling, A.; Green, R.J.; Boyko, T.D.; Skorikov, N.A.; Kurmaev, E.Z.; Neumann, M.; Finkelstein, L.D.; Ni, Ni; Thaler, Alexander; Budko, Serguei L.; Canfield, Paul; Moewes, A.

    2012-04-25

    The electronic structure of BaFe2As2 doped with Co, Ni and Cu has been studied by a variety of experimental and theoretical methods, but a clear picture of the dopant 3d states has not yet emerged. Herein we provide experimental evidence of the distribution of Co, Ni and Cu 3d states in the valence band. We conclude that the Co and Ni 3d states provide additional free carriers to the Fermi level, while the Cu 3d states are found at the bottom of the valence band in a localized 3d10 shell. These findings help shed light on why superconductivity can occur in BaFe2As2 doped with Co and Ni but not Cu.

  14. Deformable registration of 3D vessel structures to a single projection image

    NASA Astrophysics Data System (ADS)

    Zikic, Darko; Groher, Martin; Khamene, Ali; Navab, Nassir

    2008-03-01

    Alignment of angiographic preoperative 3D scans to intraoperative 2D projections is an important issue for 3D depth perception and navigation during interventions. Currently, in a setting where only one 2D projection is available, methods employing a rigid transformation model present the state of the art for this problem. In this work, we introduce a method capable of deformably registering 3D vessel structures to a respective single projection of the scene. Our approach addresses the inherent ill-posedness of the problem by incorporating a priori knowledge about the vessel structures into the formulation. We minimize the distance between the 2D points and corresponding projected 3D points together with regularization terms encoding the properties of length preservation of vessel structures and smoothness of deformation. We demonstrate the performance and accuracy of the proposed method by quantitative tests on synthetic examples as well as real angiographic scenes.

  15. Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images

    SciTech Connect

    Babu, S; Liao, P; Shin, M C; Tsap, L V

    2004-04-28

    The objectives of this work include automatic recovery and visualization of a 3D chromosome structure from a sequence of 2D tomographic reconstruction images taken through the nucleus of a cell. Structure is very important for biologists as it affects chromosome functions, behavior of the cell and its state. Chromosome analysis is significant in the detection of deceases and in monitoring environmental gene mutations. The algorithm incorporates thresholding based on a histogram analysis with a polyline splitting algorithm, contour extraction via active contours, and detection of the 3D chromosome structure by establishing corresponding regions throughout the slices. Visualization using point cloud meshing generates a 3D surface. The 3D triangular mesh of the chromosomes provides surface detail and allows a user to interactively analyze chromosomes using visualization software.

  16. Contribution of 3D inversion of Electrical Resistivity Tomography data applied to volcanic structures

    NASA Astrophysics Data System (ADS)

    Portal, Angélie; Fargier, Yannick; Lénat, Jean-François; Labazuy, Philippe

    2016-04-01

    The electrical resistivity tomography (ERT) method, initially developed for environmental and engineering exploration, is now commonly used for geological structures imaging. Such structures can present complex characteristics that conventional 2D inversion processes cannot perfectly integrate. Here we present a new 3D inversion algorithm named EResI, firstly developed for levee investigation, and presently applied to the study of a complex lava dome (the Puy de Dôme volcano, France). EResI algorithm is based on a conventional regularized Gauss-Newton inversion scheme and a 3D non-structured discretization of the model (double grid method based on tetrahedrons). This discretization allows to accurately model the topography of investigated structure (without a mesh deformation procedure) and also permits a precise location of the electrodes. Moreover, we demonstrate that a complete 3D unstructured discretization limits the number of inversion cells and is better adapted to the resolution capacity of tomography than a structured discretization. This study shows that a 3D inversion with a non-structured parametrization has some advantages compared to classical 2D inversions. The first advantage comes from the fact that a 2D inversion leads to artefacts due to 3D effects (3D topography, 3D internal resistivity). The second advantage comes from the fact that the capacity to experimentally align electrodes along an axis (for 2D surveys) depends on the constrains on the field (topography...). In this case, a 2D assumption induced by 2.5D inversion software prevents its capacity to model electrodes outside this axis leading to artefacts in the inversion result. The last limitation comes from the use of mesh deformation techniques used to accurately model the topography in 2D softwares. This technique used for structured discretization (Res2dinv) is prohibed for strong topography (>60 %) and leads to a small computational errors. A wide geophysical survey was carried out

  17. 3D high-resolution two-photon crosslinked hydrogel structures for biological studies.

    PubMed

    Brigo, Laura; Urciuolo, Anna; Giulitti, Stefano; Giustina, Gioia Della; Tromayer, Maximilian; Liska, Robert; Elvassore, Nicola; Brusatin, Giovanna

    2017-03-25

    Hydrogels are widely used as matrices for cell growth due to the their tuneable chemical and physical properties, which mimic the extracellular matrix of natural tissue. The microfabrication of hydrogels into arbitrarily complex 3D structures is becoming essential for numerous biological applications, and in particular for investigating the correlation between cell shape and cell function in a 3D environment. Micrometric and sub-micrometric resolution hydrogel scaffolds are required to deeply investigate molecular mechanisms behind cell-matrix interaction and downstream cellular processes. We report the design and development of high resolution 3D gelatin hydrogel woodpile structures by two-photon crosslinking. Hydrated structures of lateral linewidth down to 0.5 µm, lateral and axial resolution down to a few µm are demonstrated. According to the processing parameters, different degrees of polymerization are obtained, resulting in hydrated scaffolds of variable swelling and deformation. The 3D hydrogels are biocompatible and promote cell adhesion and migration. Interestingly, according to the polymerization degree, 3D hydrogel woodpile structures show variable extent of cell adhesion and invasion. Human BJ cell lines show capability of deforming 3D micrometric resolved hydrogel structures.

  18. Mesh Convolutional Restricted Boltzmann Machines for Unsupervised Learning of Features With Structure Preservation on 3-D Meshes.

    PubMed

    Han, Zhizhong; Liu, Zhenbao; Han, Junwei; Vong, Chi-Man; Bu, Shuhui; Chen, Chun Long Philip

    2016-06-30

    Discriminative features of 3-D meshes are significant to many 3-D shape analysis tasks. However, handcrafted descriptors and traditional unsupervised 3-D feature learning methods suffer from several significant weaknesses: 1) the extensive human intervention is involved; 2) the local and global structure information of 3-D meshes cannot be preserved, which is in fact an important source of discriminability; 3) the irregular vertex topology and arbitrary resolution of 3-D meshes do not allow the direct application of the popular deep learning models; 4) the orientation is ambiguous on the mesh surface; and 5) the effect of rigid and nonrigid transformations on 3-D meshes cannot be eliminated. As a remedy, we propose a deep learning model with a novel irregular model structure, called mesh convolutional restricted Boltzmann machines (MCRBMs). MCRBM aims to simultaneously learn structure-preserving local and global features from a novel raw representation, local function energy distribution. In addition, multiple MCRBMs can be stacked into a deeper model, called mesh convolutional deep belief networks (MCDBNs). MCDBN employs a novel local structure preserving convolution (LSPC) strategy to convolve the geometry and the local structure learned by the lower MCRBM to the upper MCRBM. LSPC facilitates resolving the challenging issue of the orientation ambiguity on the mesh surface in MCDBN. Experiments using the proposed MCRBM and MCDBN were conducted on three common aspects: global shape retrieval, partial shape retrieval, and shape correspondence. Results show that the features learned by the proposed methods outperform the other state-of-the-art 3-D shape features.

  19. Partial order optimum likelihood (POOL): maximum likelihood prediction of protein active site residues using 3D Structure and sequence properties.

    PubMed

    Tong, Wenxu; Wei, Ying; Murga, Leonel F; Ondrechen, Mary Jo; Williams, Ronald J

    2009-01-01

    A new monotonicity-constrained maximum likelihood approach, called Partial Order Optimum Likelihood (POOL), is presented and applied to the problem of functional site prediction in protein 3D structures, an important current challenge in genomics. The input consists of electrostatic and geometric properties derived from the 3D structure of the query protein alone. Sequence-based conservation information, where available, may also be incorporated. Electrostatics features from THEMATICS are combined with multidimensional isotonic regression to form maximum likelihood estimates of probabilities that specific residues belong to an active site. This allows likelihood ranking of all ionizable residues in a given protein based on THEMATICS features. The corresponding ROC curves and statistical significance tests demonstrate that this method outperforms prior THEMATICS-based methods, which in turn have been shown previously to outperform other 3D-structure-based methods for identifying active site residues. Then it is shown that the addition of one simple geometric property, the size rank of the cleft in which a given residue is contained, yields improved performance. Extension of the method to include predictions of non-ionizable residues is achieved through the introduction of environment variables. This extension results in even better performance than THEMATICS alone and constitutes to date the best functional site predictor based on 3D structure only, achieving nearly the same level of performance as methods that use both 3D structure and sequence alignment data. Finally, the method also easily incorporates such sequence alignment data, and when this information is included, the resulting method is shown to outperform the best current methods using any combination of sequence alignments and 3D structures. Included is an analysis demonstrating that when THEMATICS features, cleft size rank, and alignment-based conservation scores are used individually or in combination

  20. FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms

    PubMed Central

    Kaltdorf, Kristin Verena; Schulze, Katja; Helmprobst, Frederik; Kollmannsberger, Philip; Stigloher, Christian

    2017-01-01

    Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation

  1. Super-resolution imaging of the cytokinetic Z ring in live bacteria using fast 3D-structured illumination microscopy (f3D-SIM).

    PubMed

    Turnbull, Lynne; Strauss, Michael P; Liew, Andrew T F; Monahan, Leigh G; Whitchurch, Cynthia B; Harry, Elizabeth J

    2014-09-29

    Imaging of biological samples using fluorescence microscopy has advanced substantially with new technologies to overcome the resolution barrier of the diffraction of light allowing super-resolution of live samples. There are currently three main types of super-resolution techniques - stimulated emission depletion (STED), single-molecule localization microscopy (including techniques such as PALM, STORM, and GDSIM), and structured illumination microscopy (SIM). While STED and single-molecule localization techniques show the largest increases in resolution, they have been slower to offer increased speeds of image acquisition. Three-dimensional SIM (3D-SIM) is a wide-field fluorescence microscopy technique that offers a number of advantages over both single-molecule localization and STED. Resolution is improved, with typical lateral and axial resolutions of 110 and 280 nm, respectively and depth of sampling of up to 30 µm from the coverslip, allowing for imaging of whole cells. Recent advancements (fast 3D-SIM) in the technology increasing the capture rate of raw images allows for fast capture of biological processes occurring in seconds, while significantly reducing photo-toxicity and photobleaching. Here we describe the use of one such method to image bacterial cells harboring the fluorescently-labelled cytokinetic FtsZ protein to show how cells are analyzed and the type of unique information that this technique can provide.

  2. Super-resolution Imaging of the Cytokinetic Z Ring in Live Bacteria Using Fast 3D-Structured Illumination Microscopy (f3D-SIM)

    PubMed Central

    Liew, Andrew T. F.; Monahan, Leigh G.; Whitchurch, Cynthia B.; Harry, Elizabeth J.

    2014-01-01

    Imaging of biological samples using fluorescence microscopy has advanced substantially with new technologies to overcome the resolution barrier of the diffraction of light allowing super-resolution of live samples. There are currently three main types of super-resolution techniques – stimulated emission depletion (STED), single-molecule localization microscopy (including techniques such as PALM, STORM, and GDSIM), and structured illumination microscopy (SIM). While STED and single-molecule localization techniques show the largest increases in resolution, they have been slower to offer increased speeds of image acquisition. Three-dimensional SIM (3D-SIM) is a wide-field fluorescence microscopy technique that offers a number of advantages over both single-molecule localization and STED. Resolution is improved, with typical lateral and axial resolutions of 110 and 280 nm, respectively and depth of sampling of up to 30 µm from the coverslip, allowing for imaging of whole cells. Recent advancements (fast 3D-SIM) in the technology increasing the capture rate of raw images allows for fast capture of biological processes occurring in seconds, while significantly reducing photo-toxicity and photobleaching. Here we describe the use of one such method to image bacterial cells harboring the fluorescently-labelled cytokinetic FtsZ protein to show how cells are analyzed and the type of unique information that this technique can provide. PMID:25286090

  3. Edge structure preserving 3D image denoising by local surface approximation.

    PubMed

    Qiu, Peihua; Mukherjee, Partha Sarathi

    2012-08-01

    In various applications, including magnetic resonance imaging (MRI) and functional MRI (fMRI), 3D images are becoming increasingly popular. To improve the reliability of subsequent image analyses, 3D image denoising is often a necessary preprocessing step, which is the focus of the current paper. In the literature, most existing image denoising procedures are for 2D images. Their direct extensions to 3D cases generally cannot handle 3D images efficiently because the structure of a typical 3D image is substantially more complicated than that of a typical 2D image. For instance, edge locations are surfaces in 3D cases which would be much more challenging to handle compared to edge curves in 2D cases. We propose a novel 3D image denoising procedure in this paper, based on local approximation of the edge surfaces using a set of surface templates. An important property of this method is that it can preserve edges and major edge structures (e.g., intersections of two edge surfaces and pointed corners). Numerical studies show that it works well in various applications.

  4. 3D nonrigid medical image registration using a new information theoretic measure

    NASA Astrophysics Data System (ADS)

    Li, Bicao; Yang, Guanyu; Coatrieux, Jean Louis; Li, Baosheng; Shu, Huazhong

    2015-11-01

    This work presents a novel method for the nonrigid registration of medical images based on the Arimoto entropy, a generalization of the Shannon entropy. The proposed method employed the Jensen-Arimoto divergence measure as a similarity metric to measure the statistical dependence between medical images. Free-form deformations were adopted as the transformation model and the Parzen window estimation was applied to compute the probability distributions. A penalty term is incorporated into the objective function to smooth the nonrigid transformation. The goal of registration is to optimize an objective function consisting of a dissimilarity term and a penalty term, which would be minimal when two deformed images are perfectly aligned using the limited memory BFGS optimization method, and thus to get the optimal geometric transformation. To validate the performance of the proposed method, experiments on both simulated 3D brain MR images and real 3D thoracic CT data sets were designed and performed on the open source elastix package. For the simulated experiments, the registration errors of 3D brain MR images with various magnitudes of known deformations and different levels of noise were measured. For the real data tests, four data sets of 4D thoracic CT from four patients were selected to assess the registration performance of the method, including ten 3D CT images for each 4D CT data covering an entire respiration cycle. These results were compared with the normalized cross correlation and the mutual information methods and show a slight but true improvement in registration accuracy.

  5. Photometry unlocks 3D information from 2D localization microscopy data.

    PubMed

    Franke, Christian; Sauer, Markus; van de Linde, Sebastian

    2017-01-01

    We developed a straightforward photometric method, temporal, radial-aperture-based intensity estimation (TRABI), that allows users to extract 3D information from existing 2D localization microscopy data. TRABI uses the accurate determination of photon numbers in different regions of the emission pattern of single emitters to generate a z-dependent photometric parameter. This method can determine fluorophore positions up to 600 nm from the focal plane and can be combined with biplane detection to further improve axial localization.

  6. Structure of Pseudoknot PK26 Shows 3D Domain Swapping in an RNA

    NASA Technical Reports Server (NTRS)

    Lietzke, Susan E; Barnes, Cindy L.

    1998-01-01

    3D domain swapping provides a facile pathway for the evolution of oligomeric proteins and allosteric mechanisms and a means for using monomer-oligomer equilibria to regulate biological activity. The term "3D domain swapping" describes the exchange of identical domains between two protein monomers to create an oligomer. 3D domain swapping has, so far, only been recognized in proteins. In this study, the structure of the pseudoknot PK26 is reported and it is a clear example of 3D domain swapping in RNA. PK26 was chosen for study because RNA pseudoknots are required structures in several biological processes and they arise frequently in in vitro selection experiments directed against protein targets. PK26 specifically inhibits HIV-1 reverse transcriptase with nanomolar affinity. We have now determined the 3.1 A resolution crystal structure of PK26 and find that it forms a 3D domain swapped dimer. PK26 shows extensive base pairing between and within strands. Formation of the dimer requires the linker region between the pseudoknot folds to adopt a unique conformation that allows a base within a helical stem to skip one base in the stacking register. Rearrangement of the linker would permit a monomeric pseudoknot to form. This structure shows how RNA can use 3D domain swapping to build large scale oligomers like the putative hexamer in the packaging RNA of bacteriophage Phi29.

  7. ProFunc: a server for predicting protein function from 3D structure.

    PubMed

    Laskowski, Roman A; Watson, James D; Thornton, Janet M

    2005-07-01

    ProFunc (http://www.ebi.ac.uk/thornton-srv/databases/ProFunc) is a web server for predicting the likely function of proteins whose 3D structure is known but whose function is not. Users submit the coordinates of their structure to the server in PDB format. ProFunc makes use of both existing and novel methods to analyse the protein's sequence and structure identifying functional motifs or close relationships to functionally characterized proteins. A summary of the analyses provides an at-a-glance view of what each of the different methods has found. More detailed results are available on separate pages. Often where one method has failed to find anything useful another may be more forthcoming. The server is likely to be of most use in structural genomics where a large proportion of the proteins whose structures are solved are of hypothetical proteins of unknown function. However, it may also find use in a comparative analysis of members of large protein families. It provides a convenient compendium of sequence and structural information that often hold vital functional clues to be followed up experimentally.

  8. ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files.

    PubMed

    Karthikeyan, Muthukumarasamy; Vyas, Renu

    2016-01-01

    Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular information, generally from a PDF document format is a daunting task. Here we present an approach to harvest 3D molecular data from the supporting information of scientific research articles that are normally available from publisher's resources. In order to demonstrate the feasibility of extracting truly computable molecules from PDF file formats in a fast and efficient manner, we have developed a Java based application, namely ChemEngine. This program recognizes textual patterns from the supplementary data and generates standard molecular structure data (bond matrix, atomic coordinates) that can be subjected to a multitude of computational processes automatically. The methodology has been demonstrated via several case studies on different formats of coordinates data stored in supplementary information files, wherein ChemEngine selectively harvested the atomic coordinates and interpreted them as molecules with high accuracy. The reusability of extracted molecular coordinate data was demonstrated by computing Single Point Energies that were in close agreement with the original computed data provided with the articles. It is envisaged that the methodology will enable large scale conversion of molecular information from supplementary files available in the PDF format into a collection of ready- to- compute molecular data to create an automated workflow for advanced computational processes. Software along with source codes and instructions available at https://sourceforge.net/projects/chemengine/files/?source=navbar.Graphical abstract.

  9. A 3-D Puzzle Approach to Building Protein-DNA Structures.

    PubMed

    Hinton, Deborah M

    2017-02-02

    Despite recent advances in structural analysis, it is still challenging to obtain a high resolution structure for a complex of RNA polymerase, transcriptional factors, and DNA. However, using biochemical constraints, 3-D printed models of available structures, and computer modeling, one can build biologically relevant models of such supramolecular complexes.

  10. Laser fabrication of 2D and 3D metal nanoparticle structures and arrays.

    PubMed

    Kuznetsov, A I; Kiyan, R; Chichkov, B N

    2010-09-27

    A novel method for fabrication of 2D and 3D metal nanoparticle structures and arrays is proposed. This technique is based on laser-induced transfer of molten metal nanodroplets from thin metal films. Metal nanoparticles are produced by solidification of these nanodroplets. The size of the transferred nanoparticles can be controllably changed in the range from 180 nm to 1500 nm. Several examples of complex 2D and 3D microstructures generated form gold nanoparticles are demonstrated.

  11. Linear-time protein 3-D structure searching with insertions and deletions

    PubMed Central

    2010-01-01

    Background Two biomolecular 3-D structures are said to be similar if the RMSD (root mean square deviation) between the two molecules' sequences of 3-D coordinates is less than or equal to some given constant bound. Tools for searching for similar structures in biomolecular 3-D structure databases are becoming increasingly important in the structural biology of the post-genomic era. Results We consider an important, fundamental problem of reporting all substructures in a 3-D structure database of chain molecules (such as proteins) which are similar to a given query 3-D structure, with consideration of indels (i.e., insertions and deletions). This problem has been believed to be very difficult but its exact computational complexity has not been known. In this paper, we first prove that the problem in unbounded dimensions is NP-hard. We then propose a new algorithm that dramatically improves the average-case time complexity of the problem in 3-D in case the number of indels k is bounded by a constant. Our algorithm solves the above problem for a query of size m and a database of size N in average-case O(N) time, whereas the time complexity of the previously best algorithm was O(Nmk+1). Conclusions Our results show that although the problem of searching for similar structures in a database based on the RMSD measure with indels is NP-hard in the case of unbounded dimensions, it can be solved in 3-D by a simple average-case linear time algorithm when the number of indels is bounded by a constant. PMID:20047663

  12. Tailored complex 3D vortex lattice structures by perturbed multiples of three-plane waves.

    PubMed

    Xavier, Jolly; Vyas, Sunil; Senthilkumaran, Paramasivam; Joseph, Joby

    2012-04-20

    As three-plane waves are the minimum number required for the formation of vortex-embedded lattice structures by plane wave interference, we present our experimental investigation on the formation of complex 3D photonic vortex lattice structures by a designed superposition of multiples of phase-engineered three-plane waves. The unfolding of the generated complex photonic lattice structures with higher order helical phase is realized by perturbing the superposition of a relatively phase-encoded, axially equidistant multiple of three noncoplanar plane waves. Through a programmable spatial light modulator assisted single step fabrication approach, the unfolded 3D vortex lattice structures are experimentally realized, well matched to our computer simulations. The formation of higher order intertwined helices embedded in these 3D spiraling vortex lattice structures by the superposition of the multiples of phase-engineered three-plane waves interference is also studied.

  13. Building Proteins in a Day: Efficient 3D Molecular Structure Estimation with Electron Cryomicroscopy.

    PubMed

    Punjani, Ali; Brubaker, Marcus A; Fleet, David J

    2017-04-01

    Discovering the 3D atomic-resolution structure of molecules such as proteins and viruses is one of the foremost research problems in biology and medicine. Electron Cryomicroscopy (cryo-EM) is a promising vision-based technique for structure estimation which attempts to reconstruct 3D atomic structures from a large set of 2D transmission electron microscope images. This paper presents a new Bayesian framework for cryo-EM structure estimation that builds on modern stochastic optimization techniques to allow one to scale to very large datasets. We also introduce a novel Monte-Carlo technique that reduces the cost of evaluating the objective function during optimization by over five orders of magnitude. The net result is an approach capable of estimating 3D molecular structure from large-scale datasets in about a day on a single CPU workstation.

  14. Stereomicroscopic 3D-pattern profiling of murine and human intestinal inflammation reveals unique structural phenotypes

    PubMed Central

    Rodriguez-Palacios, Alex; Kodani, Tomohiro; Kaydo, Lindsey; Pietropaoli, Davide; Corridoni, Daniele; Howell, Scott; Katz, Jeffry; Xin, Wei; Pizarro, Theresa T.; Cominelli, Fabio

    2015-01-01

    Histology is fundamental to assess two-dimensional intestinal inflammation; however, inflammatory bowel diseases (IBDs) are often indistinguishable microscopically on the basis of mucosal biopsies. Here, we use stereomicroscopy (SM) to rapidly profile the entire intestinal topography and assess inflammation. We examine the mucosal surface of >700 mice (encompassing >16 strains and various IBD-models), create a profiling catalogue of 3D-stereomicroscopic abnormalities and demonstrate that mice with comparable histological scores display unique sub-clusters of 3D-structure-patterns of IBD pathology, which we call 3D-stereoenterotypes, and which are otherwise indiscernible histologically. We show that two ileal IBD-stereoenterotypes (‘cobblestones' versus ‘villous mini-aggregation') cluster separately within two distinct mouse lines of spontaneous ileitis, suggesting that host genetics drive unique and divergent inflammatory 3D-structural patterns in the gut. In humans, stereomicroscopy reveals ‘liquefaction' lesions and hierarchical fistulous complexes, enriched with clostridia/segmented filamentous bacteria, running under healthy mucosa in Crohn's disease. We suggest that stereomicroscopic (3D-SMAPgut) profiling can be easily implemented and enable the comprehensive study of inflammatory 3D structures, genetics and flora in IBD. PMID:26154811

  15. Efficient global wave propagation adapted to 3-D structural complexity: a pseudospectral/spectral-element approach

    NASA Astrophysics Data System (ADS)

    Leng, Kuangdai; Nissen-Meyer, Tarje; van Driel, Martin

    2016-12-01

    We present a new, computationally efficient numerical method to simulate global seismic wave propagation in realistic 3-D Earth models. We characterize the azimuthal dependence of 3-D wavefields in terms of Fourier series, such that the 3-D equations of motion reduce to an algebraic system of coupled 2-D meridian equations, which is then solved by a 2-D spectral element method (SEM). Computational efficiency of such a hybrid method stems from lateral smoothness of 3-D Earth models and axial singularity of seismic point sources, which jointly confine the Fourier modes of wavefields to a few lower orders. We show novel benchmarks for global wave solutions in 3-D structures between our method and an independent, fully discretized 3-D SEM with remarkable agreement. Performance comparisons are carried out on three state-of-the-art tomography models, with seismic period ranging from 34 s down to 11 s. It turns out that our method has run up to two orders of magnitude faster than the 3-D SEM, featured by a computational advantage expanding with seismic frequency.

  16. Gene3D: structural assignments for the biologist and bioinformaticist alike

    PubMed Central

    Buchan, Daniel W. A.; Rison, Stuart C. G.; Bray, James E.; Lee, David; Pearl, Frances; Thornton, Janet M.; Orengo, Christine A.

    2003-01-01

    The Gene3D database (http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/) provides structural assignments for genes within complete genomes. These are available via the internet from either the World Wide Web or FTP. Assignments are made using PSI-BLAST and subsequently processed using the DRange protocol. The DRange protocol is an empirically benchmarked method for assessing the validity of structural assignments made using sequence searching methods where appropriate assignment statistics are collected and made available. Gene3D links assignments to their appropriate entries in relevent structural and classification resources (PDBsum, CATH database and the Dictionary of Homologous Superfamilies). Release 2.0 of Gene3D includes 62 genomes, 2 eukaryotes, 10 archaea and 40 bacteria. Currently, structural assignments can be made for between 30 and 40 percent of any given genome. In any genome, around half of those genes assigned a structural domain are assigned a single domain and the other half of the genes are assigned multiple structural domains. Gene3D is linked to the CATH database and is updated with each new update of CATH. PMID:12520054

  17. Segmentation of vascular structures and hematopoietic cells in 3D microscopy images and quantitative analysis

    NASA Astrophysics Data System (ADS)

    Mu, Jian; Yang, Lin; Kamocka, Malgorzata M.; Zollman, Amy L.; Carlesso, Nadia; Chen, Danny Z.

    2015-03-01

    In this paper, we present image processing methods for quantitative study of how the bone marrow microenvironment changes (characterized by altered vascular structure and hematopoietic cell distribution) caused by diseases or various factors. We develop algorithms that automatically segment vascular structures and hematopoietic cells in 3-D microscopy images, perform quantitative analysis of the properties of the segmented vascular structures and cells, and examine how such properties change. In processing images, we apply local thresholding to segment vessels, and add post-processing steps to deal with imaging artifacts. We propose an improved watershed algorithm that relies on both intensity and shape information and can separate multiple overlapping cells better than common watershed methods. We then quantitatively compute various features of the vascular structures and hematopoietic cells, such as the branches and sizes of vessels and the distribution of cells. In analyzing vascular properties, we provide algorithms for pruning fake vessel segments and branches based on vessel skeletons. Our algorithms can segment vascular structures and hematopoietic cells with good quality. We use our methods to quantitatively examine the changes in the bone marrow microenvironment caused by the deletion of Notch pathway. Our quantitative analysis reveals property changes in samples with deleted Notch pathway. Our tool is useful for biologists to quantitatively measure changes in the bone marrow microenvironment, for developing possible therapeutic strategies to help the bone marrow microenvironment recovery.

  18. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

    PubMed

    Capra, John A; Laskowski, Roman A; Thornton, Janet M; Singh, Mona; Funkhouser, Thomas A

    2009-12-01

    Identifying a protein's functional sites is an important step towards characterizing its molecular function. Numerous structure- and sequence-based methods have been developed for this problem. Here we introduce ConCavity, a small molecule binding site prediction algorithm that integrates evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. In large-scale testing on a diverse set of single- and multi-chain protein structures, we show that ConCavity substantially outperforms existing methods for identifying both 3D ligand binding pockets and individual ligand binding residues. As part of our testing, we perform one of the first direct comparisons of conservation-based and structure-based methods. We find that the two approaches provide largely complementary information, which can be combined to improve upon either approach alone. We also demonstrate that ConCavity has state-of-the-art performance in predicting catalytic sites and drug binding pockets. Overall, the algorithms and analysis presented here significantly improve our ability to identify ligand binding sites and further advance our understanding of the relationship between evolutionary sequence conservation and structural and functional attributes of proteins. Data, source code, and prediction visualizations are available on the ConCavity web site (http://compbio.cs.princeton.edu/concavity/).

  19. 3D structure and dynamics of prominences in IRIS-Hinode collaborative observations

    NASA Astrophysics Data System (ADS)

    Okamoto, J.; De Pontieu, B.; Tarbell, T. D.; Title, A. M.

    2013-12-01

    A new solar physics satellite, Interface Region Imaging Spectrograph (IRIS), was launched on June 27, 2013. IRIS obtains UV spectra and images with high spatial resolution (0.33 arcsec) and high time cadence (1 sec / slit) of the chromosphere and transition region of the Sun. The chromosphere is located between the photosphere and the corona. Recently, the Hinode satellite has revealed that the chromosphere is highly active and suggested that it is a very important region in terms of energy deposit and transfer for coronal heating and solar wind acceleration. However, we cannot have further chromospheric information by Hinode because the Hinode Solar Optical Telescope has only a filtergraph for chromospheric observations. Now we have IRIS. IRIS performs spectroscopic observations to get the missing physical quantities of the dynamic chromosphere. Moreover, IRIS and Hinode is the most powerful collaboration to understand chromospheric activities. Hinode observes extremely high-cadence (1.6 sec) and high-spatial (0.2 arcsec) 2-D images, while IRIS measures line-of-sight velocity and Doppler width of fine structures with temperature dependence. This combination provides information about 3-D structures and dynamic phenomena of chromospheric features. Here we focus on prominence observations performed by IRIS and Hinode, and introduce the initial results of prominence dynamics and magnetic structures such as helical configurations, propagating waves and their damping mechanisms, and formation processes.

  20. EDCs DataBank: 3D-Structure database of endocrine disrupting chemicals.

    PubMed

    Montes-Grajales, Diana; Olivero-Verbel, Jesus

    2015-01-02

    Endocrine disrupting chemicals (EDCs) are a group of compounds that affect the endocrine system, frequently found in everyday products and epidemiologically associated with several diseases. The purpose of this work was to develop EDCs DataBank, the only database of EDCs with three-dimensional structures. This database was built on MySQL using the EU list of potential endocrine disruptors and TEDX list. It contains the three-dimensional structures available on PubChem, as well as a wide variety of information from different databases and text mining tools, useful for almost any kind of research regarding EDCs. The web platform was developed employing HTML, CSS and PHP languages, with dynamic contents in a graphic environment, facilitating information analysis. Currently EDCs DataBank has 615 molecules, including pesticides, natural and industrial products, cosmetics, drugs and food additives, among other low molecular weight xenobiotics. Therefore, this database can be used to study the toxicological effects of these molecules, or to develop pharmaceuticals targeting hormone receptors, through docking studies, high-throughput virtual screening and ligand-protein interaction analysis. EDCs DataBank is totally user-friendly and the 3D-structures of the molecules can be downloaded in several formats. This database is freely available at http://edcs.unicartagena.edu.co.

  1. High-resolution 3D seismic model of the crustal and uppermost mantle structure in Poland

    NASA Astrophysics Data System (ADS)

    Grad, Marek; Polkowski, Marcin; Ostaficzuk, Stanisław R.

    2016-01-01

    In the area of Poland a contact between the Precambrian and Phanerozoic Europe and the Carpathians has a complicated structure and a complex P-wave velocity of the sedimentary cover, crystalline crust, Moho depth and the uppermost mantle. The geometry of the uppermost several kilometers of sediments is relatively well recognized from over 100,000 boreholes. The vertical seismic profiling (VSP) from 1188 boreholes provided detailed velocity data for regional tectonic units and for stratigraphic successions from Permian to the Tertiary and Quaternary deposits. These data, however, do not provide information about the velocity and basement depth in the central part of the Trans-European suture zone (TESZ) and in the Carpathians. So, the data set is supplemented by 2D velocity models from 32 deep seismic sounding refraction profiles which also provide information about the crust and uppermost mantle. Together with the results of other methods: vertical seismic profiling, magnetotelluric, allow for the creation of a detailed, high-resolution 3D model for the entire Earth's crust and the uppermost mantle down to a depth of 60 km. The thinnest sedimentary cover in the Mazury-Belarus anteclise is only 0.3 to 1 km thick, which increases to 7 to 8 km along the East European Craton (EEC) margin, and 9 to 12 km in the TESZ. The Variscan domain is characterized by a 1-4 km thick sedimentary cover, while the Carpathians are characterized by very thick sedimentary layers, up to about 20 km. The crystalline crust is differentiated and has a layered structure. The crust beneath the West European Platform (WEP; Variscan domain) is characterized by P-wave velocities of 5.8-6.6 km/s. The upper and middle crusts beneath the EEC are characterized by velocities of 6.1-6.6 km/s, and are underlain by a high velocity lower crust with a velocity of about 7 km/s. A general decrease in velocity is observed from the older to the younger tectonic domains. The TESZ is associated with a steep dip

  2. Sparsity-based Ankylography for Recovering 3D molecular structures from single-shot 2D scattered light intensity

    PubMed Central

    Mutzafi, Maor; Shechtman, Yoav; Eldar, Yonina C.; Cohen, Oren; Segev, Mordechai

    2015-01-01

    Deciphering the three-dimensional (3D) structure of complex molecules is of major importance, typically accomplished with X-ray crystallography. Unfortunately, many important molecules cannot be crystallized, hence their 3D structure is unknown. Ankylography presents an alternative, relying on scattering an ultrashort X-ray pulse off a single molecule before it disintegrates, measuring the far-field intensity on a two-dimensional surface, followed by computation. However, significant information is absent due to lower dimensionality of the measurements and the inability to measure the phase. Recent Ankylography experiments attracted much interest, but it was counter-argued that Ankylography is valid only for objects containing a small number of volume pixels. Here, we propose a sparsity-based approach to reconstruct the 3D structure of molecules. Sparsity is natural for Ankylography, because molecules can be represented compactly in stoichiometric basis. Utilizing sparsity, we surpass current limits on recoverable information by orders of magnitude, paving the way for deciphering the 3D structure of macromolecules. PMID:26289358

  3. Digital structural interpretation of mountain-scale photogrammetric 3D models (Kamnik Alps, Slovenia)

    NASA Astrophysics Data System (ADS)

    Dolžan, Erazem; Vrabec, Marko

    2015-04-01

    From the earliest days of geological science, mountainous terrains with their extreme topographic relief and sparse to non-existent vegetation were utilized to a great advantage for gaining 3D insight into geological structure. But whereas Alpine vistas may offer perfect panoramic views of geology, the steep mountain slopes and vertical cliffs make it very time-consuming and difficult (if not impossible) to acquire quantitative mapping data such as precisely georeferenced traces of geological boundaries and attitudes of structural planes. We faced this problem in mapping the central Kamnik Alps of northern Slovenia, which are built up from Mid to Late Triassic succession of carbonate rocks. Polyphase brittle tectonic evolution, monotonous lithology and the presence of temporally and spatially irregular facies boundary between bedded platform carbonates and massive reef limestones considerably complicate the structural interpretation of otherwise perfectly exposed, but hardly accessible massif. We used Agisoft Photoscan Structure-from-Motion photogrammetric software to process a series of overlapping high-resolution (~0.25 m ground resolution) vertical aerial photographs originally acquired by the Geodetic Authority of the Republic of Slovenia for surveying purposes, to derive very detailed 3D triangular mesh models of terrain and associated photographic textures. Phototextures are crucial for geological interpretation of the models as they provide additional levels of detail and lithological information which is not resolvable from geometrical mesh models alone. We then exported the models to Paradigm Gocad software to refine and optimize the meshing. Structural interpretation of the models, including mapping of traces and surfaces of faults and stratigraphic boundaries and determining dips of structural planes, was performed in MVE Move suite which offers a range of useful tools for digital mapping and interpretation. Photogrammetric model was complemented by

  4. Lithographically-generated 3D lamella layers and their structural color.

    PubMed

    Zhang, Sichao; Chen, Yifang; Lu, Bingrui; Liu, Jianpeng; Shao, Jinhai; Xu, Chen

    2016-04-28

    Inspired by the structural color from the multilayer nanophotonic structures in Morpho butterfly wing scales, 3D lamellae layers in dielectric polymers (polymethyl methacrylate, PMMA) with n ∼ 1.5 were designed and fabricated by standard top-down electron beam lithography with one-step exposure followed by an alternating development/dissolution process of PMMA/LOR (lift-off resist) multilayers. This work offers direct proof of the structural blue/green color via lithographically-replicated PMMA/air multilayers, analogous to those in real Morpho butterfly wings. The success of nanolithography in this work for the 3D lamellae structures in dielectric polymers not only enables us to gain deeper insight into the mysterious blue color of the Morpho butterfly wings, but also breaks through the bottleneck in technical development toward broad applications in gas/liquid sensors, 3D meta-materials, coloring media, and infrared imaging devices, etc.

  5. Lithographically-generated 3D lamella layers and their structural color

    NASA Astrophysics Data System (ADS)

    Zhang, Sichao; Chen, Yifang; Lu, Bingrui; Liu, Jianpeng; Shao, Jinhai; Xu, Chen

    2016-04-01

    Inspired by the structural color from the multilayer nanophotonic structures in Morpho butterfly wing scales, 3D lamellae layers in dielectric polymers (polymethyl methacrylate, PMMA) with n ~ 1.5 were designed and fabricated by standard top-down electron beam lithography with one-step exposure followed by an alternating development/dissolution process of PMMA/LOR (lift-off resist) multilayers. This work offers direct proof of the structural blue/green color via lithographically-replicated PMMA/air multilayers, analogous to those in real Morpho butterfly wings. The success of nanolithography in this work for the 3D lamellae structures in dielectric polymers not only enables us to gain deeper insight into the mysterious blue color of the Morpho butterfly wings, but also breaks through the bottleneck in technical development toward broad applications in gas/liquid sensors, 3D meta-materials, coloring media, and infrared imaging devices, etc.

  6. 3-D seismic velocity and attenuation structures in the geothermal field

    SciTech Connect

    Nugraha, Andri Dian; Syahputra, Ahmad; Fatkhan,; Sule, Rachmat

    2013-09-09

    We conducted delay time tomography to determine 3-D seismic velocity structures (Vp, Vs, and Vp/Vs ratio) using micro-seismic events in the geothermal field. The P-and S-wave arrival times of these micro-seismic events have been used as input for the tomographic inversion. Our preliminary seismic velocity results show that the subsurface condition of geothermal field can be fairly delineated the characteristic of reservoir. We then extended our understanding of the subsurface physical properties through determining of attenuation structures (Qp, Qs, and Qs/Qp ratio) using micro-seismic waveform. We combined seismic velocities and attenuation structures to get much better interpretation of the reservoir characteristic. Our preliminary attanuation structures results show reservoir characterization can be more clearly by using the 3-D attenuation model of Qp, Qs, and Qs/Qp ratio combined with 3-D seismic velocity model of Vp, Vs, and Vp/Vs ratio.

  7. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    Ishikawa, Takashi

    2013-01-01

    Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex.

  8. System for conveyor belt part picking using structured light and 3D pose estimation

    NASA Astrophysics Data System (ADS)

    Thielemann, J.; Skotheim, Ø.; Nygaard, J. O.; Vollset, T.

    2009-01-01

    Automatic picking of parts is an important challenge to solve within factory automation, because it can remove tedious manual work and save labor costs. One such application involves parts that arrive with random position and orientation on a conveyor belt. The parts should be picked off the conveyor belt and placed systematically into bins. We describe a system that consists of a structured light instrument for capturing 3D data and robust methods for aligning an input 3D template with a 3D image of the scene. The method uses general and robust pre-processing steps based on geometric primitives that allow the well-known Iterative Closest Point algorithm to converge quickly and robustly to the correct solution. The method has been demonstrated for localization of car parts with random position and orientation. We believe that the method is applicable for a wide range of industrial automation problems where precise localization of 3D objects in a scene is needed.

  9. 3D printing of weft knitted textile based structures by selective laser sintering of nylon powder

    NASA Astrophysics Data System (ADS)

    Beecroft, M.

    2016-07-01

    3D printing is a form of additive manufacturing whereby the building up of layers of material creates objects. The selective laser sintering process (SLS) uses a laser beam to sinter powdered material to create objects. This paper builds upon previous research into 3D printed textile based material exploring the use of SLS using nylon powder to create flexible weft knitted structures. The results show the potential to print flexible textile based structures that exhibit the properties of traditional knitted textile structures along with the mechanical properties of the material used, whilst describing the challenges regarding fineness of printing resolution. The conclusion highlights the potential future development and application of such pieces.

  10. Definition of subsurface stratigraphy, structure and rock properties from 3-D seismic data

    NASA Astrophysics Data System (ADS)

    Hart, Bruce S.

    1999-10-01

    This paper summarizes how three-dimensional (3-D) seismic technology is being used, primarily in the petroleum industry, to define subsurface structure, stratigraphy and rock properties. A 3-D seismic data volume: (a) provides a more accurate image of the subsurface than can be obtained with 2-D seismic methods; (b) is continuous, and so has a much greater spatial sampling than is obtained with 2-D seismic or other subsurface data (e.g., wells); and (c) can be viewed and interpreted interactively from a variety of perspectives, thus enhancing the interpreter's ability to generate an accurate description of subsurface features of interest. Seismic interpretation was once the almost exclusive realm of geophysicists, however, most 3-D seismic interpretation today is conducted by multidisciplinary teams that integrate geophysical, geological, petrophysical and engineering data and concepts into the 3-D seismic interpretation. These factors, plus proper survey design, help to increase the chances of success of a 3-D seismic interpretation project. Although there are cases where the technology is not appropriate or cannot be applied (for economic reasons or otherwise), the general success of 3-D seismic has led it to become a mainstay of the petroleum industry. The approach and technology, first developed in that industry, have potential applications in other applied and fundamental earth science disciplines, including mining, environmental geology, structural geology and stratigraphy.

  11. The Relationship between Oxygen A-band Photon Pathlength Distributions and 3D Structures of Heating Rate Profiles

    NASA Astrophysics Data System (ADS)

    Song, L.; Min, Q.

    2012-12-01

    Broadband heating directly drives the global atmospheric and oceanic circulation and its vertical profiles strongly depend upon cloud three-dimensional (3D) structures. Due to the complexity of cloud 3D problems and the difficulties in observations of broadband heating rate profiles (BBHRP), there are still large uncertainties in the relationship of clouds, radiation and climate feedback. Oxygen A-band photon pathlength distributions (PPLD) contain rich information about the 3D structures of clouds and BBHRP and can be observed by both ground based and space based measurements. Therefore, it is meaningful to explore the possibility of connecting A-band PPLD and BBHRP and consequently to describe the internal relationship between them together with the cloud 3D effects on BBHRP. A 3D Monte Carlo radiative transfer model is applied to simulate solar broadband heating rate profiles and oxygen A-band photon pathlength distributions of several ideal cloud fields and two typical cloud fields generated by cloud resolving model (CRM). Principal components (PCs) and the first four moments are selected to represent the vertical structures of BBHRP and PPLD, respectively. In ideal cloud fields, the moments show clear constraint to PCs of BBHRP. The results demonstrate the feasibility to describe the vertical structures of BBHRP by PPLD. The relationship between moments and PCs turns complicated in CRM cloud fields due to the composition of various 3D effects. However, detailed analysis still show that the moments, the PCs and total cloud optical depth are effective factors in defining BBHRP, especially for the vertical structures of relative low clouds. Further, a statistical fitting between the PCs and the moments by a two-layer neural network is applied to provide a quantitative representation of the linkages.

  12. Function and 3D Structure of the N-Glycans on Glycoproteins

    PubMed Central

    Nagae, Masamichi; Yamaguchi, Yoshiki

    2012-01-01

    Glycosylation is one of the most common post-translational modifications in eukaryotic cells and plays important roles in many biological processes, such as the immune response and protein quality control systems. It has been notoriously difficult to study glycoproteins by X-ray crystallography since the glycan moieties usually have a heterogeneous chemical structure and conformation, and are often mobile. Nonetheless, recent technical advances in glycoprotein crystallography have accelerated the accumulation of 3D structural information. Statistical analysis of “snapshots” of glycoproteins can provide clues to understanding their structural and dynamic aspects. In this review, we provide an overview of crystallographic analyses of glycoproteins, in which electron density of the glycan moiety is clearly observed. These well-defined N-glycan structures are in most cases attributed to carbohydrate-protein and/or carbohydrate-carbohydrate interactions and may function as “molecular glue” to help stabilize inter- and intra-molecular interactions. However, the more mobile N-glycans on cell surface receptors, the electron density of which is usually missing on X-ray crystallography, seem to guide the partner ligand to its binding site and prevent irregular protein aggregation by covering oligomerization sites away from the ligand-binding site. PMID:22942711

  13. Characterisation of the surface structure of 3D printed scaffolds for cell infiltration and surgical suturing.

    PubMed

    Ruiz-Cantu, Laura; Gleadall, Andrew; Faris, Callum; Segal, Joel; Shakesheff, Kevin; Yang, Jing

    2016-03-01

    3D printing is of great interest for tissue engineering scaffolds due to the ability to form complex geometries and control internal structures, including porosity and pore size. The porous structure of scaffolds plays an important role in cell ingrowth and nutrition infusion. Although the internal porosity and pore size of 3D printed scaffolds have been frequently studied, the surface porosity and pore size, which are critical for cell infiltration and mass transport, have not been investigated. The surface geometry can differ considerably from the internal scaffold structure depending on the 3D printing process. It is vital to be able to control the surface geometry of scaffolds as well as the internal structure to fabricate optimal architectures. This work presents a method to control the surface porosity and pore size of 3D printed scaffolds. Six scaffold designs have been printed with surface porosities ranging from 3% to 21%. We have characterised the overall scaffold porosity and surface porosity using optical microscopy and microCT. It has been found that surface porosity has a significant impact on cell infiltration and proliferation. In addition, the porosity of the surface has been found to have an effect on mechanical properties and on the forces required to penetrate the scaffold with a surgical suturing needle. To the authors' knowledge, this study is the first to investigate the surface geometry of extrusion-based 3D printed scaffolds and demonstrates the importance of surface geometry in cell infiltration and clinical manipulation.

  14. Novel scanning electron microscopy methods for analyzing the 3D structure of the Golgi apparatus.

    PubMed

    Koga, Daisuke; Ushiki, Tatsuo; Watanabe, Tsuyoshi

    2017-01-01

    The structure of the Golgi apparatus has been extensively examined by light and electron microscopy, but details of its three-dimensional (3D) structure have remained unclear because of the technical limitations of conventional microscopy techniques. To overcome this problem, we have developed several novel scanning electron microscopy (SEM) methods for observing the 3D structure of subcellular organelles including the Golgi apparatus: (1) an osmium maceration method that facilitates SEM observation of membranous organelles, including the Golgi apparatus, by selectively removing soluble cytoplasmic proteins, (2) an osmium impregnation/maceration method that combines an osmium impregnation method with the osmium maceration method to determine the polarity of the Golgi apparatus by SEM, (3) a correlative light and SEM method that combines a cryosectioning technique with the osmium maceration method to enable correlation of the immunocytochemical distribution of molecules with the 3D ultrastructure of the Golgi apparatus, and (4) array tomography based on the systematic collection and integration of SEM images of serial ultrathin sections on glass slides for revealing the 3D ultrastructure of the entire Golgi apparatus. Together, the novel SEM techniques listed above can reveal the complete 3D structure of the Golgi apparatus in different cell types.

  15. A GIS-based 3D online information system for underground energy storage in northern Germany

    NASA Astrophysics Data System (ADS)

    Nolde, Michael; Malte, Schwanebeck; Ehsan, Biniyaz; Rainer, Duttmann

    2015-04-01

    We would like to present the concept and current state of development of a GIS-based 3D online information system for underground energy storage. Its aim is to support the local authorities through pre-selection of possible sites for thermal, electrical and substantial underground energy storages. Since the extension of renewable energies has become legal requirement in Germany, the underground storing of superfluously produced green energy (such as during a heavy wind event) in the form of compressed air, gas or heated water has become increasingly important. However, the selection of suitable sites is a complex task. The presented information system uses data of geological features such as rock layers, salt domes and faults enriched with attribute data such as rock porosity and permeability. This information is combined with surface data of the existing energy infrastructure, such as locations of wind and biogas stations, powerline arrangement and cable capacity, and energy distribution stations. Furthermore, legal obligations such as protected areas on the surface and current underground mining permissions are used for the process of pre-selecting sites suitable for energy storage. Not only the current situation but also prospective scenarios, such as expected growth in produced amount of energy are incorporated in the system. While the process of pre-selection itself is completely automated, the user has full control of the weighting of the different factors via the web interface. The system is implemented as an online 3D server GIS environment, so that it can easily be utilized in any web browser. The results are visualized online as interactive 3d graphics. The information system is implemented in the Python programming language in combination with current Web standards, and is build using only free and open source software. It is being developed at Kiel University as part of the ANGUS+ project (lead by Prof. Sebastian Bauer) for the federal state of

  16. 3D modeling of soil structure in urban groundwater areas: case studies in Kolpene, Rovaniemi, Finland

    NASA Astrophysics Data System (ADS)

    Kupila, Juho

    2015-04-01

    3D modeling of groundwater areas is an important research method in groundwater surveys. Model of geological soil structure improves the knowledge of linkage between land use planning and groundwater protection. Results can be used as base information when developing the water supply services and anticipating and performing the measures needed in case of environmental accidents. Also, collected information is utilized when creating the groundwater flow model. In Finland, structure studies have been conducted in cooperation (among others) with the municipalities and local water suppliers and with the authorities from the Centre for Economic Development, Transport and the Environment. Geological Survey of Finland carries out project "Structure studies in Kolpene groundwater area" in Rovaniemi, Finnish Lapland. Study site is located in northern Finland, in the vicinity of the city center of Rovaniemi. Extent of the area is about 13 square kilometers and there are lots of urban residential areas and other human activities. The objective of this project is to determine the geological structure of the Kolpene groundwater area so that the results can be used to estimate the validity of the present exclusion area and possible risks to the groundwater caused by the land use. Soil layers of the groundwater area are studied by means of collecting information by heavy drilling, geophysical surveying (ground penetrating radar and gravimeter measurements) and water sampling from the installed observation pipes. Also the general geological and hydrological mappings are carried out. Main results which will be produced are: 1) the model of the bedrock surface, 2) the model of the surface of the ground water and flow directions, 3) the thickness of ground water saturated soil layers and 4) location and main characteristics of the soil layers which are significant to the ground water conditions. The preparing studies have been started at the end of 2013 and the results will be

  17. Effects of haptic information on the perception of dynamic 3-D movement.

    PubMed

    Umemura, Hiroyuki

    2014-01-01

    This study examined effects of hand movement on visual perception of 3-D movement. I used an apparatus in which a cursor position in a simulated 3-D space and the position of a stylus on a haptic device could coincide using a mirror. In three experiments, participants touched the center of a rectangle in the visual display with the stylus of the force-feedback device. Then the rectangle's surface stereoscopically either protruded toward a participant or indented away from the participant. Simultaneously, the stylus either pushed back participant's hand, pulled away, or remained static. Visual and haptic information were independently manipulated. Participants judged whether the rectangle visually protruded or dented. Results showed that when the hand was pulled away, subjects were biased to perceive rectangles indented; however, when the hand was pushed back, no effect of haptic information was observed (Experiment 1). This effect persisted even when the cursor position was spatially separated from the hand position (Experiment 2). But, when participants touched an object different from the visual stimulus, this effect disappeared (Experiment 3). These results suggest that the visual system tried to integrate the dynamic visual and haptic information when they coincided cognitively, and the effect of haptic information on visually perceived depth was direction-dependent.

  18. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae’s Colliding Winds Using 3D Prints of Smoothed Particle Hydrodynamics Simulations

    NASA Astrophysics Data System (ADS)

    Madura, Thomas; Gull, Theodore R.; Clementel, Nicola; Paardekooper, Jan-Pieter; Kruip, Chael; Corcoran, Michael F.; Hamaguchi, Kenji; Teodoro, Mairan

    2015-01-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (>120 MSun), highly eccentric (e ~ 0.9) binary Eta Carinae. Using a consumer-grade 3D printer (Makerbot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of Eta Carinae's inner (r ~110 AU) wind-wind collision interface at multiple orbital phases. These 3D prints reveal important, previously unknown 'finger-like' structures at orbital phases shortly after periastron (φ ~1.045) that protrude radially outward from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. Rayleigh-Taylor) that arise at the interface between the radiatively-cooled layer of dense post-shock primary-star wind and the hot, adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unknown physical features highlight the important role 3D printing can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

  19. 3D multi-layered fibrous cellulose structure using an electrohydrodynamic process for tissue engineering.

    PubMed

    Kim, Minseong; Kim, GeunHyung

    2015-11-01

    Micro/nanofibrous structures have been applied widely in various tissue-engineering applications because the topological structures are similar to the extracellular matrix (ECM), which encourages a high degree of cell adhesion and growth. However, it has been difficult to produce a three-dimensional (3D) fibrous structure using controllable macro-pores. Recently, cellulose has been considered a high-potential natural-origin biomaterial, but its use in 3D biomedical structures has been limited due to its narrow processing window. Here, we suggest a new 3D cellulose scaffold consisting of multi-layered struts made of submicron-sized entangled fibers that were fabricated using an electrohydrodynamic direct jet (EHDJ) process that is spin-printing. By optimizing processing conditions (electric field strength, cellulose feeding rate, and distance between nozzle and target), we can achieve a multi-layered cellulose structure consisting of the cylindrically entangled cellulose fibers. To compare the properties of the fabricated 3D cellulose structure, we used a PCL fibrous scaffold, which has a similar fibrous morphology and pore geometry, as a control. The physical and in vitro biocompatibilities of both fibrous scaffolds were assessed using human dermal fibroblasts, and the cellulose structure showed higher cell adhesion and metabolic activities compared with the control. These results suggest the EHDJ process to be an effective fabricating tool for tissue engineering and the cellulose scaffold has high potential as a tissue regenerative material.

  20. Enhanced genome annotation using structural profiles in the program 3D-PSSM.

    PubMed

    Kelley, L A; MacCallum, R M; Sternberg, M J

    2000-06-02

    A method (three-dimensional position-specific scoring matrix, 3D-PSSM) to recognise remote protein sequence homologues is described. The method combines the power of multiple sequence profiles with knowledge of protein structure to provide enhanced recognition and thus functional assignment of newly sequenced genomes. The method uses structural alignments of homologous proteins of similar three-dimensional structure in the structural classification of proteins (SCOP) database to obtain a structural equivalence of residues. These equivalences are used to extend multiply aligned sequences obtained by standard sequence searches. The resulting large superfamily-based multiple alignment is converted into a PSSM. Combined with secondary structure matching and solvation potentials, 3D-PSSM can recognise structural and functional relationships beyond state-of-the-art sequence methods. In a cross-validated benchmark on 136 homologous relationships unambiguously undetectable by position-specific iterated basic local alignment search tool (PSI-Blast), 3D-PSSM can confidently assign 18 %. The method was applied to the remaining unassigned regions of the Mycoplasma genitalium genome and an additional 13 regions were assigned with 95 % confidence. 3D-PSSM is available to the community as a web server: http://www.bmm.icnet.uk/servers/3dpssm

  1. Low-Cost 3D Laser Scanning in Air or Water Using Self-Calibrating Structured Light

    NASA Astrophysics Data System (ADS)

    Bleier, M.; Nüchter, A.

    2017-02-01

    In-situ calibration of structured light scanners in underwater environments is time-consuming and complicated. This paper presents a self-calibrating line laser scanning system, which enables the creation of dense 3D models with a single fixed camera and a freely moving hand-held cross line laser projector. The proposed approach exploits geometric constraints, such as coplanarities, to recover the depth information and is applicable without any prior knowledge of the position and orientation of the laser projector. By employing an off-the-shelf underwater camera and a waterproof housing with high power line lasers an affordable 3D scanning solution can be built. In experiments the performance of the proposed technique is studied and compared with 3D reconstruction using explicit calibration. We demonstrate that the scanning system can be applied to above-the-water as well as underwater scenes.

  2. Spatial orientation in 3-D desktop displays: using rooms for organizing information.

    PubMed

    Colle, Herbert A; Reid, Gary B

    2003-01-01

    Understanding how spatial knowledge is acquired is important for spatial navigation and for improving the design of 3-D perspective interfaces. Configural spatial knowledge of object locations inside rooms is learned rapidly and easily (Colle & Reid, 1998), possibly because rooms afford local viewing in which objects are directly viewed or, alternatively, because of their structural features. The local viewing hypothesis predicts that the layout of objects outside of rooms also should be rapidly acquired when walls are removed and rooms are sufficiently close that participants can directly view and identify objects. It was evaluated using pointing and sketch map measures of configural knowledge with and without walls by varying distance, lighting levels, and observation instructions. Although within-room spatial knowledge was uniformly good, local viewing was not sufficient for improving spatial knowledge of objects in different rooms. Implications for navigation and 3-D interface design are discussed. Actual or potential applications of this research include the design of user interfaces, especially interfaces with 3-D displays.

  3. Structure light telecentric stereoscopic vision 3D measurement system based on Scheimpflug condition

    NASA Astrophysics Data System (ADS)

    Mei, Qing; Gao, Jian; Lin, Hui; Chen, Yun; Yunbo, He; Wang, Wei; Zhang, Guanjin; Chen, Xin

    2016-11-01

    We designed a new three-dimensional (3D) measurement system for micro components: a structure light telecentric stereoscopic vision 3D measurement system based on the Scheimpflug condition. This system creatively combines the telecentric imaging model and the Scheimpflug condition on the basis of structure light stereoscopic vision, having benefits of a wide measurement range, high accuracy, fast speed, and low price. The system measurement range is 20 mm×13 mm×6 mm, the lateral resolution is 20 μm, and the practical vertical resolution reaches 2.6 μm, which is close to the theoretical value of 2 μm and well satisfies the 3D measurement needs of micro components such as semiconductor devices, photoelectron elements, and micro-electromechanical systems. In this paper, we first introduce the principle and structure of the system and then present the system calibration and 3D reconstruction. We then present an experiment that was performed for the 3D reconstruction of the surface topography of a wafer, followed by a discussion. Finally, the conclusions are presented.

  4. Towards an efficient compression of 3D coordinates of macromolecular structures

    PubMed Central

    Valasatava, Yana; Bradley, Anthony R.; Rose, Alexander S.; Duarte, Jose M.; Prlić, Andreas

    2017-01-01

    The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format. PMID:28362865

  5. Towards an efficient compression of 3D coordinates of macromolecular structures.

    PubMed

    Valasatava, Yana; Bradley, Anthony R; Rose, Alexander S; Duarte, Jose M; Prlić, Andreas; Rose, Peter W

    2017-01-01

    The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format.

  6. Simulation approach of atomic layer deposition in large 3D structures

    NASA Astrophysics Data System (ADS)

    Schwille, Matthias C.; Barth, Jonas; Schössler, Timo; Schön, Florian; Bartha, Johann W.; Oettel, Martin

    2017-04-01

    We present a new simulation method predicting thicknesses of thin films obtained by atomic layer deposition in high aspect ratio 3D geometries as they appear in MEMS manufacturing. The method features a Monte-Carlo computation of film deposition in free molecular flow, as well as in the Knudsen and diffusive gas regime, applicable for large structures. We compare our approach to analytic and simulation results from the literature. The capability of the method is demonstrated by a comparison to experimental film thicknesses in a large 3D structure. Finally, the feasability to extract process parameters, i.e. sticking coefficients is shown.

  7. 3D-information fusion from very high resolution satellite sensors

    NASA Astrophysics Data System (ADS)

    Krauss, T.; d'Angelo, P.; Kuschk, G.; Tian, J.; Partovi, T.

    2015-04-01

    In this paper we show the pre-processing and potential for environmental applications of very high resolution (VHR) satellite stereo imagery like these from WorldView-2 or Pl'eiades with ground sampling distances (GSD) of half a metre to a metre. To process such data first a dense digital surface model (DSM) has to be generated. Afterwards from this a digital terrain model (DTM) representing the ground and a so called normalized digital elevation model (nDEM) representing off-ground objects are derived. Combining these elevation based data with a spectral classification allows detection and extraction of objects from the satellite scenes. Beside the object extraction also the DSM and DTM can directly be used for simulation and monitoring of environmental issues. Examples are the simulation of floodings, building-volume and people estimation, simulation of noise from roads, wave-propagation for cellphones, wind and light for estimating renewable energy sources, 3D change detection, earthquake preparedness and crisis relief, urban development and sprawl of informal settlements and much more. Also outside of urban areas volume information brings literally a new dimension to earth oberservation tasks like the volume estimations of forests and illegal logging, volume of (illegal) open pit mining activities, estimation of flooding or tsunami risks, dike planning, etc. In this paper we present the preprocessing from the original level-1 satellite data to digital surface models (DSMs), corresponding VHR ortho images and derived digital terrain models (DTMs). From these components we present how a monitoring and decision fusion based 3D change detection can be realized by using different acquisitions. The results are analyzed and assessed to derive quality parameters for the presented method. Finally the usability of 3D information fusion from VHR satellite imagery is discussed and evaluated.

  8. SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.

    PubMed

    Magnus, Marcin; Boniecki, Michał J; Dawson, Wayne; Bujnicki, Janusz M

    2016-07-08

    RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb.

  9. 3D flexible NiTi-braided elastomer composites for smart structure applications

    NASA Astrophysics Data System (ADS)

    Heller, L.; Vokoun, D.; Šittner, P.; Finckh, H.

    2012-04-01

    While outstanding functional properties of thin NiTi wires are nowadays well recognized and beneficially utilized in medical NiTi devices, development of 2D/3D wire structures made out of these NiTi wires remains challenging and mostly unexplored. The research is driven by the idea of creating novel 2D/3D smart structures which inherit the functional properties of NiTi wires and actively utilize geometrical deformations within the structure to create new/improved functional properties. Generally, textile technology provides attractive processing methods for manufacturing 2D/3D smart structures made out of NiTi wires. Such structures may be beneficially combined with soft elastomers to create smart deformable composites. Following this route, we carried out experimental work focused on development of 3D flexible NiTi-braided elastomer composites involving their design, laboratory manufacture and thermomechanical testing. We describe the manufacturing technology and structural properties of these composites; and perform thermomechanical tests on the composites, focusing particularly on quasistatic tensile properties, energy absorption, damping and actuation under tensile loading. Functional thermomechanical properties of the composites are discussed with regard to the mechanical properties of the components and architecture of the composites. It is found that the composites indeed inherit all important features of the thermomechanical behavior of NiTi wires but, due to their internal architecture, outperform single NiTi wires in some features such as the magnitude of recoverable strain, superelastic damping capacity and thermally induced actuation strain.

  10. Segmented images and 3D images for studying the anatomical structures in MRIs

    NASA Astrophysics Data System (ADS)

    Lee, Yong Sook; Chung, Min Suk; Cho, Jae Hyun

    2004-05-01

    For identifying the pathological findings in MRIs, the anatomical structures in MRIs should be identified in advance. For studying the anatomical structures in MRIs, an education al tool that includes the horizontal, coronal, sagittal MRIs of entire body, corresponding segmented images, 3D images, and browsing software is necessary. Such an educational tool, however, is hard to obtain. Therefore, in this research, such an educational tool which helps medical students and doctors study the anatomical structures in MRIs was made as follows. A healthy, young Korean male adult with standard body shape was selected. Six hundred thirteen horizontal MRIs of the entire body were scanned and inputted to the personal computer. Sixty anatomical structures in the horizontal MRIs were segmented to make horizontal segmented images. Coronal, sagittal MRIs and coronal, sagittal segmented images were made. 3D images of anatomical structures in the segmented images were reconstructed by surface rendering method. Browsing software of the MRIs, segmented images, and 3D images was composed. This educational tool that includes horizontal, coronal, sagittal MRIs of entire body, corresponding segmented images, 3D images, and browsing software is expected to help medical students and doctors study anatomical structures in MRIs.

  11. RGB-D SLAM Based on Extended Bundle Adjustment with 2D and 3D Information

    PubMed Central

    Di, Kaichang; Zhao, Qiang; Wan, Wenhui; Wang, Yexin; Gao, Yunjun

    2016-01-01

    In the study of SLAM problem using an RGB-D camera, depth information and visual information as two types of primary measurement data are rarely tightly coupled during refinement of camera pose estimation. In this paper, a new method of RGB-D camera SLAM is proposed based on extended bundle adjustment with integrated 2D and 3D information on the basis of a new projection model. First, the geometric relationship between the image plane coordinates and the depth values is constructed through RGB-D camera calibration. Then, 2D and 3D feature points are automatically extracted and matched between consecutive frames to build a continuous image network. Finally, extended bundle adjustment based on the new projection model, which takes both image and depth measurements into consideration, is applied to the image network for high-precision pose estimation. Field experiments show that the proposed method has a notably better performance than the traditional method, and the experimental results demonstrate the effectiveness of the proposed method in improving localization accuracy. PMID:27529256

  12. ROI-preserving 3D video compression method utilizing depth information

    NASA Astrophysics Data System (ADS)

    Ti, Chunli; Xu, Guodong; Guan, Yudong; Teng, Yidan

    2015-09-01

    Efficiently transmitting the extra information of three dimensional (3D) video is becoming a key issue of the development of 3DTV. 2D plus depth format not only occupies the smaller bandwidth and is compatible transmission under the condition of the existing channel, but also can provide technique support for advanced 3D video compression in some extend. This paper proposes an ROI-preserving compression scheme to further improve the visual quality at a limited bit rate. According to the connection between the focus of Human Visual System (HVS) and depth information, region of interest (ROI) can be automatically selected via depth map progressing. The main improvement from common method is that a meanshift based segmentation is executed to the depth map before foreground ROI selection to keep the integrity of scene. Besides, the sensitive areas along the edges are also protected. The Spatio-temporal filtering adapting to H.264 is used to the non-ROI of both 2D video and depth map before compression. Experiments indicate that, the ROI extracted by this method is more undamaged and according with subjective feeling, and the proposed method can keep the key high-frequency information more effectively while the bit rate is reduced.

  13. Seismic source inversion using Green's reciprocity and a 3-D structural model for the Japanese Islands

    NASA Astrophysics Data System (ADS)

    Simutė, S.; Fichtner, A.

    2015-12-01

    We present a feasibility study for seismic source inversions using a 3-D velocity model for the Japanese Islands. The approach involves numerically calculating 3-D Green's tensors, which is made efficient by exploiting Green's reciprocity. The rationale for 3-D seismic source inversion has several aspects. For structurally complex regions, such as the Japan area, it is necessary to account for 3-D Earth heterogeneities to prevent unknown structure polluting source solutions. In addition, earthquake source characterisation can serve as a means to delineate existing faults. Source parameters obtained for more realistic Earth models can then facilitate improvements in seismic tomography and early warning systems, which are particularly important for seismically active areas, such as Japan. We have created a database of numerically computed 3-D Green's reciprocals for a 40°× 40°× 600 km size area around the Japanese Archipelago for >150 broadband stations. For this we used a regional 3-D velocity model, recently obtained from full waveform inversion. The model includes attenuation and radial anisotropy and explains seismic waveform data for periods between 10 - 80 s generally well. The aim is to perform source inversions using the database of 3-D Green's tensors. As preliminary steps, we present initial concepts to address issues that are at the basis of our approach. We first investigate to which extent Green's reciprocity works in a discrete domain. Considering substantial amounts of computed Green's tensors we address storage requirements and file formatting. We discuss the importance of the initial source model, as an intelligent choice can substantially reduce the search volume. Possibilities to perform a Bayesian inversion and ways to move to finite source inversion are also explored.

  14. Advanced resin systems and 3D textile preforms for low cost composite structures

    NASA Technical Reports Server (NTRS)

    Shukla, J. G.; Bayha, T. D.

    1993-01-01

    Advanced resin systems and 3D textile preforms are being evaluated at Lockheed Aeronautical Systems Company (LASC) under NASA's Advanced Composites Technology (ACT) Program. This work is aimed towards the development of low-cost, damage-tolerant composite fuselage structures. Resin systems for resin transfer molding and powder epoxy towpreg materials are being evaluated for processability, performance and cost. Three developmental epoxy resin systems for resin transfer molding (RTM) and three resin systems for powder towpregging are being investigated. Various 3D textile preform architectures using advanced weaving and braiding processes are also being evaluated. Trials are being conducted with powdered towpreg, in 2D weaving and 3D braiding processes for their textile processability and their potential for fabrication in 'net shape' fuselage structures. The progress in advanced resin screening and textile preform development is reviewed here.

  15. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression

    PubMed Central

    Jacob, J. Augustin; Kumar, N. Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation. PMID:26601120

  16. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression.

    PubMed

    Jacob, J Augustin; Kumar, N Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation.

  17. 3D watershed-based segmentation of internal structures within MR brain images

    NASA Astrophysics Data System (ADS)

    Bueno, Gloria; Musse, Olivier; Heitz, Fabrice; Armspach, Jean-Paul

    2000-06-01

    In this paper an image-based method founded on mathematical morphology is presented in order to facilitate the segmentation of cerebral structures on 3D magnetic resonance images (MRIs). The segmentation is described as an immersion simulation, applied to the modified gradient image, modeled by a generated 3D region adjacency graph (RAG). The segmentation relies on two main processes: homotopy modification and contour decision. The first one is achieved by a marker extraction stage where homogeneous 3D regions are identified in order to attribute an influence zone only to relevant minima of the image. This stage uses contrasted regions from morphological reconstruction and labeled flat regions constrained by the RAG. The goal of the decision stage is to precisely locate the contours of regions detected by the marker extraction. This decision is performed by a 3D extension of the watershed transform. Upon completion of the segmentation, the outcome of the preceding process is presented to the user for manual selection of the structures of interest (SOI). Results of this approach are described and illustrated with examples of segmented 3D MRIs of the human head.

  18. 3D shape shearography with integrated structured light projection for strain inspection of curved objects

    NASA Astrophysics Data System (ADS)

    Anisimov, Andrei G.; Groves, Roger M.

    2015-05-01

    Shearography (speckle pattern shearing interferometry) is a non-destructive testing technique that provides full-field surface strain characterization. Although real-life objects especially in aerospace, transport or cultural heritage are not flat (e.g. aircraft leading edges or sculptures), their inspection with shearography is of interest for both hidden defect detection and material characterization. Accurate strain measuring of a highly curved or free form surface needs to be performed by combining inline object shape measuring and processing of shearography data in 3D. Previous research has not provided a general solution. This research is devoted to the practical questions of 3D shape shearography system development for surface strain characterization of curved objects. The complete procedure of calibration and data processing of a 3D shape shearography system with integrated structured light projector is presented. This includes an estimation of the actual shear distance and a sensitivity matrix correction within the system field of view. For the experimental part a 3D shape shearography system prototype was developed. It employs three spatially-distributed shearing cameras, with Michelson interferometers acting as the shearing devices, one illumination laser source and a structured light projector. The developed system performance was evaluated with a previously reported cylinder specimen (length 400 mm, external diameter 190 mmm) loaded by internal pressure. Further steps for the 3D shape shearography prototype and the technique development are also proposed.

  19. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGES

    Zhang, Xing; Zhang, Lei; Tong, Huimin; ...

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, wemore » derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.« less

  20. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    SciTech Connect

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.

  1. Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions

    PubMed Central

    Shi, Ya-Zhou; Jin, Lei; Wang, Feng-Hua; Zhu, Xiao-Long; Tan, Zhi-Jie

    2015-01-01

    A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility, and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a three-bead coarse-grained predictive model with implicit salt/solvent potentials. In this study, we further develop the model by improving the implicit-salt electrostatic potential and including a sequence-dependent coaxial stacking potential to enable the model to simulate RNA 3D structure folding in divalent/monovalent ion solutions. The model presented here can predict 3D structures of RNA hairpins with bulges/internal loops (<77 nucleotides) from their sequences at the corresponding experimental ion conditions with an overall improved accuracy compared to the experimental data; the model also makes reliable predictions for the flexibility of RNA hairpins with bulge loops of different lengths at several divalent/monovalent ion conditions. In addition, the model successfully predicts the stability of RNA hairpins with various loops/stems in divalent/monovalent ion solutions. PMID:26682822

  2. Neurally and ocularly informed graph-based models for searching 3D environments

    NASA Astrophysics Data System (ADS)

    Jangraw, David C.; Wang, Jun; Lance, Brent J.; Chang, Shih-Fu; Sajda, Paul

    2014-08-01

    Objective. As we move through an environment, we are constantly making assessments, judgments and decisions about the things we encounter. Some are acted upon immediately, but many more become mental notes or fleeting impressions—our implicit ‘labeling’ of the world. In this paper, we use physiological correlates of this labeling to construct a hybrid brain-computer interface (hBCI) system for efficient navigation of a 3D environment. Approach. First, we record electroencephalographic (EEG), saccadic and pupillary data from subjects as they move through a small part of a 3D virtual city under free-viewing conditions. Using machine learning, we integrate the neural and ocular signals evoked by the objects they encounter to infer which ones are of subjective interest to them. These inferred labels are propagated through a large computer vision graph of objects in the city, using semi-supervised learning to identify other, unseen objects that are visually similar to the labeled ones. Finally, the system plots an efficient route to help the subjects visit the ‘similar’ objects it identifies. Main results. We show that by exploiting the subjects’ implicit labeling to find objects of interest instead of exploring naively, the median search precision is increased from 25% to 97%, and the median subject need only travel 40% of the distance to see 84% of the objects of interest. We also find that the neural and ocular signals contribute in a complementary fashion to the classifiers’ inference of subjects’ implicit labeling. Significance. In summary, we show that neural and ocular signals reflecting subjective assessment of objects in a 3D environment can be used to inform a graph-based learning model of that environment, resulting in an hBCI system that improves navigation and information delivery specific to the user’s interests.

  3. Verification of 3d Building Models Using Mutual Information in Airborne Oblique Images

    NASA Astrophysics Data System (ADS)

    Nyaruhuma, A. P.; Gerke, M.; Vosselman, G.

    2012-07-01

    This paper describes a method for automatic verification of 3D building models using airborne oblique images. The problem being tackled is identifying buildings that are demolished or changed since the models were constructed or identifying wrong models using the images. The models verified are of CityGML LOD2 or higher since their edges are expected to coincide with actual building edges. The verification approach is based on information theory. Corresponding variables between building models and oblique images are used for deriving mutual information for individual edges, faces or whole buildings, and combined for all perspective images available for the building. The wireframe model edges are projected to images and verified using low level image features - the image pixel gradient directions. A building part is only checked against images in which it may be visible. The method has been tested with models constructed using laser points against Pictometry images that are available for most cities of Europe and may be publically viewed in the so called Birds Eye view of the Microsoft Bing Maps. Results are that nearly all buildings are correctly categorised as existing or demolished. Because we now concentrate only on roofs we also used the method to test and compare results from nadir images. This comparison made clear that especially height errors in models can be more reliably detected in oblique images because of the tilted view. Besides overall building verification, results per individual edges can be used for improving the 3D building models.

  4. Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling.

    PubMed

    Meier, Armin; Söding, Johannes

    2015-10-01

    Homology modeling predicts the 3D structure of a query protein based on the sequence alignment with one or more template proteins of known structure. Its great importance for biological research is owed to its speed, simplicity, reliability and wide applicability, covering more than half of the residues in protein sequence space. Although multiple templates have been shown to generally increase model quality over single templates, the information from multiple templates has so far been combined using empirically motivated, heuristic approaches. We present here a rigorous statistical framework for multi-template homology modeling. First, we find that the query proteins' atomic distance restraints can be accurately described by two-component Gaussian mixtures. This insight allowed us to apply the standard laws of probability theory to combine restraints from multiple templates. Second, we derive theoretically optimal weights to correct for the redundancy among related templates. Third, a heuristic template selection strategy is proposed. We improve the average GDT-ha model quality score by 11% over single template modeling and by 6.5% over a conventional multi-template approach on a set of 1000 query proteins. Robustness with respect to wrong constraints is likewise improved. We have integrated our multi-template modeling approach with the popular MODELLER homology modeling software in our free HHpred server http://toolkit.tuebingen.mpg.de/hhpred and also offer open source software for running MODELLER with the new restraints at https://bitbucket.org/soedinglab/hh-suite.

  5. Proteopedia: A Collaborative, Virtual 3D Web-Resource for Protein and Biomolecule Structure and Function

    ERIC Educational Resources Information Center

    Hodis, Eran; Prilusky, Jaime, Sussman, Joel L.

    2010-01-01

    Protein structures are hard to represent on paper. They are large, complex, and three-dimensional (3D)--four-dimensional if conformational changes count! Unlike most of their substrates, which can easily be drawn out in full chemical formula, drawing every atom in a protein would usually be a mess. Simplifications like showing only the surface of…

  6. Graphene originated 3D structures grown on the assembled nickel particles

    NASA Astrophysics Data System (ADS)

    Paronyan, Tereza; Harutyunyan, Avetik; Honda Research Institute USA Inc. Team

    2013-03-01

    Recently, the fabrication of various morphologies of graphene originated structures became very important due to the perspective of wide range of new applications. Particularly, free standing 3D structured graphene foams could be imperative in energy related areas . Here, we present the new approach of the CVD growth of 3D graphene network by using primarily sintered Ni particle's (~40 μm size) assembles as a template-catalyst via decomposition of low rate of CH4 at 1100° C based on synthesis method described earlier. SEM and Raman spectra analysis revealed the formation of graphene structure containing a single up to few layers grown on the sintered metal particles served as a catalyst-template. After etching the metal frame without using any support polymer, 3D free-standing graphene microporous structure was formed demonstrating high BET surface area. Two probe measurements of frame resistance were ~2-8 Ω. Our approach allows controllable tune the pore size and thereby the surface area of 3D graphene network through the variation of the template-catalyst particles size.

  7. Ion Beam Etching: Replication of Micro Nano-structured 3D Stencil Masks

    SciTech Connect

    Weber, Patrick; Guibert, Edouard; Mikhailov, Serguei; Bruegger, Juergen; Villanueva, Guillermo

    2009-03-10

    Ion beam LIGA allows the etching of 3D nano-structures by direct writing with a nano-sized beam. However, this is a relatively time consuming process. We propose here another approach for etching structures on large surfaces and faster, compared to the direct writing process. This approach consists of replicating 3D structured masks, by scanning an unfocused ion beam. A polymer substrate is placed behind the mask, as in UV photolithography. But the main advantage is that the 3D structure of the mask can be replicated into the polymer. For that purpose, the masks (developped at LMIS1, EPFL) are made of a silicon nitride membrane 100 nm thick, on which 3D gold structures up to 200 nm thick, are deposited. The 3D Au structures are made with the nanostencil method, based on successive gold deposition. The IMA institute, from HE-Arc, owns a High Voltage Engineering 1.7 MV Tandetron with both solid and gaseous negative ion sources, able to generate ions from almost every chemical element in a broad range of energies comprised between 400 keV and 6.8 MeV. The beam composition and energy are chosen in such a way, that ions lose a significant fraction of their energy when passing through the thickest regions of the mask. Ions passing through thinner regions of the mask loose a smaller fraction of their energy and etch the polymer with larger thicknesses, allowing a replication of the mask into the polymer. For our trials, we have used a carbon beam with an energy of 500 keV. The beam was focussed to a diameter of 5 mm with solid slits, in order to avoid border effects and thus ensure a homogeneous dose distribution on the beam diameter. The feasibility of this technique has been demonstrated, allowing industrial applications for micro-mould fabrication, micro-fluidics and micro-optics.

  8. Analysis of the variation in OCT measurements of a structural bottle neck for eye-brain transfer of visual information from 3D-volumes of the optic nerve head, PIMD-Average [02π

    NASA Astrophysics Data System (ADS)

    Söderberg, Per G.; Malmberg, Filip; Sandberg-Melin, Camilla

    2016-03-01

    The present study aimed to analyze the clinical usefulness of the thinnest cross section of the nerve fibers in the optic nerve head averaged over the circumference of the optic nerve head. 3D volumes of the optic nerve head of the same eye was captured at two different visits spaced in time by 1-4 weeks, in 13 subjects diagnosed with early to moderate glaucoma. At each visit 3 volumes containing the optic nerve head were captured independently with a Topcon OCT- 2000 system. In each volume, the average shortest distance between the inner surface of the retina and the central limit of the pigment epithelium around the optic nerve head circumference, PIMD-Average [02π], was determined semiautomatically. The measurements were analyzed with an analysis of variance for estimation of the variance components for subjects, visits, volumes and semi-automatic measurements of PIMD-Average [0;2π]. It was found that the variance for subjects was on the order of five times the variance for visits, and the variance for visits was on the order of 5 times higher than the variance for volumes. The variance for semi-automatic measurements of PIMD-Average [02π] was 3 orders of magnitude lower than the variance for volumes. A 95 % confidence interval for mean PIMD-Average [02π] was estimated to 1.00 +/-0.13 mm (D.f. = 12). The variance estimates indicate that PIMD-Average [02π] is not suitable for comparison between a onetime estimate in a subject and a population reference interval. Cross-sectional independent group comparisons of PIMD-Average [02π] averaged over subjects will require inconveniently large sample sizes. However, cross-sectional independent group comparison of averages of within subject difference between baseline and follow-up can be made with reasonable sample sizes. Assuming a loss rate of 0.1 PIMD-Average [02π] per year and 4 visits per year it was found that approximately 18 months follow up is required before a significant change of PIMDAverage [02π] can

  9. Non-contact 3D fingerprint scanner using structured light illumination

    NASA Astrophysics Data System (ADS)

    Troy, Mike; Hassebrook, Laurence; Yalla, Veeraganesh; Daley, Raymond

    2011-03-01

    As crime prevention and national security remain a top priority, requirements for the use of fingerprints for identification continue to grow. While the size of fingerprint databases continues to expand, new technologies that can improve accuracy and ultimately matching performance will become more critical to maintain the effectiveness of the systems. FlashScan3D has developed non-contact, fingerprint scanners based on the principles of Structured Light Illumination (SLI) that capture 3Dimensional data of fingerprints quickly, accurately and independently of an operator. FlashScan3D will present findings from various research projects performed for the US Army and the Department of Homeland Security.

  10. A Patterned 3D Silicon Anode Fabricated by Electrodeposition on a Virus-Structured Current Collector

    SciTech Connect

    Chen, X L; Gerasopoulos, K; Guo, J C; Brown, A; Wang, Chunsheng; Ghodssi, Reza; Culver, J N

    2010-11-09

    Electrochemical methods were developed for the deposition of nanosilicon onto a 3D virus-structured nickel current collector. This nickel current collector is composed of self-assembled nanowire-like rods of genetically modified tobacco mosaic virus (TMV1cys), chemically coated in nickel to create a complex high surface area conductive substrate. The electrochemically depo­sited 3D silicon anodes demonstrate outstanding rate performance, cycling stability, and rate capability. Electrodeposition thus provides a unique means of fabricating silicon anode materials on complex substrates at low cost.

  11. Studies of the 3D Structure of the Nucleon at Jlab

    SciTech Connect

    Avakian, Harut

    2016-07-01

    Studies of the 3D structure of the nucleon encoded in Transverse Momentum Dependent distribution and fragmentation functions of partons and Generalized Parton Distributions are among the key objectives of the JLab 12 GeV upgrade and the Electron Ion Collider. Main challenges in extracting 3D partonic distributions from precision measurements of hard scattering processes include clear understanding of leading twist QCD fundamentals, higher twist effects, and also correlations of hadron production in target and current fragmentation regions. In this contribution we discuss some ongoing studies and future measurements of spin-orbit correlations at Jefferson Lab.

  12. Prediction of spin-dependent electronic structure in 3d-transition-metal doped antimonene

    NASA Astrophysics Data System (ADS)

    Yang, L. F.; Song, Y.; Mi, W. B.; Wang, X. C.

    2016-07-01

    We investigate the geometric structure and electronic and magnetic properties of 3d-transition-metal atom doped antimonene using spin-polarized first-principles calculations. Strong orbital hybridization exhibits between 3d-transition-metal and Sb atoms, where covalent bonds form in antimonene. A spin-polarized semiconducting state appears in Cr-doped antimonene, while half-metallic states appear by doping Ti, V, and Mn. These findings indicate that once combined with doping states, the bands of antimonene systems offer a variety of features. Specific dopants lead to half-metallic characters with high spin polarization that has potential application in spintronics.

  13. Holographic particle velocimetry - A 3D measurement technique for vortex interactions, coherent structures and turbulence

    NASA Astrophysics Data System (ADS)

    Meng, Hui; Hussain, Fazle

    1991-10-01

    To understand the topology and dynamics of coherent structures (CS), the interactions of CS with fine-scale turbulence, and the effects of CS on entrainment, mixing and combustion, experimental tools are needed that can measure velocity (preferably vorticity) vector fields in both 3D space and time. While traditional measurement techniques are not able to serve this purpose, holographic particle velocimetry (HPV) appears to be promising. In a demonstration experiment, the instantaneous 3D velocity vector fields in some simple vortical flows have been obtained using the HPV technique. In this preliminary report, the principles of the HPV technique are illustrated and the key issues in its implementation are discussed.

  14. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells.

    PubMed

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L; Han, Jessica H; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H; Bussey, Kimberly J; Meldrum, Deirdre R

    2016-08-09

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an 'epigenetic' drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat's differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action.

  15. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells

    PubMed Central

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L.; Han, Jessica H.; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H.; Bussey, Kimberly J.; Meldrum, Deirdre R.

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an ‘epigenetic’ drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat’s differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  16. Recursive estimation of 3D motion and surface structure from local affine flow parameters.

    PubMed

    Calway, Andrew

    2005-04-01

    A recursive structure from motion algorithm based on optical flow measurements taken from an image sequence is described. It provides estimates of surface normals in addition to 3D motion and depth. The measurements are affine motion parameters which approximate the local flow fields associated with near-planar surface patches in the scene. These are integrated over time to give estimates of the 3D parameters using an extended Kalman filter. This also estimates the camera focal length and, so, the 3D estimates are metric. The use of parametric measurements means that the algorithm is computationally less demanding than previous optical flow approaches and the recursive filter builds in a degree of noise robustness. Results of experiments on synthetic and real image sequences demonstrate that the algorithm performs well.

  17. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures

    PubMed Central

    Zenou, M.; Sa’ar, A.; Kotler, Z.

    2015-01-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures. PMID:26602432

  18. 3D electrical structure of porphyry copper deposit: A case study of Shaxi copper deposit

    NASA Astrophysics Data System (ADS)

    Chen, Xiang-Bin; Lü, Qing-Tian; Yan, Jia-Yong

    2012-06-01

    Located in Lu-Zong ore concentration area, middle-lower Yangtze metallogenic belt, ShaXi porphyry copper deposit is a typical hydrothermal deposit. To investigate the distribution of deep ore bodies and spatial characteristics of host structures, an AMT survey was conducted in mining area. Eighteen pseudo-2D resistivity sections were constructed through careful processing and inversion. These sections clearly show resistivity difference between the Silurian sandstones formation and quartz diorite porphyry and this porphyry copper formation was controlled by the highly resistive anticlines. Using 3D block Kriging interpolation method and 3D visualization techniques, we constructed a detailed 3D resistivity model of quartz diorite porphyry which shows the shape and spatial distribution of deep ore bodies. This case study can serve as a good example for future ore prospecting in and around this mining area.

  19. 3D shape measurement of shoeprint impression with structured illumination and fringe pattern analysis

    NASA Astrophysics Data System (ADS)

    Su, Xianyu; Cao, Yiping; Xiang, Liqun; Chen, Wenjing

    2002-06-01

    The shoeprint impressions of suspect left at the crime scene can sometimes tell investigators what type of shoes to be looked for. These shoeprint impressions as one of the important evidence are useful in the detection of criminals. In this paper we propose a novel technique for identifying and analyzing the 3D characteristics of shoeprint impressions. We also design 3D shoeprint impression analysis system based on the combination the 3D shape measurement with structured illumination and fringe pattern analysis. We give a detail discussion on the principle and configuration of the system. Laboratory experiments show the technique is efficient in the detection of shoeprint and in the offering the reference for judicial evidence.

  20. 3D printed low-loss THz waveguide based on Kagome photonic crystal structure.

    PubMed

    Yang, Jing; Zhao, Jiayu; Gong, Cheng; Tian, Haolin; Sun, Lu; Chen, Ping; Lin, Lie; Liu, Weiwei

    2016-10-03

    A low-loss hollow core terahertz waveguide based on Kagome photonic crystal structure has been designed and fabricated by 3D printing. The 3D printed waveguide has been characterized by using THz time-domain spectroscopy. The results demonstrate that the obtained waveguide features average power propagation loss of 0.02 cm-1 for 0.2-1.0 THz (the minimum is about 0.002 cm-1 at 0.75 THz). More interesting, it could be simply mechanically spliced without any additional alignment, while maintaining the excellent performance. The 3D printing technique will be a promising solution to fabricate Kagome THz waveguide with well controllable characteristics and low cost.

  1. Human Sinoatrial Node Structure: 3D Microanatomy of Sinoatrial Conduction Pathways

    PubMed Central

    Csepe, Thomas A.; Zhao, Jichao; Hansen, Brian J.; Li, Ning; Sul, Lidiya V.; Lim, Praise; Wang, Yufeng; Simonetti, Orlando P.; Kilic, Ahmet; Mohler, Peter J.; Janssen, Paul ML.; Fedorov, Vadim V.

    2016-01-01

    Introduction Despite a century of extensive study on the human sinoatrial node (SAN), the structure-to-function features of specialized SAN conduction pathways (SACP) are still unknown and debated. We report a new method for direct analysis of the SAN microstructure in optically-mapped human hearts with and without clinical history of SAN dysfunction. Methods Two explanted donor human hearts were coronary-perfused and optically-mapped. Structural analyses of histological sections parallel to epicardium (~13-21μm intervals) were integrated with optical maps to create 3D computational reconstructions of the SAN complex. High-resolution fiber fields were obtained using 3D Eigen-analysis of the structure tensor, and used to analyze SACP microstructure with a fiber-tracking approach. Results Optical mapping revealed normal SAN activation of the atria through a lateral SACP proximal to the crista terminalis in Heart #1 but persistent SAN exit block in diseased Heart #2. 3D structural analysis displayed a functionally-observed SAN border composed of fibrosis, fat, and/or discontinuous fibers between SAN and atria, which was only crossed by several branching myofiber tracts in SACP regions. Computational 3D fiber-tracking revealed that myofiber tracts of SACPs created continuous connections between SAN #1 and atria, but in SAN #2, SACP region myofiber tracts were discontinuous due to fibrosis and fat. Conclusions We developed a new integrative functional, structural and computational approach that allowed for the resolution of the specialized 3D microstructure of human SACPs for the first time. Application of this integrated approach will shed new light on the role of the specialized SAN microanatomy in maintaining sinus rhythm. PMID:26743207

  2. Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity.

    PubMed

    Lee, Karen J I; Calder, Grant M; Hindle, Christopher R; Newman, Jacob L; Robinson, Simon N; Avondo, Jerome J H Y; Coen, Enrico S

    2016-12-26

    Optical projection tomography (OPT) is a well-established method for visualising gene activity in plants and animals. However, a limitation of conventional OPT is that the specimen upper size limit precludes its application to larger structures. To address this problem we constructed a macro version called Macro OPT (M-OPT). We apply M-OPT to 3D live imaging of gene activity in growing whole plants and to visualise structural morphology in large optically cleared plant and insect specimens up to 60 mm tall and 45 mm deep. We also show how M-OPT can be used to image gene expression domains in 3D within fixed tissue and to visualise gene activity in 3D in clones of growing young whole Arabidopsis plants. A further application of M-OPT is to visualise plant-insect interactions. Thus M-OPT provides an effective 3D imaging platform that allows the study of gene activity, internal plant structures and plant-insect interactions at a macroscopic scale.

  3. Modeling and characterization of 2-D and 3-D textile structural composites

    SciTech Connect

    Yang, J.M.

    1986-01-01

    This dissertation studies the analytical modeling and experimental characterization of various two-dimensional and three-dimensional textile structure composites. In the analytical approach, various theoretical models were established to predict the stiffness, strength, nonlinear deformation, and failure behavior of triaxial woven-fabric composites, 3-D braided composites, and multilayer multidirectional warp knit fabric composites in polymer and metal matrices. The structure performance maps of various textile structural composites were also established, based upon these analytical methods. In the experimental approach, extensive mechanical testing and microstructural characterization were performed to investigate the thermomechanical properties and failure behavior of 3-D braided FP/Al composites. Results of this research will serve as the basis for assessing the potential of textile composites for structural applications.

  4. Parametric estimation of 3D tubular structures for diffuse optical tomography

    PubMed Central

    Larusson, Fridrik; Anderson, Pamela G.; Rosenberg, Elizabeth; Kilmer, Misha E.; Sassaroli, Angelo; Fantini, Sergio; Miller, Eric L.

    2013-01-01

    We explore the use of diffuse optical tomography (DOT) for the recovery of 3D tubular shapes representing vascular structures in breast tissue. Using a parametric level set method (PaLS) our method incorporates the connectedness of vascular structures in breast tissue to reconstruct shape and absorption values from severely limited data sets. The approach is based on a decomposition of the unknown structure into a series of two dimensional slices. Using a simplified physical model that ignores 3D effects of the complete structure, we develop a novel inter-slice regularization strategy to obtain global regularity. We report on simulated and experimental reconstructions using realistic optical contrasts where our method provides a more accurate estimate compared to an unregularized approach and a pixel based reconstruction. PMID:23411913

  5. Cryo-EM structure of a 3D DNA-origami object

    PubMed Central

    Bai, Xiao-chen; Martin, Thomas G.; Scheres, Sjors H. W.; Dietz, Hendrik

    2012-01-01

    A key goal for nanotechnology is to design synthetic objects that may ultimately achieve functionalities known today only from natural macromolecular complexes. Molecular self-assembly with DNA has shown potential for creating user-defined 3D scaffolds, but the level of attainable positional accuracy has been unclear. Here we report the cryo-EM structure and a full pseudoatomic model of a discrete DNA object that is almost twice the size of a prokaryotic ribosome. The structure provides a variety of stable, previously undescribed DNA topologies for future use in nanotechnology and experimental evidence that discrete 3D DNA scaffolds allow the positioning of user-defined structural motifs with an accuracy that is similar to that observed in natural macromolecules. Thereby, our results indicate an attractive route to fabricate nanoscale devices that achieve complex functionalities by DNA-templated design steered by structural feedback. PMID:23169645

  6. Parametric estimation of 3D tubular structures for diffuse optical tomography.

    PubMed

    Larusson, Fridrik; Anderson, Pamela G; Rosenberg, Elizabeth; Kilmer, Misha E; Sassaroli, Angelo; Fantini, Sergio; Miller, Eric L

    2013-02-01

    We explore the use of diffuse optical tomography (DOT) for the recovery of 3D tubular shapes representing vascular structures in breast tissue. Using a parametric level set method (PaLS) our method incorporates the connectedness of vascular structures in breast tissue to reconstruct shape and absorption values from severely limited data sets. The approach is based on a decomposition of the unknown structure into a series of two dimensional slices. Using a simplified physical model that ignores 3D effects of the complete structure, we develop a novel inter-slice regularization strategy to obtain global regularity. We report on simulated and experimental reconstructions using realistic optical contrasts where our method provides a more accurate estimate compared to an unregularized approach and a pixel based reconstruction.

  7. An Interdisciplinary Conservation Module for Condition Survey on Cultural Heritages with a 3d Information System

    NASA Astrophysics Data System (ADS)

    Pedelì, C.

    2013-07-01

    In order to make the most of the digital outsourced documents, based on new technologies (e.g.: 3D LASER scanners, photogrammetry, etc.), a new approach was followed and a new ad hoc information system was implemented. The obtained product allow to the final user to reuse and manage the digital documents providing graphic tools and an integrated specific database to manage the entire documentation and conservation process, starting from the condition assessment until the conservation / restoration work. The system is organised on two main modules: Archaeology and Conservation. This paper focus on the features and the advantages of the second one. In particular it is emphasized its logical organisation, the possibility to easily mapping by using a very precise 3D metric platform, to benefit of the integrated relational database which allows to well organise, compare, keep and manage different kind of information at different level. Conservation module can manage along the time the conservation process of a site, monuments, object or excavation and conservation work in progress. An alternative approach called OVO by the author of this paper, force the surveyor to observe and describe the entity decomposing it on functional components, materials and construction techniques. Some integrated tools as the "ICOMOS-ISCS Illustrated glossary … " help the user to describe pathologies with a unified approach and terminology. Also the conservation project phase is strongly supported to envision future intervention and cost. A final section is devoted to record the conservation/restoration work already done or in progress. All information areas of the conservation module are interconnected to each other to allows to the system a complete interchange of graphic and alphanumeric data. The conservation module it self is connected to the archaeological one to create an interdisciplinary daily tool.

  8. Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D

    PubMed Central

    Fabris, Daniele; Yu, Eizadora T.

    2010-01-01

    Chemical probing represents a very versatile alternative for studying the structure and dynamics of substrates that are intractable by established high-resolution techniques. The implementation of MS-based strategies for the characterization of probing products has not only extended the range of applicability to virtually all types of biopolymers, but has also paved the way for the introduction of new reagents that would not have been viable with traditional analytical platforms. As the availability of probing data is steadily increasing on the wings of the development of dedicated interpretation aids, powerful computational approaches have been explored to enable the effective utilization of such information to generate valid molecular models. This combination of factors has contributed to making the possibility of obtaining actual 3D structures by MS-based technologies (MS3D) a reality. Although approaches for achieving structure determination of unknown substrates or assessing the dynamics of known structures may share similar reagents and development trajectories, they clearly involve distinctive experimental strategies, analytical concerns, and interpretation paradigms. This Perspective offers a commentary on methods aimed at obtaining distance constraints for the modeling of full-fledged structures, while highlighting common elements, salient distinctions, and complementary capabilities exhibited by methods employed in dynamics studies. We discuss critical factors to be addressed for completing effective structural determinations and expose possible pitfalls of chemical methods. We survey programs developed for facilitating the interpretation of experimental data and discuss possible computational strategies for translating sparse spatial constraints into all-atom models. Examples are provided to illustrate how the concerted application of very diverse probing techniques can lead to the solution of actual biological substrates. PMID:20648672

  9. 3D scanning of internal structure in gel engineering materials with visual scanning microscopic light scattering

    NASA Astrophysics Data System (ADS)

    Watanabe, Yosuke; Gong, Jing; Masato, Makino; Kabir, M. Hasnat; Furukawa, Hidemitsu

    2014-04-01

    The 3D printing technology, causing much attention from the beginning of 2013, will be possibly an alternative method to fabricate the biological soft tissues. Recently our group of Yamagata University has developed the world-first 3D Gel Printer to fabricate the complicated gel-materials with high-strength and biocompatibility. However, there are no 3D scanners that collect the data from the internal structure of complicated gel objects such as eye lens. It means that a new system for scanning the internal structure is needed now. In this study, firstly, we have tried to investigate the gel network of synthetic and biological gel with scanning microscopic light scattering (SMILS). We calculated the Young's modulus of synthetic gels with the SMILS and with the tensile test, and precisely compared the results between them. The temperature dependences of the inside structure and the transparency are observed in the pig crystalline lens. The quantitative analysis indicates the importance of the internal structure of real object. Secondary, we show the new system named Gel-scanner that can provide the 2-dimentional data of the internal structure. From examining our findings, the scanning of internal structure will enable us to expect physical properties of the real object. We convince that the gelscanner will play major role in the various fields.

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

    PubMed

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

    2017-02-23

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

  11. Novel 3D bismuth-based coordination polymers: Synthesis, structure, and second harmonic generation properties

    NASA Astrophysics Data System (ADS)

    Wibowo, Arief C.; Smith, Mark D.; Yeon, Jeongho; Halasyamani, P. Shiv; zur Loye, Hans-Conrad

    2012-11-01

    Two new 3D bismuth containing coordination polymers are reported along with their single crystal structures and SHG properties. Compound 1: Bi2O2(pydc) (pydc=pyridine-2, 5-dicarboxylate), crystallizes in the monoclinic, polar space group, P21 (a=9.6479(9) Å, b=4.2349(4) Å, c=11.9615(11) Å, β=109.587(1)°), which contains Bi2O2 chains that are connected into a 3D structure via the pydc ligands. Compound 2: Bi4Na4(1R3S-cam)8(EtOH)3.1(H2O)3.4 (1R3S cam=1R3S-camphoric acid) crystallizes in the monoclinic, polar space group, P21 (a=19.0855(7) Å, b=13.7706(5) Å, c=19.2429(7) Å, β=90.701(1)°) and is a true 3D coordination polymer. These are two example of SHG compounds prepared using unsymmetric ligands (compound 1) or chiral ligands (compound 2), together with metals that often exhibit stereochemically-active lone pairs, such as Bi3+, a synthetic approach that resulted in polar, non-centrosymmetric, 3D metal-organic coordination polymer.

  12. Structural and functional imaging of 3D microfluidic mixers using optical coherence tomography.

    PubMed

    Xi, Chuanwu; Marks, Daniel L; Parikh, Devang S; Raskin, Lutgarde; Boppart, Stephen A

    2004-05-18

    To achieve high mixing efficiency in microfluidic devices, complex designs are often required. Microfluidic devices have been evaluated with light and confocal microscopy, but fluid-flow characteristics at different depths are difficult to separate from the en face images produced. By using optical coherence tomography (OCT), an imaging modality capable of imaging 3D microstructures at micrometer-scale resolutions over millimeter-size scales, we obtained 3D dynamic functional and structural data for three representative microfluidic mixers: a Y channel mixer, a 3D serpentine mixer, and a vortex mixer. In the serpentine mixer, OCT image analysis revealed that the mixing efficiency was linearly dependent on the Reynolds number, whereas it appeared to have exponential dependence when imaged with light microscopy. The visual overlap of fluid flows in light-microscopy images leads to an overestimation of the mixing efficiency, an effect that was eliminated with OCT imaging. Doppler OCT measurements determined velocity profiles at various points in the serpentine mixer. Mixing patterns in the vortex mixer were compared with light-microscopy and OCT image analysis. These results demonstrate that OCT can significantly improve the characterization of 3D microfluidic device structure and function.

  13. Generation of 3-D surface maps in waste storage silos using a structured light source

    NASA Technical Reports Server (NTRS)

    Burks, B. L.; Rowe, J. C.; Dinkins, M. A.; Christensen, B.; Selleck, C.; Jacoboski, D.; Markus, R.

    1992-01-01

    Surface contours inside the large waste storage tanks typical of the Department of Energy (DOE) complex are, in general, highly irregular. In addition to pipes and other pieces of equipment in the tanks, the surfaces may have features such as mounds, fissures, crystalline structures, and mixed solid and liquid forms. Prior to remediation activities, it will be necessary to characterize the waste to determine the most effective remediation approaches. Surface contour data will be required both prior to and during remediation. The use is described of a structured light source to generate 3-D surface contour maps of the interior of waste storage silos at the Feed Materials Production Center at Fernald, OH. The landscape inside these large waste storage tanks bears a strong resemblance to some of the landscapes that might be encountered during lunar or planetary exploration. Hence, these terrestrial 3-D mapping techniques may be directly applicable to extraterrestrial exploration. In further development, it will be demonstrated that these 3-D data can be used for robotic task planning just as 3-D surface contour data of a satellite could be used to plan maintenance tasks for a space-based servicing robot.

  14. Factors Affecting Dimensional Accuracy of 3-D Printed Anatomical Structures Derived from CT Data.

    PubMed

    Ogden, Kent M; Aslan, Can; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Soman, Pranav

    2015-12-01

    Additive manufacturing and bio-printing, with the potential for direct fabrication of complex patient-specific anatomies derived from medical scan data, are having an ever-increasing impact on the practice of medicine. Anatomic structures are typically derived from CT or MRI scans, and there are multiple steps in the model derivation process that influence the geometric accuracy of the printed constructs. In this work, we compare the dimensional accuracy of 3-D printed constructs of an L1 vertebra derived from CT data for an ex vivo cadaver T-L spine with the original vertebra. Processing of segmented structures using binary median filters and various surface extraction algorithms is evaluated for the effect on model dimensions. We investigate the effects of changing CT reconstruction kernels by scanning simple geometric objects and measuring the impact on the derived model dimensions. We also investigate if there are significant differences between physical and virtual model measurements. The 3-D models were printed using a commercial 3-D printer, the Replicator 2 (MakerBot, Brooklyn, NY) using polylactic acid (PLA) filament. We found that changing parameters during the scan reconstruction, segmentation, filtering, and surface extraction steps will have an effect on the dimensions of the final model. These effects need to be quantified for specific situations that rely on the accuracy of 3-D printed models used in medicine or tissue engineering applications.

  15. Optimal Image Stitching for Concrete Bridge Bottom Surfaces Aided by 3d Structure Lines

    NASA Astrophysics Data System (ADS)

    Liu, Yahui; Yao, Jian; Liu, Kang; Lu, Xiaohu; Xia, Menghan

    2016-06-01

    Crack detection for bridge bottom surfaces via remote sensing techniques is undergoing a revolution in the last few years. For such applications, a large amount of images, acquired with high-resolution industrial cameras close to the bottom surfaces with some mobile platform, are required to be stitched into a wide-view single composite image. The conventional idea of stitching a panorama with the affine model or the homographic model always suffers a series of serious problems due to poor texture and out-of-focus blurring introduced by depth of field. In this paper, we present a novel method to seamlessly stitch these images aided by 3D structure lines of bridge bottom surfaces, which are extracted from 3D camera data. First, we propose to initially align each image in geometry based on its rough position and orientation acquired with both a laser range finder (LRF) and a high-precision incremental encoder, and these images are divided into several groups with the rough position and orientation data. Secondly, the 3D structure lines of bridge bottom surfaces are extracted from the 3D cloud points acquired with 3D cameras, which impose additional strong constraints on geometrical alignment of structure lines in adjacent images to perform a position and orientation optimization in each group to increase the local consistency. Thirdly, a homographic refinement between groups is applied to increase the global consistency. Finally, we apply a multi-band blending algorithm to generate a large-view single composite image as seamlessly as possible, which greatly eliminates both the luminance differences and the color deviations between images and further conceals image parallax. Experimental results on a set of representative images acquired from real bridge bottom surfaces illustrate the superiority of our proposed approaches.

  16. Pipeline inwall 3D measurement system based on the cross structured light

    NASA Astrophysics Data System (ADS)

    Shen, Da; Lin, Zhipeng; Xue, Lei; Zheng, Qiang; Wang, Zichi

    2014-01-01

    In order to accurately realize the defect detection of pipeline inwall, this paper proposes a measurement system made up of cross structured light, single CCD camera and a smart car, etc. Based on structured light measurement technology, this paper mainly introduces the structured light measurement system, the imaging mathematical model, and the parameters and method of camera calibration. Using these measuring principles and methods, the camera in remote control car platform achieves continuous shooting of objects and real-time rebound processing as well as utilizing established model to extract 3D point cloud coordinate to reconstruct pipeline defects, so it is possible to achieve 3D automatic measuring, and verifies the correctness and feasibility of this system. It has been found that this system has great measurement accuracy in practice.

  17. Proteopedia: Exciting Advances in the 3D Encyclopedia of Biomolecular Structure

    NASA Astrophysics Data System (ADS)

    Prilusky, Jaime; Hodis, Eran; Sussman, Joel L.

    Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other structures. Proteopedia ( http://www.proteopedia.org ) presents 3D biomolecule structures in a broadly accessible manner to a diverse scientific audience through easy-to-use molecular visualization tools integrated into a wiki environment that anyone with a user account can edit. We describe recent advances in the web resource in the areas of content and software. In terms of content, we describe a large growth in user-added content as well as improvements in automatically-generated content for all PDB entry pages in the resource. In terms of software, we describe new features ranging from the capability to create pages hidden from public view to the capability to export pages for offline viewing. New software features also include an improved file-handling system and availability of biological assemblies of protein structures alongside their asymmetric units.

  18. The crystal structure of Aspergillus fumigatus cyclophilin reveals 3D domain swapping of a central element.

    PubMed

    Limacher, Andreas; Kloer, Daniel P; Flückiger, Sabine; Folkers, Gerd; Crameri, Reto; Scapozza, Leonardo

    2006-02-01

    The crystal structure of Aspergillus fumigatus cyclophilin (Asp f 11) was solved by the multiwavelength anomalous dispersion method and was refined to a resolution of 1.85 A with R and R(free) values of 18.9% and 21.4%, respectively. Many cyclophilin structures have been solved to date, all showing the same monomeric conformation. In contrast, the structure of A. fumigatus cyclophilin reveals dimerization by 3D domain swapping and represents one of the first proteins with a swapped central domain. The domain-swapped element consists of two beta strands and a subsequent loop carrying a conserved tryptophan. The tryptophan binds into the active site, inactivating cis-trans isomerization. This might be a means of biological regulation. The two hinge loops leave the protein prone to misfolding. In this context, alternative forms of 3D domain swapping that can lead to N- or C-terminally swapped dimers, oligomers, and aggregates are discussed.

  19. Band like Electronic Structures in Square Hollow Quantum Dots by 3D-MHFKS Calculation

    NASA Astrophysics Data System (ADS)

    Takizawa, Tokihiro; Okada, Hoshihito; Matsuse, Takehiro

    To find novel aspects of the electronic structures in quantum dots (QD) from a view point of spatial broken symmetry, 3-dimensional-mesh Hartree-Fock-Kohn-Sham (3D-MHFKS) calculations1 are applied to the interacting electron system of electron number N in a symmetry broken hollow QD. For the case of a square hollow quantum dot confined in square hard wall (HW) potential (SSHQD), the magnetic (B) field dependence of the obtained single particle energy levels and chemical potentials in B-N diagram are shown to have a band like electronic structures over the wide B-field range up to 20T. To clarify the origin of the band like electronic structures in SSHQD, 3D-MHFKS calculations are also applied for the mixed symmetry QD's with a circular hollow in square HW potential (SCHQD) and with a square hollow in circular HW potential (CSHQD).

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

    PubMed

    Zhang, Xiao-Long; Lin, Xiao-Li

    2010-09-01

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

  1. Oscillating optical tweezer-based 3-D confocal microrheometer for investigating the intracellular micromechanics and structures

    NASA Astrophysics Data System (ADS)

    Ou-Yang, H. D.; Rickter, E. A.; Pu, C.; Latinovic, O.; Kumar, A.; Mengistu, M.; Lowe-Krentz, L.; Chien, S.

    2005-08-01

    Mechanical properties of living biological cells are important for cells to maintain their shapes, support mechanical stresses and move through tissue matrix. The use of optical tweezers to measure micromechanical properties of cells has recently made significant progresses. This paper presents a new approach, the oscillating optical tweezer cytorheometer (OOTC), which takes advantage of the coherent detection of harmonically modulated particle motions by a lock-in amplifier to increase sensitivity, temporal resolution and simplicity. We demonstrate that OOTC can measure the dynamic mechanical modulus in the frequency range of 0.1-6,000 Hz at a rate as fast as 1 data point per second with submicron spatial resolution. More importantly, OOTC is capable of distinguishing the intrinsic non-random temporal variations from random fluctuations due to Brownian motion; this capability, not achievable by conventional approaches, is particular useful because living systems are highly dynamic and often exhibit non-thermal, rhythmic behavior in a broad time scale from a fraction of a second to hours or days. Although OOTC is effective in measuring the intracellular micromechanical properties, unless we can visualize the cytoskeleton in situ, the mechanical property data would only be as informative as that of "Blind men and the Elephant". To solve this problem, we take two steps, the first, to use of fluorescent imaging to identify the granular structures trapped by optical tweezers, and second, to integrate OOTC with 3-D confocal microscopy so we can take simultaneous, in situ measurements of the micromechanics and intracellular structure in living cells. In this paper, we discuss examples of applying the oscillating tweezer-based cytorheometer for investigating cultured bovine endothelial cells, the identification of caveolae as some of the granular structures in the cell as well as our approach to integrate optical tweezers with a spinning disk confocal microscope.

  2. ICARE-HS: atmospheric correction of airborne hyperspectral urban images using 3D information

    NASA Astrophysics Data System (ADS)

    Ceamanos, Xavier; Briottet, Xavier; Roussel, Guillaume; Gilardy, Hugo

    2016-10-01

    The algorithm ICARE-HS (Inversion Code for urban Areas Reflectance Extraction using HyperSpectral imagery) is presented in this paper. ICARE-HS processes airborne hyperspectral images for atmospheric compensation taking into account the strong relief of urban areas. A digital surface model is used to provide the 3D information, which is key to simulating relief-related effects such as shadow casting, multiple reflections between objects and variable illumination depending on local solid angle of view of the sky. Some of these effects are modeled using ray tracing techniques. ICARE-HS is applied to airborne hyperspectral data of the city center of Toulouse, which are also processed by a standard atmospheric correction method for comparison.

  3. Fabrication of 3D embedded hollow structures inside polymer dielectric PMMA with femtosecond laser

    NASA Astrophysics Data System (ADS)

    Zheng, Chong; Chen, Tao; Hu, Anming; Liu, Shibing; Li, Junwei

    2016-11-01

    Recent progresses in femtosecond laser (fs) manufacturing have already proved that fs laser is a powerful tool in three dimensional internal structure fabrications. However, most studies are mainly focused on realize such structures in inorganic transparent dielectric, such as photosensitive glass and fused silica, etc. In this study, we present two methods to fabricate embedded internal 3D structures in a polymer dielectric material polymethyl methacrylate (PMMA). Both continuous hollow structure such as microfluidic channels and discrete hollow structures such as single microcavities are successfully fabricated with the help of femtosecond lasers. Among them, complicated 3D microchannel with a total length longer than 10mm and diameters around 80μm to 200μm are fabricated with a low repetition rate Ti: sapphire femtosecond laser by direct laser writing at a speed ranging from 25μm/s to 2000μm/s microcavities which function as concave microball lenses (CMBLs) and can be applied in super-wide-angle imaging are fabricated with a high repetition rate femtosecond fiber laser due to the distinct heat accumulation effect after 5s irradiation with the tightly focused fs laser beam. These new approaches proved that femtosecond laser direct writing technology has great application potential in 3D integrated devices manufacturing in the future.

  4. Proteins without unique 3D structures: biotechnological applications of intrinsically unstable/disordered proteins.

    PubMed

    Uversky, Vladimir N

    2015-03-01

    Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are functional proteins or regions that do not have unique 3D structures under functional conditions. Therefore, from the viewpoint of their lack of stable 3D structure, IDPs/IDPRs are inherently unstable. As much as structure and function of normal ordered globular proteins are determined by their amino acid sequences, the lack of unique 3D structure in IDPs/IDPRs and their disorder-based functionality are also encoded in the amino acid sequences. Because of their specific sequence features and distinctive conformational behavior, these intrinsically unstable proteins or regions have several applications in biotechnology. This review introduces some of the most characteristic features of IDPs/IDPRs (such as peculiarities of amino acid sequences of these proteins and regions, their major structural features, and peculiar responses to changes in their environment) and describes how these features can be used in the biotechnology, for example for the proteome-wide analysis of the abundance of extended IDPs, for recombinant protein isolation and purification, as polypeptide nanoparticles for drug delivery, as solubilization tools, and as thermally sensitive carriers of active peptides and proteins.

  5. 3D Documentation and BIM Modeling of Cultural Heritage Structures Using UAVs: The Case of the Foinikaria Church

    NASA Astrophysics Data System (ADS)

    Themistocleous, K.; Agapiou, A.; Hadjimitsis, D.

    2016-10-01

    The documentation of architectural cultural heritage sites has traditionally been expensive and labor-intensive. New innovative technologies, such as Unmanned Aerial Vehicles (UAVs), provide an affordable, reliable and straightforward method of capturing cultural heritage sites, thereby providing a more efficient and sustainable approach to documentation of cultural heritage structures. In this study, hundreds of images of the Panagia Chryseleousa church in Foinikaria, Cyprus were taken using a UAV with an attached high resolution camera. The images were processed to generate an accurate digital 3D model by using Structure in Motion techniques. Building Information Model (BIM) was then used to generate drawings of the church. The methodology described in the paper provides an accurate, simple and cost-effective method of documenting cultural heritage sites and generating digital 3D models using novel techniques and innovative methods.

  6. 3D Printed Modeling of the Mitral Valve for Catheter-Based Structural Interventions.

    PubMed

    Vukicevic, Marija; Puperi, Daniel S; Jane Grande-Allen, K; Little, Stephen H

    2017-02-01

    As catheter-based structural heart interventions become increasingly complex, the ability to effectively model patient-specific valve geometry as well as the potential interaction of an implanted device within that geometry will become increasingly important. Our aim with this investigation was to combine the technologies of high-spatial resolution cardiac imaging, image processing software, and fused multi-material 3D printing, to demonstrate that patient-specific models of the mitral valve apparatus could be created to facilitate functional evaluation of novel trans-catheter mitral valve repair strategies. Clinical 3D transesophageal echocardiography and computed tomography images were acquired for three patients being evaluated for a catheter-based mitral valve repair. Target anatomies were identified, segmented and reconstructed into 3D patient-specific digital models. For each patient, the mitral valve apparatus was digitally reconstructed from a single or fused imaging data set. Using multi-material 3D printing methods, patient-specific anatomic replicas of the mitral valve were created. 3D print materials were selected based on the mechanical testing of elastomeric TangoPlus materials (Stratasys, Eden Prairie, Minnesota, USA) and were compared to freshly harvested porcine leaflet tissue. The effective bending modulus of healthy porcine MV tissue was significantly less than the bending modulus of TangoPlus (p < 0.01). All TangoPlus varieties were less stiff than the maximum tensile elastic modulus of mitral valve tissue (3697.2 ± 385.8 kPa anterior leaflet; 2582.1 ± 374.2 kPa posterior leaflet) (p < 0.01). However, the slopes of the stress-strain toe regions of the mitral valve tissues (532.8 ± 281.9 kPa anterior leaflet; 389.0 ± 156.9 kPa posterior leaflet) were not different than those of the Shore 27, Shore 35, and Shore 27 with Shore 35 blend TangoPlus material (p > 0.95). We have demonstrated that patient-specific mitral valve models can be

  7. 3D structure and conductive thermal field of the Upper Rhine Graben

    NASA Astrophysics Data System (ADS)

    Freymark, Jessica; Sippel, Judith; Scheck-Wenderoth, Magdalena; Bär, Kristian; Stiller, Manfred; Fritsche, Johann-Gerhard; Kracht, Matthias

    2016-04-01

    The Upper Rhine Graben (URG) was formed as part of the European Cenozoic Rift System in a complex extensional setting. At present-day, it has a large socioeconomic relevance as it provides a great potential for geothermal energy production in Germany and France. For the utilisation of this energy resource it is crucial to understand the structure and the observed temperature anomalies in the rift basin. In the framework of the EU-funded "IMAGE" project (Integrated Methods for Advanced Geothermal Exploration), we apply a data-driven numerical modelling approach to quantify the processes and properties controlling the spatial distribution of subsurface temperatures. Typically, reservoir-scale numerical models are developed for predictions on the subsurface hydrothermal conditions and for reducing the risk of drilling non-productive geothermal wells. One major problem related to such models is setting appropriate boundary conditions that define, for instance, how much heat enters the reservoir from greater depths. Therefore, we first build a regional lithospheric-scale 3D structural model, which covers not only the entire URG but also adjacent geological features like the Black Forest and the Vosges Mountains. In particular, we use a multidisciplinary dataset (e.g. well data, seismic reflection data, existing structural models, gravity) to construct the geometries of the sediments, the crust and the lithospheric mantle that control the spatial distribution of thermal conductivity and radiogenic heat production and hence temperatures. By applying a data-based and lithology-dependent parameterisation of this lithospheric-scale 3D structural model and a 3D finite element method, we calculate the steady-state conductive thermal field for the entire region. Available measured temperatures (down to depths of up to 5 km) are considered to validate the 3D thermal model. We present major characteristics of the lithospheric-scale 3D structural model and results of the 3D

  8. 3D structure tensor analysis of light microscopy data for validating diffusion MRI

    PubMed Central

    Khan, Ahmad Raza; Cornea, Anda; Leigland, Lindsey A.; Kohama, Steven G.; Jespersen, Sune Nørhøj; Kroenke, Christopher D.

    2015-01-01

    Diffusion magnetic resonance imaging (d-MRI) is a powerful non-invasive and non-destructive technique for characterizing brain tissue on the microscopic scale. However, the lack of validation of d-MRI by independent experimental means poses an obstacle to accurate interpretation of data acquired using this method. Recently, structure tensor analysis has been applied to light microscopy images, and this technique holds promise to be a powerful validation strategy for d-MRI. Advantages of this approach include its similarity to d-MRI in terms of averaging the effects of a large number of cellular structures, and its simplicity, which enables it to be implemented in a high-throughput manner. However, a drawback of previous implementations of this technique arises from it being restricted to 2D. As a result, structure tensor analyses have been limited to tissue sectioned in a direction orthogonal to the direction of interest. Here we describe the analytical framework for extending structure tensor analysis to 3D, and utilize the results to analyze serial image “stacks” acquired with confocal microscopy of rhesus macaque hippocampal tissue. Implementation of 3D structure tensor procedures requires removal of sources of anisotropy introduced in tissue preparation and confocal imaging. This is accomplished with image processing steps to mitigate the effects of anisotropic tissue shrinkage, and the effects of anisotropy in the point spread function (PSF). In order to address the latter confound, we describe procedures for measuring the dependence of PSF anisotropy on distance from the microscope objective within tissue. Prior to microscopy, ex vivo d-MRI measurements performed on the hippocampal tissue revealed three regions of tissue with mutually orthogonal directions of least restricted diffusion that correspond to CA1, alveus and inferior longitudinal fasciculus. We demonstrate the ability of 3D structure tensor analysis to identify structure tensor orientations

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

    PubMed

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

    2010-12-01

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

  10. 3D printing of layered brain-like structures using peptide modified gellan gum substrates.

    PubMed

    Lozano, Rodrigo; Stevens, Leo; Thompson, Brianna C; Gilmore, Kerry J; Gorkin, Robert; Stewart, Elise M; in het Panhuis, Marc; Romero-Ortega, Mario; Wallace, Gordon G

    2015-10-01

    The brain is an enormously complex organ structured into various regions of layered tissue. Researchers have attempted to study the brain by modeling the architecture using two dimensional (2D) in vitro cell culturing methods. While those platforms attempt to mimic the in vivo environment, they do not truly resemble the three dimensional (3D) microstructure of neuronal tissues. Development of an accurate in vitro model of the brain remains a significant obstacle to our understanding of the functioning of the brain at the tissue or organ level. To address these obstacles, we demonstrate a new method to bioprint 3D brain-like structures consisting of discrete layers of primary neural cells encapsulated in hydrogels. Brain-like structures were constructed using a bio-ink consisting of a novel peptide-modified biopolymer, gellan gum-RGD (RGD-GG), combined with primary cortical neurons. The ink was optimized for a modified reactive printing process and developed for use in traditional cell culturing facilities without the need for extensive bioprinting equipment. Furthermore the peptide modification of the gellan gum hydrogel was found to have a profound positive effect on primary cell proliferation and network formation. The neural cell viability combined with the support of neural network formation demonstrated the cell supportive nature of the matrix. The facile ability to form discrete cell-containing layers validates the application of this novel printing technique to form complex, layered and viable 3D cell structures. These brain-like structures offer the opportunity to reproduce more accurate 3D in vitro microstructures with applications ranging from cell behavior studies to improving our understanding of brain injuries and neurodegenerative diseases.

  11. Low-cost impact detection and location for automated inspections of 3D metallic based structures.

    PubMed

    Morón, Carlos; Portilla, Marina P; Somolinos, José A; Morales, Rafael

    2015-05-28

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach.

  12. Rapid Fabrication of Cell-Laden Alginate Hydrogel 3D Structures by Micro Dip-Coating

    PubMed Central

    Ghanizadeh Tabriz, Atabak; Mills, Christopher G.; Mullins, John J.; Davies, Jamie A.; Shu, Wenmiao

    2017-01-01

    Development of a simple, straightforward 3D fabrication method to culture cells in 3D, without relying on any complex fabrication methods, remains a challenge. In this paper, we describe a new technique that allows fabrication of scalable 3D cell-laden hydrogel structures easily, without complex machinery: the technique can be done using only apparatus already available in a typical cell biology laboratory. The fabrication method involves micro dip-coating of cell-laden hydrogels covering the surface of a metal bar, into the cross-linking reagents calcium chloride or barium chloride to form hollow tubular structures. This method can be used to form single layers with thickness ranging from 126 to 220 µm or multilayered tubular structures. This fabrication method uses alginate hydrogel as the primary biomaterial and a secondary biomaterial can be added depending on the desired application. We demonstrate the feasibility of this method, with survival rate over 75% immediately after fabrication and normal responsiveness of cells within these tubular structures using mouse dermal embryonic fibroblast cells and human embryonic kidney 293 cells containing a tetracycline-responsive, red fluorescent protein (tHEK cells). PMID:28286747

  13. Low-Cost Impact Detection and Location for Automated Inspections of 3D Metallic Based Structures

    PubMed Central

    Morón, Carlos; Portilla, Marina P.; Somolinos, José A.; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  14. LigandBox: A database for 3D structures of chemical compounds.

    PubMed

    Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

    2013-01-01

    A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.

  15. Low-cost structured-light based 3D capture system design

    NASA Astrophysics Data System (ADS)

    Dong, Jing; Bengtson, Kurt R.; Robinson, Barrett F.; Allebach, Jan P.

    2014-03-01

    Most of the 3D capture products currently in the market are high-end and pricey. They are not targeted for consumers, but rather for research, medical, or industrial usage. Very few aim to provide a solution for home and small business applications. Our goal is to fill in this gap by only using low-cost components to build a 3D capture system that can satisfy the needs of this market segment. In this paper, we present a low-cost 3D capture system based on the structured-light method. The system is built around the HP TopShot LaserJet Pro M275. For our capture device, we use the 8.0 Mpixel camera that is part of the M275. We augment this hardware with two 3M MPro 150 VGA (640 × 480) pocket projectors. We also describe an analytical approach to predicting the achievable resolution of the reconstructed 3D object based on differentials and small signal theory, and an experimental procedure for validating that the system under test meets the specifications for reconstructed object resolution that are predicted by our analytical model. By comparing our experimental measurements from the camera-projector system with the simulation results based on the model for this system, we conclude that our prototype system has been correctly configured and calibrated. We also conclude that with the analytical models, we have an effective means for specifying system parameters to achieve a given target resolution for the reconstructed object.

  16. Propagation of Coronal Mass Ejections in 3D and the Structure of the Inner Heliosphere

    NASA Astrophysics Data System (ADS)

    Gallagher, P. T.; Byrne, J. P.; Maloney, S. A.; McAteer, J.

    2011-12-01

    Solar coronal mass ejections (CMEs) are the most significant drivers of adverse space weather on Earth, but the physics governing their propagation through the heliosphere is not well understood. Although stereoscopic imaging of CMEs with NASA's Solar Terrestrial Relations Observatory (STEREO) has provided some insight into their three-dimensional (3D) propagation, the mechanisms governing their evolution remain unclear because of difficulties in reconstructing their true 3D structure. In this talk I will describe the use of an elliptical tie-pointing technique to reconstruct a CME front in 3D, enabling us to quantify its deflected trajectory from high latitudes along the ecliptic, and measure its increasing angular width and propagation. At large distances from the Sun (>7 R_sun), I will describe how its motion is determined by drag effects in the solar wind, using ENLIL simulations of the inner heliosphere. By combining a 3D reconstruction with modelling of the solar wind, we predict an arrival time within 30 mins of the in-situ detection of the CME at ACE

  17. 3D analysis of vortical structures in an abdominal aortic aneurysm by stereoscopic PIV

    NASA Astrophysics Data System (ADS)

    Deplano, Valérie; Guivier-Curien, Carine; Bertrand, Eric

    2016-11-01

    The present work presents an experimental in vitro three-dimensional analysis of the flow dynamics in an abdominal aortic aneurysm (AAA) through stereoscopic particle image velocimetry (SPIV) measurements. The experimental set-up mimics the pathophysiological context involving a shear thinning blood analogue fluid, compliant AAA and aorto-iliac bifurcation walls and controlled inlet and outlet flow rate and pressure waveforms as well as working fluid temperature. SPIV was carefully calibrated and conducted to assess the three velocity components in the AAA volume. For the first time in the literature, the 3D vortex ring genesis, propagation, and vanishing in the AAA bulge are experimentally described and quantified. In comparison with classical 2-component PIV measurements (2C PIV), the third component of the velocity vector was shown to be of importance in such a geometry, especially, during the deceleration phase of the flow rate. The 3D velocity magnitude reached up more than 20 % of the 2D one showing that 2C PIV are definitively not accurate enough to provide a complete description of flow behaviour in an AAA. In addition to potential clinical implications of a full 3D vortex ring description in AAA evolution, the 3D in vitro experimental quantification of the flow dynamics carried out in the present study offers an interesting tool for the validation of fluid-structure interaction numerical studies dealing with AAA.

  18. Walsh-Hadamard Based 3D Steganography for Protecting Sensitive Information in Point-of-Care.

    PubMed

    Abuadbba, Alsharif; Khalil, Ibrahim

    2016-11-29

    Remote points-of-care has recently had a lot of attention for their advantages such as saving lives and cost reduction. The transmitted streams usually contain (1) normal biomedical signals (e.g. ECG) and (2) highly private information (e.g. patient identity). Despite the obvious advantages, the primary concerns are privacy and authenticity of the transferred data. Therefore, this paper introduces a novel steganographic mechanism that ensures (1) strong privacy preservation of private information by random concealing inside the transferred signals employing a key, and (2) evidence of originality for the biomedical signals. To maximize hiding, Fast Walsh-Hadamard Transform is utilized to transform the signals into a group of coefficients. To ensure the lowest distortion, only less-significant values of coefficients are employed. To strengthen security, the key is utilized in a 3-Dimensional random coefficients' reform to produce a 3D order employed in the concealing process. The resultant distortion has been thoroughly measured in all stages. After extensive experiments on three types of signals, it has been proven that the algorithm has little impact on the genuine signals (< 1 %). The security evaluation also confirms that unlawful retrieval of the hidden information within rational time is mightily improbable.

  19. Determination and validation of mTOR kinase-domain 3D structure by homology modeling.

    PubMed

    Lakhlili, Wiame; Chevé, Gwénaël; Yasri, Abdelaziz; Ibrahimi, Azeddine

    2015-01-01

    The AKT/mammalian target of rapamycin (mTOR) pathway is considered as one of the commonly activated and deregulated signaling pathways in human cancer. mTOR is associated with other proteins in two molecular complexes: mTOR complex 1/Raptor and the mTOR complex 2/Rictor. Using the crystal structure of the related lipid kinase PI3Kγ, we built a model of the catalytic region of mTOR. The modeling of the three-dimensional (3D) structure of the mTOR was performed by homology modeling program SWISS-MODEL. The quality and validation of the obtained model were performed using PROCHECK and PROVE softwares. The overall stereochemical property of the protein was assessed by the Ramachandran plot. The model validation was also done by docking of known inhibitors. In this paper, we describe and validate a 3D model for the mTOR catalytic site.

  20. Utilizing in-situ resources and 3D printing structures for a manned Mars mission

    NASA Astrophysics Data System (ADS)

    Kading, Benjamin; Straub, Jeremy

    2015-02-01

    This paper presents a manned Mars mission, which is based on the use of in-situ resources for the fabrication of structures. First, it provides an overview of the two-phase mission. In phase one, robotic construction units prepare a functional base for phase-two human habitation. Then, it describes a set of prospective structures that can be created utilizing additive manufacturing (commonly known as 3D printing) techniques and in situ materials. Next, the technological advancements required to allow this type of mission are considered and their feasibility is discussed. Specific focus is given to the topics of basalt 3D printing and the maintenance of the pressure environment. The process of the construction of the base is also discussed. Finally the proposed approach is analyzed through comparison to prior missions, before concluding.

  1. Novel 3D bio-macromolecular bilinear descriptors for protein science: Predicting protein structural classes.

    PubMed

    Marrero-Ponce, Yovani; Contreras-Torres, Ernesto; García-Jacas, César R; Barigye, Stephen J; Cubillán, Néstor; Alvarado, Ysaías J

    2015-06-07

    In the present study, we introduce novel 3D protein descriptors based on the bilinear algebraic form in the ℝ(n) space on the coulombic matrix. For the calculation of these descriptors, macromolecular vectors belonging to ℝ(n) space, whose components represent certain amino acid side-chain properties, were used as weighting schemes. Generalization approaches for the calculation of inter-amino acidic residue spatial distances based on Minkowski metrics are proposed. The simple- and double-stochastic schemes were defined as approaches to normalize the coulombic matrix. The local-fragment indices for both amino acid-types and amino acid-groups are presented in order to permit characterizing fragments of interest in proteins. On the other hand, with the objective of taking into account specific interactions among amino acids in global or local indices, geometric and topological cut-offs are defined. To assess the utility of global and local indices a classification model for the prediction of the major four protein structural classes, was built with the Linear Discriminant Analysis (LDA) technique. The developed LDA-model correctly classifies the 92.6% and 92.7% of the proteins on the training and test sets, respectively. The obtained model showed high values of the generalized square correlation coefficient (GC(2)) on both the training and test series. The statistical parameters derived from the internal and external validation procedures demonstrate the robustness, stability and the high predictive power of the proposed model. The performance of the LDA-model demonstrates the capability of the proposed indices not only to codify relevant biochemical information related to the structural classes of proteins, but also to yield suitable interpretability. It is anticipated that the current method will benefit the prediction of other protein attributes or functions.

  2. 3D reconstruction of internal structure of animal body using near-infrared light

    NASA Astrophysics Data System (ADS)

    Tran, Trung Nghia; Yamamoto, Kohei; Namita, Takeshi; Kato, Yuji; Shimizu, Koichi

    2014-03-01

    To realize three-dimensional (3D) optical imaging of the internal structure of animal body, we have developed a new technique to reconstruct CT images from two-dimensional (2D) transillumination images. In transillumination imaging, the image is blurred due to the strong scattering in the tissue. We had developed a scattering suppression technique using the point spread function (PSF) for a fluorescent light source in the body. In this study, we have newly proposed a technique to apply this PSF for a light source to the image of unknown light-absorbing structure. The effectiveness of the proposed technique was examined in the experiments with a model phantom and a mouse. In the phantom experiment, the absorbers were placed in the tissue-equivalent medium to simulate the light-absorbing organs in mouse body. Near-infrared light was illuminated from one side of the phantom and the image was recorded with CMOS camera from another side. Using the proposed techniques, the scattering effect was efficiently suppressed and the absorbing structure can be visualized in the 2D transillumination image. Using the 2D images obtained in many different orientations, we could reconstruct the 3D image. In the mouse experiment, an anesthetized mouse was held in an acrylic cylindrical holder. We can visualize the internal organs such as kidneys through mouse's abdomen using the proposed technique. The 3D image of the kidneys and a part of the liver were reconstructed. Through these experimental studies, the feasibility of practical 3D imaging of the internal light-absorbing structure of a small animal was verified.

  3. Analysis and 3D visualization of structures of animal brains obtained from histological sections

    NASA Astrophysics Data System (ADS)

    Forero-Vargas, Manuel G.; Fuentes, Veronica; Lopez, D.; Moscoso, A.; Merchan, Miguel A.

    2002-11-01

    This paper presents a new application for the analysis of histological sections and their 3D visualization. The process is performed in few steps. First, a manual process is necessary to determine the regions of interest, including image digitalization, drawing of borders and alignment between all images. Then, a reconstruction process is made. After sampling the contour, the structure of interest is displayed. The application is experimentally validated and some results on histological sections of a rodent's brain (hamster and rat) are shown.

  4. UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling

    PubMed Central

    Bhattacharya, Debswapna; Cao, Renzhi; Cheng, Jianlin

    2016-01-01

    Motivation: Recent experimental studies have suggested that proteins fold via stepwise assembly of structural units named ‘foldons’ through the process of sequential stabilization. Alongside, latest developments on computational side based on probabilistic modeling have shown promising direction to perform de novo protein conformational sampling from continuous space. However, existing computational approaches for de novo protein structure prediction often randomly sample protein conformational space as opposed to experimentally suggested stepwise sampling. Results: Here, we develop a novel generative, probabilistic model that simultaneously captures local structural preferences of backbone and side chain conformational space of polypeptide chains in a united-residue representation and performs experimentally motivated conditional conformational sampling via stepwise synthesis and assembly of foldon units that minimizes a composite physics and knowledge-based energy function for de novo protein structure prediction. The proposed method, UniCon3D, has been found to (i) sample lower energy conformations with higher accuracy than traditional random sampling in a small benchmark of 6 proteins; (ii) perform comparably with the top five automated methods on 30 difficult target domains from the 11th Critical Assessment of Protein Structure Prediction (CASP) experiment and on 15 difficult target domains from the 10th CASP experiment; and (iii) outperform two state-of-the-art approaches and a baseline counterpart of UniCon3D that performs traditional random sampling for protein modeling aided by predicted residue-residue contacts on 45 targets from the 10th edition of CASP. Availability and Implementation: Source code, executable versions, manuals and example data of UniCon3D for Linux and OSX are freely available to non-commercial users at http://sysbio.rnet.missouri.edu/UniCon3D/. Contact: chengji@missouri.edu Supplementary information: Supplementary data are

  5. Dynamic Characteristics of a Model and Prototype for 3D-RC Structure

    NASA Astrophysics Data System (ADS)

    Moniuddin, Md. Khaja; Vasanthalakshmi, G.; Chethan, K.; Babu, R. Ramesh

    2016-06-01

    Infill walls provide durable and economical partitions that have relatively excellent thermal and sound insulation with high fire resistance. Monolithic infilled walls are provided within RC structures without being analyzed as a combination of concrete and brick elements, although in reality they act as a single unit during earthquakes. The performance of such structures during earthquakes has proved to be superior in comparison to bare frames in terms of stiffness, strength and energy dissipation. To know the dynamic characteristics of monolithic infill wall panels and masonry infill, modal, response spectrum and time history analyses have been carried out on a model and prototype of a 3D RC structure for a comparative study.

  6. 3-D Structure of the Slave and Rae Cratons Provides Clues to Their Construction

    NASA Astrophysics Data System (ADS)

    Snyder, D. B.

    2013-12-01

    Deep geologic structures within cratons that make up continental cores were long neglected. Recently acquired geophysical data from large observational arrays and geochemical data resulting from exploration for diamond has now made possible co-registration of large-scale (400-km depth), truly 3-dimensional data sets. P-waves, surface waves and magnetotelluric observations provide 3-D wavespeed and conductivity models. Multi-azimuthal receiver functions map seismic discontinuity surfaces in 3-D. Xenolith suites erupted in kimberlites provide rock samples at key lithospheric depths, albeit at sparsely distributed locations. These multi-disciplinary models are becoming available for several key cratons worldwide; here the deep structure of the Slave and Rae cratons of the Canadian Shield is described. Lithospheric layers with tapered, wedge-shaped margins are common. Slave craton layers are sub-horizontal and indicate construction of the craton core at 2.7 Ga by underthrusting and flat stacking of lithosphere. The central Rae craton has predominantly dipping discontinuities that indicate construction at 1.9 Ga by thrusting similar to that observed in crustal ';thick-skinned' fold-and-thrust belts. 3-D mapping of conductivity and metasomatism, the latter via mineral recrystallization and resetting of isotopic ages, overprints primary structures in both cratons. Distribution of more conductivitve mantle suggests that assumed causative pervasive metasomatism occurs at 100-200 km depths with ';chimneys' reaching to shallower depths, typically in locations where kimberlites or mineralization has occurred.

  7. SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures

    PubMed Central

    Nadzirin, Nurul; Gardiner, Eleanor J.; Willett, Peter; Artymiuk, Peter J.; Firdaus-Raih, Mohd

    2012-01-01

    Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function. In contrast, a 3D pattern of interest can be searched for existing occurrences in available PDB structures using ASSAM. Both programs are freely accessible without any login requirement. SPRITE is available at http://mfrlab.org/grafss/sprite/ while ASSAM can be accessed at http://mfrlab.org/grafss/assam/. PMID:22573174

  8. Enhanced hybrid search algorithm for protein structure prediction using the 3D-HP lattice model.

    PubMed

    Zhou, Changjun; Hou, Caixia; Zhang, Qiang; Wei, Xiaopeng

    2013-09-01

    The problem of protein structure prediction in the hydrophobic-polar (HP) lattice model is the prediction of protein tertiary structure. This problem is usually referred to as the protein folding problem. This paper presents a method for the application of an enhanced hybrid search algorithm to the problem of protein folding prediction, using the three dimensional (3D) HP lattice model. The enhanced hybrid search algorithm is a combination of the particle swarm optimizer (PSO) and tabu search (TS) algorithms. Since the PSO algorithm entraps local minimum in later evolution extremely easily, we combined PSO with the TS algorithm, which has properties of global optimization. Since the technologies of crossover and mutation are applied many times to PSO and TS algorithms, so enhanced hybrid search algorithm is called the MCMPSO-TS (multiple crossover and mutation PSO-TS) algorithm. Experimental results show that the MCMPSO-TS algorithm can find the best solutions so far for the listed benchmarks, which will help comparison with any future paper approach. Moreover, real protein sequences and Fibonacci sequences are verified in the 3D HP lattice model for the first time. Compared with the previous evolutionary algorithms, the new hybrid search algorithm is novel, and can be used effectively to predict 3D protein folding structure. With continuous development and changes in amino acids sequences, the new algorithm will also make a contribution to the study of new protein sequences.

  9. Minimizing camera-eye optical aberrations during the 3D reconstruction of retinal structures

    NASA Astrophysics Data System (ADS)

    Aldana-Iuit, Javier; Martinez-Perez, M. Elena; Espinosa-Romero, Arturo; Diaz-Uribe, Rufino

    2010-05-01

    3D reconstruction of blood vessels is a powerful visualization tool for physicians, since it allows them to refer to qualitative representation of their subject of study. In this paper we propose a 3D reconstruction method of retinal vessels from fundus images. The reconstruction method propose herein uses images of the same retinal structure in epipolar geometry. Images are preprocessed by RISA system for segmenting blood vessels and obtaining feature points for correspondences. The correspondence points process is solved using correlation. The LMedS analysis and Graph Transformation Matching algorithm are used for outliers suppression. Camera projection matrices are computed with the normalized eight point algorithm. Finally, we retrieve 3D position of the retinal tree points by linear triangulation. In order to increase the power of visualization, 3D tree skeletons are represented by surfaces via generalized cylinders whose radius correspond to morphological measurements obtained by RISA. In this paper the complete calibration process including the fundus camera and the optical properties of the eye, the so called camera-eye system is proposed. On one hand, the internal parameters of the fundus camera are obtained by classical algorithms using a reference pattern. On the other hand, we minimize the undesirable efects of the aberrations induced by the eyeball optical system assuming that contact enlarging lens corrects astigmatism, spherical and coma aberrations are reduced changing the aperture size and eye refractive errors are suppressed adjusting camera focus during image acquisition. Evaluation of two self-calibration proposals and results of 3D blood vessel surface reconstruction are presented.

  10. Novel 3D bismuth-based coordination polymers: Synthesis, structure, and second harmonic generation properties

    SciTech Connect

    Wibowo, Arief C.; Smith, Mark D.; Yeon, Jeongho; Halasyamani, P. Shiv; Loye, Hans-Conrad zur

    2012-11-15

    Two new 3D bismuth containing coordination polymers are reported along with their single crystal structures and SHG properties. Compound 1: Bi{sub 2}O{sub 2}(pydc) (pydc=pyridine-2, 5-dicarboxylate), crystallizes in the monoclinic, polar space group, P2{sub 1} (a=9.6479(9) A, b=4.2349(4) A, c=11.9615(11) A, {beta}=109.587(1) Degree-Sign ), which contains Bi{sub 2}O{sub 2} chains that are connected into a 3D structure via the pydc ligands. Compound 2: Bi{sub 4}Na{sub 4}(1R3S-cam){sub 8}(EtOH){sub 3.1}(H{sub 2}O){sub 3.4} (1R3S cam=1R3S-camphoric acid) crystallizes in the monoclinic, polar space group, P2{sub 1} (a=19.0855(7) A, b=13.7706(5) A, c=19.2429(7) A, {beta}=90.701(1) Degree-Sign ) and is a true 3D coordination polymer. These are two example of SHG compounds prepared using unsymmetric ligands (compound 1) or chiral ligands (compound 2), together with metals that often exhibit stereochemically-active lone pairs, such as Bi{sup 3+}, a synthetic approach that resulted in polar, non-centrosymmetric, 3D metal-organic coordination polymer. - Graphical Abstract: Structures of two new, polar, 3D Bismuth(III)-based coordination polymers: Bi{sub 2}O{sub 2}(pydc) (compound 1), and Bi{sub 4}Na{sub 4}(1R3S-cam){sub 8}(EtOH){sub 3.1}(H{sub 2}O){sub 3.4} (compound 2). Highlights: Black-Right-Pointing-Pointer New, polar, 3D Bismuth(III)-based coordination polymers. Black-Right-Pointing-Pointer First polar bismuth-based coordination polymers synthesized via a 'hybrid' strategy. Black-Right-Pointing-Pointer Combination of stereochemically-active lone pairs and unsymmetrical or chiral ligands. Black-Right-Pointing-Pointer Synthesis of class C-SHG materials based on Kurtz-Perry categories.

  11. 3-D Radar Imaging Reveals Deep Structures and Buried Craters Within the Martian Polar Caps

    NASA Astrophysics Data System (ADS)

    Putzig, N. E.; Foss, F. J., II; Campbell, B. A.; Phillips, R. J.; Smith, I. B.

    2015-12-01

    We use Shallow Radar (SHARAD) observations on thousands of orbital passes by the Mars Reconnaissance Orbiter to produce fully imaged 3-D data volumes encompassing both polar ice caps of Mars. Greatly clarifying the view of subsurface features, a completed volume for Planum Boreum provides new constraints on the nature and timing of emplacement of the northern polar deposits and their relationship to climate. The standard method of mapping subsurface features with single-pass 2-D radargrams has been very fruitful (see Brothers et al. 2015, JGR 120 in press, and references therein), but a full assessment of internal structures has been hindered by interfering off-nadir echoes from spiral troughs and other variable topography prevalent on both caps. By assembling the SHARAD radargrams into a volume and applying a 3-D imaging process (migration) borrowed from seismic processing techniques, we enhance the signal-to-noise ratio while repositioning the echoes to their proper locations, thereby unraveling the interference. As part of the process, we correct ionospheric distortions and delays of the radar echoes (Campbell et al. 2014, IEEE GRSL 11 #3). Interfaces painstakingly mapped in radargrams (e.g., the basal-unit surface, a buried chasma) are clearly visible in the 3-D volume, and new features are revealed. Structures may now be mapped through trough-rich regions, including a widespread sequence that provides corroborative evidence of recent ice ages (Smith et al. 2015, LPSC XLVI #2574). Distinctive radar signatures associated with known, partially buried craters also occur elsewhere in the volume but without surface expression. Presumably, these are fully buried craters that may provide a new means to estimate the age of the deposits. Preliminary work for Planum Australe demonstrates that the 3-D processing currently underway will illuminate deep structures that are broadly obfuscated in 2-D radargrams by a shallow scatterer (Campbell et al. 2015, LPSC XLVI #2366).

  12. Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA.

    PubMed

    Mrozek, Dariusz; Brożek, Miłosz; Małysiak-Mrozek, Bożena

    2014-02-01

    Searching for similar 3D protein structures is one of the primary processes employed in the field of structural bioinformatics. However, the computational complexity of this process means that it is constantly necessary to search for new methods that can perform such a process faster and more efficiently. Finding molecular substructures that complex protein structures have in common is still a challenging task, especially when entire databases containing tens or even hundreds of thousands of protein structures must be scanned. Graphics processing units (GPUs) and general purpose graphics processing units (GPGPUs) can perform many time-consuming and computationally demanding processes much more quickly than a classical CPU can. In this paper, we describe the GPU-based implementation of the CASSERT algorithm for 3D protein structure similarity searching. This algorithm is based on the two-phase alignment of protein structures when matching fragments of the compared proteins. The GPU (GeForce GTX 560Ti: 384 cores, 2GB RAM) implementation of CASSERT ("GPU-CASSERT") parallelizes both alignment phases and yields an average 180-fold increase in speed over its CPU-based, single-core implementation on an Intel Xeon E5620 (2.40GHz, 4 cores). In this paper, we show that massive parallelization of the 3D structure similarity search process on many-core GPU devices can reduce the execution time of the process, allowing it to be performed in real time. GPU-CASSERT is available at: http://zti.polsl.pl/dmrozek/science/gpucassert/cassert.htm.

  13. Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities

    PubMed Central

    Dai, Chao; Li, Wenyuan; Tjong, Harianto; Hao, Shengli; Zhou, Yonggang; Li, Qingjiao; Chen, Lin; Zhu, Bing; Alber, Frank; Jasmine Zhou, Xianghong

    2016-01-01

    Three-dimensional (3D) genome structures vary from cell to cell even in an isogenic sample. Unlike protein structures, genome structures are highly plastic, posing a significant challenge for structure-function mapping. Here we report an approach to comprehensively identify 3D chromatin clusters that each occurs frequently across a population of genome structures, either deconvoluted from ensemble-averaged Hi-C data or from a collection of single-cell Hi-C data. Applying our method to a population of genome structures (at the macrodomain resolution) of lymphoblastoid cells, we identify an atlas of stable inter-chromosomal chromatin clusters. A large number of these clusters are enriched in binding of specific regulatory factors and are therefore defined as ‘Regulatory Communities.' We reveal two major factors, centromere clustering and transcription factor binding, which significantly stabilize such communities. Finally, we show that the regulatory communities differ substantially from cell to cell, indicating that expression variability could be impacted by genome structures. PMID:27240697

  14. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

    PubMed Central

    Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.

    2015-01-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations. PMID:26346202

  15. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers.

    PubMed

    Mao, Yiqi; Yu, Kai; Isakov, Michael S; Wu, Jiangtao; Dunn, Martin L; Jerry Qi, H

    2015-09-08

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations.

  16. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

    NASA Astrophysics Data System (ADS)

    Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.

    2015-09-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations.

  17. Characterization of ABS specimens produced via the 3D printing technology for drone structural components

    NASA Astrophysics Data System (ADS)

    Ferro, Carlo Giovanni; Brischetto, Salvatore; Torre, Roberto; Maggiore, Paolo

    2016-07-01

    The Fused Deposition Modelling (FDM) technology is widely used in rapid prototyping. 3D printers for home desktop applications are usually employed to make non-structural objects. When the mechanical stresses are not excessive, this technology can also be successfully employed to produce structural objects, not only in prototyping stage but also in the realization of series pieces. The innovative idea of the present work is the application of this technology, implemented in a desktop 3D printer, to the realization of components for aeronautical use, especially for unmanned aerial systems. For this purpose, the paper is devoted to the statistical study of the performance of a desktop 3D printer to understand how the process performs and which are the boundary limits of acceptance. Mechanical and geometrical properties of ABS (Acrylonitrile Butadiene Styrene) specimens, such as tensile strength and stiffness, have been evaluated. ASTM638 type specimens have been used. A capability analysis has been applied for both mechanical and dimensional performances. Statistically stable limits have been determined using experimentally collected data.

  18. Development of biologically active compounds by combining 3D QSAR and structure-based design methods

    NASA Astrophysics Data System (ADS)

    Sippl, Wolfgang

    2002-11-01

    One of the major challenges in computational approaches to drug design is the accurate prediction of the binding affinity of novel biomolecules. In the present study an automated procedure which combines docking and 3D-QSAR methods was applied to several drug targets. The developed receptor-based 3D-QSAR methodology was tested on several sets of ligands for which the three-dimensional structure of the target protein has been solved - namely estrogen receptor, acetylcholine esterase and protein-tyrosine-phosphatase 1B. The molecular alignments of the studied ligands were determined using the docking program AutoDock and were compared with the X-ray structures of the corresponding protein-ligand complexes. The automatically generated protein-based ligand alignment obtained was subsequently taken as basis for a comparative field analysis applying the GRID/GOLPE approach. Using GRID interaction fields and applying variable selection procedures, highly predictive models were obtained. It is expected that concepts from receptor-based 3D QSAR will be valuable tools for the analysis of high-throughput screening as well as virtual screening data

  19. 3D Density Structure and LOS Observations of a Model CME

    NASA Astrophysics Data System (ADS)

    Manchester, W. B.; Lugaz, N.; Gombosi, T.; de Zeeuw, D.; Sokolov, I.; Toth, G.

    2004-12-01

    We present synthetic Thomson-scattered white-light images of a simulated coronal mass ejection (CME). The simulations are based on a 3-D MHD model of a CME propagating through a bimodal solar wind characteristic of solar minimum. The CME is driven by a 3-D Gibson-Low flux rope inserted in the helmet streamer of the steady-state corona. Synthetic coronograph images are produced that follow the evolution of the CME to 1 AU from several points of view. The white light images provide a basis for comparison with wide angle coronographs, like those of SMEI or STEREO. We find that a large amount of plasma is swept up from the solar wind by the CME-driven shock wave, which dominates the density structure far from the Sun. We also find that the shape of this compressed plasma is highly distorted by the variation in speed of the ambient solar wind. Comparisons of 2-D integrated images to the 3-D density structure show that the viewing angle severely effects the line-of-sight appearance of the CME, as well as the estimated mass of the CME from such 2D images.

  20. The lithospheric-scale 3D structural configuration of the North Alpine Foreland Basin constrained by gravity modelling and the calculation of the 3D load distribution

    NASA Astrophysics Data System (ADS)

    Przybycin, Anna M.; Scheck-Wenderoth, Magdalena; Schneider, Michael

    2014-05-01

    The North Alpine Foreland Basin is situated in the northern front of the European Alps and extends over parts of France, Switzerland, Germany and Austria. It formed as a wedge shaped depression since the Tertiary in consequence of the Euro - Adriatic continental collision and the Alpine orogeny. The basin is filled with clastic sediments, the Molasse, originating from erosional processes of the Alps and underlain by Mesozoic sedimentary successions and a Paleozoic crystalline crust. For our study we have focused on the German part of the basin. To investigate the deep structure, the isostatic state and the load distribution of this region we have constructed a 3D structural model of the basin and the Alpine area using available depth and thickness maps, regional scale 3D structural models as well as seismic and well data for the sedimentary part. The crust (from the top Paleozoic down to the Moho (Grad et al. 2008)) has been considered as two-parted with a lighter upper crust and a denser lower crust; the partition has been calculated following the approach of isostatic equilibrium of Pratt (1855). By implementing a seismic Lithosphere-Asthenosphere-Boundary (LAB) (Tesauro 2009) the crustal scale model has been extended to the lithospheric-scale. The layer geometry and the assigned bulk densities of this starting model have been constrained by means of 3D gravity modelling (BGI, 2012). Afterwards the 3D load distribution has been calculated using a 3D finite element method. Our results show that the North Alpine Foreland Basin is not isostatically balanced and that the configuration of the crystalline crust strongly controls the gravity field in this area. Furthermore, our results show that the basin area is influenced by varying lateral load differences down to a depth of more than 150 km what allows a first order statement of the required compensating horizontal stress needed to prevent gravitational collapse of the system. BGI (2012). The International

  1. Shape optimization of 3D continuum structures via force approximation techniques

    NASA Technical Reports Server (NTRS)

    Vanderplaats, Garret N.; Kodiyalam, Srinivas

    1988-01-01

    The existing need to develop methods whereby the shape design efficiency can be improved through the use of high quality approximation methods is addressed. An efficient approximation method for stress constraints in 3D shape design problems is proposed based on expanding the nodal forces in Taylor series with respect to shape variations. The significance of this new method is shown through elementary beam theory calculations and via numerical computations using 3D solid finite elements. Numerical examples including the classical cantilever beam structure and realistic automotive parts like the engine connecting rod are designed for optimum shape using the proposed method. The numerical results obtained from these methods are compared with other published results, to assess the efficiency and the convergence rate of the proposed method.

  2. Structured light 3D tracking system for measuring motions in PET brain imaging

    NASA Astrophysics Data System (ADS)

    Olesen, Oline V.; Jørgensen, Morten R.; Paulsen, Rasmus R.; Højgaard, Liselotte; Roed, Bjarne; Larsen, Rasmus

    2010-02-01

    Patient motion during scanning deteriorates image quality, especially for high resolution PET scanners. A new proposal for a 3D head tracking system for motion correction in high resolution PET brain imaging is set up and demonstrated. A prototype tracking system based on structured light with a DLP projector and a CCD camera is set up on a model of the High Resolution Research Tomograph (HRRT). Methods to reconstruct 3D point clouds of simple surfaces based on phase-shifting interferometry (PSI) are demonstrated. The projector and camera are calibrated using a simple stereo vision procedure where the projector is treated as a camera. Additionally, the surface reconstructions are corrected for the non-linear projector output prior to image capture. The results are convincing and a first step toward a fully automated tracking system for measuring head motions in PET imaging.

  3. Imaging and 3D reconstruction of cerebrovascular structures in embryonic zebrafish.

    PubMed

    Ethell, Douglas W; Cameron, D Joshua

    2014-04-22

    Zebrafish are a powerful tool to study developmental biology and pathology in vivo. The small size and relative transparency of zebrafish embryos make them particularly useful for the visual examination of processes such as heart and vascular development. In several recent studies transgenic zebrafish that express EGFP in vascular endothelial cells were used to image and analyze complex vascular networks in the brain and retina, using confocal microscopy. Descriptions are provided to prepare, treat and image zebrafish embryos that express enhanced green fluorescent protein (EGFP), and then generate comprehensive 3D renderings of the cerebrovascular system. Protocols include the treatment of embryos, confocal imaging, and fixation protocols that preserve EGFP fluorescence. Further, useful tips on obtaining high-quality images of cerebrovascular structures, such as removal the eye without damaging nearby neural tissue are provided. Potential pitfalls with confocal imaging are discussed, along with the steps necessary to generate 3D reconstructions from confocal image stacks using freely available open source software.

  4. Determining the 3-D structure and motion of objects using a scanning laser range sensor

    NASA Astrophysics Data System (ADS)

    Nandhakumar, N.; Smith, Philip W.

    1993-12-01

    In order for the EVAHR robot to autonomously track and grasp objects, its vision system must be able to determine the 3-D structure and motion of an object from a sequence of sensory images. This task is accomplished by the use of a laser radar range sensor which provides dense range maps of the scene. Unfortunately, the currently available laser radar range cameras use a sequential scanning approach which complicates image analysis. Although many algorithms have been developed for recognizing objects from range images, none are suited for use with single beam, scanning, time-of-flight sensors because all previous algorithms assume instantaneous acquisition of the entire image. This assumption is invalid since the EVAHR robot is equipped with a sequential scanning laser range sensor. If an object is moving while being imaged by the device, the apparent structure of the object can be significantly distorted due to the significant non-zero delay time between sampling each image pixel. If an estimate of the motion of the object can be determined, this distortion can be eliminated; but, this leads to the motion-structure paradox - most existing algorithms for 3-D motion estimation use the structure of objects to parameterize their motions. The goal of this research is to design a rigid-body motion recovery technique which overcomes this limitation. The method being developed is an iterative, linear, feature-based approach which uses the non-zero image acquisition time constraint to accurately recover the motion parameters from the distorted structure of the 3-D range maps. Once the motion parameters are determined, the structural distortion in the range images is corrected.

  5. Integrating 3D geological information with a national physically-based hydrological modelling system

    NASA Astrophysics Data System (ADS)

    Lewis, Elizabeth; Parkin, Geoff; Kessler, Holger; Whiteman, Mark

    2016-04-01

    Robust numerical models are an essential tool for informing flood and water management and policy around the world. Physically-based hydrological models have traditionally not been used for such applications due to prohibitively large data, time and computational resource requirements. Given recent advances in computing power and data availability, a robust, physically-based hydrological modelling system for Great Britain using the SHETRAN model and national datasets has been created. Such a model has several advantages over less complex systems. Firstly, compared with conceptual models, a national physically-based model is more readily applicable to ungauged catchments, in which hydrological predictions are also required. Secondly, the results of a physically-based system may be more robust under changing conditions such as climate and land cover, as physical processes and relationships are explicitly accounted for. Finally, a fully integrated surface and subsurface model such as SHETRAN offers a wider range of applications compared with simpler schemes, such as assessments of groundwater resources, sediment and nutrient transport and flooding from multiple sources. As such, SHETRAN provides a robust means of simulating numerous terrestrial system processes which will add physical realism when coupled to the JULES land surface model. 306 catchments spanning Great Britain have been modelled using this system. The standard configuration of this system performs satisfactorily (NSE > 0.5) for 72% of catchments and well (NSE > 0.7) for 48%. Many of the remaining 28% of catchments that performed relatively poorly (NSE < 0.5) are located in the chalk in the south east of England. As such, the British Geological Survey 3D geology model for Great Britain (GB3D) has been incorporated, for the first time in any hydrological model, to pave the way for improvements to be made to simulations of catchments with important groundwater regimes. This coupling has involved

  6. 1d, 2d, and 3d periodic structures: Electromagnetic characterization, design, and measurement

    NASA Astrophysics Data System (ADS)

    Brockett, Timothy John

    Periodic structures have many useful applications in electromagnetics including phased arrays, frequency selective surfaces, and absorbing interfaces. Their unique properties can be used to provide increased performance in antenna gain, electromagnetic propagation, and electromagnetic absorption. In antenna arrays, repeating elements create a larger eective aperture, increasing the gain of the antenna and the ability to scan the direction of the main beam. Three-dimensional periodic structures, such as an array of shaped pillars such as columns, cones, or prisms have the potential of improving electromagnetic absorption, improving performance in applications such as solar cell eciency and absorbing interfaces. Furthermore, research into periodic structures is a continuing endeavor where novel approaches and analysis in appropriate applications can be sought. This dissertation will address the analysis, diagnostics, and enhancement of 1D, 2D, and 3D periodic structures for antenna array applications and solar cell technology. In particular, a unique approach to array design will be introduced to prevent the appearance of undesirable grating lobes in large antenna arrays that employ subarrays. This approach, named the distortion diagnostic procedure, can apply directly to 1D and 2D periodic structures in the form of planar antenna arrays. Interesting corollaries included here are developments in millimeter-wave antenna measurements including spiral planar scanning, phaseless measurements, and addressing antennas that feature an internal source. Finally, analysis and enhancement of 3D periodic structures in nanostructure photovoltaic arrays and absorbing interfaces will be examined for their behavior and basic operation in regards to improved absorption of electromagnetic waves.

  7. Loading mode dependent effective properties of octet-truss lattice structures using 3D-printing

    NASA Astrophysics Data System (ADS)

    Challapalli, Adithya

    Cellular materials, often called lattice materials, are increasingly receiving attention for their ultralight structures with high specific strength, excellent impact absorption, acoustic insulation, heat dissipation media and compact heat exchangers. In alignment with emerging additive manufacturing (AM) technology, realization of the structural applications of the lattice materials appears to be becoming faster. Considering the direction dependent material properties of the products with AM, by directionally dependent printing resolution, effective moduli of lattice structures appear to be directionally dependent. In this paper, a constitutive model of a lattice structure, which is an octet-truss with a base material having an orthotropic material property considering AM is developed. In a case study, polyjet based 3D printing material having an orthotropic property with a 9% difference in the principal direction provides difference in the axial and shear moduli in the octet-truss by 2.3 and 4.6%. Experimental validation for the effective properties of a 3D printed octet-truss is done for uniaxial tension and compression test. The theoretical value based on the micro-buckling of truss member are used to estimate the failure strength. Modulus value appears a little overestimate compared with the experiment. Finite element (FE) simulations for uniaxial compression and tension of octettruss lattice materials are conducted. New effective properties for the octet-truss lattice structure are developed considering the observed behavior of the octet-truss structure under macroscopic compression and tension trough simulations.

  8. 3D visualization of deformation structures and potential fluid pathways at the Grimsel Test Site

    NASA Astrophysics Data System (ADS)

    Schneeberger, Raphael; Kober, Florian; Berger, Alfons; Spillmann, Thomas; Herwegh, Marco

    2015-04-01

    Knowledge on the ability of fluids to infiltrate subsurface rocks is of major importance for underground constructions, geothermal or radioactive waste disposal projects. In this study, we focus on the characterization of water infiltration pathways, their 3D geometries and origins. Based on surface and subsurface mapping in combination with drill core data, we developed by the use of MoveTM (Midland Valley Exploration Ltd.) a 3D structural model of the Grimsel Test Site (GTS). GTS is an underground laboratory operated by NAGRA, the Swiss organisation responsible for the management of nuclear waste. It is located within a suite of post-Variscan magmatic bodies comprising former granitic and granodioritic melts, which are dissected by mafic and aplitic dikes. During Alpine orogeny, the suite was tectonically overprinted within two stages of ductile deformation (Wehrens et al., in prep.) followed by brittle overprint of some of the shear zones during the retrograde exhumation history. It is this brittle deformation, which controls today's water infiltration network. However, the associated fractures, cataclasites and fault gouges are controlled themselves by aforementioned pre-existing mechanical discontinuities, whose origin ranges back as far as to the magmatic stage. For example, two sets of vertically oriented mafic dikes (E-W and NW-SE striking) and compositional heterogeneities induced by magmatic segregation processes in the plutonic host rocks served as nucleation sites for Alpine strain localization. Subsequently, NE-SW, E-W and NW-SE striking ductile shear zones were formed, in combination with high temperature fracturing while dissecting the host rocks in a complex 3D pattern (Wehrens et al, in prep.). Whether the ductile shear zones have been subjected to brittle reactivation and can serve as infiltration pathways or not, depends strongly on their orientations with respect to the principal stress field. Especially where deformation structures intersect

  9. 3D crustal and lithospheric structure of the Pyrenean orogenic wedge

    NASA Astrophysics Data System (ADS)

    Theunissen, Thomas; Chevrot, Sébastien; Sylvander, Matthieu; Monteiller, Vadim; Villasenor, Antonio; Benahmed, Sébastien; Calvet, Marie

    2013-04-01

    The Pyrenean orogenic wedge is the consequence of the collision between the Iberian microplate and the southwesternmost part of the Eurasian plate from 55 to 25 Ma (Eocene to Oligocene). The shortening began since Late Cretaceous, about 100 My ago, leading to about 75 km from the west to 125 km to the east of continental crustal shortening. Before this period of time, the region was characterized by a sedimentary basin associated with a very important thinning that later controlled the deformation during the shortening process. Mantle outcrops are therefore present along and north of the North Pyrenean Fault with a scattered localization to the west toward the Mauleon basin. Today, the horizontal deformation rate is very low and the recent seismicity, mainly normal faulting mechanisms, is certainly caused by coupling between erosion and isostatic readjustments. Images from seismic reflection, gravity modeling, local and teleseismic seismic waves inversions and magnetotellurics inversions are in agreement with the subduction of Iberia beneath Aquitania. The 3D crustal structure reveals the presence of an important thickening of the continental crust associated with the subduction of the Iberian lower crust through the north beneath Aquitania at the favor of a detachment. Lateral variations of the geometry (including that of the Moho) and the wave propagation properties are important. In order to better analyze waveforms from local, regional or teleseismic earthquakes and to better constrain the geodynamical evolution of the Pyrenean chain over the time, PYROPE and TOPO-IBERIA projects were born. Two temporary seismic arrays (using broadband seismometers), on the French and Spanish sides, have been deployed between 2010 and 2013. We present here preliminary results on 3D crustal structures (approximately in the window 40° N-45° N and -4° E and 5° E) from arrival-times of about 20000 earthquakes recorded at about 200 seismic stations between 1978 and 2012

  10. The “lnc” between 3D Chromatin Structure and X Chromosome Inactivation

    PubMed Central

    Pandya-Jones, Amy; Plath, Kathrin

    2016-01-01

    The long non-coding RNA Xist directs a remarkable instance of developmentally regulated, epigenetic change known as X Chromosome Inactivation (XCI). By spreading in cis across the X chromosome from which it is expressed, Xist RNA facilities the creation of a heritably silent, heterochromatic nuclear territory that displays a three-dimensional structure distinct from that of the active X chromosome. How Xist RNA attaches to and propagates across a chromosome and its influence over the three-dimensional (3D) structure of the inactive X are aspects of XCI that have remained largely unclear. Here, we discuss studies that have made significant contributions towards answering these open questions. PMID:27062886

  11. Protein contact maps: A binary depiction of protein 3D structures

    NASA Astrophysics Data System (ADS)

    Emerson, Isaac Arnold; Amala, Arumugam

    2017-01-01

    In recent years, there has been a considerable interest in examining the structure and dynamics of complex networks. Proteins in 3D space may also be considered as complex systems emerged through the interactions of their constituent amino acids. This representation provides a powerful framework to uncover the general organized principle of protein contact network. Here we reviewed protein contact map in terms of protein structure prediction and analyses. In addition, we had also discussed the various computational techniques for the prediction of protein contact maps and the tools to visualize contact maps.

  12. Monolithic 3D titania with ultrathin nanoshell structures for enhanced photocatalytic activity and recyclability

    NASA Astrophysics Data System (ADS)

    Ahn, Changui; Park, Junyong; Kim, Donghyuk; Jeon, Seokwoo

    2013-10-01

    nanoshell titania increases the photocatalytic performance more than three-fold relative to that of a thin film of equivalent sample size. Also, the monolithic form of titania enables it to be reused without any degradation of photocatalytic activity. The newly developed nanomaterials in this study can serve as an efficient and reusable photocatalyst for water purification systems. Electronic supplementary information (ESI) available: Further details of SEM images of 3D nanoshell titania and a P25 film, thickness of coated titania measured by AFM, photocatalytic performance of a P25 film and a thin film, a detailed unit cell model of 3D nanostructures for calculation of the theoretical surface area, and comparison data of photocatalytic performances with references. See DOI: 10.1039/c3nr03115b

  13. A 3D model describing the initial structure of an artificial hydrological catchment

    NASA Astrophysics Data System (ADS)

    Maurer, T.; Schneider, A.; Buczko, U.; Gerke, H. H.

    2009-04-01

    The initial development stages of artificially constructed hydrologic catchments are characterized by the absence of vegetation, soil organic matter and soil horizons. This results in increased surface runoff and favors erosion processes that dominate the initial phase. Hydraulic conditions on artificial catchments thus are governed by rapidly changing surface structures as well as by the primary internal structural framework. Contemporary hydrological modeling does not consider any dynamic change of relevant structural features but rather assumes a stable, invariant landscape. The objective of this study was the digital visualization and quantitative description of the initial state and its early structural dynamics, exemplified for the small artificial hydrological catchment "Huehnerwasser" near Cottbus, Germany. Photogrammetric surveys of surface and internal structural units (clay basis liner) during the construction phase provided spatially and temporally resolved data for digital elevation models (DEM). Interpolated physical and chemical soil properties obtained at a borehole grid (e.g., texture) are used for the visualization of spatial distribution of relevant (hydraulic) parameters. The data are merged in a database and visualized in the 3D-GIS application GoCAD. The specific technological construction processes determines the internal structure of the artificial catchment. Resulting differences in bulk density and texture are supposed to have considerable impact on hydraulic properties. A structure generator program was implemented to reproduce the initial structure of the sediment layer as closely as possible. Results of the digital structure generation are checked with non-invasive geophysical measurements, on-site bore holes data and off-site 2D vertical spoil exploration. The accuracy of structure generator results will be compared with predictions of different interpolation methods. Thus, the structure model will serve as a basis for deriving the 3D

  14. Generating 3D hyperspectral information with lightweight UAV snapshot cameras for vegetation monitoring: From camera calibration to quality assurance

    NASA Astrophysics Data System (ADS)

    Aasen, Helge; Burkart, Andreas; Bolten, Andreas; Bareth, Georg

    2015-10-01

    This paper describes a novel method to derive 3D hyperspectral information from lightweight snapshot cameras for unmanned aerial vehicles for vegetation monitoring. Snapshot cameras record an image cube with one spectral and two spatial dimensions with every exposure. First, we describe and apply methods to radiometrically characterize and calibrate these cameras. Then, we introduce our processing chain to derive 3D hyperspectral information from the calibrated image cubes based on structure from motion. The approach includes a novel way for quality assurance of the data which is used to assess the quality of the hyperspectral data for every single pixel in the final data product. The result is a hyperspectral digital surface model as a representation of the surface in 3D space linked with the hyperspectral information emitted and reflected by the objects covered by the surface. In this study we use the hyperspectral camera Cubert UHD 185-Firefly, which collects 125 bands from 450 to 950 nm. The obtained data product has a spatial resolution of approximately 1 cm for the spatial and 21 cm for the hyperspectral information. The radiometric calibration yields good results with less than 1% offset in reflectance compared to an ASD FieldSpec 3 for most of the spectral range. The quality assurance information shows that the radiometric precision is better than 0.13% for the derived data product. We apply the approach to data from a flight campaign in a barley experiment with different varieties during the growth stage heading (BBCH 52 - 59) to demonstrate the feasibility for vegetation monitoring in the context of precision agriculture. The plant parameters retrieved from the data product correspond to in-field measurements of a single date field campaign for plant height (R2 = 0.7), chlorophyll (BGI2, R2 = 0.52), LAI (RDVI, R2 = 0.32) and biomass (RDVI, R2 = 0.29). Our approach can also be applied for other image-frame cameras as long as the individual bands of the

  15. Towards Automated Seismic Moment Tensor Inversion in Australia Using 3D Structural Model

    NASA Astrophysics Data System (ADS)

    Hingee, M.; Tkalcic, H.; Fichtner, A.; Sambridge, M.; Kennett, B. L.; Gorbatov, A.

    2009-12-01

    There is significant seismic activity in the region around Australia, largely due to the plate boundaries to the north and to the east of the mainland. This seismicity poses serious seismic and tsunamigenic hazard in a wider region, and risk to coastal areas of Australia, and is monitored by Geoscience Australia (GA) using a network of permanent broadband seismometers within Australia. Earthquake and tsunami warning systems were established by the Australian Government and have been using the waveforms from the GA seismological network. The permanent instruments are augmented by non-GA seismic stations based both within and outside of Australia. In particular, seismic moment tensor (MT) solutions for events around Australia as well as local distances are useful for both warning systems and geophysical studies in general. These monitoring systems, however, currently use only one dimensional, spherically-symmetric models of the Earth for source parameter determination. Recently, a novel 3D model of Australia and the surrounding area has been developed from spectral element simulations [1], taking into account not only velocity heterogeneities, but also radial anisotropy and seismic attenuation. This development, inter alia, introduces the potential of providing significant improvements in MT solution accuracy. Allowing reliable MT solutions with reduced dependence on non-GA stations is a secondary advantage. We studied the feasibility of using 1D versus 3D structural models. The accuracy of the 3D model has been investigated, confirming that these models are in most cases superior to the 1D models. A full MT inversion method using a point source approximation was developed as the first step, keeping in mind that for more complex source time functions, a finite source inversion will be needed. Synthetic experiments have been performed with random noise added to the signal to test the code in the both 1D and 3D setting, using a precomputed library of structural Greens

  16. Molecular Phylogeny and Predicted 3D Structure of Plant beta-D-N-Acetylhexosaminidase

    PubMed Central

    Hossain, Md. Anowar

    2014-01-01

    beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom. PMID:25165734

  17. Molecular phylogeny and predicted 3D structure of plant beta-D-N-acetylhexosaminidase.

    PubMed

    Hossain, Md Anowar; Roslan, Hairul Azman

    2014-01-01

    beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom.

  18. Uncovering the structural basis of protein interactions with efficient clustering of 3-D interaction interfaces.

    PubMed

    Aung, Z; Tan, S-H; Ng, S-K; Tan, K-L

    2007-01-01

    The biological mechanisms with which proteins interact with one another are best revealed by studying the structural interfaces between interacting proteins. Protein-protein interfaces can be extracted from 3-D structural data of protein complexes and then clustered to derive biological insights. However, conventional protein interface clustering methods lack computational scalability and statistical support. In this work, we present a new method named "PPiClust" to systematically encode, cluster and analyze similar 3-D interface patterns in protein complexes efficiently. Experimental results showed that our method is effective in discovering visually consistent and statistically significant clusters of interfaces, and at the same time sufficiently time-efficient to be performed on a single computer. The interface clusters are also useful for uncovering the structural basis of protein interactions. Analysis of the resulting interface clusters revealed groups of structurally diverse proteins having similar interface patterns. We also found, in some of the interface clusters, the presence of well-known linear binding motifs which were non-contiguous in the primary sequences. These results suggest that PPiClust can discover not only statistically significant but also biologically significant protein interface clusters from protein complex structural data.

  19. A Method for Developing 3D User Interfaces of Information Systems

    NASA Astrophysics Data System (ADS)

    Calleros, Juan Manuel González; Vanderdonckt, Jean; Arteaga, Jaime Muñoz

    A transformational method for developing tri-dimensional user interfaces of interactive information systems is presented that starts from a task model and a domain model to progressively derive a final user interface. This method consists of three steps: deriving one or many abstract user interfaces from a task model and a domain model, deriving one or many concrete user interfaces from each abstract interface, and producing the code of the final user interfaces corresponding to each concrete interface. To ensure the two first steps, trans-formations are encoded as graph transformations performed on the involved models expressed in their graph equivalent. In addition, a graph grammar gathers relevant graph transformations for accomplishing the sub-steps involved in each step. Once a concrete user interface is resulting from these two first steps, it is converted in a development environment for 3D user interfaces where it can be edited for fine tuning and personalization. From this environment, the user interface code is automatically generated. The method is defined by its steps, input/output, and exemplified on a case study. By expressing the steps of the method through transformations between models, the method adheres to Model-Driven Engineering paradigm where models and transformations are explicitly defined and used

  20. Construction of topological structure of 3D coronary vessels for analysis of catheter navigation in interventional cardiology simulation

    NASA Astrophysics Data System (ADS)

    Wang, Yaoping; Chui, Cheekong K.; Cai, Yiyu; Mak, KoonHou

    1998-06-01

    This study presents an approach to build a 3D vascular system of coronary for the development of a virtual cardiology simulator. The 3D model of the coronary arterial tree is reconstructed from the geometric information segmented from the Visible Human data set for physical analysis of catheterization. The process of segmentation is guided by a 3D topologic hierarchy structure of coronary vessels which is obtained from a mechanical model by using Coordinate Measuring Machine (CMM) probing. This mechanical professional model includes all major coronary arterials ranging from right coronary artery to atrioventricular branch and from left main trunk to left anterior descending branch. All those branches are considered as the main operating sites for cardiology catheterization. Along with the primary arterial vasculature and accompanying secondary and tertiary networks obtained from a previous work, a more complete vascular structure can then be built for the simulation of catheterization. A novel method has been developed for real time Finite Element Analysis of catheter navigation based on this featured vasculature of vessels.

  1. Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure.

    PubMed

    Tokheim, Collin; Bhattacharya, Rohit; Niknafs, Noushin; Gygax, Derek M; Kim, Rick; Ryan, Michael; Masica, David L; Karchin, Rachel

    2016-07-01

    The impact of somatic missense mutation on cancer etiology and progression is often difficult to interpret. One common approach for assessing the contribution of missense mutations in carcinogenesis is to identify genes mutated with statistically nonrandom frequencies. Even given the large number of sequenced cancer samples currently available, this approach remains underpowered to detect drivers, particularly in less studied cancer types. Alternative statistical and bioinformatic approaches are needed. One approach to increase power is to focus on localized regions of increased missense mutation density or hotspot regions, rather than a whole gene or protein domain. Detecting missense mutation hotspot regions in three-dimensional (3D) protein structure may also be beneficial because linear sequence alone does not fully describe the biologically relevant organization of codons. Here, we present a novel and statistically rigorous algorithm for detecting missense mutation hotspot regions in 3D protein structures. We analyzed approximately 3 × 10(5) mutations from The Cancer Genome Atlas (TCGA) and identified 216 tumor-type-specific hotspot regions. In addition to experimentally determined protein structures, we considered high-quality structural models, which increase genomic coverage from approximately 5,000 to more than 15,000 genes. We provide new evidence that 3D mutation analysis has unique advantages. It enables discovery of hotspot regions in many more genes than previously shown and increases sensitivity to hotspot regions in tumor suppressor genes (TSG). Although hotspot regions have long been known to exist in both TSGs and oncogenes, we provide the first report that they have different characteristic properties in the two types of driver genes. We show how cancer researchers can use our results to link 3D protein structure and the biologic functions of missense mutations in cancer, and to generate testable hypotheses about driver mechanisms. Our results

  2. Colloidal and polyelectrolyte inks for direct-write assembly of 3D periodic structures

    NASA Astrophysics Data System (ADS)

    Gratson, Gregory Michael

    Novel inks were developed for the direct-write assembly of 3D periodic structures with varying feature size. Specifically, two ink designs were pursued: (1) a model colloidal ink (feature size > 100 mum) and (2) a polyelectrolyte ink (feature size ˜ 1 mum). The rheological properties of both inks were specifically tailored for our direct-write assembly process, which involves ink deposition through a fine scale nozzle that is robotically controlled using a 3-axis stage. Central to this approach is the design of inks that are capable of flowing through deposition nozzles of varying size and then "setting" immediately to facilitate shape retention of the deposited features. In addition, the inks must contain a high solid volume fraction to minimize drying-induced shrinkage after assembly is complete. First, a model colloidal ink based on monodisperse silica microspheres was designed for 3D periodic structures. These colloidal inks suffer difficulties (e.g., nozzle clogging) when used to fabricate structures with feature sizes below ˜ 100 mum, so a different ink design was pursued based on polyelectrolyte complexes. These inks rapidly solidified upon deposition into an IPA/water coagulation reservoir, and the exact coagulation mechanism depended strongly on reservoir composition. The water/IPA ratio in the reservoir (83--88 % IPA) was carefully tailored to produce filaments that could maintain their shape while spanning unsupported regions in the structure, yet were flexible enough to adhere to the substrate or underlying layers. Several micro-periodic structures of varying design were fabricated, revealing the facile nature of our approach. 3D micro-periodic scaffolds were used to create photonic crystals with high refractive index contrast. Silica chemical vapor deposition was performed under ambient conditions to produce a thin inorganic layer around the polymer, which facilitated further high-temperature steps. The polymer was removed through burnout at 475

  3. Color influence on accuracy of 3D scanners based on structured light

    NASA Astrophysics Data System (ADS)

    Voisin, Sophie; Page, David L.; Foufou, Sebti; Truchetet, Frédéric; Abidi, Mongi A.

    2006-02-01

    The characterization of commercial 3D scanners allows acquiring precise and useful data. The accuracy of range and, more recently, color for 3D scanners is usually studied separately, but when the 3D scanner is based on structured light with a color coding pattern, color influence on range accuracy should be investigated. The commercial product that we have tested has the particularity that it can acquire data under ambient light instead of a controlled environment as it is with most available scanners. Therefore, based on related work in the literature and on experiments we have done on a variety of standard illuminants, we have designed an interesting setup to control illuminant interference. Basically, the setup consists of acquiring the well-known Macbeth ColorChecker under a controlled environment and also ambient daylight. The results have shown variations with respect to the color. We have performed several statistical studies to show how the range results evolve with respect to the RGB and the HSV channels. In addition, a systematic noise error has also been identified. This noise depends on the object color. A subset of colors shows strong noise errors while other colors have minimal or even no systematic error under the same illuminant.

  4. Modeling the Impact of Drizzle and 3D Cloud Structure on Remote Sensing of Effective Radius

    NASA Technical Reports Server (NTRS)

    Platnick, Steven; Zinner, Tobias; Ackerman, S.

    2008-01-01

    Remote sensing of cloud particle size with passive sensors like MODIS is an important tool for cloud microphysical studies. As a measure of the radiatively relevant droplet size, effective radius can be retrieved with different combinations of visible through shortwave infrared channels. MODIS observations sometimes show significantly larger effective radii in marine boundary layer cloud fields derived from the 1.6 and 2.1 pm channel observations than for 3.7 pm retrievals. Possible explanations range from 3D radiative transport effects and sub-pixel cloud inhomogeneity to the impact of drizzle formation on the droplet distribution. To investigate the potential influence of these factors, we use LES boundary layer cloud simulations in combination with 3D Monte Carlo simulations of MODIS observations. LES simulations of warm cloud spectral microphysics for cases of marine stratus and broken stratocumulus, each for two different values of cloud condensation nuclei density, produce cloud structures comprising droplet size distributions with and without drizzle size drops. In this study, synthetic MODIS observations generated from 3D radiative transport simulations that consider the full droplet size distribution will be generated for each scene. The operational MODIS effective radius retrievals will then be applied to the simulated reflectances and the results compared with the LES microphysics.

  5. PACS-based interface for 3D anatomical structure visualization and surgical planning

    NASA Astrophysics Data System (ADS)

    Koehl, Christophe; Soler, Luc; Marescaux, Jacques

    2002-05-01

    The interpretation of radiological image is routine but it remains a rather difficult task for physicians. It requires complex mental processes, that permit translation from 2D slices into 3D localization and volume determination of visible diseases. An easier and more extensive visualization and exploitation of medical images can be reached through the use of computer-based systems that provide real help from patient admission to post-operative followup. In this way, we have developed a 3D visualization interface linked to a PACS database that allows manipulation and interaction on virtual organs delineated from CT-scan or MRI. This software provides the 3D real-time surface rendering of anatomical structures, an accurate evaluation of volumes and distances and the improvement of radiological image analysis and exam annotation through a negatoscope tool. It also provides a tool for surgical planning allowing the positioning of an interactive laparoscopic instrument and the organ resection. The software system could revolutionize the field of computerized imaging technology. Indeed, it provides a handy and portable tool for pre-operative and intra-operative analysis of anatomy and pathology in various medical fields. This constitutes the first step of the future development of augmented reality and surgical simulation systems.

  6. Algorithms for extraction of structural attitudes from 3D outcrop models

    NASA Astrophysics Data System (ADS)

    Duelis Viana, Camila; Endlein, Arthur; Ademar da Cruz Campanha, Ginaldo; Henrique Grohmann, Carlos

    2016-05-01

    The acquisition of geological attitudes on rock cuts using traditional field compass survey can be a time consuming, dangerous, or even impossible task depending on the conditions and location of outcrops. The importance of this type of data in rock-mass classifications and structural geology has led to the development of new techniques, in which the application of photogrammetric 3D digital models has had an increasing use. In this paper we present two algorithms for extraction of attitudes of geological discontinuities from virtual outcrop models: ply2atti and scanline, implemented with the Python programming language. The ply2atti algorithm allows for the virtual sampling of planar discontinuities appearing on the 3D model as individual exposed surfaces, while the scanline algorithm allows the sampling of discontinuities (surfaces and traces) along a virtual scanline. Application to digital models of a simplified test setup and a rock cut demonstrated a good correlation between the surveys undertaken using traditional field compass reading and virtual sampling on 3D digital models.

  7. Proof of Concept of Integrated Load Measurement in 3D Printed Structures

    PubMed Central

    Hinderdael, Michaël; Jardon, Zoé; Lison, Margot; De Baere, Dieter; Devesse, Wim; Strantza, Maria; Guillaume, Patrick

    2017-01-01

    Currently, research on structural health monitoring systems is focused on direct integration of the system into a component or structure. The latter results in a so-called smart structure. One example of a smart structure is a component with integrated strain sensing for continuous load monitoring. Additive manufacturing, or 3D printing, now also enables such integration of functions inside components. As a proof-of-concept, the Fused Deposition Modeling (FDM) technique was used to integrate a strain sensing element inside polymer (ABS) tensile test samples. The strain sensing element consisted of a closed capillary filled with a fluid and connected to an externally mounted pressure sensor. The volumetric deformation of the integrated capillary resulted in pressure changes in the fluid. The obtained pressure measurements during tensile testing are reported in this paper and compared to state-of-the-art extensometer measurements. The sensitivity of the 3D printed pressure-based strain sensor is primarily a function of the compressibility of the capillary fluid. Air- and watertightness are of critical importance for the proper functioning of the 3D printed pressure-based strain sensor. Therefore, the best after-treatment procedure was selected on basis of a comparative analysis. The obtained pressure measurements are linear with respect to the extensometer readings, and the uncertainty on the strain measurement of a capillary filled with water (incompressible fluid) is ±3.1 µstrain, which is approximately three times less sensitive than conventional strain gauges (±1 µstrain), but 32 times more sensitive than the same sensor based on air (compressible fluid) (±101 µstrain). PMID:28208779

  8. Proof of Concept of Integrated Load Measurement in 3D Printed Structures.

    PubMed

    Hinderdael, Michaël; Jardon, Zoé; Lison, Margot; De Baere, Dieter; Devesse, Wim; Strantza, Maria; Guillaume, Patrick

    2017-02-09

    Currently, research on structural health monitoring systems is focused on direct integration of the system into a component or structure. The latter results in a so-called smart structure. One example of a smart structure is a component with integrated strain sensing for continuous load monitoring. Additive manufacturing, or 3D printing, now also enables such integration of functions inside components. As a proof-of-concept, the Fused Deposition Modeling (FDM) technique was used to integrate a strain sensing element inside polymer (ABS) tensile test samples. The strain sensing element consisted of a closed capillary filled with a fluid and connected to an externally mounted pressure sensor. The volumetric deformation of the integrated capillary resulted in pressure changes in the fluid. The obtained pressure measurements during tensile testing are reported in this paper and compared to state-of-the-art extensometer measurements. The sensitivity of the 3D printed pressure-based strain sensor is primarily a function of the compressibility of the capillary fluid. Air- and watertightness are of critical importance for the proper functioning of the 3D printed pressure-based strain sensor. Therefore, the best after-treatment procedure was selected on basis of a comparative analysis. The obtained pressure measurements are linear with respect to the extensometer readings, and the uncertainty on the strain measurement of a capillary filled with water (incompressible fluid) is ±3.1 µstrain, which is approximately three times less sensitive than conventional strain gauges (±1 µstrain), but 32 times more sensitive than the same sensor based on air (compressible fluid) (±101 µstrain).

  9. Experimental Investigation of the Near Wall Flow Structure of a Low Reynolds Number 3-D Turbulent Boundary Layer

    NASA Technical Reports Server (NTRS)

    Fleming, J. L.; Simpson, R. L.

    1997-01-01

    Laser Doppler velocimetry (LDV) measurements and hydrogen bubble flow visualization techniques were used to examine the near-wall flow structure of 2D and 3D turbulent boundary layers (TBLs) over a range of low Reynolds numbers. The goals of this research were (1) an increased understanding of the flow physics in the near wall region of turbulent boundary layers,(2) to observe and quantify differences between 2D and 3D TBL flow structures, and (3) to document Reynolds number effects for 3D TBLs. The LDV data have provided results detailing the turbulence structure of the 2D and 3D TBLs. These results include mean Reynolds stress distributions, flow skewing results, and U and V spectra. Effects of Reynolds number for the 3D flow were also examined. Comparison to results with the same 3D flow geometry but at a significantly higher Reynolds number provided unique insight into the structure of 3D TBLs. While the 3D mean and fluctuating velocities were found to be highly dependent on Reynolds number, a previously defined shear stress parameter was discovered to be invariant with Reynolds number. The hydrogen bubble technique was used as a flow visualization tool to examine the near-wall flow structure of 2D and 3D TBLs. Both the quantitative and qualitative results displayed larger turbulent fluctuations with more highly concentrated vorticity regions for the 2D flow.

  10. Generation of (3 + d)-dimensional superspace groups for describing the symmetry of modulated crystalline structures.

    PubMed

    Stokes, Harold T; Campbell, Branton J; van Smaalen, Sander

    2011-01-01

    A complete table of (3 + 1)D, (3 + 2)D and (3 + 3)D superspace groups (SSGs) has been enumerated that corrects omissions and duplicate entries in previous tables of superspace groups and Bravais classes. The theoretical methods employed are not new, though the implementation is both novel and robust. The paper also describes conventions for assigning a unique one-line symbol for each group in the table. Finally, a new online data repository is introduced that delivers more complete information about each SSG than has been presented previously.

  11. Comparative 3D genome structure analysis of the fission and the budding yeast.

    PubMed

    Gong, Ke; Tjong, Harianto; Zhou, Xianghong Jasmine; Alber, Frank

    2015-01-01

    We studied the 3D structural organization of the fission yeast genome, which emerges from the tethering of heterochromatic regions in otherwise randomly configured chromosomes represented as flexible polymer chains in an nuclear environment. This model is sufficient to explain in a statistical manner many experimentally determined distinctive features of the fission yeast genome, including chromatin interaction patterns from Hi-C experiments and the co-locations of functionally related and co-expressed genes, such as genes expressed by Pol-III. Our findings demonstrate that some previously described structure-function correlations can be explained as a consequence of random chromatin collisions driven by a few geometric constraints (mainly due to centromere-SPB and telomere-NE tethering) combined with the specific gene locations in the chromosome sequence. We also performed a comparative analysis between the fission and budding yeast genome structures, for which we previously detected a similar organizing principle. However, due to the different chromosome sizes and numbers, substantial differences are observed in the 3D structural genome organization between the two species, most notably in the nuclear locations of orthologous genes, and the extent of nuclear territories for genes and chromosomes. However, despite those differences, remarkably, functional similarities are maintained, which is evident when comparing spatial clustering of functionally related genes in both yeasts. Functionally related genes show a similar spatial clustering behavior in both yeasts, even though their nuclear locations are largely different between the yeast species.

  12. Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates

    PubMed Central

    Matthew Ward, R.; Venner, Eric; Daines, Bryce; Murray, Stephen; Erdin, Serkan; Kristensen, David M.; Lichtarge, Olivier

    2009-01-01

    Summary:The Evolutionary Trace Annotation (ETA) Server predicts enzymatic activity. ETA starts with a structure of unknown function, such as those from structural genomics, and with no prior knowledge of its mechanism uses the phylogenetic Evolutionary Trace (ET) method to extract key functional residues and propose a function-associated 3D motif, called a 3D template. ETA then searches previously annotated structures for geometric template matches that suggest molecular and thus functional mimicry. In order to maximize the predictive value of these matches, ETA next applies distinctive specificity filters—evolutionary similarity, function plurality and match reciprocity. In large scale controls on enzymes, prediction coverage is 43% but the positive predictive value rises to 92%, thus minimizing false annotations. Users may modify any search parameter, including the template. ETA thus expands the ET suite for protein structure annotation, and can contribute to the annotation efforts of metaservers. Availability:The ETA Server is a web application available at http://mammoth.bcm.tmc.edu/eta/. Contact: lichtarge@bcm.edu PMID:19307237

  13. GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.

    PubMed

    Boudard, Mélanie; Bernauer, Julie; Barth, Dominique; Cohen, Johanne; Denise, Alain

    2015-01-01

    Cellular processes involve large numbers of RNA molecules. The functions of these RNA molecules and their binding to molecular machines are highly dependent on their 3D structures. One of the key challenges in RNA structure prediction and modeling is predicting the spatial arrangement of the various structural elements of RNA. As RNA folding is generally hierarchical, methods involving coarse-grained models hold great promise for this purpose. We present here a novel coarse-grained method for sampling, based on game theory and knowledge-based potentials. This strategy, GARN (Game Algorithm for RNa sampling), is often much faster than previously described techniques and generates large sets of solutions closely resembling the native structure. GARN is thus a suitable starting point for the molecular modeling of large RNAs, particularly those with experimental constraints. GARN is available from: http://garn.lri.fr/.

  14. Evaluation of geological conditions for coalbed methane occurrence based on 3D seismic information: a case study in Fowa region, Xinjing coal mine, China

    NASA Astrophysics Data System (ADS)

    Li, Juanjuan; Li, Fanjia; Hu, Mingshun; Zhang, Wei; Pan, Dongming

    2017-03-01

    The research on geological conditions of coalbed methane (CBM) occurrence is of great significance for predicting the high abundance CBM rich region and gas outburst risk area pre-warning. The No. 3 coal seam, in Yangquan coalfield of Qinshui basin, is the research target studied by 3D seismic exploration technique. The geological factors which affect CBM occurrence are interpreted based on the 3D seismic information. First, the geological structure (faults, folds, and collapse columns) is found out by the 3D seismic structural interpretation and the information of buried depth and thickness of the coal seam is calculated by the seismic horizons. Second, 3D elastic impedance (EI) and natural gamma attribute volumes are generated by prestack EI inversion and multi-attribute probabilistic neural network (PNN) inversion techniques which reflect the information of coal structure types and lithology of the roof and floor. Then, the information of metamorphic degree of seam and hydrogeology conditions can be obtained by the geological data. Consequently, geological conditions of CBM occurrence in No. 3 coal seam are evaluated which will provide scientific reference for high abundance CBM rich region prediction and gas outburst risk area pre-warning.

  15. 3D P-wave velocity structure of the deep Galicia rifted margin: A first analysis of the Galicia 3D wide-angle seismic dataset

    NASA Astrophysics Data System (ADS)

    Bayrakci, Gaye; Minshull, Timothy A.; Davy, Richard G.; Karplus, Marianne S.; Kaeschen, Dirk; Papenberg, Cord; Krabbenhoeft, Anne; Sawyer, Dale; Reston, Timothy J.; Shillington, Donna J.; Ranero, César R.

    2014-05-01

    Galicia 3D, a reflection-refraction and long offset seismic experiment was carried out from May through September 2013, at the Galicia rifted margin (in the northeast Atlantic Ocean, west of Spain) as a collaboration between US, UK, German and Spanish groups. The 3D multichannel seismic acquisition conducted by R/V Marcus Langseth covered a 64 km by 20 km (1280 km2) zone where the main geological features are the Peridotite Ridge (PR), composed of serpentinized peridotite and thought be upper mantle exhumed to the seafloor during rifting, and the S reflector which has been interpreted to be a low angle detachment fault overlain by fault bounded, rotated, continental crustal blocks. In the 3D box, two airgun arrays of 3300 cu.in. were fired alternately (in flip-flop configuration) every 37.5 m. All shots are recorded by 44 short period four component ocean bottom seismometers (OBS) and 26 ocean bottom hydrophones (OBH) deployed and recovered by R/V Poseidon, as well as four 6 km hydrophone streamers with 12.5 m channel spacing towed by R/V Marcus Langseth. We present the preliminary results of the first arrival time tomography study which is carried out with a subset of the wide-angle dataset, in order to generate a 3D P-wave velocity volume for the entire depth sampled by the reflection data. After the relocation of OBSs and OBHs, an automatic first-arrival time picking approach is applied to a subset of the dataset, which comprises more than 5.5 million source-receiver pairs. Then, the first-arrival times are checked visually, in 3-dimensions. The a priori model used for the first-arrival time tomography is built up using information from previous seismic surveys carried out at the Galicia margin (e.g. ISE, 1997). The FAST algorithm of Zelt and Barton (1998) is used for the first-arrival time inversion. The 3D P-wave velocity volume can be used in interpreting the reflection dataset, as a starting point for migration, to quantify the thinning of the crustal layers

  16. Cross modality registration of video and magnetic tracker data for 3D appearance and structure modeling

    NASA Astrophysics Data System (ADS)

    Sargent, Dusty; Chen, Chao-I.; Wang, Yuan-Fang

    2010-02-01

    The paper reports a fully-automated, cross-modality sensor data registration scheme between video and magnetic tracker data. This registration scheme is intended for use in computerized imaging systems to model the appearance, structure, and dimension of human anatomy in three dimensions (3D) from endoscopic videos, particularly colonoscopic videos, for cancer research and clinical practices. The proposed cross-modality calibration procedure operates this way: Before a colonoscopic procedure, the surgeon inserts a magnetic tracker into the working channel of the endoscope or otherwise fixes the tracker's position on the scope. The surgeon then maneuvers the scope-tracker assembly to view a checkerboard calibration pattern from a few different viewpoints for a few seconds. The calibration procedure is then completed, and the relative pose (translation and rotation) between the reference frames of the magnetic tracker and the scope is determined. During the colonoscopic procedure, the readings from the magnetic tracker are used to automatically deduce the pose (both position and orientation) of the scope's reference frame over time, without complicated image analysis. Knowing the scope movement over time then allows us to infer the 3D appearance and structure of the organs and tissues in the scene. While there are other well-established mechanisms for inferring the movement of the camera (scope) from images, they are often sensitive to mistakes in image analysis, error accumulation, and structure deformation. The proposed method using a magnetic tracker to establish the camera motion parameters thus provides a robust and efficient alternative for 3D model construction. Furthermore, the calibration procedure does not require special training nor use expensive calibration equipment (except for a camera calibration pattern-a checkerboard pattern-that can be printed on any laser or inkjet printer).

  17. Spectral element method for band-structure calculations of 3D phononic crystals

    NASA Astrophysics Data System (ADS)

    Shi, Linlin; Liu, Na; Zhou, Jianyang; Zhou, Yuanguo; Wang, Jiamin; Huo Liu, Qing

    2016-11-01

    The spectral element method (SEM) is a special kind of high-order finite element method (FEM) which combines the flexibility of a finite element method with the accuracy of a spectral method. In contrast to the traditional FEM, the SEM exhibits advantages in the high-order accuracy as the error decreases exponentially with the increase of interpolation degree by employing the Gauss-Lobatto-Legendre (GLL) polynomials as basis functions. In this study, the spectral element method is developed for the first time for the determination of band structures of 3D isotropic/anisotropic phononic crystals (PCs). Based on the Bloch theorem, we present a novel, intuitive discretization formulation for Navier equation in the SEM scheme for periodic media. By virtue of using the orthogonal Legendre polynomials, the generalized eigenvalue problem is converted to a regular one in our SEM implementation to improve the efficiency. Besides, according to the specific geometry structure, 8-node and 27-node hexahedral elements as well as an analytic mesh have been used to accurately capture curved PC models in our SEM scheme. To verify its accuracy and efficiency, this study analyses the phononic-crystal plates with square and triangular lattice arrangements, and the 3D cubic phononic crystals consisting of simple cubic (SC), bulk central cubic (BCC) and faced central cubic (FCC) lattices with isotropic or anisotropic scatters. All the numerical results considered demonstrate that SEM is superior to the conventional FEM and can be an efficient alternative method for accurate determination of band structures of 3D phononic crystals.

  18. Monte Carlo generators for studies of the 3D structure of the nucleon

    DOE PAGES

    Avakian, Harut; D'Alesio, U.; Murgia, F.

    2015-01-23

    In this study, extraction of transverse momentum and space distributions of partons from measurements of spin and azimuthal asymmetries requires development of a self consistent analysis framework, accounting for evolution effects, and allowing control of systematic uncertainties due to variations of input parameters and models. Development of realistic Monte-Carlo generators, accounting for TMD evolution effects, spin-orbit and quark-gluon correlations will be crucial for future studies of quark-gluon dynamics in general and 3D structure of the nucleon in particular.

  19. Photopolymerization of 3D conductive polypyrrole structures via digital light processing

    NASA Astrophysics Data System (ADS)

    Price, Aaron D.

    2016-04-01

    The intrinsically conductive polymer polypyrrole is conventionally synthesized as monolithic films that exhibit significant actuation strains when subjected to an applied electric potential. Though numerous linear and bending actuators based on polypyrrole films have been investigated, the limitations inherent to planar film geometries inhibit the realization of more complex behaviours. Hence, three-dimensional polypyrrole structures are sought to greatly expand the potential applications for conductive polymer actuators. This research aims to develop a novel additive manufacturing method for the fabrication of three-dimensional structures of conductive polypyrrole. In this investigation, radiation-curing techniques are employed by means of digital light processing (DLP) technology. DLP is an additive manufacturing technique where programmed light patterns emitted from a dedicated source are used to selectively cure a specially formulated polymer resin. Successive curing operations lead to a layered 3D structure into which fine features may be incorporated. Energy dispersive spectroscopy (EDS) is subsequently employed to examine the unique microstructural features of the resultant 3D printed polymer morphology in order to elucidate the nature of the conductivity. These polymer microstructures are highly desirable since actuation response times are highly dependent on ion transport distances, and hence the ability to fabricate fine features offers a potential mechanism to improve actuator performance.

  20. 3D X-rays application for precision measurement of the cell structure of extruded polystyrene

    NASA Astrophysics Data System (ADS)

    Lim, J. Y.; Kim, K. Y.; Shin, H. S.; Yeom, S.; Lee, S. E.

    2015-12-01

    While the thermal performance of existing insulation materials have been determined by blister gases, the thermal performance of future insulation materials will be dependent on the cell size and independent foam content as we use eco-friendly blister gases with a higher thermal conductivity. However, with the current technology we are only able to guess the whole cell size and independent foam content through SEM applied 2D fragmentary scanning but are still far from the level of accurate cell structure data extraction. Under this situation, we utilized X-ray CT scanned 3D images to identify and shape the cell structure and proposed a method of inferring the whole distribution and independent foam content as accurately as possible. According to X-ray CT scanning images and SEM images, the shape was similar but according to tracer applied CT scanning images, the cell size distribution was 380∼400 pm within the range of the general insulation diameter distribution which had the highest reliability. As for extrusion foaming polystyrene, we need additional image processing to identify the independent foam content as its density is too low. So, it is recommended to raise the 3D cell structure completeness of XPS by improving the scanning accuracy.

  1. Robotic extrusion processes for direct ink writing of 3D conductive polyaniline structures

    NASA Astrophysics Data System (ADS)

    Holness, F. Benjamin; Price, Aaron D.

    2016-04-01

    The intractable nature of intrinsically conductive polymers (ICP) leads to practical limitations in the fabrication of ICP-based transducers having complex three-dimensional geometries. Conventional ICP device fabrication processes have focused primarily on thin-film deposition techniques; therefore this study explores novel additive manufacturing processes specifically developed for ICP with the ultimate goal of increasing the functionality of ICP sensors and actuators. Herein we employ automated polymer paste extrusion processes for the direct ink writing of 3D conductive polyaniline (PANI) structures. Realization of these structures is enabled through a modified fused filament fabrication delta robot equipped with an integrated polymer paste extruder. This unique robot-controlled additive manufacturing platform is capable of fabricating high-resolution 3D conductive PANI and has been utilized to produce structures with a minimum feature size of 1.5 mm. The required processability of PANI is achieved by means of a counter-ion induced thermal doping method. Using this method, a viscous paste is formulated as the extrudate and a thermo-chemical treatment is applied post extrusion to finalize the complexation.

  2. Lamina 3D display: projection-type depth-fused display using polarization-encoded depth information.

    PubMed

    Park, Soon-gi; Yoon, Sangcheol; Yeom, Jiwoon; Baek, Hogil; Min, Sung-Wook; Lee, Byoungho

    2014-10-20

    In order to realize three-dimensional (3D) displays, various multiplexing methods have been proposed to add the depth dimension to two-dimensional scenes. However, most of these methods have faced challenges such as the degradation of viewing qualities, the requirement of complicated equipment, and large amounts of data. In this paper, we further developed our previous concept, polarization distributed depth map, to propose the Lamina 3D display as a method for encoding and reconstructing depth information using the polarization status. By adopting projection optics to the depth encoding system, reconstructed 3D images can be scaled like images of 2D projection displays. 3D reconstruction characteristics of the polarization-encoded images are analyzed with simulation and experiment. The experimental system is also demonstrated to show feasibility of the proposed method.

  3. Correlative Nanoscale 3D Imaging of Structure and Composition in Extended Objects

    PubMed Central

    Xu, Feng; Helfen, Lukas; Suhonen, Heikki; Elgrabli, Dan; Bayat, Sam; Reischig, Péter; Baumbach, Tilo; Cloetens, Peter

    2012-01-01

    Structure and composition at the nanoscale determine the behavior of biological systems and engineered materials. The drive to understand and control this behavior has placed strong demands on developing methods for high resolution imaging. In general, the improvement of three-dimensional (3D) resolution is accomplished by tightening constraints: reduced manageable specimen sizes, decreasing analyzable volumes, degrading contrasts, and increasing sample preparation efforts. Aiming to overcome these limitations, we present a non-destructive and multiple-contrast imaging technique, using principles of X-ray laminography, thus generalizing tomography towards laterally extended objects. We retain advantages that are usually restricted to 2D microscopic imaging, such as scanning of large areas and subsequent zooming-in towards a region of interest at the highest possible resolution. Our technique permits correlating the 3D structure and the elemental distribution yielding a high sensitivity to variations of the electron density via coherent imaging and to local trace element quantification through X-ray fluorescence. We demonstrate the method by imaging a lithographic nanostructure and an aluminum alloy. Analyzing a biological system, we visualize in lung tissue the subcellular response to toxic stress after exposure to nanotubes. We show that most of the nanotubes are trapped inside alveolar macrophages, while a small portion of the nanotubes has crossed the barrier to the cellular space of the alveolar wall. In general, our method is non-destructive and can be combined with different sample environmental or loading conditions. We therefore anticipate that correlative X-ray nano-laminography will enable a variety of in situ and in operando 3D studies. PMID:23185554

  4. 3D Surveying, Modeling and Geo-Information System of the New Campus of ITB-Indonesia

    NASA Astrophysics Data System (ADS)

    Suwardhi, D.; Trisyanti, S. W.; Ainiyah, N.; Fajri, M. N.; Hanan, H.; Virtriana, R.; Edmarani, A. A.

    2016-10-01

    The new campus of ITB-Indonesia, which is located at Jatinangor, requires good facilities and infrastructures to supporting all of campus activities. Those can not be separated from procurement and maintenance activities. Technology for procurement and maintenance of facilities and infrastructures -based computer (information system)- has been known as Building Information Modeling (BIM). Nowadays, that technology is more affordable with some of free software that easy to use and tailored to user needs. BIM has some disadvantages and it requires other technologies to complete it, namely Geographic Information System (GIS). BIM and GIS require surveying data to visualized landscape and buildings on Jatinangor ITB campus. This paper presents the on-going of an internal service program conducted by the researcher, academic staff and students for the university. The program including 3D surveying to support the data requirements for 3D modeling of buildings in CityGML and Industry Foundation Classes (IFC) data model. The entire 3D surveying will produce point clouds that can be used to make 3D model. The 3D modeling is divided into low and high levels of detail modeling. The low levels model is stored in 3D CityGML database, and the high levels model including interiors is stored in BIM Server. 3D model can be used to visualized the building and site of Jatinangor ITB campus. For facility management of campus, an geo-information system is developed that can be used for planning, constructing, and maintaining Jatinangor ITB's facilities and infrastructures. The system uses openMAINT, an open source solution for the Property & Facility Management.

  5. Investigating the Use of 3d Geovisualizations for Urban Design in Informal Settlement Upgrading in South Africa

    NASA Astrophysics Data System (ADS)

    Rautenbach, V.; Coetzee, S.; Çöltekin, A.

    2016-06-01

    Informal settlements are a common occurrence in South Africa, and to improve in-situ circumstances of communities living in informal settlements, upgrades and urban design processes are necessary. Spatial data and maps are essential throughout these processes to understand the current environment, plan new developments, and communicate the planned developments. All stakeholders need to understand maps to actively participate in the process. However, previous research demonstrated that map literacy was relatively low for many planning professionals in South Africa, which might hinder effective planning. Because 3D visualizations resemble the real environment more than traditional maps, many researchers posited that they would be easier to interpret. Thus, our goal is to investigate the effectiveness of 3D geovisualizations for urban design in informal settlement upgrading in South Africa. We consider all involved processes: 3D modelling, visualization design, and cognitive processes during map reading. We found that procedural modelling is a feasible alternative to time-consuming manual modelling, and can produce high quality models. When investigating the visualization design, the visual characteristics of 3D models and relevance of a subset of visual variables for urban design activities of informal settlement upgrades were qualitatively assessed. The results of three qualitative user experiments contributed to understanding the impact of various levels of complexity in 3D city models and map literacy of future geoinformatics and planning professionals when using 2D maps and 3D models. The research results can assist planners in designing suitable 3D models that can be used throughout all phases of the process.

  6. Smart three-dimensional lightweight structure triggered from a thin composite sheet via 3D printing technique

    PubMed Central

    Zhang, Quan; Zhang, Kai; Hu, Gengkai

    2016-01-01

    Complex fabrication process and expensive materials have restricted the development of smart three-dimensional (3D) lightweight structures, which are expected to possess self-shaping, self-folding and self-unfolding performances. Here we present a simple approach to fabricate smart lightweight structures by triggering shape transformation from thin printed composite sheets. The release of the internal strain in printed polymer materials enables the printed composite sheet to keep flat under heating and transform into a designed 3D configuration when cooled down to room temperature. The 3D lightweight structure can be switched between flat and 3D configuration under appropriate thermal stimuli. Our work exploits uniform internal strain in printed materials as a controllable tool to fabricate smart 3D lightweight structures, opening an avenue for possible applications in engineering fields. PMID:26926357

  7. Smart three-dimensional lightweight structure triggered from a thin composite sheet via 3D printing technique

    NASA Astrophysics Data System (ADS)

    Zhang, Quan; Zhang, Kai; Hu, Gengkai

    2016-02-01

    Complex fabrication process and expensive materials have restricted the development of smart three-dimensional (3D) lightweight structures, which are expected to possess self-shaping, self-folding and self-unfolding performances. Here we present a simple approach to fabricate smart lightweight structures by triggering shape transformation from thin printed composite sheets. The release of the internal strain in printed polymer materials enables the printed composite sheet to keep flat under heating and transform into a designed 3D configuration when cooled down to room temperature. The 3D lightweight structure can be switched between flat and 3D configuration under appropriate thermal stimuli. Our work exploits uniform internal strain in printed materials as a controllable tool to fabricate smart 3D lightweight structures, opening an avenue for possible applications in engineering fields.

  8. Smart three-dimensional lightweight structure triggered from a thin composite sheet via 3D printing technique.

    PubMed

    Zhang, Quan; Zhang, Kai; Hu, Gengkai

    2016-02-29

    Complex fabrication process and expensive materials have restricted the development of smart three-dimensional (3D) lightweight structures, which are expected to possess self-shaping, self-folding and self-unfolding performances. Here we present a simple approach to fabricate smart lightweight structures by triggering shape transformation from thin printed composite sheets. The release of the internal strain in printed polymer materials enables the printed composite sheet to keep flat under heating and transform into a designed 3D configuration when cooled down to room temperature. The 3D lightweight structure can be switched between flat and 3D configuration under appropriate thermal stimuli. Our work exploits uniform internal strain in printed materials as a controllable tool to fabricate smart 3D lightweight structures, opening an avenue for possible applications in engineering fields.

  9. Nanoimprint of a 3D structure on an optical fiber for light wavefront manipulation.

    PubMed

    Calafiore, Giuseppe; Koshelev, Alexander; Allen, Frances I; Dhuey, Scott; Sassolini, Simone; Wong, Edward; Lum, Paul; Munechika, Keiko; Cabrini, Stefano

    2016-09-16

    Integration of complex photonic structures onto optical fiber facets enables powerful platforms with unprecedented optical functionalities. Conventional nanofabrication technologies, however, do not permit viable integration of complex photonic devices onto optical fibers owing to their low throughput and high cost. In this paper we report the fabrication of a three-dimensional structure achieved by direct nanoimprint lithography on the facet of an optical fiber. Nanoimprint processes and tools were specifically developed to enable a high lithographic accuracy and coaxial alignment of the optical device with respect to the fiber core. To demonstrate the capability of this new approach, a 3D beam splitter has been designed, imprinted and optically characterized. Scanning electron microscopy and optical measurements confirmed the good lithographic capabilities of the proposed approach as well as the desired optical performance of the imprinted structure. The inexpensive solution presented here should enable advancements in areas such as integrated optics and sensing, achieving enhanced portability and versatility of fiber optic components.

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

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  11. 3D lattice distortions and defect structures in ion-implanted nano-crystals

    DOE PAGES

    Hofmann, Felix; Robinson, Ian K.; Tarleton, Edmund; ...

    2017-04-06

    The ability of Focused Ion Beam (FIB) techniques to cut solid matter at the nano-scale revolutionized the study of material structure across the life-, earth- and material sciences. But a detailed understanding of the damage caused by the ion beam and its effect on material properties remains elusive. We examine this damage in 3D using coherent X-ray diffraction to measure the full lattice strain tensor in FIB-milled gold nano-crystals. We also found that even very low ion doses, previously thought to be negligible, cause substantial lattice distortions. At higher doses, extended self-organized defect structures appear. Combined with detailed numerical calculations,more » these observations allow fundamental insight into the nature of the damage created and the structural instabilities that lead to a surprisingly inhomogeneous morphology.« less

  12. Nanoimprint of a 3D structure on an optical fiber for light wavefront manipulation

    NASA Astrophysics Data System (ADS)

    Calafiore, Giuseppe; Koshelev, Alexander; Allen, Frances I.; Dhuey, Scott; Sassolini, Simone; Wong, Edward; Lum, Paul; Munechika, Keiko; Cabrini, Stefano

    2016-09-01

    Integration of complex photonic structures onto optical fiber facets enables powerful platforms with unprecedented optical functionalities. Conventional nanofabrication technologies, however, do not permit viable integration of complex photonic devices onto optical fibers owing to their low throughput and high cost. In this paper we report the fabrication of a three-dimensional structure achieved by direct nanoimprint lithography on the facet of an optical fiber. Nanoimprint processes and tools were specifically developed to enable a high lithographic accuracy and coaxial alignment of the optical device with respect to the fiber core. To demonstrate the capability of this new approach, a 3D beam splitter has been designed, imprinted and optically characterized. Scanning electron microscopy and optical measurements confirmed the good lithographic capabilities of the proposed approach as well as the desired optical performance of the imprinted structure. The inexpensive solution presented here should enable advancements in areas such as integrated optics and sensing, achieving enhanced portability and versatility of fiber optic components.

  13. Quantification of spatial structure of human proximal tibial bone biopsies using 3D measures of complexity

    NASA Astrophysics Data System (ADS)

    Saparin, Peter I.; Skovhus Thomsen, Jesper; Prohaska, Steffen; Zaikin, Alexei; Kurths, Jürgen; Hege, Hans-Christian; Gowin, Wolfgang

    2005-05-01

    Changes in trabecular bone composition during development of osteoporosis are used as a model for bone loss in microgravity conditions during a space flight. Symbolic dynamics and measures of complexity are proposed and applied to assess quantitatively the structural composition of bone tissue from 3D data sets of human tibia bone biopsies acquired by a micro-CT scanner. In order to justify the newly proposed approach, the measures of complexity of the bone architecture were compared with the results of traditional 2D bone histomorphometry. The proposed technique is able to quantify the structural loss of the bone tissue and may help to diagnose and to monitor changes in bone structure of patients on Earth as well as of the space-flying personnel.

  14. Observed 3D Structure, Generation, and Dissipation of Oceanic Mesoscale Eddies in the South China Sea

    NASA Astrophysics Data System (ADS)

    Zhang, Zhiwei; Tian, Jiwei; Qiu, Bo; Zhao, Wei; Chang, Ping; Wu, Dexing; Wan, Xiuquan

    2016-04-01

    Oceanic mesoscale eddies with horizontal scales of 50–300 km are the most energetic form of flows in the ocean. They are the oceanic analogues of atmospheric storms and are effective transporters of heat, nutrients, dissolved carbon, and other biochemical materials in the ocean. Although oceanic eddies have been ubiquitously observed in the world oceans since 1960s, our understanding of their three-dimensional (3D) structure, generation, and dissipation remains fragmentary due to lack of systematic full water-depth measurements. To bridge this knowledge gap, we designed and conducted a multi-months field campaign, called the South China Sea Mesoscale Eddy Experiment (S-MEE), in the northern South China Sea in 2013/2014. The S-MEE for the first time captured full-depth 3D structures of an anticyclonic and cyclonic eddy pair, which are characterized by a distinct vertical tilt of their axes. By observing the eddy evolution at an upstream versus downstream location and conducting an eddy energy budget analysis, the authors further proposed that generation of submesoscale motions most likely constitutes the dominant dissipation mechanism for the observed eddies.

  15. Observed 3D Structure, Generation, and Dissipation of Oceanic Mesoscale Eddies in the South China Sea.

    PubMed

    Zhang, Zhiwei; Tian, Jiwei; Qiu, Bo; Zhao, Wei; Chang, Ping; Wu, Dexing; Wan, Xiuquan

    2016-04-14

    Oceanic mesoscale eddies with horizontal scales of 50-300 km are the most energetic form of flows in the ocean. They are the oceanic analogues of atmospheric storms and are effective transporters of heat, nutrients, dissolved carbon, and other biochemical materials in the ocean. Although oceanic eddies have been ubiquitously observed in the world oceans since 1960s, our understanding of their three-dimensional (3D) structure, generation, and dissipation remains fragmentary due to lack of systematic full water-depth measurements. To bridge this knowledge gap, we designed and conducted a multi-months field campaign, called the South China Sea Mesoscale Eddy Experiment (S-MEE), in the northern South China Sea in 2013/2014. The S-MEE for the first time captured full-depth 3D structures of an anticyclonic and cyclonic eddy pair, which are characterized by a distinct vertical tilt of their axes. By observing the eddy evolution at an upstream versus downstream location and conducting an eddy energy budget analysis, the authors further proposed that generation of submesoscale motions most likely constitutes the dominant dissipation mechanism for the observed eddies.

  16. Electrohydrodynamic-assisted Assembly of Hierarchically Structured, 3D Crumpled Nanostructures for Efficient Solar Conversions

    PubMed Central

    Ishihara, Hidetaka; Chen, Yen-Chang; De Marco, Nicholas; Lin, Oliver; Huang, Chih-Meng; Limsakoune, Vipawee; Chou, Yi-Chia; Yang, Yang; Tung, Vincent

    2016-01-01

    The tantalizing prospect of harnessing the unique properties of graphene crumpled nanostructures continues to fuel tremendous interest in energy storage and harvesting applications. However, the paper ball-like, hard texture, and closed-sphere morphology of current 3D graphitic nanostructure production not only constricts the conductive pathways but also limits the accessible surface area. Here, we report new insights into electrohydrodynamically-generated droplets as colloidal nanoreactors in that the stimuli-responsive nature of reduced graphene oxide can lead to the formation of crumpled nanostructures with a combination of open structures and doubly curved, saddle-shaped edges. In particular, the crumpled nanostructures dynamically adapt to non-spherical, polyhedral shapes under continuous deposition, ultimately assembling into foam-like microstructures with a highly accessible surface area and spatially interconnected transport pathways. The implementation of such crumpled nanostructures as three-dimensional rear contacts for solar conversion applications realize benefits of a high aspect ratio, electrically addressable and energetically favorable interfaces, and substantial enhancement of both short-circuit currents and fill-factors compared to those made of planar graphene counterparts. Further, the 3D crumpled nanostructures may shed lights onto the development of effective electrocatalytic electrodes due to their open structure that simultaneously allows for efficient water flow and hydrogen escape. PMID:27924857

  17. Electrohydrodynamic-assisted Assembly of Hierarchically Structured, 3D Crumpled Nanostructures for Efficient Solar Conversions

    NASA Astrophysics Data System (ADS)

    Ishihara, Hidetaka; Chen, Yen-Chang; De Marco, Nicholas; Lin, Oliver; Huang, Chih-Meng; Limsakoune, Vipawee; Chou, Yi-Chia; Yang, Yang; Tung, Vincent

    2016-12-01

    The tantalizing prospect of harnessing the unique properties of graphene crumpled nanostructures continues to fuel tremendous interest in energy storage and harvesting applications. However, the paper ball-like, hard texture, and closed-sphere morphology of current 3D graphitic nanostructure production not only constricts the conductive pathways but also limits the accessible surface area. Here, we report new insights into electrohydrodynamically-generated droplets as colloidal nanoreactors in that the stimuli-responsive nature of reduced graphene oxide can lead to the formation of crumpled nanostructures with a combination of open structures and doubly curved, saddle-shaped edges. In particular, the crumpled nanostructures dynamically adapt to non-spherical, polyhedral shapes under continuous deposition, ultimately assembling into foam-like microstructures with a highly accessible surface area and spatially interconnected transport pathways. The implementation of such crumpled nanostructures as three-dimensional rear contacts for solar conversion applications realize benefits of a high aspect ratio, electrically addressable and energetically favorable interfaces, and substantial enhancement of both short-circuit currents and fill-factors compared to those made of planar graphene counterparts. Further, the 3D crumpled nanostructures may shed lights onto the development of effective electrocatalytic electrodes due to their open structure that simultaneously allows for efficient water flow and hydrogen escape.

  18. 3D-Printed Broadband Dielectric Tube Terahertz Waveguide with Anti-Reflection Structure

    NASA Astrophysics Data System (ADS)

    Vogt, Dominik Walter; Leonhardt, Rainer

    2016-11-01

    We demonstrate broadband, low loss, and close-to-zero dispersion guidance of terahertz (THz) radiation in a dielectric tube with an anti-reflection structure (AR-tube waveguide) in the frequency range from 0.2 to 1.0 THz. The anti-reflection structure (ARS) consists of close-packed cones in a hexagonal lattice arranged on the outer surface of the tube cladding. The feature size of the ARS is in the order of the wavelength between 0.2 and 1.0 THz. The waveguides are fabricated with the versatile and cost efficient 3D-printing method. Terahertz time-domain spectroscopy (THz-TDS) measurements as well as 3D finite-difference time-domain simulations (FDTD) are performed to extensively characterize the AR-tube waveguides. Spectrograms, attenuation spectra, effective phase refractive indices, and the group-velocity dispersion parameters β 2 of the AR-tube waveguides are presented. Both the experimental and numerical results confirm the extended bandwidth and smaller group-velocity dispersion of the AR-tube waveguide compared to a low loss plain dielectric tube THz waveguide. The AR-tube waveguide prototypes show an attenuation spectrum close to the theoretical limit given by the infinite cladding tube waveguide.

  19. Electrohydrodynamic-assisted Assembly of Hierarchically Structured, 3D Crumpled Nanostructures for Efficient Solar Conversions.

    PubMed

    Ishihara, Hidetaka; Chen, Yen-Chang; De Marco, Nicholas; Lin, Oliver; Huang, Chih-Meng; Limsakoune, Vipawee; Chou, Yi-Chia; Yang, Yang; Tung, Vincent

    2016-12-07

    The tantalizing prospect of harnessing the unique properties of graphene crumpled nanostructures continues to fuel tremendous interest in energy storage and harvesting applications. However, the paper ball-like, hard texture, and closed-sphere morphology of current 3D graphitic nanostructure production not only constricts the conductive pathways but also limits the accessible surface area. Here, we report new insights into electrohydrodynamically-generated droplets as colloidal nanoreactors in that the stimuli-responsive nature of reduced graphene oxide can lead to the formation of crumpled nanostructures with a combination of open structures and doubly curved, saddle-shaped edges. In particular, the crumpled nanostructures dynamically adapt to non-spherical, polyhedral shapes under continuous deposition, ultimately assembling into foam-like microstructures with a highly accessible surface area and spatially interconnected transport pathways. The implementation of such crumpled nanostructures as three-dimensional rear contacts for solar conversion applications realize benefits of a high aspect ratio, electrically addressable and energetically favorable interfaces, and substantial enhancement of both short-circuit currents and fill-factors compared to those made of planar graphene counterparts. Further, the 3D crumpled nanostructures may shed lights onto the development of effective electrocatalytic electrodes due to their open structure that simultaneously allows for efficient water flow and hydrogen escape.

  20. Observed 3D Structure, Generation, and Dissipation of Oceanic Mesoscale Eddies in the South China Sea

    PubMed Central

    Zhang, Zhiwei; Tian, Jiwei; Qiu, Bo; Zhao, Wei; Chang, Ping; Wu, Dexing; Wan, Xiuquan

    2016-01-01

    Oceanic mesoscale eddies with horizontal scales of 50–300 km are the most energetic form of flows in the ocean. They are the oceanic analogues of atmospheric storms and are effective transporters of heat, nutrients, dissolved carbon, and other biochemical materials in the ocean. Although oceanic eddies have been ubiquitously observed in the world oceans since 1960s, our understanding of their three-dimensional (3D) structure, generation, and dissipation remains fragmentary due to lack of systematic full water-depth measurements. To bridge this knowledge gap, we designed and conducted a multi-months field campaign, called the South China Sea Mesoscale Eddy Experiment (S-MEE), in the northern South China Sea in 2013/2014. The S-MEE for the first time captured full-depth 3D structures of an anticyclonic and cyclonic eddy pair, which are characterized by a distinct vertical tilt of their axes. By observing the eddy evolution at an upstream versus downstream location and conducting an eddy energy budget analysis, the authors further proposed that generation of submesoscale motions most likely constitutes the dominant dissipation mechanism for the observed eddies. PMID:27074710

  1. A crust-scale 3D structural model of the Beaufort-Mackenzie Basin (Arctic Canada)

    NASA Astrophysics Data System (ADS)

    Sippel, Judith; Scheck-Wenderoth, Magdalena; Lewerenz, Björn; Kroeger, Karsten Friedrich

    2013-04-01

    The Beaufort-Mackenzie Basin was initiated in the Early Jurassic as part of an Arctic rifted passive continental margin which soon after became overprinted by Cordilleran foreland tectonics. Decades of industrial exploration and scientific research in this petroliferous region have produced a wide spectrum of geological and geophysical data as well as geoscientific knowledge. We have integrated available grids of sedimentary horizons, well data, seismic reflection and refraction data, and the observed regional gravity field into the first crust-scale 3D structural model of the Beaufort-Mackenzie Basin. Many characteristics of this model reflect the complex geodynamic and tectonostratigraphic history of the basin. The Mesozoic-Cenozoic sedimentary part of the model comprises seven clastic units (predominantly sandy shales) of which the modelled thickness distributions allow to retrace the well-established history of the basin comprising a gradual north(east)ward shift of the main depocentres as well as diverse phases of localised erosion. As a result of this development, the present-day configuration of the basin reveals that the sedimentary units tend to be younger, more porous, and thus less dense towards the north at a constant depth level. By integrating three refraction seismic profiles and performing combined isostatic and 3D gravity modelling, we have modelled the sub-sedimentary basement of the Beaufort-Mackenzie Basin. The continental basement spans from unstretched domains (as thick as about 42 km) in the south to extremely thinned domains (of less than 5 km thickness) in the north where it probably represents transitional crust attached to the oceanic crust of the Canada Basin. The uppermost parts of the continental crust are less dense (ρ = 2710 kg/m3) and most probably made up by pre-Mesozoic meta-sediments overlying a heavier igneous and metamorphic crust (ρ = 2850 kg/m3). The presented crust-scale 3D structural model shows that the greatest

  2. Analysis of simple 2-D and 3-D metal structures subjected to fragment impact

    NASA Technical Reports Server (NTRS)

    Witmer, E. A.; Stagliano, T. R.; Spilker, R. L.; Rodal, J. J. A.

    1977-01-01

    Theoretical methods were developed for predicting the large-deflection elastic-plastic transient structural responses of metal containment or deflector (C/D) structures to cope with rotor burst fragment impact attack. For two-dimensional C/D structures both, finite element and finite difference analysis methods were employed to analyze structural response produced by either prescribed transient loads or fragment impact. For the latter category, two time-wise step-by-step analysis procedures were devised to predict the structural responses resulting from a succession of fragment impacts: the collision force method (CFM) which utilizes an approximate prediction of the force applied to the attacked structure during fragment impact, and the collision imparted velocity method (CIVM) in which the impact-induced velocity increment acquired by a region of the impacted structure near the impact point is computed. The merits and limitations of these approaches are discussed. For the analysis of 3-d responses of C/D structures, only the CIVM approach was investigated.

  3. Modeling the effects of 3-D slab geometry and oblique subduction on subduction zone thermal structure

    NASA Astrophysics Data System (ADS)

    Wada, I.; Wang, K.; He, J.

    2013-12-01

    In this study, we revisit the effects of along-strike variation in slab geometry and oblique subduction on subduction zone thermal structures. Along-strike variations in slab dip cause changes in the descending rate of the slab and generate trench-parallel pressure gradients that drive trench-parallel mantle flow (e.g., Kneller and van Keken, 2007). Oblique subduction also drives trench-parallel mantle flow. In this study, we use a finite element code PGCtherm3D and examine a range of generic subduction geometries and parameters to investigate the effects of the above two factors. This exercise is part of foundational work towards developing detailed 3-D thermal models for NE Japan, Nankai, and Cascadia to better constrain their 3-D thermal structures and to understand the role of temperature in controlling metamorphic, seismogenic, and volcanic processes. The 3-D geometry of the subducting slabs in the forearc and arc regions are well delineated at these three subduction zones. Further, relatively large compilations of surface heat flow data at these subduction zones make them excellent candidates for this study. At NE Japan, a megathrust earthquake occurred on March 11, 2011; at Nankai and Cascadia, there has been a great effort to constrain the scale of the next subduction thrust earthquake for the purpose of disaster prevention. Temperature influences the slip behavior of subduction faults by (1) affecting the rheology of the interface material and (2) controlling dehydration reactions, which can lead to elevated pore fluid pressure. Beyond the depths of subduction thrust earthquakes, the thermal structure is affected strongly by the pattern of mantle wedge flow. This flow is driven by viscous coupling between the subducting slab and the overriding mantle, and it brings in hot flowing mantle into the wedge. The trench-ward (up-dip) extent of the slab-mantle coupling is thus a key factor that controls the thermal structure. Slab-mantle decoupling at shallow

  4. Evaluating the utility of 3D TRUS image information in guiding intra-procedure registration for motion compensation

    NASA Astrophysics Data System (ADS)

    De Silva, Tharindu; Cool, Derek W.; Romagnoli, Cesare; Fenster, Aaron; Ward, Aaron D.

    2014-03-01

    In targeted 3D transrectal ultrasound (TRUS)-guided biopsy, patient and prostate movement during the procedure can cause target misalignments that hinder accurate sampling of pre-planned suspicious tissue locations. Multiple solutions have been proposed for motion compensation via registration of intra-procedural TRUS images to a baseline 3D TRUS image acquired at the beginning of the biopsy procedure. While 2D TRUS images are widely used for intra-procedural guidance, some solutions utilize richer intra-procedural images such as bi- or multi-planar TRUS or 3D TRUS, acquired by specialized probes. In this work, we measured the impact of such richer intra-procedural imaging on motion compensation accuracy, to evaluate the tradeoff between cost and complexity of intra-procedural imaging versus improved motion compensation. We acquired baseline and intra-procedural 3D TRUS images from 29 patients at standard sextant-template biopsy locations. We used the planes extracted from the 3D intra-procedural scans to simulate 2D and 3D information available in different clinically relevant scenarios for registration. The registration accuracy was evaluated by calculating the target registration error (TRE) using manually identified homologous fiducial markers (micro-calcifications). Our results indicate that TRE improves gradually when the number of intra-procedural imaging planes used in registration is increased. Full 3D TRUS information helps the registration algorithm to robustly converge to more accurate solutions. These results can also inform the design of a fail-safe workflow during motion compensation in a system using a tracked 2D TRUS probe, by prescribing rotational acquisitions that can be performed quickly and easily by the physician immediately prior to needle targeting.

  5. Generalized Hough transform based time invariant action recognition with 3D pose information

    NASA Astrophysics Data System (ADS)

    Muench, David; Huebner, Wolfgang; Arens, Michael

    2014-10-01

    Human action recognition has emerged as an important field in the computer vision community due to its large number of applications such as automatic video surveillance, content based video-search and human robot interaction. In order to cope with the challenges that this large variety of applications present, recent research has focused more on dev