WorldWideScience

Sample records for 3d protein structure

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

    Science.gov (United States)

    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.

  2. Comparison of the 3D Protein Structure Prediction Algorithms

    OpenAIRE

    Fadhl M. Al-Akwaa,; Husam Elhetari

    2014-01-01

    Determining protein 3D structure is important to known protein functions. Protein structure could be determined experimentally and computationally. Experimental methods are expensive and time consuming whereas computational methods are the alternative solution. From the other hand, computational methods require strong computing power, assumed models and effective algorithms. In this paper we compare the performance of these algorithms. We find that Genetic Algorithm with impro...

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

    Directory of Open Access Journals (Sweden)

    Debora S Marks

    Full Text Available 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

  4. 3D complex: a structural classification of protein complexes.

    Directory of Open Access Journals (Sweden)

    Emmanuel D Levy

    2006-11-01

    Full Text Available Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Pei, Jimin; Grishin, Nick V

    2014-01-01

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

  7. Protein contact maps: A binary depiction of protein 3D structures

    Science.gov (United States)

    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.

  8. Modeling of 3D-structure for regular fragments of low similarity unknown structure proteins

    Institute of Scientific and Technical Information of China (English)

    Peng Zhihong; Chen Jie; Lin Xiwen; Sang Yanchao

    2007-01-01

    Because it is hard to search similar structure for low similarity unknown structure proteins dimefly from the Protein Data Bank(PDB)database,3D-structure is modeled in this paper for secondary structure regular fragments(α-Helices,β-Strands)of such proteins by the protein secondary structure prediction software,the Basic Local Alignment Search Tool(BLAST)and the side chain construction software SCWRL3.First.the protein secondary structure prediction software is adopted to extract secondary structure fragments from the unknown structure proteins.Then.regular fragments are regulated by BLAST based on comparative modeling,providing main chain configurations.Finally,SCWRL3 is applied to assemble side chains for regular fragments,so that 3D-structure of regular fragments of low similarity un known structure protein is obtained.Regular fragments of several neurotoxins ale used for test.Simulation results show that the prediction errors are less than 0.06nm for regular fragments less than 10 amino acids,implying the simpleness and effectiveness of the proposed method.

  9. The PPI3D web server for searching, analyzing and modeling protein-protein interactions in the context of 3D structures.

    Science.gov (United States)

    Dapkūnas, Justas; Timinskas, Albertas; Olechnovič, Kliment; Margelevičius, Mindaugas; Dičiūnas, Rytis; Venclovas, Česlovas

    2016-12-22

    The PPI3D web server is focused on searching and analyzing the structural data on protein-protein interactions. Reducing the data redundancy by clustering and analyzing the properties of interaction interfaces using Voronoi tessellation makes this software a highly effective tool for addressing different questions related to protein interactions.

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  13. FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Rapacki, Krzysztof; Stærfeldt, Hans Henrik;

    2006-01-01

    FeatureMap3D is a web-based tool that maps protein features onto 3D structures. The user provides sequences annotated with any feature of interest, such as post-translational modifications, protease cleavage sites or exonic structure and FeatureMap3D will then search the Protein Data Bank (PDB) f...

  14. Predicting DNA-binding sites of proteins based on sequential and 3D structural information.

    Science.gov (United States)

    Li, Bi-Qing; Feng, Kai-Yan; Ding, Juan; Cai, Yu-Dong

    2014-06-01

    Protein-DNA interactions play important roles in many biological processes. To understand the molecular mechanisms of protein-DNA interaction, it is necessary to identify the DNA-binding sites in DNA-binding proteins. In the last decade, computational approaches have been developed to predict protein-DNA-binding sites based solely on protein sequences. In this study, we developed a novel predictor based on support vector machine algorithm coupled with the maximum relevance minimum redundancy method followed by incremental feature selection. We incorporated not only features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure, solvent accessibility, but also five three-dimensional (3D) structural features calculated from PDB data to predict the protein-DNA interaction sites. Feature analysis showed that 3D structural features indeed contributed to the prediction of DNA-binding site and it was demonstrated that the prediction performance was better with 3D structural features than without them. It was also shown via analysis of features from each site that the features of DNA-binding site itself contribute the most to the prediction. Our prediction method may become a useful tool for identifying the DNA-binding sites and the feature analysis described in this paper may provide useful insights for in-depth investigations into the mechanisms of protein-DNA interaction.

  15. Enhanced hybrid search algorithm for protein structure prediction using the 3D-HP lattice model.

    Science.gov (United States)

    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.

  16. Biological insights from topology independent comparison of protein 3D structures.

    Science.gov (United States)

    Nguyen, Minh N; Madhusudhan, M S

    2011-08-01

    Comparing and classifying the three-dimensional (3D) structures of proteins is of crucial importance to molecular biology, from helping to determine the function of a protein to determining its evolutionary relationships. Traditionally, 3D structures are classified into groups of families that closely resemble the grouping according to their primary sequence. However, significant structural similarities exist at multiple levels between proteins that belong to these different structural families. In this study, we propose a new algorithm, CLICK, to capture such similarities. The method optimally superimposes a pair of protein structures independent of topology. Amino acid residues are represented by the Cartesian coordinates of a representative point (usually the C(α) atom), side chain solvent accessibility, and secondary structure. Structural comparison is effected by matching cliques of points. CLICK was extensively benchmarked for alignment accuracy on four different sets: (i) 9537 pair-wise alignments between two structures with the same topology; (ii) 64 alignments from set (i) that were considered to constitute difficult alignment cases; (iii) 199 pair-wise alignments between proteins with similar structure but different topology; and (iv) 1275 pair-wise alignments of RNA structures. The accuracy of CLICK alignments was measured by the average structure overlap score and compared with other alignment methods, including HOMSTRAD, MUSTANG, Geometric Hashing, SALIGN, DALI, GANGSTA(+), FATCAT, ARTS and SARA. On average, CLICK produces pair-wise alignments that are either comparable or statistically significantly more accurate than all of these other methods. We have used CLICK to uncover relationships between (previously) unrelated proteins. These new biological insights include: (i) detecting hinge regions in proteins where domain or sub-domains show flexibility; (ii) discovering similar small molecule binding sites from proteins of different folds and (iii

  17. Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA.

    Science.gov (United States)

    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.

  18. 3D structure determination of protein using TEM single particle analysis.

    Science.gov (United States)

    Sato, Chikara; Mio, Kazuhiro; Kawata, Masaaki; Ogura, Toshihiko

    2014-11-01

    Proteins play important roles in cell functions such as enzymes, cell trafficking, neurotransmission, muscle contraction and hormone secretion. However, some proteins are very difficult to be crystallized and their structures are undetermined. Several techniques have been developed to elucidate the structure of macromolecules; X-ray or electron crystallography, nuclear magnetic resonance spectroscopy, and high-resolution electron microscopy. Among them, electron microscopy based single particle reconstruction (SPA) technique is a computer-aided structure determination method. This method reconstructs the 3D structure from projection images of dispersed protein. A large number of two-dimensional particle images are picked up from EM films, aligned and classified to generate 2D averages, and used to reconstruct the 3D structure by assigning the Euler angle of each 2D average. Due to the necessity of elaborate collaboration between the classical biology and the innovative information technology including parallel computing, scientists needed to break unseen barriers to get a start of this analysis. However, recent progresses in electron microscopes, mathematical algorithms, and computational abilities greatly reduced the height of barriers and expanded targets that are considered to be primarily addressable using single particle analysis. Membrane proteins are one of these targets to which the single particle analysis is successfully applied for the understanding of their 3D structures. For this purpose, we have developed various SPA methods [1-5] and applied them to different proteins [6-8].Here, we introduce reconstructed proteins, and discuss the availability of this technique. The intramembrane-cleaving proteases (I-CLiPs) that sever the transmembrane domains of their substrates have been identified in a range of organisms and play a variety of roles in biological conditions. I-CLiPs have been classified into three groups: serine-, aspartyl- and metalloprotease

  19. Pseudocontact Shift-Driven Iterative Resampling for 3D Structure Determinations of Large Proteins.

    Science.gov (United States)

    Pilla, Kala Bharath; Otting, Gottfried; Huber, Thomas

    2016-01-29

    Pseudocontact shifts (PCSs) induced by paramagnetic lanthanides produce pronounced effects in nuclear magnetic resonance spectra, which are easily measured and which deliver valuable long-range structure restraints. Even sparse PCS data greatly enhance the success rate of 3D (3-dimensional) structure predictions of proteins by the modeling program Rosetta. The present work extends this approach to 3D structures of larger proteins, comprising more than 200 residues, which are difficult to model by Rosetta without additional experimental restraints. The new algorithm improves the fragment assembly method of Rosetta by utilizing PCSs generated from paramagnetic lanthanide ions attached at four different sites as the only experimental restraints. The sparse PCS data are utilized at multiple stages, to identify native-like local structures, to rank the best structural models and to rebuild the fragment libraries. The fragment libraries are refined iteratively until convergence. The PCS-driven iterative resampling algorithm is strictly data dependent and shown to generate accurate models for a benchmark set of eight different proteins, ranging from 100 to 220 residues, using solely PCSs of backbone amide protons.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    John A Capra

    2009-12-01

    Full Text Available 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/.

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

    Science.gov (United States)

    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/).

  3. A 3D model of the membrane protein complex formed by the white spot syndrome virus structural proteins.

    Directory of Open Access Journals (Sweden)

    Yun-Shiang Chang

    Full Text Available BACKGROUND: Outbreaks of white spot disease have had a large negative economic impact on cultured shrimp worldwide. However, the pathogenesis of the causative virus, WSSV (whit spot syndrome virus, is not yet well understood. WSSV is a large enveloped virus. The WSSV virion has three structural layers surrounding its core DNA: an outer envelope, a tegument and a nucleocapsid. In this study, we investigated the protein-protein interactions of the major WSSV structural proteins, including several envelope and tegument proteins that are known to be involved in the infection process. PRINCIPAL FINDINGS: In the present report, we used coimmunoprecipitation and yeast two-hybrid assays to elucidate and/or confirm all the interactions that occur among the WSSV structural (envelope and tegument proteins VP51A, VP19, VP24, VP26 and VP28. We found that VP51A interacted directly not only with VP26 but also with VP19 and VP24. VP51A, VP19 and VP24 were also shown to have an affinity for self-interaction. Chemical cross-linking assays showed that these three self-interacting proteins could occur as dimers. CONCLUSIONS: From our present results in conjunction with other previously established interactions we construct a 3D model in which VP24 acts as a core protein that directly associates with VP26, VP28, VP38A, VP51A and WSV010 to form a membrane-associated protein complex. VP19 and VP37 are attached to this complex via association with VP51A and VP28, respectively. Through the VP26-VP51C interaction this envelope complex is anchored to the nucleocapsid, which is made of layers of rings formed by VP664. A 3D model of the nucleocapsid and the surrounding outer membrane is presented.

  4. "SP-G", a putative new surfactant protein--tissue localization and 3D structure.

    Directory of Open Access Journals (Sweden)

    Felix Rausch

    Full Text Available Surfactant proteins (SP are well known from human lung. These proteins assist the formation of a monolayer of surface-active phospholipids at the liquid-air interface of the alveolar lining, play a major role in lowering the surface tension of interfaces, and have functions in innate and adaptive immune defense. During recent years it became obvious that SPs are also part of other tissues and fluids such as tear fluid, gingiva, saliva, the nasolacrimal system, and kidney. Recently, a putative new surfactant protein (SFTA2 or SP-G was identified, which has no sequence or structural identity to the already know surfactant proteins. In this work, computational chemistry and molecular-biological methods were combined to localize and characterize SP-G. With the help of a protein structure model, specific antibodies were obtained which allowed the detection of SP-G not only on mRNA but also on protein level. The localization of this protein in different human tissues, sequence based prediction tools for posttranslational modifications and molecular dynamic simulations reveal that SP-G has physicochemical properties similar to the already known surfactant proteins B and C. This includes also the possibility of interactions with lipid systems and with that, a potential surface-regulatory feature of SP-G. In conclusion, the results indicate SP-G as a new surfactant protein which represents an until now unknown surfactant protein class.

  5. Computational 3D structures of drug-targeting proteins in the 2009-H1N1 influenza A virus

    Science.gov (United States)

    Du, Qi-Shi; Wang, Shu-Qing; Huang, Ri-Bo; Chou, Kuo-Chen

    2010-01-01

    The neuraminidase (NA) and M2 proton channel of influenza virus are the drug-targeting proteins, based on which several drugs were developed. However these once powerful drugs encountered drug-resistant problem to the H5N1 and H1N1 flu. To address this problem, the computational 3D structures of NA and M2 proteins of 2009-H1N1 influenza virus were built using the molecular modeling technique and computational chemistry method. Based on the models the structure features of NA and M2 proteins were analyzed, the docking structures of drug-protein complexes were computed, and the residue mutations were annotated. The results may help to solve the drug-resistant problem and stimulate designing more effective drugs against 2009-H1N1 influenza pandemic.

  6. Automated Assignment of MS/MS Cleavable Cross-Links in Protein 3D-Structure Analysis

    Science.gov (United States)

    Götze, Michael; Pettelkau, Jens; Fritzsche, Romy; Ihling, Christian H.; Schäfer, Mathias; Sinz, Andrea

    2015-01-01

    CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com .

  7. Representation of protein 3D structures in spherical (ρ, ϕ, θ) coordinates and two of its potential applications.

    Science.gov (United States)

    Reyes, Vicente M

    2011-09-01

    Three-dimensional objects can be represented using cartesian, spherical or cylindrical coordinate systems, among many others. Currently all protein 3D structures in the PDB are in cartesian coordinates. We wanted to explore the possibility that protein 3D structures, especially the globular type (spheroproteins), when represented in spherical coordinates might find useful novel applications. A Fortran program was written to transform protein 3D structure files in cartesian coordinates (x,y,z) to spherical coordinates (ρ, ϕ, θ), with the centroid of the protein molecule as origin. We present here two applications, namely, (1) separation of the protein outer layer (OL) from the inner core (IC); and (2) identifying protrusions and invaginations on the protein surface. In the first application, ϕ and θ were partitioned into suitable intervals and the point with maximum ρ in each such 'ϕ-θ bin' was determined. A suitable cutoff value for ρ is adopted, and for each ϕ-θ bin, all points with ρ values less than the cutoff are considered part of the IC, and those with ρ values equal to or greater than the cutoff are considered part of the OL. We show that this separation procedure is successful as it gives rise to an OL that is significantly more enriched in hydrophilic amino acid residues, and an IC that is significantly more enriched in hydrophobic amino acid residues, as expected. In the second application, the point with maximum ρ in each ϕ-θ bin are sequestered and their frequency distribution constructed (i.e., maximum ρ's sorted from lowest to highest, collected into 1.50Å-intervals, and the frequency in each interval plotted). We show in such plots that invaginations on the protein surface give rise to subpeaks or shoulders on the lagging side of the main peak, while protrusions give rise to similar subpeaks or shoulders, but on the leading side of the main peak. We used the dataset of Laskowski et al. (1996) to demonstrate both applications.

  8. In Vitro Model of the Epidermis: Connecting Protein Function to 3D Structure.

    Science.gov (United States)

    Arnette, Christopher; Koetsier, Jennifer L; Hoover, Paul; Getsios, Spiro; Green, Kathleen J

    2016-01-01

    Much of our understanding of the biological processes that underlie cellular functions in humans, such as cell-cell communication, intracellular signaling, and transcriptional and posttranscriptional control of gene expression, has been acquired from studying cells in a two-dimensional (2D) tissue culture environment. However, it has become increasingly evident that the 2D environment does not support certain cell functions. The need for more physiologically relevant models prompted the development of three-dimensional (3D) cultures of epithelial, endothelial, and neuronal tissues (Shamir & Ewald, 2014). These models afford investigators with powerful tools to study the contribution of spatial organization, often in the context of relevant extracellular matrix and stromal components, to cellular and tissue homeostasis in normal and disease states.

  9. PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.

    Science.gov (United States)

    Lee, Woonghee; Stark, Jaime L; Markley, John L

    2014-11-01

    Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727-1728. doi: 10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets ((13)C- and/or (15)N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625-626. doi: 10.1038/nmeth0909-625 , 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1-2 days.

  10. Probing Protein 3D Structures and Conformational Changes Using Electrochemistry-Assisted Isotope Labeling Cross-Linking Mass Spectrometry

    Science.gov (United States)

    Zheng, Qiuling; Zhang, Hao; Wu, Shiyong; Chen, Hao

    2016-05-01

    This study presents a new chemical cross-linking mass spectrometry (MS) method in combination with electrochemistry and isotope labeling strategy for probing both protein three-dimensional (3D) structures and conformational changes. For the former purpose, the target protein/protein complex is cross-linked with equal mole of premixed light and heavy isotope labeled cross-linkers carrying electrochemically reducible disulfide bonds (i.e., DSP-d0 and DSP-d8 in this study, DSP = dithiobis[succinimidyl propionate]), digested and then electrochemically reduced followed with online MS analysis. Cross-links can be quickly identified because of their reduced intensities upon electrolysis and the presence of doublet isotopic peak characteristics. In addition, electroreduction converts cross-links into linear peptides, facilitating MS/MS analysis to gain increased information about their sequences and modification sites. For the latter purpose of probing protein conformational changes, an altered procedure is adopted, in which the protein in two different conformations is cross-linked using DSP-d0 and DSP-d8 separately, and then the two protein samples are mixed in 1:1 molar ratio. The merged sample is subjected to digestion and electrochemical mass spectrometric analysis. In such a comparative cross-linking experiment, cross-links could still be rapidly recognized based on their responses to electrolysis. More importantly, the ion intensity ratios of light and heavy isotope labeled cross-links reveal the conformational changes of the protein, as exemplified by examining the effect of Ca2+ on calmodulin conformation alternation. This new cross-linking MS method is fast and would have high value in structural biology.

  11. SCOWLP update: 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds

    Directory of Open Access Journals (Sweden)

    Schreiber Sven

    2011-10-01

    Full Text Available Abstract Background Protein interactions are essential for coordinating cellular functions. Proteomic studies have already elucidated a huge amount of protein-protein interactions that require detailed functional analysis. Understanding the structural basis of each individual interaction through their structural determination is necessary, yet an unfeasible task. Therefore, computational tools able to predict protein binding regions and recognition modes are required to rationalize putative molecular functions for proteins. With this aim, we previously created SCOWLP, a structural classification of protein binding regions at protein family level, based on the information obtained from high-resolution 3D protein-protein and protein-peptide complexes. Description We present here a new version of SCOWLP that has been enhanced by the inclusion of protein-nucleic acid and protein-saccharide interactions. SCOWLP takes interfacial solvent into account for a detailed characterization of protein interactions. In addition, the binding regions obtained per protein family have been enriched by the inclusion of predicted binding regions, which have been inferred from structurally related proteins across all existing folds. These inferences might become very useful to suggest novel recognition regions and compare structurally similar interfaces from different families. Conclusions The updated SCOWLP has new functionalities that allow both, detection and comparison of protein regions recognizing different types of ligands, which include other proteins, peptides, nucleic acids and saccharides, within a solvated environment. Currently, SCOWLP allows the analysis of predicted protein binding regions based on structure-based inferences across fold space. These predictions may have a unique potential in assisting protein docking, in providing insights into protein interaction networks, and in guiding rational engineering of protein ligands. The newly designed

  12. 3D structure of muscle dihydropyridine receptor

    Directory of Open Access Journals (Sweden)

    Montserrat Samsó

    2015-01-01

    Full Text Available Excitation contraction coupling, the rapid and massive Ca2+ release under control of an action potential that triggers muscle contraction, takes places at specialized regions of the cell called triad junctions. There, a highly ordered supramolecular complex between the dihydropyridine receptor (DHPR and the ryanodine receptor (RyR1 mediates the quasi‐instantaneous conversion from T‐tubule depolarization into Ca2+ release from the sarcoplasmic reticulum (SR. The DHPR has several key modules required for EC coupling: the voltage sensors and II‐III loop in the alpha1s subunit, and the beta subunit. To gain insight into their molecular organization, this review examines the most updated 3D structure of the DHPR as obtained by transmission electron microscopy and image reconstruction. Although structure determination of a heteromeric membrane protein such as the DHPR is challenging, novel technical advances in protein expression and 3D labeling facilitated this task. The 3D structure of the DHPR complex consists of a main body with five irregular corners around its perimeter encompassing the transmembrane alpha 1s subunit besides the intracellular beta subunit, an extended extracellular alpha 2 subunit, and a bulky intracellular II‐III loop. The structural definition attained at 19 Å resolution enabled docking of the atomic coordinates of structural homologs of the alpha1s and beta subunits. These structural features, together with their relative location with respect to the RyR1, are discussed in the context of the functional data.

  13. Calibration for 3D Structured Light Measurement

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A calibration procedure was developed for three-dimensional(3D) binocular structured light measurement systems. In virtue of a specially designed pattern, matching points in stereo images are extracted. And then sufficient 3D space points are obtained through pairs of images with the intrinsic and extrinsic parameters of each camera estimated prior and consequently some lights are calibrated by means of multi point fitting. Finally, a mathematical model is applied to interpolate and approximate all dynamic scanning lights based on geometry. The process of calibration method is successfully used in the binocular 3D measurement system based on structured lights and the 3D reconstruction results are satisfying.

  14. Combining Amine-Reactive Cross-Linkers and Photo-Reactive Amino Acids for 3D-Structure Analysis of Proteins and Protein Complexes.

    Science.gov (United States)

    Lössl, Philip; Sinz, Andrea

    2016-01-01

    During the last 15 years, the combination of chemical cross-linking and high-resolution mass spectrometry (MS) has matured into an alternative approach for analyzing 3D-structures of proteins and protein complexes. Using the distance constraints imposed by the cross-links, models of the protein or protein complex under investigation can be created. The majority of cross-linking studies are currently conducted with homobifunctional amine-reactive cross-linkers. We extend this "traditional" cross-linking/MS strategy by adding complementary photo-cross-linking data. For this, the diazirine-containing unnatural amino acids photo-leucine and photo-methionine are incorporated into the proteins and cross-link formation is induced by UV-A irradiation. The advantage of the photo-cross-linking strategy is that it is not restricted to lysine residues and that hydrophobic regions in proteins can be targeted, which is advantageous for investigating membrane proteins. We consider the strategy of combining cross-linkers with orthogonal reactivities and distances to be ideally suited for maximizing the amount of structural information that can be gained from a cross-linking experiment.

  15. Protein functional-group 3D motif and its applications

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Representing and recognizing protein active sites sequence motif (1D motif) and structural motif (3D motif) is an important topic for predicting and designing protein function. Prevalent methods for extracting and searching 3D motif always consider residue as the minimal unit, which have limited sensitivity. Here we present a new spatial representation of protein active sites, called "functional-group 3D motif ", based on the fact that the functional groups inside a residue contribute mostly to its function. Relevant algorithm and computer program are developed, which could be widely used in the function prediction and the study of structural-function relationship of proteins. As a test, we defined a functional-group 3D motif of the catalytic triad and oxyanion hole with the structure of porcine trypsin (PDB code: 1mct) as the template. With our motif-searching program, we successfully found similar sub-structures in trypsins, subtilisins and a/b hydrolases, which show distinct folds but share similar catalytic mechanism. Moreover, this motif can be used to elucidate the structural basis of other proteins with variant catalytic triads by comparing it to those proteins. Finally, we scanned this motif against a non-redundant protein structure database to find its matches, and the results demonstrated the potential application of functional group 3D motif in function prediction. Above all, compared with the other 3D-motif representations on residues, the functional group 3D motif achieves better representation of protein active region, which is more sensitive for protein function prediction.

  16. [Chaotic artificial bee colony algorithm: a new approach to the problem of minimization of energy of the 3D protein structure].

    Science.gov (United States)

    Wang, Y; Guo, G D; Chen, L F

    2013-01-01

    Frediction of the three-dimensional structure of a protein from its amino acid sequence can be considered as a global optimization problem. In this paper, the Chaotic Artificial Bee Colony (CABC) algorithm was introduced and applied to 3D protein structure prediction. Based on the 3D off-lattice AB model, the CABC algorithm combines global search and local search of the Artificial Bee Colony (ABC) algorithm with the Chaotic search algorithm to avoid the problem of premature convergence and easily trapping the local optimum solution. The experiments carried out with the popular Fibonacci sequences demonstrate that the proposed algorithm provides an effective and high-performance method for protein structure prediction.

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

    Science.gov (United States)

    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

  18. G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures

    OpenAIRE

    Solomon, Oz; Kunik, Vered; Simon, Amos; Kol, Nitzan; Barel, Ortal; Lev, Atar; Amariglio, Ninette; Somech, Raz; Rechavi, Gidi; Eyal, Eran

    2016-01-01

    Background Evaluation of the possible implications of genomic variants is an increasingly important task in the current high throughput sequencing era. Structural information however is still not routinely exploited during this evaluation process. The main reasons can be attributed to the partial structural coverage of the human proteome and the lack of tools which conveniently convert genomic positions, which are the frequent output of genomic pipelines, to proteins and structure coordinates...

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

    Directory of Open Access Journals (Sweden)

    Chia-Han Chu

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

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

    Science.gov (United States)

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

    2010-10-14

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

  1. Structured light field 3D imaging.

    Science.gov (United States)

    Cai, Zewei; Liu, Xiaoli; Peng, Xiang; Yin, Yongkai; Li, Ameng; Wu, Jiachen; Gao, Bruce Z

    2016-09-05

    In this paper, we propose a method by means of light field imaging under structured illumination to deal with high dynamic range 3D imaging. Fringe patterns are projected onto a scene and modulated by the scene depth then a structured light field is detected using light field recording devices. The structured light field contains information about ray direction and phase-encoded depth, via which the scene depth can be estimated from different directions. The multidirectional depth estimation can achieve high dynamic 3D imaging effectively. We analyzed and derived the phase-depth mapping in the structured light field and then proposed a flexible ray-based calibration approach to determine the independent mapping coefficients for each ray. Experimental results demonstrated the validity of the proposed method to perform high-quality 3D imaging for highly and lowly reflective surfaces.

  2. Solving a 3D structural puzzle

    DEFF Research Database (Denmark)

    Hoeck, Casper

    to spatial structural information using NMR spectroscopy. Experimental distances from nuclear Overhauser effect (NOE) correlations, and dihedral angles from 3JHH-coupling constants, were used to obtain 3D structural information for several natural and synthetic compounds. The stereochemistry of novel natural...... samples, which allows for RDCs to be extracted. The number of internuclear vectors for the correlation of RDCs to 3D structures is often limited for small molecules. Homonuclear RDCs were extracted by use of the homonuclear S3 HMBC that correlated well to alignment tensors from 1DCH-coupling constants......-calculation of RDCs from 3D structures was developed and tested, which copes better with multiple conformers than the commonly used SVD methodology. The approach thus resulted in good conformer populations for several small molecules, including multiple cinchona alkaloids....

  3. GANDivAWeb: A web server for detecting early folding units ("foldons" from protein 3D structures

    Directory of Open Access Journals (Sweden)

    Krishnan Arun

    2008-03-01

    Full Text Available Abstract Background It has long been known that small regions of proteins tend to fold independently and are then stabilized by interactions between these distinct subunits or modules. Such units, also known as autonomous folding units (AFUs or"foldons" play a key role in protein folding. A knowledge of such early folding units has diverse applications in protein engineering as well as in developing an understanding of the protein folding process. Such AFUs can also be used as model systems in order to study the structural organization of proteins. Results In an earlier work, we had utilized a global network partitioning algorithm to identify modules in proteins. We had shown that these modules correlate well with AFUs. In this work, we have developed a webserver, GANDivAWeb, to identify early folding units or "foldons" in networks using the algorithm described earlier. The website has three functionalities: (a It is able to display information on the modularity of a database of 1420 proteins used in the original work, (b It can take as input an uploaded PDB file, identify the modules using the GANDivA algorithm and email the results back to the user and (c It can take as input an uploaded PDB file and a results file (obtained from functionality (b and display the results using the embedded viewer. The results include the module decomposition of the protein, plots of cartoon representations of the protein colored by module identity and connectivity as well as contour plots of the hydrophobicity and relative accessible surface area (RASA distributions. Conclusion We believe that the GANDivAWeb server, will be a useful tool for scientists interested in the phenomena of protein folding as well as in protein engineering. Our tool not only provides a knowledge of the AFUs through a natural graph partitioning approach but is also able to identify residues that are critical during folding. It is our intention to use this tool to study the topological

  4. PONDEROSA-C/S: client–server based software package for automated protein 3D structure determination

    OpenAIRE

    Lee, Woonghee; Stark, Jaime L.; Markley, John L.

    2014-01-01

    Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727–1728. doi:10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nucle...

  5. 3D Structure and Nuclear Targets

    CERN Document Server

    Dupré, R

    2015-01-01

    Recent experimental and theoretical ideas are laying the ground for a new era in the knowledge of the parton structure of nuclei. We report on two promising directions beyond inclusive deep inelastic scattering experiments, aimed at, among other goals, unveiling the three dimensional structure of the bound nucleon. The 3D structure in coordinate space can be accessed through deep exclusive processes, whose non-perturbative content is parametrized in terms of generalized parton distributions. In this way the distribution of partons in the transverse plane will be obtained, providing a pictorial view of the realization of the European Muon Collaboration effect. In particular, we show how, through the generalized parton distribution framework, non nucleonic degrees of freedom in nuclei can be unveiled. Analogously, the momentum space 3D structure can be accessed by studying transverse momentum dependent parton distributions in semi-inclusive deep inelastic scattering processes. The status of measurements is also...

  6. Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach

    Directory of Open Access Journals (Sweden)

    Khader Shameer

    2010-06-01

    Full Text Available 3-dimensional domain swapping is a mechanism where two or more protein molecules form higher order oligomers by exchanging identical or similar subunits. Recently, this phenomenon has received much attention in the context of prions and neuro-degenerative diseases, due to its role in the functional regulation, formation of higher oligomers, protein misfolding, aggregation etc. While 3-dimensional domain swap mechanism can be detected from three-dimensional structures, it remains a formidable challenge to derive common sequence or structural patterns from proteins involved in swapping. We have developed a SVM-based classifier to predict domain swapping events using a set of features derived from sequence and structural data. The SVM classifier was trained on features derived from 150 proteins reported to be involved in 3D domain swapping and 150 proteins not known to be involved in swapped conformation or related to proteins involved in swapping phenomenon. The testing was performed using 63 proteins from the positive dataset and 63 proteins from the negative dataset. We obtained 76.33% accuracy from training and 73.81% accuracy from testing. Due to high diversity in the sequence, structure and functions of proteins involved in domain swapping, availability of such an algorithm to predict swapping events from sequence and structure-derived features will be an initial step towards identification of more putative proteins that may be involved in swapping or proteins involved in deposition disease. Further, the top features emerging in our feature selection method may be analysed further to understand their roles in the mechanism of domain swapping.

  7. Vectorial FDBPM 3D waveguide structures

    Science.gov (United States)

    Li, Daoping; van Brug, Hedser H.; Frankena, Hans J.

    1994-08-01

    A fully vectorial finite difference beam propagation method for 3D waveguide structures, including longitudinally variant structures is presented. The transparent boundary conditions are utilized in the edges of the computational window. Both Gaussian beams and exact fields of the guided modes are launched as the starting field. Propagating fields are calculated and the power attenuation is evaluated. The choice of step size, finite difference scheme parameter and reference propagation constant is discussed. The applicability and accuracy are demonstrated for two particular waveguide structures.

  8. 3D structure prediction of histone acetyltransferase (HAC proteins of the p300/CBP family and their interactome in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Amar Cemanovic

    2014-09-01

    Full Text Available Histone acetylation is an important posttranslational modification correlated with gene activation. In Arabidopsis thaliana the histone acetyltransferase (HAC proteins of the CBP family are homologous to animal p300/CREB (cAMP-responsive element-binding proteins, which are important histone acetyltransferases participating in many physiological processes, including proliferation, differentiation, and apoptosis. In this study the 3-D structure of all HAC protein subunits in Arabidopsis thaliana: HAC1, HAC2, HAC4, HAC5 and HAC12 is predicted by homology modeling and confirmed by Ramachandran plot analysis. The amino acid sequences HAC family members are highly similar to the sequences of the homologous human p300/CREB protein. Conservation of p300/CBP domains among the HAC proteins was examined further by sequence alignment and pattern search. The domains of p300/CBP required for the HAC function, such as PHD, TAZ and ZZ domains, are conserved in all HAC proteins. Interactome analysis revealed that HAC1, HAC5 and HAC12 proteins interact with S-adenosylmethionine-dependent methyltransferase domaincontaining protein that shows methyltransferase activity, suggesting an additional function of the HAC proteins. Additionally, HAC5 has a strong interaction value for the putative c-myb-like transcription factor MYB3R-4, which suggests that it also may have a function in regulation of DNA replication.

  9. The Voronoi diagram of half-balls and its application to the prediction of the 3D structure of proteins

    DEFF Research Database (Denmark)

    Anton, François; Hamelryck, Thomas

    2009-01-01

    The calculation of the overlap volume of half-spheres or ellipsoids is of direct interest in structural bioinformatics, which is concerned with the computational study of biological macromolecules on a genomic scale. We present an algorithm for computing the Delaunay graph and the overlap volume...

  10. Molecular cloning, expression pattern, and 3D structural prediction of the cold inducible RNA-binding protein (CIRP) in Japanese flounder ( Paralichthys olivaceus)

    Science.gov (United States)

    Yang, Xiao; Gao, Jinning; Ma, Liman; Li, Zan; Wang, Wenji; Wang, Zhongkai; Yu, Haiyang; Qi, Jie; Wang, Xubo; Wang, Zhigang; Zhang, Quanqi

    2015-02-01

    Cold-inducible RNA-binding protein (CIRP) is a kind of RNA binding proteins that plays important roles in many physiological processes. The CIRP has been widely studied in mammals and amphibians since it was first cloned from mammals. On the contrary, there are little reports in teleosts. In this study, the Po CIRP gene of the Japanese flounder was cloned and sequenced. The genomic sequence consists of seven exons and six introns. The putative PoCIRP protein of flounder was 198 amino acid residues long containing the RNA recognition motif (RRM). Phylogenetic analysis showed that the flounder PoCIRP is highly conserved with other teleost CIRPs. The 5' flanking sequence was cloned by genome walking and many transcription factor binding sites were identified. There is a CpGs region located in promoter and exon I region and the methylation state is low. Quantitative real-time PCR analysis uncovered that Po CIRP gene was widely expressed in adult tissues with the highest expression level in the ovary. The mRNA of the Po CIRP was maternally deposited and the expression level of the gene was regulated up during the gastrula and neurula stages. In order to gain the information how the protein interacts with mRNA, we performed the modeling of the 3D structure of the flounder PoCIRP. The results showed a cleft existing the surface of the molecular. Taken together, the results indicate that the CIRP is a multifunctional molecular in teleosts and the findings about the structure provide valuable information for understanding the basis of this protein's function.

  11. Protein-Assisted Assembly of Modular 3D Plasmonic Raspberry-like Core/Satellite Nanoclusters: Correlation of Structure and Optical Properties.

    Science.gov (United States)

    Höller, Roland P M; Dulle, Martin; Thomä, Sabrina; Mayer, Martin; Steiner, Anja Maria; Förster, Stephan; Fery, Andreas; Kuttner, Christian; Chanana, Munish

    2016-06-28

    We present a bottom-up assembly route for a large-scale organization of plasmonic nanoparticles (NPs) into three-dimensional (3D) modular assemblies with core/satellite structure. The protein-assisted assembly of small spherical gold or silver NPs with a hydrophilic protein shell (as satellites) onto larger metal NPs (as cores) offers high modularity in sizes and composition at high satellite coverage (close to the jamming limit). The resulting dispersions of metal/metal nanoclusters exhibit high colloidal stability and therefore allow for high concentrations and a precise characterization of the nanocluster architecture in dispersion by small-angle X-ray scattering (SAXS). Strong near-field coupling between the building blocks results in distinct regimes of dominant satellite-to-satellite and core-to-satellite coupling. High robustness against satellite disorder was proved by UV/vis diffuse reflectance (integrating sphere) measurements. Generalized multiparticle Mie theory (GMMT) simulations were employed to describe the electromagnetic coupling within the nanoclusters. The close correlation of structure and optical property allows for the rational design of core/satellite nanoclusters with tailored plasmonics and well-defined near-field enhancement, with perspectives for applications such as surface-enhanced spectroscopies.

  12. 3D printing of functional structures

    NARCIS (Netherlands)

    Krijnen, G.J.M.

    2016-01-01

    The technology colloquial known as ‘3D printing’ has developed in such diversity in printing technologies and application fields that meanwhile it seems anything is possible. However, clearly the ideal 3D Printer, with high resolution, multi-material capability, fast printing, etc. is yet to be deve

  13. Molecular Cloning, Expression Pattern, and 3D Structural Prediction of the Cold Inducible RNA - Binding Protein (CIRP) in Japanese Flounder (Paralichthys olivaceus)

    Institute of Scientific and Technical Information of China (English)

    YANG Xiao; WANG Zhigang; ZHANG Quanqi; GAO Jinning; MA Liman; LI Zan; WANG Wenji; WANG Zhongkai; YU Haiyang; QI Jie; WANG Xubo

    2015-01-01

    Cold-inducible RNA-binding protein (CIRP) is a kind of RNA binding proteins that plays important roles in many physiological processes. The CIRP has been widely studied in mammals and amphibians since it was first cloned from mammals. On the contrary, there are little reports in teleosts. In this study, the PoCIRP gene of the Japanese flounder was cloned and sequenced. The genomic sequence consists of seven exons and six introns. The putative PoCIRP protein of flounder was 198 amino acid residues long containing the RNA recognition motif (RRM). Phylogenetic analysis showed that the flounder PoCIRP is highly conserved with other teleost CIRPs. The 5’ flanking sequence was cloned by genome walking and many transcription factor binding sites were iden-tified. There is a CpGs region located in promoter and exon I region and the methylation state is low. Quantitative real-time PCR analysis uncovered that PoCIRP gene was widely expressed in adult tissues with the highest expression level in the ovary. The mRNA of the PoCIRP was maternally deposited and the expression level of the gene was regulated up during the gastrula and neu-rula stages. In order to gain the information how the protein interacts with mRNA, we performed the modeling of the 3D structure of the flounder PoCIRP. The results showed a cleft existing the surface of the molecular. Taken together, the results indicate that the CIRP is a multifunctional molecular in teleosts and the findings about the structure provide valuable information for understanding the basis of this protein’s function.

  14. A New Approach for Investigating the Molecular Recognition of Protein: Toward Structure-Based Drug Design Based on the 3D-RISM Theory.

    Science.gov (United States)

    Kiyota, Yasuomi; Yoshida, Norio; Hirata, Fumio

    2011-11-08

    A new approach to investigate a molecular recognition process of protein is presented based on the three-dimensional reference interaction site model (3D-RISM) theory, a statistical mechanics theory of molecular liquids. Numerical procedure for solving the conventional 3D-RISM equation consists of two steps. In step 1, we solve ordinary RISM (or 1D-RISM) equations for a solvent mixture including target ligands in order to obtain the density pair correlation functions (PCF) among molecules in the solution. Then, we solve the 3D-RISM equation for a solute-solvent system to find three-dimensional density distribution functions (3D-DDF) of solvent species around a protein, using PCF obtained in the first step. A key to the success of the method was to regard a target ligand as one of "solvent" species. However, the success is limited due to a difficulty of solving the 1D-RISM equation for a solvent mixture, including large ligand molecules. In the present paper, we propose a method which eases the limitation concerning solute size in the conventional method. In this approach, we solve a solute-solute 3D-RISM equations for a protein-ligand system in which both proteins and ligands are regarded as "solutes" at infinite dilution. The 3D- and 1D-RISM equations are solved for protein-solvent and ligand-solvent systems, respectively, in order to obtain the 3D- and 1D-DDF of solvent around the solutes, which are required for solving the solute-solute 3D-RISM equation. The method is applied to two practical and noteworthy examples concerning pharmaceutical design. One is an odorant binding protein in the Drosophila melanogaster , which binds an ethanol molecule. The other is phospholipase A2, which is known as a receptor of acetylsalicylic acid or aspirin. The result indicates that the method successfully reproduces the binding mode of the ligand molecules in the binding sites measured by the experiments.

  15. p3d – Python module for structural bioinformatics

    Directory of Open Access Journals (Sweden)

    Fufezan Christian

    2009-08-01

    Full Text Available Abstract Background High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. Results p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files. p3d's strength arises from the combination of a very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP tree, b set theory and c functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. Conclusion p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

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

    Science.gov (United States)

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

    Science.gov (United States)

    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/.

  18. DESIGN OF 3D TOPOLOGICAL DATA STRUCTURE FOR 3D CADASTRE OBJECTS

    Directory of Open Access Journals (Sweden)

    N. A. Zulkifli

    2016-09-01

    Full Text Available This paper describes the design of 3D modelling and topological data structure for cadastre objects based on Land Administration Domain Model (LADM specifications. Tetrahedral Network (TEN is selected as a 3D topological data structure for this project. Data modelling is based on the LADM standard and it is used five classes (i.e. point, boundary face string, boundary face, tetrahedron and spatial unit. This research aims to enhance the current cadastral system by incorporating 3D topology model based on LADM standard.

  19. Design of 3d Topological Data Structure for 3d Cadastre Objects

    Science.gov (United States)

    Zulkifli, N. A.; Rahman, A. Abdul; Hassan, M. I.

    2016-09-01

    This paper describes the design of 3D modelling and topological data structure for cadastre objects based on Land Administration Domain Model (LADM) specifications. Tetrahedral Network (TEN) is selected as a 3D topological data structure for this project. Data modelling is based on the LADM standard and it is used five classes (i.e. point, boundary face string, boundary face, tetrahedron and spatial unit). This research aims to enhance the current cadastral system by incorporating 3D topology model based on LADM standard.

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

    Science.gov (United States)

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

    2010-01-01

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

  1. Plasticized protein for 3D printing by fused deposition modeling

    Science.gov (United States)

    Chaunier, Laurent; Leroy, Eric; Della Valle, Guy; Lourdin, Denis

    2016-10-01

    The developments of Additive Manufacturing (AM) by Fused Deposition Modeling (FDM) now target new 3D printable materials, leading to novel properties like those given by biopolymers such as proteins: degradability, biocompatibility and edibility. Plasticized materials from zein, a storage protein issued from corn, present interesting thermomechanical and rheological properties, possibly matching with AM-FDM specifications. Thus commercial zein plasticized with 20% glycerol has a glass transition temperature (Tg) at about 42°C, after storage at intermediate relative humidity (RH=59%). Its principal mechanical relaxation at Tα ≈ 50°C leads to a drop of the elastic modulus from about 1.1 GPa, at ambient temperature, to 0.6 MPa at Tα+100°C. These values are in the same range as values obtained in the case of standard polymers for AM-FDM processing, as PLA and ABS, although relaxation mechanisms are likely different in these materials. Such results lead to the setting up of zein-based compositions printable by AM-FDM and allow processing bioresorbable printed parts, with designed 3D geometry and structure.

  2. Representation of 3D Woven Structures by Parametric Method

    Institute of Scientific and Technical Information of China (English)

    DING Xin; YI Hong-lei

    2005-01-01

    A parametric method is developed to quantitatively represent the microstructure of 3D woven structures. Different binding patterns, such as angle interlock and orthogonal interlock with through-thickness or layer-to-layer bindings, are classified. A unit cell of 3D woven structure is defined with four constituent yarn systems represented by nine structural parameters. A mapping relationship between the 3D woven structure and corresponding representative parameters is thus established. The study indicates that four out of the nine parameters are necessary to represent a 3D woven structure with an angle interlock binding, and that five parameters are required to describe a 3D woven structure with an orthogonal interlock binding. Once the structural parameters are determined, the pattern of 3D woven structures can be unambiguously identified, and vice versa. In addition to the purpose of structure presentation, the method can be further used as a means for designing 3D woven structure to meet the performance requirements of 3D woven composites.

  3. Contact prediction for beta and alpha-beta proteins using integer linear optimization and its impact on the first principles 3D structure prediction method ASTRO-FOLD.

    Science.gov (United States)

    Rajgaria, R; Wei, Y; Floudas, C A

    2010-06-01

    An integer linear optimization model is presented to predict residue contacts in beta, alpha + beta, and alpha/beta proteins. The total energy of a protein is expressed as sum of a C(alpha)-C(alpha) distance dependent contact energy contribution and a hydrophobic contribution. The model selects contact that assign lowest energy to the protein structure as satisfying a set of constraints that are included to enforce certain physically observed topological information. A new method based on hydrophobicity is proposed to find the beta-sheet alignments. These beta-sheet alignments are used as constraints for contacts between residues of beta-sheets. This model was tested on three independent protein test sets and CASP8 test proteins consisting of beta, alpha + beta, alpha/beta proteins and it was found to perform very well. The average accuracy of the predictions (separated by at least six residues) was approximately 61%. The average true positive and false positive distances were also calculated for each of the test sets and they are 7.58 A and 15.88 A, respectively. Residue contact prediction can be directly used to facilitate the protein tertiary structure prediction. This proposed residue contact prediction model is incorporated into the first principles protein tertiary structure prediction approach, ASTRO-FOLD. The effectiveness of the contact prediction model was further demonstrated by the improvement in the quality of the protein structure ensemble generated using the predicted residue contacts for a test set of 10 proteins.

  4. Programming structure into 3D nanomaterials

    Directory of Open Access Journals (Sweden)

    Dara Van Gough

    2009-06-01

    Full Text Available Programming three dimensional nanostructures into materials is becoming increasingly important given the need for ever more highly functional solids. Applications for materials with complex programmed structures include solar energy harvesting, energy storage, molecular separation, sensors, pharmaceutical agent delivery, nanoreactors and advanced optical devices. Here we discuss examples of molecular and optical routes to program the structure of three-dimensional nanomaterials with exquisite control over nanomorphology and the resultant properties and conclude with a discussion of the opportunities and challenges of such an approach.

  5. 3DSwap: Curated knowledgebase of proteins involved in 3D domain swapping

    KAUST Repository

    Shameer, Khader

    2011-09-29

    Three-dimensional domain swapping is a unique protein structural phenomenon where two or more protein chains in a protein oligomer share a common structural segment between individual chains. This phenomenon is observed in an array of protein structures in oligomeric conformation. Protein structures in swapped conformations perform diverse functional roles and are also associated with deposition diseases in humans. We have performed in-depth literature curation and structural bioinformatics analyses to develop an integrated knowledgebase of proteins involved in 3D domain swapping. The hallmark of 3D domain swapping is the presence of distinct structural segments such as the hinge and swapped regions. We have curated the literature to delineate the boundaries of these regions. In addition, we have defined several new concepts like \\'secondary major interface\\' to represent the interface properties arising as a result of 3D domain swapping, and a new quantitative measure for the \\'extent of swapping\\' in structures. The catalog of proteins reported in 3DSwap knowledgebase has been generated using an integrated structural bioinformatics workflow of database searches, literature curation, by structure visualization and sequence-structure-function analyses. The current version of the 3DSwap knowledgebase reports 293 protein structures, the analysis of such a compendium of protein structures will further the understanding molecular factors driving 3D domain swapping. The Author(s) 2011.

  6. 3-D Radiative Transfer Modeling of Structured Winds in Massive Hot Stars with Wind3D

    CERN Document Server

    Lobel, A; Blomme, R

    2010-01-01

    We develop 3-D models of the structured winds of massive hot stars with the Wind3D radiative transfer (RT) code. We investigate the physical properties of large-scale structures observed in the wind of the B-type supergiant HD 64760 with detailed line profile fits to Discrete Absorption Components (DACs) and rotational modulations observed with IUE in Si IV {\\lambda}1395. We develop parameterized input models Wind3D with large-scale equatorial wind density- and velocity-structures, or so-called `Co-rotating Interaction Regions' (CIRs) and `Rotational Modulation Regions' (RMRs). The parameterized models offer important advantages for high-performance RT calculations over ab-initio hydrodynamic input models. The acceleration of the input model calculations permits us to simulate and investigate a wide variety of physical conditions in the extended winds of massive hot stars. The new modeling method is very flexible for constraining the dynamic and geometric wind properties of RMRs in HD 64760. We compute that t...

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

    Science.gov (United States)

    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.

  8. Acquisition of 3-D Map Structures for Mobile Robots

    Science.gov (United States)

    2007-11-02

    U.S.N.A. — Trident Scholar project report; no. 295 (2002) Acquisition of 3-D Map Structures for Mobile Robots by Midshipman Edward H.L. Fong, Class...REPORT TYPE 3. DATES COVERED (FROM - TO) xx-xx-2002 to xx-xx-2002 4. TITLE AND SUBTITLE Acquisition of 3-D Map Structures for Mobile Robots Unclassified...AND SUBTITLE Acquisition of 3-D map structures for mobile robots 6. AUTHOR(S) Fong, Edward H. L. (Edward Hsiang Lung), 1980- 5. FUNDING NUMBERS 7

  9. Differentiation of infection from vaccination in foot-and-mouth disease by the detection of antibodies to the non-structural proteins 3D, 3AB and 3ABC in ELISA using antigens expressed in baculovirus

    DEFF Research Database (Denmark)

    Sørensen, K.J.; Madsen, K.G.; Madsen, E.S.;

    1998-01-01

    a positive result in both the 3AB and the 3ABC ELISA's. Two cattle that had been both vaccinated and infected also gave, positive results in both tests, suggesting that the 3AB and 3ABC ELISA's, but not the 3D ELISA might represent a reliable means of detecting infection in a vaccinated population.......The baculovirus expression system was found to be efficient at expressing the 3D, the 3AB and the 3ABC non-structural proteins (NSP) of foot-and-mouth disease virus (FMDV) as antigens recognised by immune sera in ELISA. ELISA's using 3D, 3AB and 3ABC detected antibodies from day 8 and 10 after...... experimental infection of susceptible cattle and sheep and cattle remained seropositive for more than 395 days. The ELISA's detected antibodies against any of the seven serotypes of FMDV. The 3D ELISA was specific and precise and as sensitive as established ELISA's which measure antibody to structural proteins...

  10. Beyond Textbook Illustrations: Hand-Held Models of Ordered DNA and Protein Structures as 3D Supplements to Enhance Student Learning of Helical Biopolymers

    Science.gov (United States)

    Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

    2010-01-01

    Textbook illustrations of 3D biopolymers on printed paper, regardless of how detailed and colorful, suffer from its two-dimensionality. For beginners, computer screen display of skeletal models of biopolymers and their animation usually does not provide the at-a-glance 3D perception and details, which can be done by good hand-held models. Here, we…

  11. Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D

    Directory of Open Access Journals (Sweden)

    Meller Jaroslaw

    2007-08-01

    Full Text Available Abstract Background Macromolecular visualization as well as automated structural and functional annotation tools play an increasingly important role in the post-genomic era, contributing significantly towards the understanding of molecular systems and processes. For example, three dimensional (3D models help in exploring protein active sites and functional hot spots that can be targeted in drug design. Automated annotation and visualization pipelines can also reveal other functionally important attributes of macromolecules. These goals are dependent on the availability of advanced tools that integrate better the existing databases, annotation servers and other resources with state-of-the-art rendering programs. Results We present a new tool for protein structure analysis, with the focus on annotation and visualization of protein complexes, which is an extension of our previously developed POLYVIEW web server. By integrating the web technology with state-of-the-art software for macromolecular visualization, such as the PyMol program, POLYVIEW-3D enables combining versatile structural and functional annotations with a simple web-based interface for creating publication quality structure rendering, as well as animated images for Powerpoint™, web sites and other electronic resources. The service is platform independent and no plug-ins are required. Several examples of how POLYVIEW-3D can be used for structural and functional analysis in the context of protein-protein interactions are presented to illustrate the available annotation options. Conclusion POLYVIEW-3D server features the PyMol image rendering that provides detailed and high quality presentation of macromolecular structures, with an easy to use web-based interface. POLYVIEW-3D also provides a wide array of options for automated structural and functional analysis of proteins and their complexes. Thus, the POLYVIEW-3D server may become an important resource for researches and educators in

  12. 3D-DART: a DNA structure modelling server

    NARCIS (Netherlands)

    van Dijk, M.; Bonvin, A.M.J.J.

    2009-01-01

    There is a growing interest in structural studies of DNA by both experimental and computational approaches. Often, 3D-structural models of DNA are required, for instance, to serve as templates for homology modeling, as starting structures for macro-molecular docking or as scaffold for NMR structure

  13. Formal representation of 3D structural geological models

    Science.gov (United States)

    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.

  14. ProteinVista: a fast molecular visualization system using Microsoft Direct3D.

    Science.gov (United States)

    Park, Chan-Yong; Park, Sung-Hee; Park, Soo-Jun; Park, Sun-Hee; Hwang, Chi-Jung

    2008-09-01

    Many tools have been developed to visualize protein and molecular structures. Most high quality protein visualization tools use the OpenGL graphics library as a 3D graphics system. Currently, the performance of recent 3D graphics hardware has rapidly improved. Recent high-performance 3D graphics hardware support Microsoft Direct3D graphics library more than OpenGL and have become very popular in personal computers (PCs). In this paper, a molecular visualization system termed ProteinVista is proposed. ProteinVista is well-designed visualization system using the Microsoft Direct3D graphics library. It provides various visualization styles such as the wireframe, stick, ball and stick, space fill, ribbon, and surface model styles, in addition to display options for 3D visualization. As ProteinVista is optimized for recent 3D graphics hardware platforms and because it uses a geometry instancing technique, its rendering speed is 2.7 times faster compared to other visualization tools.

  15. 3D-printed supercapacitor-powered electrochemiluminescent protein immunoarray.

    Science.gov (United States)

    Kadimisetty, Karteek; Mosa, Islam M; Malla, Spundana; Satterwhite-Warden, Jennifer E; Kuhns, Tyler M; Faria, Ronaldo C; Lee, Norman H; Rusling, James F

    2016-03-15

    Herein we report a low cost, sensitive, supercapacitor-powered electrochemiluminescent (ECL) protein immunoarray fabricated by an inexpensive 3-dimensional (3D) printer. The immunosensor detects three cancer biomarker proteins in serum within 35 min. The 3D-printed device employs hand screen printed carbon sensors with gravity flow for sample/reagent delivery and washing. Prostate cancer biomarker proteins, prostate specific antigen (PSA), prostate specific membrane antigen (PSMA) and platelet factor-4 (PF-4) in serum were captured on the antibody-coated carbon sensors followed by delivery of detection-antibody-coated Ru(bpy)3(2+) (RuBPY)-doped silica nanoparticles in a sandwich immunoassay. ECL light was initiated from RuBPY in the silica nanoparticles by electrochemical oxidation with tripropylamine (TPrA) co-reactant using supercapacitor power and ECL was captured with a CCD camera. The supercapacitor was rapidly photo-recharged between assays using an inexpensive solar cell. Detection limits were 300-500f gmL(-1) for the 3 proteins in undiluted calf serum. Assays of 6 prostate cancer patient serum samples gave good correlation with conventional single protein ELISAs. This technology could provide sensitive onsite cancer diagnostic tests in resource-limited settings with the need for only moderate-level training.

  16. In vitro biological characterization of macroporous 3D Bonelike structures prepared through a 3D machining technique

    Energy Technology Data Exchange (ETDEWEB)

    Laranjeira, M.S.; Dias, A.G. [INEB - Instituto de Engenharia Biomedica, Divisao de Biomateriais, Universidade do Porto, Rua do Campo Alegre, 823, 4150-180 Porto (Portugal); Santos, J.D. [INEB - Instituto de Engenharia Biomedica, Divisao de Biomateriais, Universidade do Porto, Rua do Campo Alegre, 823, 4150-180 Porto (Portugal); Universidade do Porto, Faculdade de Engenharia, Departamento de Engenharia Metalurgica e Materiais, Rua Dr. Roberto Frias, 4200-465 Porto - Portugal (Portugal); Fernandes, M.H., E-mail: mhrf@portugalmail.pt [Universidade do Porto, Faculdade de Medicina Dentaria, Laboratorio de Farmacologia e Biocompatibilidade Celular, Rua Dr. Manuel Pereira da Silva, 4200-392 Porto (Portugal)

    2009-04-30

    3D bioactive macroporous structures were prepared using a 3D machining technique. A virtual 3D structure model was created and a computer numerically controlled (CNC) milling device machined Bonelike samples. The resulting structures showed a reproducible macroporosity and interconnective structure. Macropores size after sintering was approximately 2000 {mu}m. In vitro testing using human bone marrow stroma showed that cells were able to adhere and proliferate on 3D structures surface and migrate into all macropore channels. In addition, these cells were able to differentiate, since mineralized globular structures associated with cell layer were identified. Results obtained showed that 3D structures of Bonelike successfully allow cell migration into all macropores, and allow human bone marrow stromal cells to proliferate and differentiate. This innovative technique may be considered as a step-forward preparation for 3D interconnective macroporous structures that allow bone ingrowth while maintaining mechanical integrity.

  17. 3-D structures viewed with the architect's approach

    DEFF Research Database (Denmark)

    Vanggaard, Ole

    2002-01-01

    The complexity of teaching structures to architects is described in this article on the basis of the subject: 3-D surface structures and the need to give an insight into the theoretical background. Attention is given to the value of optimised structures, and the use of geometrical systems...

  18. Toward mobile 3D visualization for structural biologists.

    Science.gov (United States)

    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.

  19. 3D local structure around copper site of rabbit prion-related protein: Quantitative determination by XANES spectroscopy combined with multiple-scattering calculations

    Science.gov (United States)

    Cui, P. X.; Lian, F. L.; Wang, Y.; Wen, Yi; Chu, W. S.; Zhao, H. F.; Zhang, S.; Li, J.; Lin, D. H.; Wu, Z. Y.

    2014-02-01

    Prion-related protein (PrP), a cell-surface copper-binding glycoprotein, is considered to be responsible for a number of transmissible spongiform encephalopathies (TSEs). The structural conversion of PrP from the normal cellular isoform (PrPC) to the post-translationally modified form (PrPSc) is thought to be relevant to Cu2+ binding to histidine residues. Rabbits are one of the few mammalian species that appear to be resistant to TSEs, because of the structural characteristics of the rabbit prion protein (RaPrPC) itself. Here we determined the three-dimensional local structure around the C-terminal high-affinity copper-binding sites using X-ray absorption near-edge structure combined with ab initio calculations in the framework of the multiple-scattering (MS) theory. Result shows that two amino acid resides, Gln97 and Met108, and two histidine residues, His95 and His110, are involved in binding this copper(II) ion. It might help us understand the roles of copper in prion conformation conversions, and the molecular mechanisms of prion-involved diseases.

  20. 3D Ultrasonic Wave Simulations for Structural Health Monitoring

    Science.gov (United States)

    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.

  1. 3D Modelling with Structured Light GAMMA Calibration

    Directory of Open Access Journals (Sweden)

    Eser Sert

    2014-01-01

    Full Text Available Structured light method is one of the non-contact measurement methods used for high resolution and high sensitive 3D modeling. In this method, a projector, camera and computer are used. Projector projects patterns that are generated with specific coding strategies onto the object that will be 3D modeled. Camera receives these patterns. By processing the images received by the camera, object is 3D modeled. Light intensity that is emitted from the projector generally not a linear function of the signal input. This causes brightness problems in the patterns projected. Thus, images received from the camera needs to the gamma corrected. In this study, gamma calibration method is proposed to overcome this problem. Test results show that proposed calibration system improves the accuracy and quality of the 3D modeling.

  2. Automatic generation of 3D motifs for classification of protein binding sites

    Directory of Open Access Journals (Sweden)

    Herzyk Pawel

    2007-08-01

    Full Text Available Abstract Background Since many of the new protein structures delivered by high-throughput processes do not have any known function, there is a need for structure-based prediction of protein function. Protein 3D structures can be clustered according to their fold or secondary structures to produce classes of some functional significance. A recent alternative has been to detect specific 3D motifs which are often associated to active sites. Unfortunately, there are very few known 3D motifs, which are usually the result of a manual process, compared to the number of sequential motifs already known. In this paper, we report a method to automatically generate 3D motifs of protein structure binding sites based on consensus atom positions and evaluate it on a set of adenine based ligands. Results Our new approach was validated by generating automatically 3D patterns for the main adenine based ligands, i.e. AMP, ADP and ATP. Out of the 18 detected patterns, only one, the ADP4 pattern, is not associated with well defined structural patterns. Moreover, most of the patterns could be classified as binding site 3D motifs. Literature research revealed that the ADP4 pattern actually corresponds to structural features which show complex evolutionary links between ligases and transferases. Therefore, all of the generated patterns prove to be meaningful. Each pattern was used to query all PDB proteins which bind either purine based or guanine based ligands, in order to evaluate the classification and annotation properties of the pattern. Overall, our 3D patterns matched 31% of proteins with adenine based ligands and 95.5% of them were classified correctly. Conclusion A new metric has been introduced allowing the classification of proteins according to the similarity of atomic environment of binding sites, and a methodology has been developed to automatically produce 3D patterns from that classification. A study of proteins binding adenine based ligands showed that

  3. Computational modeling and validation studies of 3-D structure of neuraminidase protein of H1N1 influenza A virus and subsequent in silico elucidation of piceid analogues as its potent inhibitors.

    Science.gov (United States)

    Gupta, Chhedi Lal; Akhtar, Salman; Bajpaib, Preeti; Kandpal, K N; Desai, G S; Tiwari, Ashok K

    2013-01-01

    Emergence of the drug resistant variants of the Influenza A virus in the recent years has aroused a great need for the development of novel neuraminidase inhibitors for controlling the pandemic. The neuraminidase (NA) protein of the influenza virus has been the most potential target for the anti-influenza. However, in the absence of any experimental structure of the drug targeting NA protein of H1N1 influenza A virus as zanamivir and oseltamivir, the comprehensive study of the interaction of the drug molecules with the target protein has been missing. Hence in this study a computational 3-D structure of neuraminidase of H1N1 influenza A virus has been developed using homology modeling technique, and the same was validated for its reliability by ProSA web server in term of energy profile & Z scores and PROCHECK program followed by Ramachandran plot. Further, the developed 3-D model had been employed for docking studies with the class of compounds as Piceid and its analogs. In this context, two novel compounds (ChemBank ID 2110359 and 3075417) were found to be more potent inhibitors of neuraminidase than control drugs as zanamivir and oseltamivir in terms of their robust binding energies, strong inhibition constant (Ki) and better hydrogen bond interactions between the protein-ligand complex. The interaction of these compounds with NA protein has been significantly studied at the molecular level.

  4. 3D structure and immunogenicity of Plasmodium falciparum sporozoite induced associated protein peptides as components of fully-protective anti-malarial vaccine.

    Science.gov (United States)

    Alba, Martha P; Almonacid, Hannia; Calderón, Dayana; Chacón, Edgar A; Poloche, Luis A; Patarroyo, Manuel A; Patarroyo, Manuel E

    2011-12-16

    SIAP-1 and SIAP-2 are proteins which are implicated in early events involving Plasmodium falciparum infection of the Anopheles mosquito vector and the human host. High affinity HeLa and HepG2 cell binding conserved peptides have been previously identified in these proteins, i.e. SIAP-1 34893 ((421)KVQGLSYLLRRKNGTKHPVY(440)) and SIAP-1 34899 ((541)YVLNSKLLNSRSFDKFKWIQ(560)) and SIAP-2 36879 ((181)LLLYSTNSEDNLDISFGELQ(200)). When amino acid sequences have been properly modified (replacements shown in bold) they have induced high antibody titres against sporozoites in Aotus monkeys (assessed by IFA) and in the corresponding recombinant proteins (determined by ELISA and Western blot). (1)H NMR studies of these conserved native and modified high activity binding peptides (HABPs) revealed that all had α-helical structures in different locations and lengths. Conserved and corresponding modified HABPs displayed different lengths between the residues fitting into MHCII molecule pockets 1-9 and different amino acid orientation based on their different HLA-DRβ1(∗) binding motifs and binding registers, suggesting that such modifications were associated with making them immunogenic. The results suggested that these modified HAPBs could be potential targets for inclusion as components of a fully-effective, minimal sub-unit based, multi-epitope, and multistage anti-malarial vaccine.

  5. 3D printing of nano- and micro-structures

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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. 3D Images of Materials Structures Processing and Analysis

    CERN Document Server

    Ohser, Joachim

    2009-01-01

    Taking and analyzing images of materials' microstructures is essential for quality control, choice and design of all kind of products. Today, the standard method still is to analyze 2D microscopy images. But, insight into the 3D geometry of the microstructure of materials and measuring its characteristics become more and more prerequisites in order to choose and design advanced materials according to desired product properties. This first book on processing and analysis of 3D images of materials structures describes how to develop and apply efficient and versatile tools for geometric analysis

  8. Mathematical structure of three - dimensional (3D) Ising model

    CERN Document Server

    Zhang, Zhi-dong

    2013-01-01

    An overview of the mathematical structure of the three-dimensional (3D) Ising model is given, from the viewpoints of topologic, algebraic and geometric aspects. By analyzing the relations among transfer matrices of the 3D Ising model, Reidemeister moves in the knot theory, Yang-Baxter and tetrahedron equations, the following facts are illustrated for the 3D Ising model: 1) The complexified quaternion basis constructed for the 3D Ising model represents naturally the rotation in a (3 + 1) - dimensional space-time, as a relativistic quantum statistical mechanics model, which is consistent with the 4-fold integrand of the partition function by taking the time average. 2) A unitary transformation with a matrix being a spin representation in 2^(nlo)-space corresponds to a rotation in 2nlo-space, which serves to smooth all the crossings in the transfer matrices and contributes as the non-trivial topologic part of the partition function of the 3D Ising model. 3) A tetrahedron relation would ensure the commutativity o...

  9. Tangible 3D modeling of coherent and themed structures

    DEFF Research Database (Denmark)

    Walther, Jeppe Ullè; Bærentzen, J. Andreas; Aanæs, Henrik

    2016-01-01

    , allows the user to tangibly build structures of greater details than the blocks provide in and of themselves. We show a number of shapes that have been modeled by users and are indicative of the expressive power of the system. Furthermore, we demonstrate the scalability of the tangible interface which......We present CubeBuilder, a system for interactive, tangible 3D shape modeling. CubeBuilder allows the user to create a digital 3D model by placing physical, non-interlocking cubic blocks. These blocks may be placed in a completely arbitrary fashion and combined with other objects. In effect......, this turns the task of 3D modeling into a playful activity that hardly requires any learning on the part of the user. The blocks are registered using a depth camera and entered into the cube graph where each block is a node and adjacent blocks are connected by edges. From the cube graph, we transform...

  10. Underwater 3D Surface Scanning using Structured Light

    OpenAIRE

    Törnblom, Nils

    2010-01-01

    In this thesis project, an underwater 3D scanner based on structured light has been constructed and developed. Two other scanners, based on stereoscopy and a line-swept laser, were also tested. The target application is to examine objects inside the water filled reactor vessel of nuclear power plants. Structured light systems (SLS) use a projector to illuminate the surface of the scanned object, and a camera to capture the surfaces' reflection. By projecting a series of specific line-patterns...

  11. Multifunctional 3D printing of heterogeneous hydrogel structures

    OpenAIRE

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

    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 filame...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Thuy Tuong Nguyen

    2015-07-01

    Full Text Available 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.

  15. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine.

    Science.gov (United States)

    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

    2017-02-14

    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).

  16. Formation of coherent structures in 3D laminar mixing flows

    Science.gov (United States)

    Speetjens, Michel; Clercx, Herman

    2009-11-01

    Mixing under laminar flow conditions is key to a wide variety of industrial systems of size extending from microns to meters. Examples range from the traditional (and still very relevant) mixing of viscous fluids via compact processing equipment down to emerging micro-fluidics applications. Profound insight into laminar mixing mechanisms is imperative for further advancement of mixing technology (particularly for complex micro-fluidics systems) yet remains limited to date. The present study concentrates on a fundamental transport phenomenon of potential relevance to laminar mixing: the formation of coherent structures in the web of 3D fluid trajectories due to fluid inertia. Such coherent structures geometrically determine the transport properties of the flow and better understanding of their formation and characteristics may offer ways to control and manipulate the mixing properties of laminar flows. The formation of coherent structures and its impact upon 3D transport properties is demonstrated by way of examples.

  17. Protein-protein docking using region-based 3D Zernike descriptors

    Directory of Open Access Journals (Sweden)

    Sael Lee

    2009-12-01

    Full Text Available Abstract Background Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur. Results We present a novel protein docking algorithm based on the use of 3D Zernike descriptors as regional features of molecular shape. The key motivation of using these descriptors is their invariance to transformation, in addition to a compact representation of local surface shape characteristics. Docking decoys are generated using geometric hashing, which are then ranked by a scoring function that incorporates a buried surface area and a novel geometric complementarity term based on normals associated with the 3D Zernike shape description. Our docking algorithm was tested on both bound and unbound cases in the ZDOCK benchmark 2.0 dataset. In 74% of the bound docking predictions, our method was able to find a near-native solution (interface C-αRMSD ≤ 2.5 Å within the top 1000 ranks. For unbound docking, among the 60 complexes for which our algorithm returned at least one hit, 60% of the cases were ranked within the top 2000. Comparison with existing shape-based docking algorithms shows that our method has a better performance than the others in unbound docking while remaining competitive for bound docking cases. Conclusion We show for the first time that the 3D Zernike descriptors are adept in capturing shape complementarity at the protein-protein interface and useful for

  18. 3D Printing of Protein Models in an Undergraduate Laboratory: Leucine Zippers

    Science.gov (United States)

    Meyer, Scott C.

    2015-01-01

    An upper-division undergraduate laboratory experiment is described that explores the structure/function relationship of protein domains, namely leucine zippers, through a molecular graphics computer program and physical models fabricated by 3D printing. By generating solvent accessible surfaces and color-coding hydrophobic, basic, and acidic amino…

  19. Skeleton-Sectional Structural Analysis for 3D Printing

    Institute of Scientific and Technical Information of China (English)

    Wen-Peng Xu; Wei Li; Li-Gang Liu

    2016-01-01

    3D printing has become popular and has been widely used in various applications in recent years. More and more home users have motivation to design their own models and then fabricate them using 3D printers. However, the printed objects may have some structural or stress defects as the users may be lack of knowledge on stress analysis on 3D models. In this paper, we present an approach to help users analyze a model’s structural strength while designing its shape. We adopt sectional structural analysis instead of conventional FEM (Finite Element Method) analysis which is computationally expensive. Based on sectional structural analysis, our approach imports skeletons to assist in integrating mesh designing, strength computing and mesh correction well. Skeletons can also guide sections building and load calculation for analysis. For weak regions with high stress over a threshold value in the model from analysis result, our system corrects them by scaling the corresponding bones of skeleton so as to make these regions stiff enough. A number of experiments have demonstrated the applicability and practicability of our approach.

  20. Combined shape and topology optimization of 3D structures

    DEFF Research Database (Denmark)

    Christiansen, Asger Nyman; Bærentzen, Jakob Andreas; Nobel-Jørgensen, Morten

    2015-01-01

    We present a method for automatic generation of 3D models based on shape and topology optimization. The optimization procedure, or model generation process, is initialized by a set of boundary conditions, an objective function, constraints and an initial structure. Using this input, the method...... will automatically deform and change the topology of the initial structure such that the objective function is optimized subject to the specified constraints and boundary conditions. For example, this tool can be used to improve the stiffness of a structure before printing, reduce the amount of material needed...

  1. 3D reconstruction methods of coronal structures by radio observations

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  4. Manufacturing of a 3D complex hyperstable Cesic structure

    Science.gov (United States)

    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.

  5. Structure and magnetic exchange in heterometallic 3d-3d transition metal triethanolamine clusters.

    Science.gov (United States)

    Langley, Stuart K; Chilton, Nicholas F; Moubaraki, Boujemaa; Murray, Keith S

    2012-01-21

    Synthetic methods are described that have resulted in the formation of seven heterometallic complexes, all of which contain partially deprotonated forms of the ligand triethanolamine (teaH(3)). These compounds are [Mn(III)(4)Co(III)(2)Co(II)(2)O(2)(teaH(2))(2)(teaH)(0.82)(dea)(3.18)(O(2)CMe)(2)(OMe)(2)](BF(4))(2)(O(2)CMe)(2)·3.18MeOH·H(2)O (1), [Mn(II)(2)Mn(III)(2)Co(III)(2)(teaH)(4)(OMe)(2)(acac)(4)](NO(3))(2)·2MeOH (2), [Mn(III)(2)Ni(II)(4)(teaH)(4)(O(2)CMe)(6)]·2MeCN (3), [Mn(III)(2)Co(II)(2)(teaH)(2)(sal)(2)(acac)(2)(MeOH)(2)]·2MeOH (4), [Mn(II)(2)Fe(III)(2)(teaH)(2)(paa)(4)](NO(3))(2)·2MeOH·CH(2)Cl(2) (5), [Mn(II)Mn(III)(2)Co(III)(2)O(teaH)(2)(dea)(Iso)(OMe)(F)(2)(Phen)(2)](BF(4))(NO(3))·3MeOH (6) and [Mn(II)(2)Mn(III)Co(III)(2)(OH)(teaH)(3)(teaH(2))(acac)(3)](NO(3))(2)·3CH(2)Cl(2) (7). All of the compounds contain manganese, combined with 3d transition metal ions such as Fe, Co and Ni. The crystal structures are described and examples of 'rods', tetranuclear 'butterfly' and 'triangular' Mn(3) cluster motifs, flanked in some cases by diamagnetic cobalt(III) centres, are presented. Detailed DC and AC magnetic susceptibility and magnetization studies, combined with spin Hamiltonian analysis, have yielded J values and identified the spin ground states. In most cases, the energies of the low-lying excited states have also been obtained. The features of note include the 'inverse butterfly' spin arrangement in 2, 4 and 5. A S = 5/2 ground state occurs, for the first time, in the Mn(III)(2)Mn(II) triangular moiety within 6, the many other reported [Mn(3)O](6+) examples having S = ½ or 3/2 ground states. Compound 7 provides the first example of a Mn(II)(2)Mn(III) triangle, here within a pentanuclear Mn(3)Co(2) cluster.

  6. Polarization Control by Using Anisotropic 3D Chiral Structures

    CERN Document Server

    Chen, Menglin L N; Sha, Wei E I; Choy, Wallace C H; Itoh, Tatsuo

    2016-01-01

    Due to the mirror symmetry breaking, chiral structures show fantastic electromagnetic (EM) properties involving negative refraction, giant optical activity, and asymmetric transmission. Aligned electric and magnetic dipoles excited in chiral structures contribute to extraordinary properties. However, the chiral structures that exhibit n-fold rotational symmetry show limited tuning capability. In this paper, we proposed a compact, light, and highly tunable anisotropic chiral structure to overcome this limitation and realize a linear-to-circular polarization conversion. The anisotropy is due to simultaneous excitations of two different pairs of aligned electric and magnetic dipoles. The 3D omega-like structure, etched on two sides of one PCB board and connected by metallic vias, achieves 60% of linearto- circular conversion (transmission) efficiency at the operating frequency of 9.2 GHz. The desired 90-degree phase shift between the two orthogonal linear polarization components is not only from the finite-thick...

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

    Science.gov (United States)

    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.

  8. Advancements in 3D Structural Analysis of Geothermal Systems

    Energy Technology Data Exchange (ETDEWEB)

    Siler, Drew L [Nevada Bureau of Mines and Geology, University of Nevada, Reno; Faulds, James E [Nevada Bureau of Mines and Geology, University of Nevada, Reno; Mayhew, Brett [Nevada Bureau of Mines and Geology, University of Nevada, Reno; McNamara, David [Department of Geothermal Science, GNS Science, NZ

    2013-06-23

    Robust geothermal activity in the Great Basin, USA is a product of both anomalously high regional heat flow and active fault-controlled extension. Elevated permeability associated with some fault systems provides pathways for circulation of geothermal fluids. Constraining the local-scale 3D geometry of these structures and their roles as fluid flow conduits is crucial in order to mitigate both the costs and risks of geothermal exploration and to identify blind (no surface expression) geothermal resources. Ongoing studies have indicated that much of the robust geothermal activity in the Great Basin is associated with high density faulting at structurally complex fault intersection/interaction areas, such as accommodation/transfer zones between discrete fault systems, step-overs or relay ramps in fault systems, intersection zones between faults with different strikes or different senses of slip, and horse-tailing fault terminations. These conceptualized models are crucial for locating and characterizing geothermal systems in a regional context. At the local scale, however, pinpointing drilling targets and characterizing resource potential within known or probable geothermal areas requires precise 3D characterization of the system. Employing a variety of surface and subsurface data sets, we have conducted detailed 3D geologic analyses of two Great Basin geothermal systems. Using EarthVision (Dynamic Graphics Inc., Alameda, CA) we constructed 3D geologic models of both the actively producing Brady’s geothermal system and a ‘greenfield’ geothermal prospect at Astor Pass, NV. These 3D models allow spatial comparison of disparate data sets in 3D and are the basis for quantitative structural analyses that can aid geothermal resource assessment and be used to pinpoint discrete drilling targets. The relatively abundant data set at Brady’s, ~80 km NE of Reno, NV, includes 24 wells with lithologies interpreted from careful analysis of cuttings and core, a 1

  9. A 3D image filter for parameter-free segmentation of macromolecular structures from electron tomograms.

    Directory of Open Access Journals (Sweden)

    Rubbiya A Ali

    Full Text Available 3D image reconstruction of large cellular volumes by electron tomography (ET at high (≤ 5 nm resolution can now routinely resolve organellar and compartmental membrane structures, protein coats, cytoskeletal filaments, and macromolecules. However, current image analysis methods for identifying in situ macromolecular structures within the crowded 3D ultrastructural landscape of a cell remain labor-intensive, time-consuming, and prone to user-bias and/or error. This paper demonstrates the development and application of a parameter-free, 3D implementation of the bilateral edge-detection (BLE algorithm for the rapid and accurate segmentation of cellular tomograms. The performance of the 3D BLE filter has been tested on a range of synthetic and real biological data sets and validated against current leading filters-the pseudo 3D recursive and Canny filters. The performance of the 3D BLE filter was found to be comparable to or better than that of both the 3D recursive and Canny filters while offering the significant advantage that it requires no parameter input or optimisation. Edge widths as little as 2 pixels are reproducibly detected with signal intensity and grey scale values as low as 0.72% above the mean of the background noise. The 3D BLE thus provides an efficient method for the automated segmentation of complex cellular structures across multiple scales for further downstream processing, such as cellular annotation and sub-tomogram averaging, and provides a valuable tool for the accurate and high-throughput identification and annotation of 3D structural complexity at the subcellular level, as well as for mapping the spatial and temporal rearrangement of macromolecular assemblies in situ within cellular tomograms.

  10. A 3D image filter for parameter-free segmentation of macromolecular structures from electron tomograms.

    Science.gov (United States)

    Ali, Rubbiya A; Landsberg, Michael J; Knauth, Emily; Morgan, Garry P; Marsh, Brad J; Hankamer, Ben

    2012-01-01

    3D image reconstruction of large cellular volumes by electron tomography (ET) at high (≤ 5 nm) resolution can now routinely resolve organellar and compartmental membrane structures, protein coats, cytoskeletal filaments, and macromolecules. However, current image analysis methods for identifying in situ macromolecular structures within the crowded 3D ultrastructural landscape of a cell remain labor-intensive, time-consuming, and prone to user-bias and/or error. This paper demonstrates the development and application of a parameter-free, 3D implementation of the bilateral edge-detection (BLE) algorithm for the rapid and accurate segmentation of cellular tomograms. The performance of the 3D BLE filter has been tested on a range of synthetic and real biological data sets and validated against current leading filters-the pseudo 3D recursive and Canny filters. The performance of the 3D BLE filter was found to be comparable to or better than that of both the 3D recursive and Canny filters while offering the significant advantage that it requires no parameter input or optimisation. Edge widths as little as 2 pixels are reproducibly detected with signal intensity and grey scale values as low as 0.72% above the mean of the background noise. The 3D BLE thus provides an efficient method for the automated segmentation of complex cellular structures across multiple scales for further downstream processing, such as cellular annotation and sub-tomogram averaging, and provides a valuable tool for the accurate and high-throughput identification and annotation of 3D structural complexity at the subcellular level, as well as for mapping the spatial and temporal rearrangement of macromolecular assemblies in situ within cellular tomograms.

  11. Improving 3D structure prediction from chemical shift data

    Energy Technology Data Exchange (ETDEWEB)

    Schot, Gijs van der [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Zhang, Zaiyong [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany); Vernon, Robert [University of Washington, Department of Biochemistry (United States); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vranken, Wim F. [VIB, Department of Structural Biology (Belgium); Baker, David [University of Washington, Department of Biochemistry (United States); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany)

    2013-09-15

    We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50-100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 A RMSD from the reference)

  12. Structure-Function Analysis of PPP1R3D, a Protein Phosphatase 1 Targeting Subunit, Reveals a Binding Motif for 14-3-3 Proteins which Regulates its Glycogenic Properties.

    Science.gov (United States)

    Rubio-Villena, Carla; Sanz, Pascual; Garcia-Gimeno, Maria Adelaida

    2015-01-01

    Protein phosphatase 1 (PP1) is one of the major protein phosphatases in eukaryotic cells. It plays a key role in regulating glycogen synthesis, by dephosphorylating crucial enzymes involved in glycogen homeostasis such as glycogen synthase (GS) and glycogen phosphorylase (GP). To play this role, PP1 binds to specific glycogen targeting subunits that, on one hand recognize the substrates to be dephosphorylated and on the other hand recruit PP1 to glycogen particles. In this work we have analyzed the functionality of the different protein binding domains of one of these glycogen targeting subunits, namely PPP1R3D (R6) and studied how binding properties of different domains affect its glycogenic properties. We have found that the PP1 binding domain of R6 comprises a conserved RVXF motif (R102VRF) located at the N-terminus of the protein. We have also identified a region located at the C-terminus of R6 (W267DNND) that is involved in binding to the PP1 glycogenic substrates. Our results indicate that although binding to PP1 and glycogenic substrates are independent processes, impairment of any of them results in lack of glycogenic activity of R6. In addition, we have characterized a novel site of regulation in R6 that is involved in binding to 14-3-3 proteins (RARS74LP). We present evidence indicating that when binding of R6 to 14-3-3 proteins is prevented, R6 displays hyper-glycogenic activity although is rapidly degraded by the lysosomal pathway. These results define binding to 14-3-3 proteins as an additional pathway in the control of the glycogenic properties of R6.

  13. Dual multispectral and 3D structured light laparoscope

    Science.gov (United States)

    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.

  14. 3D Shape and Indirect Appearance by Structured Light Transport.

    Science.gov (United States)

    OToole, Matthew; Mather, John; Kutulakos, Kiriakos N

    2016-07-01

    We consider the problem of deliberately manipulating the direct and indirect light flowing through a time-varying, general scene in order to simplify its visual analysis. Our approach rests on a crucial link between stereo geometry and light transport: while direct light always obeys the epipolar geometry of a projector-camera pair, indirect light overwhelmingly does not. We show that it is possible to turn this observation into an imaging method that analyzes light transport in real time in the optical domain, prior to acquisition. This yields three key abilities that we demonstrate in an experimental camera prototype: (1) producing a live indirect-only video stream for any scene, regardless of geometric or photometric complexity; (2) capturing images that make existing structured-light shape recovery algorithms robust to indirect transport; and (3) turning them into one-shot methods for dynamic 3D shape capture.

  15. Structural Indexing for 3D Solid Digital Library

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    In a very large digital library that support computer-aidedcollabora t ive design, an indexing process is crucial whenever the retrieval process has to select among many possible designs. In this paper, we address the problem of re trieving important design and engineering information by structural indexing. A design is represented by a model dependency graph, therefor, the indexing proble m is to determine whether a graph is present or absent in a database of model de pendency graphs. we present a novel graph indexing method using polynomial chara cterization of a model dependency graph and on hashing. Such an approach is able to create an high efficient 3D solid digital library for retrieving and extract ing solid geometric model and engineering information.

  16. Tridimensional Regression for Comparing and Mapping 3D Anatomical Structures

    Directory of Open Access Journals (Sweden)

    Kendra K. Schmid

    2012-01-01

    Full Text Available Shape analysis is useful for a wide variety of disciplines and has many applications. There are many approaches to shape analysis, one of which focuses on the analysis of shapes that are represented by the coordinates of predefined landmarks on the object. This paper discusses Tridimensional Regression, a technique that can be used for mapping images and shapes that are represented by sets of three-dimensional landmark coordinates, for comparing and mapping 3D anatomical structures. The degree of similarity between shapes can be quantified using the tridimensional coefficient of determination (2. An experiment was conducted to evaluate the effectiveness of this technique to correctly match the image of a face with another image of the same face. These results were compared to the 2 values obtained when only two dimensions are used and show that using three dimensions increases the ability to correctly match and discriminate between faces.

  17. Multifunctional 3D printing of heterogeneous hydrogel structures.

    Science.gov (United States)

    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.

  18. Multifunctional 3D printing of heterogeneous hydrogel structures

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  20. 3D Imaging with Structured Illumination for Advanced Security Applications

    Energy Technology Data Exchange (ETDEWEB)

    Birch, Gabriel Carisle [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Dagel, Amber Lynn [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Kast, Brian A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Smith, Collin S. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    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.

  1. The 3D structure of Coronal Mass Ejections

    Science.gov (United States)

    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).

  2. 3D Seismic Imaging over a Potential Collapse Structure

    Science.gov (United States)

    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.

  3. Proteopedia: Exciting Advances in the 3D Encyclopedia of Biomolecular Structure

    Science.gov (United States)

    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.

  4. 3D-SURFER 2.0: web platform for real-time search and characterization of protein surfaces.

    Science.gov (United States)

    Xiong, Yi; Esquivel-Rodriguez, Juan; Sael, Lee; Kihara, Daisuke

    2014-01-01

    The increasing number of uncharacterized protein structures necessitates the development of computational approaches for function annotation using the protein tertiary structures. Protein structure database search is the basis of any structure-based functional elucidation of proteins. 3D-SURFER is a web platform for real-time protein surface comparison of a given protein structure against the entire PDB using 3D Zernike descriptors. It can smoothly navigate the protein structure space in real-time from one query structure to another. A major new feature of Release 2.0 is the ability to compare the protein surface of a single chain, a single domain, or a single complex against databases of protein chains, domains, complexes, or a combination of all three in the latest PDB. Additionally, two types of protein structures can now be compared: all-atom-surface and backbone-atom-surface. The server can also accept a batch job for a large number of database searches. Pockets in protein surfaces can be identified by VisGrid and LIGSITE (csc) . The server is available at http://kiharalab.org/3d-surfer/.

  5. 3D Vegetation Structure Extraction from Lidar Remote Sensing

    Science.gov (United States)

    Ni-Meister, W.

    2006-05-01

    Vegetation structure data are critical not only for biomass estimation and global carbon cycle studies, but also for ecosystem disturbance, species habitat and ecosystem biodiversity studies. However those data are rarely available at the global scale. Multispectral passive remote sensing has shown little success on this direction. The upcoming lidar remote sensing technology shows a great potential to measure vegetation vertical structure data globally. In this study, we present and test a Bayesian Stochastic Inversion (BSI) approach to invert a full canopy Geometric Optical and Radiative Transfer (GORT) model to retrieve 3-D vegetation structure parameters from large footprint (15m-25m diameter) vegetation lidar data. BSI approach allows us to take into account lidar-directly derived structure parameters, such as tree height and the upper and lower bounds of crown height and their uncertainties as the prior knowledge in the inversion. It provides not only the optimal estimates of model parameters, but also their uncertainties. We first assess the accuracy of vegetation structure parameter retrievals from vegetation lidar data through a comprehensive GORT input parameter sensitivity analysis. We calculated the singular value decomposition (SVD) of Jacobian matrix, which contains the partial derivatives of the combined model with respect to all relevant model input parameters and. Our analysis shows that with the prior knowledge of tree height, crown depth and crown shape, lidar waveforms is most sensitive to the tree density, then to the tree size and the least to the foliage area volume density. It indicates that tree density can be retrieved with the most accuracy and then the tree size, the least is the foliage area volume density. We also test the simplified BSI approach through a synthetic experiment. The synthetic lidar waveforms were generated based the vegetation structure data obtained from the Boreal Ecosystem Atmosphere Study (BOREAS). With the exact

  6. 3D representations of amino acids—applications to protein sequence comparison and classification

    Directory of Open Access Journals (Sweden)

    Jie Li

    2014-08-01

    Full Text Available The amino acid sequence of a protein is the key to understanding its structure and ultimately its function in the cell. This paper addresses the fundamental issue of encoding amino acids in ways that the representation of such a protein sequence facilitates the decoding of its information content. We show that a feature-based representation in a three-dimensional (3D space derived from amino acid substitution matrices provides an adequate representation that can be used for direct comparison of protein sequences based on geometry. We measure the performance of such a representation in the context of the protein structural fold prediction problem. We compare the results of classifying different sets of proteins belonging to distinct structural folds against classifications of the same proteins obtained from sequence alone or directly from structural information. We find that sequence alone performs poorly as a structure classifier. We show in contrast that the use of the three dimensional representation of the sequences significantly improves the classification accuracy. We conclude with a discussion of the current limitations of such a representation and with a description of potential improvements.

  7. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.

    Science.gov (United States)

    Wallace, A C; Borkakoti, N; Thornton, J M

    1997-11-01

    It is well established that sequence templates such as those in the PROSITE and PRINTS databases are powerful tools for predicting the biological function and tertiary structure for newly derived protein sequences. The number of X-ray and NMR protein structures is increasing rapidly and it is apparent that a 3D equivalent of the sequence templates is needed. Here, we describe an algorithm called TESS that automatically derives 3D templates from structures deposited in the Brookhaven Protein Data Bank. While a new sequence can be searched for sequence patterns, a new structure can be scanned against these 3D templates to identify functional sites. As examples, 3D templates are derived for enzymes with an O-His-O "catalytic triad" and for the ribonucleases and lysozymes. When these 3D templates are applied to a large data set of nonidentical proteins, several interesting hits are located. This suggests that the development of a 3D template database may help to identify the function of new protein structures, if unknown, as well as to design proteins with specific functions.

  8. 3D reconstruction and capsid protein characterization of grass carp reovirus

    Institute of Scientific and Technical Information of China (English)

    FANG; Qin; Shah; Sanket; LIANG; Yuyao; Z.; H.; ZHOU

    2005-01-01

    Grass carp reovirus (GCRV) is a relatively new virus first isolated in China and is a member of the Aquareovirus genus of the Reoviridae family. Recent report of genomic sequencing showed that GCRV shared high degree of homology with mammalian reovirus (MRV). As a step of our effort to understand the structural basis of GCRV pathogenesis, we determined the three-dimensional (3D) structure of GCRV capsid at 17 (A) resolution by electron cryomicroscopy. Each GCRV capsid has a multilayered organization, consisting of an RNA core, an inner, middle and outer protein layer. The outer layer is made up of 200 trimers that are arranged on an incomplete T=13 icosahedral lattice. A characteristic feature of this layer is the depression resulting from the absence of trimers around the peripentonal positions, revealing the underlying trimers on the middle layer. There are 120 subunits in the inner layer arranged with T=1 symmetry. These structural features are common to other members of the Reoviridae. Moreover, SDS-PAGE analysis showed that GCRV virions contain seven structural proteins (VP1-VP7). These structural proteins have a high degree of sequence homology to MRV, consistent with the structural similarities observed in our study. The high structural similarities of isolated GCRV and MRV suggest that future structural studies focusing on GCRV entering into and replicating within its host cell are necessary in order to fully understand the structural basis of GCRV pathogenesis.

  9. Membrane transport mechanism 3D structure and beyond

    CERN Document Server

    Ziegler, Christine

    2014-01-01

    This book provides a molecular view of membrane transport by means of numerous biochemical and biophysical techniques. The rapidly growing number of atomic structures of transporters in different conformations and the constant progress in bioinformatics have recently added deeper insights.   The unifying mechanism of energized solute transport across membranes is assumed to consist of the conformational cycling of a carrier protein to provide access to substrate binding sites from either side of a cellular membrane. Due to the central role of active membrane transport there is considerable interest in deciphering the principles of one of the most fundamental processes in nature: the alternating access mechanism.   This book brings together particularly significant structure-function studies on a variety of carrier systems from different transporter families: Glutamate symporters, LeuT-like fold transporters, MFS transporters and SMR (RND) exporters, as well as ABC-type importers.   The selected examples im...

  10. 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles.

    Science.gov (United States)

    Fantino, Erika; Chiappone, Annalisa; Roppolo, Ignazio; Manfredi, Diego; Bongiovanni, Roberta; Pirri, Candido Fabrizio; Calignano, Flaviana

    2016-05-01

    Coupling the photoreduction of a metal precursor with 3D-printing technology is shown to allow the fabrication of conductive 3D hybrid structures consisting of metal nanoparticles and organic polymers shaped in complex multilayered architectures. 3D conductive structures are fabricated incorporating silver nitrate into a photocurable oligomer in the presence of suitable photoinitiators and exposing them to a digital light system.

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

    Science.gov (United States)

    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.

  12. Mixed Structural Models for 3D Audio in Virtual Environments

    OpenAIRE

    Geronazzo, Michele

    2014-01-01

    In the world of ICT, strategies for innovation and development are increasingly focusing on applications that require spatial representation and real-time interaction with and within 3D media environments. One of the major challenges that such applications have to address is user-centricity, reflecting e.g. on developing complexity-hiding services so that people can personalize their own delivery of services. In these terms, multimodal interfaces represent a key factor for enabling an inclusi...

  13. Ultra-Rapid 2-D and 3-D Laser Microprinting of Proteins

    Science.gov (United States)

    Scott, Mark Andrew

    -D printing of full length proteins in collagen, fibrin and gelatin methacrylate scaffolds, as well as printing in agarose and agarose methacrylate scaffolds. We also present a novel method for 3-D printing collagen scaffolds at unprecedented speeds, up to 14layers per second, generating complex shapes in seconds with sub-micron resolution. Finally, we demonstrate that 3-D printing of scaffold architecture and protein cues inside the scaffold can be combined, for the first time enabling structures with complex sub-micron architectures and chemical cues for directing development. We believe that the ultra-rapid printing technology presented in this thesis will be a key enabler in the development of complex, artificially engineered tissues and organs. (Copies available exclusively from MIT Libraries, libraries.mit.edu/docs - docs mit.edu)

  14. Framework system and research flow of uncertainty in 3D geological structure models

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Uncertainty in 3D geological structure models has become a bottleneck that restricts the development and application of 3D geological modeling.In order to solve this problem during periods of accuracy assessment,error detection and dynamic correction in 3D geological structure models,we have reviewed the current situation and development trends in 3D geological modeling.The main context of uncertainty in 3D geological structure models is discussed.Major research issues and a general framework system of unce...

  15. seeMotif: exploring and visualizing sequence motifs in 3D structures.

    Science.gov (United States)

    Chang, Darby Tien-Hao; Chien, Ting-Ying; Chen, Chien-Yu

    2009-07-01

    Sequence motifs are important in the study of molecular biology. Motif discovery tools efficiently deliver many function related signatures of proteins and largely facilitate sequence annotation. As increasing numbers of motifs are detected experimentally or predicted computationally, characterizing the functional roles of motifs and identifying the potential synergetic relationships between them are important next steps. A good way to investigate novel motifs is to utilize the abundant 3D structures that have also been accumulated at an astounding rate in recent years. This article reports the development of the web service seeMotif, which provides users with an interactive interface for visualizing sequence motifs on protein structures from the Protein Data Bank (PDB). Researchers can quickly see the locations and conformation of multiple motifs among a number of related structures simultaneously. Considering the fact that PDB sequences are usually shorter than those in sequence databases and/or may have missing residues, seeMotif has two complementary approaches for selecting structures and mapping motifs to protein chains in structures. As more and more structures belonging to previously uncharacterized protein families become available, combining sequence and structure information gives good opportunities to facilitate understanding of protein functions in large-scale genome projects. Available at: http://seemotif.csie.ntu.edu.tw,http://seemotif.ee.ncku.edu.tw or http://seemotif.csbb.ntu.edu.tw.

  16. Rapid Fabrication of Cell-Laden Alginate Hydrogel 3D Structures by Micro Dip-Coating

    Science.gov (United States)

    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

  17. Coherent vortex structures and 3D enstrophy cascade

    CERN Document Server

    Dascaliuc, R

    2011-01-01

    Existence of 2D enstrophy cascade in a suitable mathematical setting, and under suitable conditions compatible with 2D turbulence phenomenology, is known both in the Fourier and in the physical scales. The goal of this paper is to show that the same geometric condition preventing the formation of singularities - 1/2-H\\"older coherence of the vorticity direction - coupled with a suitable condition on a modified Kraichnan scale, and under a certain modulation assumption on evolution of the vorticity, leads to existence of 3D enstrophy cascade in physical scales of the flow.

  18. 3D structuring of biocompatible and biodegradable polymers via stereolithography.

    Science.gov (United States)

    Gill, Andrew A; Claeyssens, Frederik

    2011-01-01

    The production of user-defined 3D microstructures from biocompatible and biodegradable materials via free-form fabrication is an important step to create off-the-shelf technologies to be used as tissue engineering scaffolds. One method of achieving this is the microstereolithography of block copolymers, allowing high resolution microstructuring of materials with tuneable physical properties. A versatile protocol for the production and photofunctionalisation of pre-polymers for microstereolithography is presented along with a discussion of the possible microstereolithography set-ups and previous work in the field.

  19. The 3D chromatin structure of the mouse β-haemoglobin gene cluster

    NARCIS (Netherlands)

    M.P.C. van de Corput (Mariëtte); T.A. Knoch (Tobias); E. de Boer (Ernie); W.A. van Cappellen (Gert); M. Lesnussa (Michael); H.J.F.M.M. Eussen (Bert)

    2010-01-01

    textabstractHere we show a 3D DNA-FISH method to visualizes the 3D structure of the β-globin locus. Geometric size and shape measurements of the 3D rendered signals (128Kb) show that the volume of the β-globin locus decreases almost two fold upon gene activation. A decrease in length and a distinc

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  2. Extracting 3D Layout From a Single Image Using Global Image Structures

    NARCIS (Netherlands)

    Lou, Z.; Gevers, T.; Hu, N.

    2015-01-01

    Extracting the pixel-level 3D layout from a single image is important for different applications, such as object localization, image, and video categorization. Traditionally, the 3D layout is derived by solving a pixel-level classification problem. However, the image-level 3D structure can be very b

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

    Science.gov (United States)

    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/.

  4. Proteopedia: a status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules.

    Science.gov (United States)

    Prilusky, Jaime; Hodis, Eran; Canner, David; Decatur, Wayne A; Oberholser, Karl; Martz, Eric; Berchanski, Alexander; Harel, Michal; Sussman, Joel L

    2011-08-01

    Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other biomolecule structures. Created as a means for communicating biomolecule structures to a diverse scientific audience, Proteopedia (http://www.proteopedia.org) presents structural annotation in an intuitive, interactive format and allows members of the scientific community to easily contribute their own annotations. Here, we provide a status report on Proteopedia by describing advances in the web resource since its inception three and a half years ago, focusing on features of potential direct use to the scientific community. We discuss its progress as a collaborative 3D-encyclopedia of structures as well as its use as a complement to scientific publications and PowerPoint presentations. We also describe Proteopedia's use for 3D visualization in structure-related pedagogy.

  5. MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures.

    Science.gov (United States)

    Niknafs, Noushin; Kim, Dewey; Kim, Ryangguk; Diekhans, Mark; Ryan, Michael; Stenson, Peter D; Cooper, David N; Karchin, Rachel

    2013-11-01

    Mutation position imaging toolbox (MuPIT) interactive is a browser-based application for single-nucleotide variants (SNVs), which automatically maps the genomic coordinates of SNVs onto the coordinates of available three-dimensional (3D) protein structures. The application is designed for interactive browser-based visualization of the putative functional relevance of SNVs by biologists who are not necessarily experts either in bioinformatics or protein structure. Users may submit batches of several thousand SNVs and review all protein structures that cover the SNVs, including available functional annotations such as binding sites, mutagenesis experiments, and common polymorphisms. Multiple SNVs may be mapped onto each structure, enabling 3D visualization of SNV clusters and their relationship to functionally annotated positions. We illustrate the utility of MuPIT interactive in rationalizing the impact of selected polymorphisms in the PharmGKB database, somatic mutations identified in the Cancer Genome Atlas study of invasive breast carcinomas, and rare variants identified in the exome sequencing project. MuPIT interactive is freely available for non-profit use at http://mupit.icm.jhu.edu .

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

    Science.gov (United States)

    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

  7. Combining 3D structure with glycan array data provides insight into the origin of glycan specificity.

    Science.gov (United States)

    Grant, Oliver C; Tessier, Matthew B; Meche, Lawrence; Mahal, Lara K; Foley, Bethany L; Woods, Robert J

    2016-07-01

    Defining how a glycan-binding protein (GBP) specifically selects its cognate glycan from among the ensemble of glycans within the cellular glycome is an area of intense study. Powerful insight into recognition mechanisms can be gained from 3D structures of GBPs complexed to glycans; however, such structures remain difficult to obtain experimentally. Here an automated 3D structure generation technique, called computational carbohydrate grafting, is combined with the wealth of specificity information available from glycan array screening. Integration of the array data with modeling and crystallography allows generation of putative co-complex structures that can be objectively assessed and iteratively altered until a high level of agreement with experiment is achieved. Given an accurate model of the co-complexes, grafting is also able to discern which binding determinants are active when multiple potential determinants are present within a glycan. In some cases, induced fit in the protein or glycan was necessary to explain the observed specificity, while in other examples a revised definition of the minimal binding determinants was required. When applied to a collection of 10 GBP-glycan complexes, for which crystallographic and array data have been reported, grafting provided a structural rationalization for the binding specificity of >90% of 1223 arrayed glycans. A webtool that enables researchers to perform computational carbohydrate grafting is available at www.glycam.org/gr (accessed 03 March 2016).

  8. 3D Printing: 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles (Adv. Mater. 19/2016).

    Science.gov (United States)

    Fantino, Erika; Chiappone, Annalisa; Roppolo, Ignazio; Manfredi, Diego; Bongiovanni, Roberta; Pirri, Candido Fabrizio; Calignano, Flaviana

    2016-05-01

    On page 3712, E. Fantino, A. Chiappone, and co-workers fabricate conductive 3D hybrid structures by coupling the photo-reduction of metal precursors with 3D printing technology. The generated structures consist of metal nanoparticles embedded in a polymer matrix shaped into complex multilayered architectures. 3D conductive structures are fabricated with a digital light-processing printer incorporating silver salt into photocurable formulations.

  9. Secondary structure and 3D homology modeling of swine leukocyte antigen class 2 (SLA-2) molecules.

    Science.gov (United States)

    Gao, Feng-Shan; Xu, Chong-bo; Long, Yi-hou; Xia, Chun

    2009-01-01

    No information to date is available to elucidate the structure of swine leukocyte antigen class I (SLA-I) molecule which is comprised by a heavy chain of SLA-I non-covalently associated with a light chain, beta(2)-microglobulin (beta(2)m) proteins. Presently, one of SLA-I gene SLA-2 and beta(2)m gene were expressed as soluble maltose binding proteins (MBP-proteins) in a pMAL-p2X/Escherichia coli TB1 system and identified by western blotting with anti-MBP polyclonal antibodies. The expressed proteins MBP-SLA-2 and MBP-beta(2)m were purified on amylose affinity columns followed by DEAE-Sepharose. The purified products were cleaved by Factor Xa, respectively, and the interest of proteins SLA-2 and beta(2)m were purified on amylose affinity columns followed by separation from MBP on DEAE-Sepharose. The secondary structures of SLA-2 and beta(2)m were analyzed by circular dichroism (CD) spectrophotometry. The three-dimensional (3D) structure of their peptide-binding domain (PBD) was modeled-based sequence homology. The content of the alpha-helix, beta-sheet, turn, and random coil in the SLA-2 protein were 76, 95, 36, and 67aa, respectively. In the 98aa of beta(2)m, the contents of the alpha-helix, beta-sheet, turn, and random coil were 0, 45, 8, and 45aa, respectively. The SLA-2 protein displayed a typical alpha-helix structure while beta(2)m protein displayed a typical beta-sheet structure. Homology modeling of the SLA-2 and beta(2)m proteins demonstrated similarities with the structure of human and mouse MHC (major histocompatibility complex) class I proteins.

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

    Science.gov (United States)

    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.

  11. The Interactorium: visualising proteins, complexes and interaction networks in a virtual 3-D cell.

    Science.gov (United States)

    Widjaja, Yose Y; Pang, Chi Nam Ignatius; Li, Simone S; Wilkins, Marc R; Lambert, Tim D

    2009-12-01

    Here, we describe the Interactorium, a tool in which a Virtual Cell is used as the context for the seamless visualisation of the yeast protein interaction network, protein complexes and protein 3-D structures. The tool has been designed to display very complex networks of up to 40 000 proteins or 6000 multiprotein complexes and has a series of toolboxes and menus to allow real-time data manipulation and control the manner in which data are displayed. It incorporates new algorithms that reduce the complexity of the visualisation by the generation of putative new complexes from existing data and by the reduction of edges through the use of protein "twins" when they occur in multiple locations. Since the Interactorium permits multi-level viewing of the molecular biology of the cell, it is a considerable advance over existing approaches. We illustrate its use for Saccharomyces cerevisiae but note that it will also be useful for the analysis of data from simpler prokaryotes and higher eukaryotes, including humans. The Interactorium is available for download at http://www.interactorium.net.

  12. Multiple 3D RNA Structure Superposition Using Neighbor Joining.

    Science.gov (United States)

    Hoksza, David; Svozil, Daniel

    2015-01-01

    Recent advances in RNA research and the steady growth of available RNA structures call for bioinformatics methods for handling and analyzing RNA structural data. Recently, we introduced SETTER-a fast and accurate method for RNA pairwise structure alignment. In this paper, we describe MultiSETTER, SETTER extension for multiple RNA structure alignment. MultiSETTER combines SETTER's decomposition of RNA structures into non-overlapping structural subunits with the multiple sequence alignment algorithm ClustalW adapted for the structure alignment. The accuracy of MultiSETTER was assessed by the automatic classification of RNA structures and its comparison to SCOR annotations. In addition, MultiSETTER classification was also compared to multiple sequence alignment-based and secondary structure alignment-based classifications provided by LocARNA and RNADistance tools, respectively. MultiSETTER precompiled Windows libraries, as well as the C++ source code, are freely available from http://siret.cz/multisetter.

  13. Focus on Novel Nanoelectromechanical 3D Structures: Fabrication and Properties

    Directory of Open Access Journals (Sweden)

    Shooji Yamada, Hiroshi Yamaguchi and Sunao Ishihara

    2009-01-01

    Full Text Available Microelectromechanical systems (MEMS are widely used small electromechanical systems made of micrometre-sized components. Presently, we are witnessing a transition from MEMS to nanoelectromechanical systems (NEMS, which comprise devices integrating electrical and mechanical functionality on the nanoscale and offer new exciting applications. Similarly to MEMS, NEMS typically include a central transistor-like nanoelectronic unit for data processing, as well as mechanical actuators, pumps, and motors; and they may combine with physical, biological and chemical sensors. In the transition from MEMS to NEMS, component sizes need to be reduced. Therefore, many fabrication methods previously developed for MEMS are unsuitable for the production of high-precision NEMS components. The key challenge in NEMS is therefore the development of new methods for routine and reproducible nanofabrication. Two complementary types of method for NEMS fabrication are available: 'top-down' and 'bottom-up'. The top-down approach uses traditional lithography technologies, whereas bottom-up techniques include molecular self-organization, self-assembly and nanodeposition.The NT2008 conference, held at Ishikawa High-Tech Conference Center, Ishikawa, Japan, between 23–25 October 2008, focused on novel NEMS fabricated from new materials and on process technologies. The topics included compound semiconductors, small mechanical structures, nanostructures for micro-fluid and bio-sensors, bio-hybrid micro-machines, as well as their design and simulation.This focus issue compiles seven articles selected from 13 submitted manuscripts. The articles by Prinz et al and Kehrbusch et al introduce the frontiers of the top-down production of various operational NEMS devices, and Kometani et al present an example of the bottom-up approach, namely ion-beam induced deposition of MEMS and NEMS. The remaining articles report novel technologies for biological sensors. Taira et al have used

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

    Science.gov (United States)

    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.

  15. A procedure to average 3D anatomical structures.

    Science.gov (United States)

    Subramanya, K; Dean, D

    2000-12-01

    Creating a feature-preserving average of three dimensional anatomical surfaces extracted from volume image data is a complex task. Unlike individual images, averages present right-left symmetry and smooth surfaces which give insight into typical proportions. Averaging multiple biological surface images requires careful superimposition and sampling of homologous regions. Our approach to biological surface image averaging grows out of a wireframe surface tessellation approach by Cutting et al. (1993). The surface delineating wires represent high curvature crestlines. By adding tile boundaries in flatter areas the 3D image surface is parametrized into anatomically labeled (homology mapped) grids. We extend the Cutting et al. wireframe approach by encoding the entire surface as a series of B-spline space curves. The crestline averaging algorithm developed by Cutting et al. may then be used for the entire surface. Shape preserving averaging of multiple surfaces requires careful positioning of homologous surface regions such as these B-spline space curves. We test the precision of this new procedure and its ability to appropriately position groups of surfaces in order to produce a shape-preserving average. Our result provides an average that well represents the source images and may be useful clinically as a deformable model or for animation.

  16. 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

    Science.gov (United States)

    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.

  17. Air-structured optical fibre drawn from a 3D-printed preform

    CERN Document Server

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

    2016-01-01

    A structured optical fibre 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 fibre manufacture.

  18. 3D Wide FOV Scanning Measurement System Based on Multiline Structured-Light Sensors

    OpenAIRE

    2014-01-01

    Structured-light three-dimensional (3D) vision measurement is currently one of the most common approaches to obtain 3D surface data. However, the existing structured-light scanning measurement systems are primarily constructed on the basis of single sensor, which inevitably generates three obvious problems: limited measurement range, blind measurement area, and low scanning efficiency. To solve these problems, we developed a novel 3D wide FOV scanning measurement system which adopted two mult...

  19. 3D structure prediction of replication factor C subunits (RFC and their interactome in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Mohamed Ragab Abdel Gawwad

    2013-06-01

    Full Text Available DNA stress can causes potentially spontaneous genome damage during DNA replication process. Proteins involved in this process are DNA-dependent ATPases, required for replication and repair. In this study the 3-D structure of RFC protein subunits in Arabidopsis thaliana: RFC1, RFC2, RFC3, RFC4 and RFC5 are predicted and confirmed by Ramachadran plot. The amino acid sequences are highly similar to the sequences of the homologous human RFC 140-, 37-, 36-, 40-, and 38 kDa subunits, respectively, and also show amino acid sequence similarity to functionally homologous proteins from E. coli. All five subunits show conserved regions characteristic of ATP/GTP-binding proteins and have significant degree of similarity among each other. The segments of conserved amino acid sequences that define a family of related proteins have been identified. RFC1 is identical to CDC44, a gene identified as a cell division cycle gene encoding a protein involved in DNA metabolism. Subcellular localization and interactions of each protein RFC protein subunit is determined. It subsequently became clear that RFC proteins and their interactome have functions in cell cycle regulation and/or DNA replication and repair processes. In addition, AtRFC subunits are controlling the biosynthesis of salicylic and salicylic acid-mediated defense responses in Arabidopsis.

  20. 3D Crustal Structure and 3D-b-value in AbuDabbab Seismogenic Source, Northern Red Sea.

    Science.gov (United States)

    Al-Arifi, Nassir; El Kherpy, Sami; Koulakov, Ivan

    2014-05-01

    Abu Dabbab seismogenic source region is of unique seismic activity located on the Egyptian Red Sea coast. It's known as earthquake Cannons where the earthquakes are accompanied by a sound of distinct rumbling similar to the sound of a distant quarry blast which is heard by humans for several generations. Seismic activity of Abu Dabbab becomes very well determined after establishing of the Egyptian National Seismic Network 1997. Joint earthquake tomography inversion of local and regional data has been performed in order to image the crustal heterogeneity and the origin of the cannons earthquakes. Most previous studies suggested that this activity is of magmatic origin. We found the seismicity forms an arc shaped cluster that surrounds an aseismic block. This aseismic block has high velocities and a low Vp/Vs ratio. The origin of this seismic activity is probably due an active fault below the non-deformed block of Precambrian Igneous rock reaching a depth of ~10 km. Spatial mapping of the frequency magnitude distribution of the earthquakes and 3D-b-value indicate a strong variation moreover high b-value (1.4) at depth downward the rigid block. The Combined interpretation of the seismic imaging and 3D b-value in addition to the seismological and the geophysical observations revealed the tectonic origin of the earthquake activity in this area which is related strongly to the evolution of the crust in the Red Sea and its tectonic activity. KEYWARD:Three dimensional Crustal Structure - Seismic activity -Three-D b-value- Red Sea tectonics- Tectonic activity

  1. Structure-Function Analysis of PPP1R3D, a Protein Phosphatase 1 Targeting Subunit, Reveals a Binding Motif for 14-3-3 Proteins which Regulates its Glycogenic Properties

    OpenAIRE

    Rubio-Villena, Carla; Sanz, Pascual; Garcia-Gimeno, Maria Adelaida

    2015-01-01

    Protein phosphatase 1 (PP1) is one of the major protein phosphatases in eukaryotic cells. It plays a key role in regulating glycogen synthesis, by dephosphorylating crucial enzymes involved in glycogen homeostasis such as glycogen synthase (GS) and glycogen phosphorylase (GP). To play this role, PP1 binds to specific glycogen targeting subunits that, on one hand recognize the substrates to be dephosphorylated and on the other hand recruit PP1 to glycogen particles. In this work we have analyz...

  2. Extracting 3D layout from a single image using global image structures.

    Science.gov (United States)

    Lou, Zhongyu; Gevers, Theo; Hu, Ninghang

    2015-10-01

    Extracting the pixel-level 3D layout from a single image is important for different applications, such as object localization, image, and video categorization. Traditionally, the 3D layout is derived by solving a pixel-level classification problem. However, the image-level 3D structure can be very beneficial for extracting pixel-level 3D layout since it implies the way how pixels in the image are organized. In this paper, we propose an approach that first predicts the global image structure, and then we use the global structure for fine-grained pixel-level 3D layout extraction. In particular, image features are extracted based on multiple layout templates. We then learn a discriminative model for classifying the global layout at the image-level. Using latent variables, we implicitly model the sublevel semantics of the image, which enrich the expressiveness of our model. After the image-level structure is obtained, it is used as the prior knowledge to infer pixel-wise 3D layout. Experiments show that the results of our model outperform the state-of-the-art methods by 11.7% for 3D structure classification. Moreover, we show that employing the 3D structure prior information yields accurate 3D scene layout segmentation.

  3. Protein folding optimization based on 3D off-lattice model via an improved artificial bee colony algorithm.

    Science.gov (United States)

    Li, Bai; Lin, Mu; Liu, Qiao; Li, Ya; Zhou, Changjun

    2015-10-01

    Protein folding is a fundamental topic in molecular biology. Conventional experimental techniques for protein structure identification or protein folding recognition require strict laboratory requirements and heavy operating burdens, which have largely limited their applications. Alternatively, computer-aided techniques have been developed to optimize protein structures or to predict the protein folding process. In this paper, we utilize a 3D off-lattice model to describe the original protein folding scheme as a simplified energy-optimal numerical problem, where all types of amino acid residues are binarized into hydrophobic and hydrophilic ones. We apply a balance-evolution artificial bee colony (BE-ABC) algorithm as the minimization solver, which is featured by the adaptive adjustment of search intensity to cater for the varying needs during the entire optimization process. In this work, we establish a benchmark case set with 13 real protein sequences from the Protein Data Bank database and evaluate the convergence performance of BE-ABC algorithm through strict comparisons with several state-of-the-art ABC variants in short-term numerical experiments. Besides that, our obtained best-so-far protein structures are compared to the ones in comprehensive previous literature. This study also provides preliminary insights into how artificial intelligence techniques can be applied to reveal the dynamics of protein folding. Graphical Abstract Protein folding optimization using 3D off-lattice model and advanced optimization techniques.

  4. Oit1/Fam3D, a gut-secreted protein displaying nutritional status-dependent regulation.

    Science.gov (United States)

    de Wit, Nicole J W; IJssennagger, Noortje; Oosterink, Els; Keshtkar, Shohreh; Hooiveld, Guido J E J; Mensink, Ronald P; Hammer, Sebastiaan; Smit, Johannes W A; Müller, Michael; van der Meer, Roelof

    2012-11-01

    Oncoprotein-induced transcript 1 (Oit1) was previously identified as a dietary fat-induced gene in the small intestine of C57Bl/6J mice. In this study, we further characterized Oit1 and its human ortholog family with sequence similarity 3, member D (Fam3D), on the messenger RNA as well as the protein level. Oit1 and Fam3D were found to be predominantly expressed in the gastrointestinal tract of mice and humans, respectively. Dietary fat induced a clear and acute up-regulation of Oit1, especially in the jejunum, whereas fasting led to a reduced gene expression in the small intestine. Regarding protein expression, we found a remarkable pattern of Oit1 along the longitudinal axis of the intestine, a predominant villus-restricted expression in the proximal small intestine and a more pronounced crypt expression in the distal parts of the intestine. Using transfection experiments, we confirmed secretion of the Oit1 protein, as was predicted by a signal peptide sequence. Detection of Oit1 and Fam3D in plasma samples indicated that both proteins are secreted to the basolateral site of enterocytes. Moreover, in human plasma samples, we also found an effect of nutritional status on Fam3D levels, with a postprandial elevation and a reduction after fasting. In conclusion, Oit1 and Fam3D are gut-derived proteins that are expressed and secreted in a nutritional status-dependent manner.

  5. On the Use of Laguerre Tessellations for Representations of 3D Grain Structures

    DEFF Research Database (Denmark)

    Lyckegaard, Allan; Lauridsen, Erik Mejdal; Ludwig, Wolfgang;

    2011-01-01

    structures from only the spatial center of mass location and the volume of the grains. The ability of Laguerre tessellations to describe accurate grain shapes and topologies of real 3D grain structures are revealed by direct comparison to 3D reconstructions of an un-deformed meta-stable β -titanium alloy...

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

    Science.gov (United States)

    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. 3-D structures viewed with the architect's approach

    DEFF Research Database (Denmark)

    Vanggaard, Ole

    2002-01-01

    to generate the surfaces. At the same time, the limited value of these means is shown, and the author tries to crawl into the difficult area between architecture and structure. This area is found to be an important, but not very appreciated area of research. Most of the figures shown relate to the Academy...

  8. Precision and Accuracy Parameters in Structured Light 3-D Scanning

    DEFF Research Database (Denmark)

    Eiríksson, Eyþór Rúnar; Wilm, Jakob; Pedersen, David Bue

    2016-01-01

    Structured light systems are popular in part because they can be constructed from off-the-shelf low cost components. In this paper we quantitatively show how common design parameters affect precision and accuracy in such systems, supplying a much needed guide for practitioners. Our quantitative m...

  9. Imaging solar coronal magnetic structures in 3D

    Science.gov (United States)

    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

  10. 3D bioprinting matrices with controlled pore structure and release function guide in vitro self-organization of sweat gland

    Science.gov (United States)

    Liu, Nanbo; Huang, Sha; Yao, Bin; Xie, Jiangfan; Wu, Xu; Fu, Xiaobing

    2016-01-01

    3D bioprinting matrices are novel platforms for tissue regeneration. Tissue self-organization is a critical process during regeneration that implies the features of organogenesis. However, it is not clear from the current evidences whether 3D printed construct plays a role in guiding tissue self-organization in vitro. Based on our previous study, we bioprinted a 3D matrix as the restrictive niche for direct sweat gland differentiation of epidermal progenitors by different pore structure (300-μm or 400-μm nozzle diameters printed) and reported a long-term gradual transition of differentiated cells into glandular morphogenesis occurs within the 3D construct in vitro. At the initial 14-day culture, an accelerated cell differentiation was achieved with inductive cues released along with gelatin reduction. After protein release completed, the 3D construct guide the self-organized formation of sweat gland tissues, which is similar to that of the natural developmental process. However, glandular morphogenesis was only observed in 300-μm–printed constructs. In the absence of 3D architectural support, glandular morphogenesis was not occurred. This striking finding made us to identify a previously unknown role of the 3D-printed structure in glandular tissue regeneration, and this self-organizing strategy can be applied to forming other tissues in vitro. PMID:27694985

  11. 3D bioprinting matrices with controlled pore structure and release function guide in vitro self-organization of sweat gland.

    Science.gov (United States)

    Liu, Nanbo; Huang, Sha; Yao, Bin; Xie, Jiangfan; Wu, Xu; Fu, Xiaobing

    2016-10-03

    3D bioprinting matrices are novel platforms for tissue regeneration. Tissue self-organization is a critical process during regeneration that implies the features of organogenesis. However, it is not clear from the current evidences whether 3D printed construct plays a role in guiding tissue self-organization in vitro. Based on our previous study, we bioprinted a 3D matrix as the restrictive niche for direct sweat gland differentiation of epidermal progenitors by different pore structure (300-μm or 400-μm nozzle diameters printed) and reported a long-term gradual transition of differentiated cells into glandular morphogenesis occurs within the 3D construct in vitro. At the initial 14-day culture, an accelerated cell differentiation was achieved with inductive cues released along with gelatin reduction. After protein release completed, the 3D construct guide the self-organized formation of sweat gland tissues, which is similar to that of the natural developmental process. However, glandular morphogenesis was only observed in 300-μm-printed constructs. In the absence of 3D architectural support, glandular morphogenesis was not occurred. This striking finding made us to identify a previously unknown role of the 3D-printed structure in glandular tissue regeneration, and this self-organizing strategy can be applied to forming other tissues in vitro.

  12. Effective Quantification of the Paper Surface 3D Structure

    OpenAIRE

    Fidjestøl, Svein

    2005-01-01

    This thesis covers the topic of image processing in relation to the segmentation and analysis of pores protruding the surface in the three dimensional surface structure of paper. The successful analysis of pores is related to a greater goal of relating such an analysis to the perceived quality of the surface of a paper sample. The first part of the thesis gives an introduction to the context of image processing in relation to paper research. Also, an overview of the image processing framewor...

  13. 3D pressure field in lipid membranes and membrane-protein complexes

    DEFF Research Database (Denmark)

    Ollila, O H Samuli; Risselada, H Jelger; Louhivuori, Martti;

    2009-01-01

    We calculate full 3D pressure fields for inhomogeneous nanoscale systems using molecular dynamics simulation data. The fields represent systems with increasing level of complexity, ranging from semivesicles and vesicles to membranes characterized by coexistence of two phases, including also...... a protein-membrane complex. We show that the 3D pressure field is distinctly different for curved and planar bilayers, the pressure field depends strongly on the phase of the membrane, and that an integral protein modulates the tension and elastic properties of the membrane....

  14. 3D Printing for Spacecraft Multi-Functional Structures

    Science.gov (United States)

    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.

  15. Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.

    Science.gov (United States)

    Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi

    2015-03-17

    Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.

  16. STRUCTURAL 3D MONITORING USING A NEW SINUSOIDAL FITTING ADJUSTMENT

    Directory of Open Access Journals (Sweden)

    I. Detchev

    2016-06-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  18. Short-range correlations of partons & 3D nucleon structure

    Directory of Open Access Journals (Sweden)

    Schweitzer P.

    2014-03-01

    Full Text Available Dynamical breaking of chiral symmetry in QCD is caused by non-perturbative interactions on a scale ρ ∼ 0.3 fm much smaller than the hadronic size R ∼ 1 fm. This has important consequences for the nucleon structure such as the prediction that the transverse momentum distribution of sea quarks is significantly broader than the pT -distribution of valence quarks due to short-range correlations between sea quarks in the nucleon’s light-cone wave function.

  19. 3D nano-structures for laser nano-manipulation

    Directory of Open Access Journals (Sweden)

    Gediminas Seniutinas

    2013-09-01

    Full Text Available 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.

  20. NUMERICAL STUDY OF 3D EXPLOSION BUBBLES ADJACENT TO STRUCTURES

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The bejavior of a bubble near a rigid structure was considered by using the local surface fitting method and the "jet prediction" method. The convergence difficulty caused by the abnormality of the elements was overcome. The flow was numerically simulated by using the boundary-integral method on the assumption that the water was inviscid and incompressible, and the bubble gas obeyed the isoentropic rule. The evolution of the bubble was investigated by means of the mixed Euler-Lagrange method, and the Runge-Kutta method. The important behavior of the bubble, such as migration and jetting, was analyzed in several examples. And the solution of one period of the explosion bubble was obtained.

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

    Science.gov (United States)

    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.

  2. Tensile Behavior Analysis on Different Structures of 3D Glass Woven Perform for Fibre Reinforced Composites

    Directory of Open Access Journals (Sweden)

    Mazhar Hussain Peerzada

    2013-01-01

    Full Text Available Three common 3D (Three Dimensional Glass woven structures were studied to analyze the tensile behavior. Each type of strand (Warp, weft and binder of 3D woven structure was studied in detail. Crimp percentage of those strands was measured by crimp meter. Standard size samples of each 3D woven structure were cut in warp and weft direction and were stretched by Instron Tensile testing computerized machine. Results reveal that hybrid possesses lowest crimp in core strands and higher strength in warp as well as weft direction. Layer to layer woven structure appeared with lower strength and higher strain value due to highest crimp percentage in core strands.

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

    OpenAIRE

    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

    2014-01-01

    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 exte...

  4. Communicating long-span timber structures with 3D computer visualization

    OpenAIRE

    Janols, Henrik

    2005-01-01

    One of the reasons for the low amount of timber in construction is a general lack of knowledge about timber engineering and how timber can be used to its full advantage. In this thesis the focus is 3D computer visualisation (3D VIZ) of non-residential long-span timber structures, used for storage, industry and sports where 3D VIZ is defined as a process where a 3D-model is enhanced with environmental information e.g. texture maps and realistic light effects. An area of interest is the possibi...

  5. Lagrangian structures, integrability and chaos for 3D dynamical equations

    CERN Document Server

    Bustamante, M D; Bustamante, Miguel D.; Hojman, Sergio A.

    2003-01-01

    In this paper we consider the general setting for constructing Action Principles for three-dimensional first order autonomous equations. We present the results for some integrable and non-integrable cases of the Lotka-Volterra equation, and we show Lagrangian descriptions which are valid for systems satisfying Shil'nikov criteria on the existence of strange attractors, though chaotic behavior or homoclinic orbits have not been verified up to now. The Euler-Lagrange equations we get for these systems usually present "time reparameterization" symmetry, though other kinds of invariance may be found according to the kernel of the associated symplectic 2-form. The formulation of a Hamiltonian structure (Poisson brackets and Hamiltonians) for these systems from the Lagrangian viewpoint leads to a method of finding new constants of the motion starting from known ones, which is applied to some systems found in the literature known to possess a constant of the motion, to find the other and thus showing their integrabi...

  6. 3D Digital Design of Cranes' Structures Based on Hybrid Software Architecture

    Institute of Scientific and Technical Information of China (English)

    WANG Chonghua; LI Hua

    2006-01-01

    3D digital design for cranes' structures based on hybrid software architecture of Client/Server and Browser/Server is introduced in this paper. Based on Pro/ENGINEER platform, 3D parametric model family is built to allow generation of feasible configurations of cranes' structures in Client/Server framework. Taking use of Visual C++, the second exploiting software kit provided by Pro/ENGINEER and ANSYS GUI/APDL modeling patterns, an integration method of 3D CAD and CAE is achieved, which includes regeneration of 3D parametric model, synchronous updating and analysis of FEA model. As in Browser/Server framework, the 3D CAD models of parts, components and the whole structure could also be displayed in the customer's browser in VRML format.

  7. 3D-structured illumination microscopy provides novel insight into architecture of human centrosomes

    Directory of Open Access Journals (Sweden)

    Katharina F. Sonnen

    2012-08-01

    Centrioles are essential for the formation of cilia and flagella. They also form the core of the centrosome, which organizes microtubule arrays important for cell shape, polarity, motility and division. Here, we have used super-resolution 3D-structured illumination microscopy to analyse the spatial relationship of 18 centriole and pericentriolar matrix (PCM components of human centrosomes at different cell cycle stages. During mitosis, PCM proteins formed extended networks with interspersed γ-Tubulin. During interphase, most proteins were arranged at specific distances from the walls of centrioles, resulting in ring staining, often with discernible density masses. Through use of site-specific antibodies, we found the C-terminus of Cep152 to be closer to centrioles than the N-terminus, illustrating the power of 3D-SIM to study protein disposition. Appendage proteins showed rings with multiple density masses, and the number of these masses was strongly reduced during mitosis. At the proximal end of centrioles, Sas-6 formed a dot at the site of daughter centriole assembly, consistent with its role in cartwheel formation. Plk4 and STIL co-localized with Sas-6, but Cep135 was associated mostly with mother centrioles. Remarkably, Plk4 formed a dot on the surface of the mother centriole before Sas-6 staining became detectable, indicating that Plk4 constitutes an early marker for the site of nascent centriole formation. Our study provides novel insights into the architecture of human centrosomes and illustrates the power of super-resolution microscopy in revealing the relative localization of centriole and PCM proteins in unprecedented detail.

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

    Science.gov (United States)

    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.

  9. Electrostatic Contributions Drive the Interaction Between Staphylococcus aureus Protein Efb-C and its Complement Target C3d

    Energy Technology Data Exchange (ETDEWEB)

    Haspel, N.; Ricklin, D.; Geisbrecht, B.V.; Kavraki, L.E.; Lambris, J.D. (UPENN); (UMKC); (Rice)

    2008-11-13

    The C3-inhibitory domain of Staphylococcus aureus extracellular fibrinogen-binding protein (Efb-C) defines a novel three-helix bundle motif that regulates complement activation. Previous crystallographic studies of Efb-C bound to its cognate subdomain of human C3 (C3d) identified Arg-131 and Asn-138 of Efb-C as key residues for its activity. In order to characterize more completely the physical and chemical driving forces behind this important interaction, we employed in this study a combination of structural, biophysical, and computational methods to analyze the interaction of C3d with Efb-C and the single-point mutants R131A and N138A. Our results show that while these mutations do not drastically affect the structure of the Efb-C/C3d recognition complex, they have significant adverse effects on both the thermodynamic and kinetic profiles of the resulting complexes. We also characterized other key interactions along the Efb-C/C3d binding interface and found an intricate network of salt bridges and hydrogen bonds that anchor Efb-C to C3d, resulting in its potent complement inhibitory properties.

  10. Multi-functional 3D printed and embedded sensors for satellite qualification structures

    NARCIS (Netherlands)

    Shemelya, Corey; Banuelos-Chacon, Luis; Melendez, Adrian; Kief, Craig; Espalin, David; Wicker, Ryan; Krijnen, Gijs; MacDonald, Eric

    2015-01-01

    Three dimensional (3D) printing has recently gained attention in a variety of industries ranging from aerospace to biomedical. However, in order to create truly functional 3D printed structures, electronic functionality must be integrated into building sequence. This work explores the integration of

  11. Low-resolution characterization of the 3D structure of the Euglena gracilis photoreceptor.

    Science.gov (United States)

    Barsanti, Laura; Coltelli, Primo; Evangelista, Valtere; Passarelli, Vincenzo; Frassanito, Anna Maria; Vesentini, Nicoletta; Gualtieri, Paolo

    2008-10-24

    This paper deals with the first characterization of the structure of the photoreceptive organelle of the unicellular alga Euglena gracilis (Euglenophyta). This organelle has a three-dimensional organization consisting of up to 50 closely stacked membrane lamellae. Ionically induced unstacking of the photoreceptor lamellae revealed ordered arrays well suited to structural analysis by electron microscopy and image analysis, which ultimately yielded a low-resolution picture of the structure. Each lamella is formed by the photoreceptive membrane protein of the cell assembled within the membrane layer in a hexagonal lattice. The first order diffraction spots in the calculated Fourier transform reveals the presence of 6-fold symmetrized topography (better resolution about 90A). The 2D and 3D structural data are very similar with those recently published on proteorodopsin, a membrane protein used by marine bacterio-plankton as light-driven proton pump. In our opinion these similarity indicate that a photoreceptive protein belonging to the same superfamily of proteorodopsin could form the Euglena photoreceptor.

  12. MuPIT Interactive: Webserver for mapping variant positions to annotated, interactive 3D structures

    Science.gov (United States)

    Niknafs, Noushin; Kim, Dewey; Kim, Ryang Guk; Diekhans, Mark; Ryan, Michael; Stenson, Peter D.; Cooper, David N.; Karchin, Rachel

    2013-01-01

    Mutation Position Imaging Toolbox (MuPIT) Interactive is a browser-based application for single nucleotide variants (SNVs), which automatically maps the genomic coordinates of SNVs onto the coordinates of available three-dimensional protein structures. The application is designed for interactive browser-based visualization of the putative functional relevance of SNVs by biologists who are not necessarily experts either in bioinformatics or protein structure. Users may submit batches of several thousand SNVs and review all protein structures that cover the SNVs, including available functional annotations such as binding sites, mutagenesis experiments, and common polymorphisms. Multiple SNVs may be mapped onto each structure, enabling 3D visualization of SNV clusters and their relationship to functionally annotated positions. We illustrate the utility of MuPIT Interactive in rationalizing the impact of selected polymorphisms in the PharmGKB database, somatic mutations identified in the Cancer Genome Atlas study of invasive breast carcinomas, and rare variants identified in the Exome Sequencing Project. MuPIT Interactive is freely available for non-profit use at http://mupit.icm.jhu.edu. PMID:23793516

  13. Molecular field analysis and 3D-quantitative structure-activity relationship study (MFA 3D-QSAR) unveil novel features of bile acid recognition at TGR5.

    Science.gov (United States)

    Macchiarulo, Antonio; Gioiello, Antimo; Thomas, Charles; Massarotti, Alberto; Nuti, Roberto; Rosatelli, Emiliano; Sabbatini, Paola; Schoonjans, Kristina; Auwerx, Johan; Pellicciari, Roberto

    2008-09-01

    Bile acids regulate nongenomic actions through the activation of TGR5, a membrane receptor that is G protein-coupled to the induction of adenylate cyclase. In this work, a training set of 43 bile acid derivatives is used to develop a molecular interaction field analysis (MFA) and a 3D-quantitative structure-activity relationship study (3D-QSAR) of TGR5 agonists. The predictive ability of the resulting model is evaluated using an external set of compounds with known TGR5 activity, and six bile acid derivatives whose unknown TGR5 activity is herein assessed with in vitro luciferase assay of cAMP formation. The results show a good predictive model and indicate a statistically relevant degree of correlation between the TGR5 activity and the molecular interaction fields produced by discrete positions of the bile acid scaffold. This information is instrumental to extend on a quantitative basis the current structure-activity relationships of bile acids as TGR5 modulators and will be fruitful to design new potent and selective agonists of the receptor.

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

    Directory of Open Access Journals (Sweden)

    Tsap Leonid V

    2006-01-01

    Full Text Available 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.

  15. 3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

    Science.gov (United States)

    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.

  16. Fabrication of 2D protein microstructures and 3D polymer-protein hybrid microstructures by two-photon polymerization

    Energy Technology Data Exchange (ETDEWEB)

    Engelhardt, Sascha [Lehrstuhl fuer Lasertechnik, RWTH Aachen, Steinbachstrasse 15, Aachen (Germany); Hoch, Eva; Tovar, Guenter E M [Institut fuer Grenzflaechenverfahrenstechnik, Universitaet Stuttgart, Nobelstrasse 12, Stuttgart (Germany); Borchers, Kirsten [Fraunhofer-Institut fuer Grenzflaechen- und Bioverfahrenstechnik, Nobelstrasse 12, Stuttgart (Germany); Meyer, Wolfdietrich; Krueger, Hartmut [Fraunhofer-Institut fuer Angewandte Polymerforschung, Geiselbergstrasse 69, Potsdam (Germany); Gillner, Arnold, E-mail: sascha.engelhardt@ilt.fraunhofer.de [Fraunhofer-Institut fuer Lasertechnik, Steinbachstrasse 15, Aachen (Germany)

    2011-06-15

    Two-photon polymerization (TPP) offers the possibility of creating artificial cell scaffolds composed of micro- and nanostructures with spatial resolutions of less than 1 {mu}m. For use in tissue engineering, the identification of a TPP-processable polymer that provides biocompatibility, biofunctionality and appropriate mechanical properties is a difficult task. ECM proteins such as collagen or fibronectin, which could mimic native tissues best, often lack the mechanical stability. Hence, by generating polymer-protein hybrid structures, the beneficial properties of proteins can be combined with the advantageous characteristics of polymers, such as sufficient mechanical stability. This study describes three steps toward facilitated application of TPP for biomaterial generation. (1) The efficiency of a low-cost ps-laser source is compared to a fs-laser source by testing several materials. A novel photoinitiator for polymerization with a ps-laser source is synthesized and proved to enable increased fabrication throughput. (2) The fabrication of 3D-microstructures with both systems and the fabrication of polymer-protein hybrid structures are demonstrated. (3) The tissue engineering capabilities of TPP are demonstrated by creating cross-linked gelatin microstructures, which clearly forced porcine chondrocytes to adapt their cell morphology.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  19. 3D Printers Can Provide an Added Dimension for Teaching Structure-Energy Relationships

    Science.gov (United States)

    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.

  20. Mu-Synthesis robust control of 3D bar structure vibration using piezo-stack actuators

    Science.gov (United States)

    Mystkowski, Arkadiusz; Koszewnik, Andrzej Piotr

    2016-10-01

    This paper presents an idea for the Mu-Synthesis robust control of 3D bar structure vibration with using a piezo-stack actuators. A model of the 3D bar structure with uncertain parameters is presented as multi-input multi-output (MIMO) dynamics. Nominal stability and nominal performances of the open-loop 3D bar structure dynamic model is developed. The uncertain model-based robust controller is derived due to voltage control signal saturation and selected parameter perturbations. The robust control performances and robustness of the system due to uncertainties influence is evaluated by using singular values and a small gain theorem. Finally, simulation investigations and experimental results shown that system response of the 3D bar structure dynamic model with taken into account perturbed parameters met desired robust stability and system limits. The proposed robust controller ensures a good dynamics of the closed-loop system, robustness, and vibration attenuation.

  1. Structure Prediction of Membrane Proteins

    Institute of Scientific and Technical Information of China (English)

    Chunlong Zhou; Yao Zheng; Yan Zhou

    2004-01-01

    There is a large gap between the number of membrane protein (MP) sequences and that of their decoded 3D structures, especially high-resolution structures, due to difficulties in crystal preparation of MPs. However, detailed knowledge of the 3D structure is required for the fundamental understanding of the function of an MP and the interactions between the protein and its inhibitors or activators. In this paper, some computational approaches that have been used to predict MP structures are discussed and compared.

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

    Institute of Scientific and Technical Information of China (English)

    Changku Sun; Li Tao; Peng Wang; Li He

    2006-01-01

    @@ 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. Model and numerical analysis of 3D corrosion layer of reinforced concrete structure

    Institute of Scientific and Technical Information of China (English)

    李永和; 葛修润

    2003-01-01

    Under the assumption that the corrosion at the end of steel bolt or steel bar is shaped like the contour line of ellipsoid, a mathematic model and formulas of calculating the thickness of corrosion layer at arbitrary point are presented in this paper. Then regarding the arbitrary points of 3D corrosion layer as patch element model of fictitious displacement discontinuity, we propose the basic solution of 3D problem of the patch element acting on discontinuous displacement. With three basic assumptions of the corrosion layer, we set up the 3D numerical discreted model, and derive the stress boundary equation for fictitious corrosion layer of 3D numerical analysis. We also make the numerical stimulating calculation of the shotcrete structure at some lane using 3D finite element method. The results show that this method is effective and reasonable.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    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

  7. TRAIL protein localization in human primary T cells by 3D microscopy using 3D interactive surface plot: a new method to visualize plasma membrane.

    Science.gov (United States)

    Gras, Christophe; Smith, Nikaïa; Sengmanivong, Lucie; Gandini, Mariana; Kubelka, Claire Fernandes; Herbeuval, Jean-Philippe

    2013-01-31

    The apoptotic ligand TNF-related apoptosis ligand (TRAIL) is expressed on the membrane of immune cells during HIV infection. The intracellular stockade of TRAIL in human primary CD4(+) T cells is not known. Here we investigated whether primary CD4(+) T cells expressed TRAIL in their intracellular compartment and whether TRAIL is relocalized on the plasma membrane under HIV activation. We found that TRAIL protein was stocked in intracellular compartment in non activated CD4(+) T cells and that the total level of TRAIL protein was not increased under HIV-1 stimulation. However, TRAIL was massively relocalized on plasma membrane when cells were cultured with HIV. Using three dimensional (3D) microscopy we localized TRAIL protein in human T cells and developed a new method to visualize plasma membrane without the need of a membrane marker. This method used the 3D interactive surface plot and bright light acquired images.

  8. Transfer printing of 3D hierarchical gold structures using a sequentially imprinted polymer stamp

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Fengxiang; Low, Hong Yee [Institute of Materials Research and Engineering, A-STAR - Agency for Science, Technology and Research, 3 Research Link, 117602 (Singapore)], E-mail: hy-low@imre.a-star.edu.sg

    2008-10-15

    Complex three-dimensional (3D) hierarchical structures on polymeric materials are fabricated through a process referred to as sequential imprinting. In this work, the sequentially imprinted polystyrene film is used as a soft stamp to replicate hierarchical structures onto gold (Au) films, and the Au structures are then transferred to a substrate by transfer printing at an elevated temperature and pressure. Continuous and isolated 3D structures can be selectively fabricated with the assistance of thermo-mechanical deformation of the polymer stamp. Hierarchical Au structures are achieved without the need for a corresponding three-dimensionally patterned mold.

  9. Protein adsorption resistant surface on polymer composite based on 2D- and 3D-controlled grafting of phospholipid moieties

    Energy Technology Data Exchange (ETDEWEB)

    Hoshi, Toru [Department of Materials Engineering, School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan); Matsuno, Ryosuke [Department of Materials Engineering, School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan); Center for NanoBio Integration, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan); Sawaguchi, Takashi [Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-surugadai, Chiyoda-ku, Tokyo 101-8308 (Japan); Konno, Tomohiro; Takai, Madoka [Department of Materials Engineering, School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan); Center for NanoBio Integration, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan); Ishihara, Kazuhiko [Department of Materials Engineering, School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan); Department of Bioengineering, School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan); Center for NanoBio Integration, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan)], E-mail: ishihara@mpc.t.u-tokyo.ac.jp

    2008-11-15

    To prepare the biocompatible surface, a phosphorylcholine (PC) group was introduced on this hydroxyl group generated by surface hydrolysis on the polymer composite composed of polyethylene (PE) and poly (vinyl acetate) (PVAc) prepared by supercritical carbon dioxide. Two different procedures such as two-dimensional (2D) modification and three-dimensional (3D) modification were applied to obtain the steady biocompatible surface. 2D modification was that PC groups were directly anchored on the surface of the polymer composite. 3D modification was that phospholipid polymer was grafted from the surface of the polymer composite by surface-initiated atom transfer radical polymerization (SI-ATRP) of 2-methacryloyloxyethyl phosphorylcholine (MPC). The surfaces were characterized by X-ray photoelectron spectroscopy, dynamic water contact angle measurements, and atomic force microscope. The effects of the poly(MPC) chain length on the protein adsorption resistivity were investigated. The protein adsorption on the polymer composite surface with PC groups modified by 2D or 3D modification was significantly reduced as compared with that on the unmodified PE. Further, the amount of protein adsorbed on the 3D modified surface that is poly(MPC)-grafted surface decreased with an increase in the chain length of the poly(MPC). The surface with an arbitrary structure and the characteristic can be constructed by using 2D and 3D modification. We conclude that the polymer composites of PE/PVAc with PC groups on the surface are useful for fabricating biomedical devices due to their good mechanical and surface properties.

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

    Science.gov (United States)

    Kaltdorf, Kristin Verena; Schulze, Katja; Helmprobst, Frederik; Kollmannsberger, Philip; Dandekar, Thomas; 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

  11. Optical Measurement of Micromechanics and Structure in a 3D Fibrin Extracellular Matrix

    Science.gov (United States)

    Kotlarchyk, Maxwell Aaron

    2011-07-01

    In recent years, a significant number of studies have focused on linking substrate mechanics to cell function using standard methodologies to characterize the bulk properties of the hydrogel substrates. However, current understanding of the correlations between the microstructural mechanical properties of hydrogels and cell function in 3D is poor, in part because of a lack of appropriate techniques. Methods for tuning extracellular matrix (ECM) mechanics in 3D cell culture that rely on increasing the concentration of either protein or cross-linking molecules fail to control important parameters such as pore size, ligand density, and molecular diffusivity. Alternatively, ECM stiffness can be modulated independently from protein concentration by mechanically loading the ECM. We have developed an optical tweezers-based microrheology system to investigate the fundamental role of ECM mechanical properties in determining cellular behavior. Further, this thesis outlines the development of a novel device for generating stiffness gradients in naturally derived ECMs, where stiffness is tuned by inducing strain, while local structure and mechanical properties are directly determined by laser tweezers-based passive and active microrheology respectively. Hydrogel substrates polymerized within 35 mm diameter Petri dishes are strained non-uniformly by the precise rotation of an embedded cylindrical post, and exhibit a position-dependent stiffness with little to no modulation of local mesh geometry. Here we present microrheological studies in the context of fibrin hydrogels. Microrheology and confocal imaging were used to directly measure local changes in micromechanics and structure respectively in unstrained hydrogels of increasing fibrinogen concentration, as well as in our strain gradient device, in which the concentration of fibrinogen is held constant. Orbital particle tracking, and raster image correlation analysis are used to quantify changes in fibrin mechanics on the

  12. Modelling a 3D structure for EgDf1 from shape Echinococcus granulosus: putative epitopes, phosphorylation motifs and ligand

    Science.gov (United States)

    Paulino, M.; Esteves, A.; Vega, M.; Tabares, G.; Ehrlich, R.; Tapia, O.

    1998-07-01

    EgDf1 is a developmentally regulated protein from the parasite Echinococcus granulosus related to a family of hydrophobic ligand binding proteins. This protein could play a crucial role during the parasite life cycle development since this organism is unable to synthetize most of their own lipids de novo. Furthermore, it has been shown that two related protein from other parasitic platyhelminths (Fh15 from Fasciola hepatica and Sm14 from Schistosoma mansoni) are able to confer protective inmunity against experimental infection in animal models. A three-dimensional structure would help establishing structure/function relationships on a knowledge based manner. 3D structures for EgDf1 protein were modelled by using myelin P2 (mP2) and intestine fatty acid binding protein (I-FABP) as templates. Molecular dynamics techniques were used to validate the models. Template mP2 yielded the best 3D structure for EgDf1. Palmitic and oleic acids were docked inside EgDf1. The present theoretical results suggest definite location in the secondary structure of the epitopic regions, consensus phosphorylation motifs and oleic acid as a good ligand candidate to EgDf1. This protein might well be involved in the process of supplying hydrophobic metabolites for membrane biosynthesis and for signaling pathways.

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

    Directory of Open Access Journals (Sweden)

    Elisee Ilunga-Mbuyamba

    2016-04-01

    Full Text Available 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-iCEUS s t a r t and after (3D-iCEUS e n d tumor resection. Based on rigid registration techniques, a preselected vascular segment in cT1MR is searched in 3D-iCEUS s t a r t and 3D-iCEUS e n d 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.

  14. Comparison of 3 methods on fabricating micro- /nano- structured surface on 3D mold cavity

    DEFF Research Database (Denmark)

    Zhang, Yang; Hansen, Hans Nørgaard; Bissacco, Giuliano

    2015-01-01

    The methods to manufacture micro- or nano- structures on surfaces have been an area of intense investigation. Demands are shown for technologies for surface structuring on real 3D parts in many fields. However, most technologies for the fabrication of micro-structured functional surfaces are stil...

  15. 3D and 4D atlas system of living human body structure.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  17. RNA 3D modules in genome-wide predictions of RNA 2D structure

    DEFF Research Database (Denmark)

    Theis, Corinna; Zirbel, Craig L; Zu Siederdissen, Christian Höner

    2015-01-01

    Recent experimental and computational progress has revealed a large potential for RNA structure in the genome. This has been driven by computational strategies that exploit multiple genomes of related organisms to identify common sequences and secondary structures. However, these computational...... approaches have two main challenges: they are computationally expensive and they have a relatively high false discovery rate (FDR). Simultaneously, RNA 3D structure analysis has revealed modules composed of non-canonical base pairs which occur in non-homologous positions, apparently by independent evolution....... These modules can, for example, occur inside structural elements which in RNA 2D predictions appear as internal loops. Hence one question is if the use of such RNA 3D information can improve the prediction accuracy of RNA secondary structure at a genome-wide level. Here, we use RNAz in combination with 3D...

  18. Cloning, Expression and 3D Structure Prediction of Chitinase from Chitinolyticbacter meiyuanensis SYBC-H1

    Directory of Open Access Journals (Sweden)

    Zhikui Hao

    2016-05-01

    Full Text Available Two CHI genes from Chitinolyticbacter meiyuanensis SYBC-H1 encoding chitinases were identified and their protein 3D structures were predicted. According to the amino acid sequence alignment, CHI1 gene encoding 166 aa had a structural domain similar to the GH18 type II chitinase, and CHI2 gene encoding 383 aa had the same catalytic domain as the glycoside hydrolase family 19 chitinase. In this study, CHI2 chitinase were expressed in Escherichia coli BL21 cells, and this protein was purified by ammonium sulfate precipitation, DEAE-cellulose, and Sephadex G-100 chromatography. Optimal activity of CHI2 chitinase occurred at a temperature of 40 °C and a pH of 6.5. The presence of metal ions Fe3+, Fe2+, and Zn2+ inhibited CHI2 chitinase activity, while Na+ and K+ promoted its activity. Furthermore, the presence of EGTA, EDTA, and β-mercaptoethanol significantly increased the stability of CHI2 chitinase. The CHI2 chitinase was active with p-NP-GlcNAc, with the Km and Vm values of 23.0 µmol/L and 9.1 mM/min at a temperature of 37 °C, respectively. Additionally, the CHI2 chitinase was characterized as an N-acetyl glucosaminidase based on the hydrolysate from chitin. Overall, our results demonstrated CHI2 chitinase with remarkable biochemical properties is suitable for bioconversion of chitin waste.

  19. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae's Inner Colliding Winds

    CERN Document Server

    Madura, Thomas I; Gull, Theodore R; Kruip, Chael J H; Paardekooper, Jan-Pieter

    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 M_Sun), highly eccentric (e ~ 0.9) binary star system Eta Carinae. We demonstrate the methodology used to incorporate 3D interactive figures into a PDF journal publication and the benefits of using 3D visualization and 3D printing as tools to analyze data from multidimensional numerical simulations. Using a consumer-grade 3D printer (MakerBot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics (SPH) simulations of Eta 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 (phi ~ 1.045) that protrude radially outward from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. thin-shell, Rayleigh-Taylor) that arise a...

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

    Science.gov (United States)

    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.

  1. Mechanical Properties Of 3D-Structure Composites Based On Warp-Knitted Spacer Fabrics

    Directory of Open Access Journals (Sweden)

    Chen Si

    2015-06-01

    Full Text Available In this paper, the mechanical properties (compression and impact behaviours of three-dimension structure (3D-structure composites based on warp-knitted spacer fabrics have been thoroughly investigated. In order to discuss the effect of fabric structural parameters on the mechanical performance of composites, six different types of warp-knitted spacer fabrics having different structural parameters (such as outer layer structure, diameter of spacer yarn, spacer yarn inclination angle and thickness were involved for comparison study. The 3D-structure composites were fabricated based on a flexible polyurethane foam. The produced composites were characterised for compression and impact properties. The findings obtained indicate that the fabric structural parameters have strong influence on the compression and impact responses of 3D-structure composites. Additionally, the impact test carried out on the 3D-structure composites shows that the impact loads do not affect the integrity of composite structure. All the results reveal that the product exhibits promising mechanical performance and its service life can be sustained.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Nugraha, Andri Dian [Global Geophysics Research Group, Faculty of Mining and Petroleum Engineering, Institute of Technology Bandung, Jalan Ganesha No. 10 Bandung, 40132 (Indonesia); Syahputra, Ahmad [Geophyisical Engineering, Faculty of Mining and Petroleum Engineering, Institute of Technology Bandung, Jalan Ganesha No. 10 Bandung, 40132 (Indonesia); Fatkhan,; Sule, Rachmat [Applied Geophysics Research Group, Faculty of Mining and Petroleum Engineering, Institute of Technology Bandung, Jalan Ganesha No. 10 Bandung, 40132 (Indonesia)

    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.

  4. 3-D seismic velocity and attenuation structures in the geothermal field

    Science.gov (United States)

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

    2013-09-01

    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.

  5. Estimating the complexity of 3D structural models using machine learning methods

    Science.gov (United States)

    Mejía-Herrera, Pablo; Kakurina, Maria; Royer, Jean-Jacques

    2016-04-01

    Quantifying the complexity of 3D geological structural models can play a major role in natural resources exploration surveys, for predicting environmental hazards or for forecasting fossil resources. This paper proposes a structural complexity index which can be used to help in defining the degree of effort necessary to build a 3D model for a given degree of confidence, and also to identify locations where addition efforts are required to meet a given acceptable risk of uncertainty. In this work, it is considered that the structural complexity index can be estimated using machine learning methods on raw geo-data. More precisely, the metrics for measuring the complexity can be approximated as the difficulty degree associated to the prediction of the geological objects distribution calculated based on partial information on the actual structural distribution of materials. The proposed methodology is tested on a set of 3D synthetic structural models for which the degree of effort during their building is assessed using various parameters (such as number of faults, number of part in a surface object, number of borders, ...), the rank of geological elements contained in each model, and, finally, their level of deformation (folding and faulting). The results show how the estimated complexity in a 3D model can be approximated by the quantity of partial data necessaries to simulated at a given precision the actual 3D model without error using machine learning algorithms.

  6. In Situ Thermal Generation of Silver Nanoparticles in 3D Printed Polymeric Structures

    Directory of Open Access Journals (Sweden)

    Erika Fantino

    2016-07-01

    Full Text Available Polymer nanocomposites have always attracted the interest of researchers and industry because of their potential combination of properties from both the nanofillers and the hosting matrix. Gathering nanomaterials and 3D printing could offer clear advantages and numerous new opportunities in several application fields. Embedding nanofillers in a polymeric matrix could improve the final material properties but usually the printing process gets more difficult. Considering this drawback, in this paper we propose a method to obtain polymer nanocomposites by in situ generation of nanoparticles after the printing process. 3D structures were fabricated through a Digital Light Processing (DLP system by disolving metal salts in the starting liquid formulation. The 3D fabrication is followed by a thermal treatment in order to induce in situ generation of metal nanoparticles (NPs in the polymer matrix. Comprehensive studies were systematically performed on the thermo-mechanical characteristics, morphology and electrical properties of the 3D printed nanocomposites.

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

    Science.gov (United States)

    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.

  8. 3D printing of weft knitted textile based structures by selective laser sintering of nylon powder

    Science.gov (United States)

    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.

  9. Automatic Generation of Structural Building Descriptions from 3D Point Cloud Scans

    DEFF Research Database (Denmark)

    Ochmann, Sebastian; Vock, Richard; Wessel, Raoul

    2013-01-01

    scans to derive high-level architectural entities like rooms and doors. Starting with a registered 3D point cloud, we probabilistically model the affiliation of each measured point to a certain room in the building. We solve the resulting clustering problem using an iterative algorithm that relies......We present a new method for automatic semantic structuring of 3D point clouds representing buildings. In contrast to existing approaches which either target the outside appearance like the facade structure or rather low-level geometric structures, we focus on the building’s interior using indoor...

  10. Protein Structure

    Science.gov (United States)

    Asmus, Elaine Garbarino

    2007-01-01

    Individual students model specific amino acids and then, through dehydration synthesis, a class of students models a protein. The students clearly learn amino acid structure, primary, secondary, tertiary, and quaternary structure in proteins and the nature of the bonds maintaining a protein's shape. This activity is fun, concrete, inexpensive and…

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

    Science.gov (United States)

    Montes-Grajales, Diana; Olivero-Verbel, Jesus

    2015-01-01

    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.

  12. Backbone cup – a structure design competition based on topology optimization and 3D printing

    Directory of Open Access Journals (Sweden)

    Zhu Ji-Hong

    2016-01-01

    Full Text Available This paper addresses a structure design competition based on topology optimization and 3D Printing, and proposes an experimental approach to efficiently and quickly measure the mechanical performance of the structures designed using topology optimization. Since the topology optimized structure designs are prone to be geometrically complex, it is extremely inconvenient to fabricate these designs with traditional machining. In this study, we not only fabricated the topology optimized structure designs using one kind of 3D Printing technology known as stereolithography (SLA, but also tested the mechanical performance of the produced prototype parts. The finite element method is used to analyze the structure responses, and the consistent results of the numerical simulations and structure experiments prove the validity of this new structure testing approach. This new approach will not only provide a rapid access to topology optimized structure designs verifying, but also cut the turnaround time of structure design significantly.

  13. Quasi-3D Waveform Inversion for Velocity Structures and Source Process Analyses Using its Results

    Science.gov (United States)

    Hikima, K.; Koketsu, K.

    2007-12-01

    In this study, we propose an efficient waveform inversion method for 2-D velocity structures and 3-D velocity structures are constructed by interpolating the results of the 2-D inversions. We apply these methods to a source process study of the 2003 Miyagi-ken Hokubu earthquake. We will first construct a velocity model, then determine the source processes of this earthquake sequence using the Green's function calculated with the resultant 3-D velocity model. We formulate the inversion procedure in a 2-D cross section. In a 2-D problem, an earthquake is forced to be a line source. Therefore, we introduce approximate transformation from a line source to a point source (Vidale and Helmberger, 1987). We use the 2-D velocity-stress staggered-grid finite difference scheme, so that the source representation is somewhat different from the original 'source box method' and we apply additional corrections to calculated waveforms. The boundary shapes of layers are expressed by connected nodes and we invert observed waveforms for layer thicknesses at the nodes. We perform 2-D velocity inversions along cross sections which involve a medium-size earthquake and observation points. We assemble the results for many stations and interpolated them to construct the 3-D velocity model. Finally, we calculate waveforms from the target earthquake by the 3-D finite difference method with this velocity model to confirm the validity of the model. We next perform waveform inversions for source processes of the 2003 Miyagi-ken Hokubu earthquake sequence using the resultant 3-D velocity model. We divide the fault plane into northern and southern subplanes, so that the southern subplane includes the hypocenter of the mainshock and the largest foreshock. The strike directions of the northern and southern subplanes were N-S and NE-SW, respectively. The Green's functions for these source inversions are calculated using the reciprocal theorem. We determine the slip models using the 3- D structure and

  14. Open Plot Project: an open-source toolkit for 3-D structural data analysis

    Directory of Open Access Journals (Sweden)

    S. Tavani

    2011-05-01

    Full Text Available In this work we present the Open Plot Project, an open-source software for structural data analysis, including a 3-D environment. The software includes many classical functionalities of structural data analysis tools, like stereoplot, contouring, tensorial regression, scatterplots, histograms and transect analysis. In addition, efficient filtering tools are present allowing the selection of data according to their attributes, including spatial distribution and orientation. This first alpha release represents a stand-alone toolkit for structural data analysis.

    The presence of a 3-D environment with digitalising tools allows the integration of structural data with information extracted from georeferenced images to produce structurally validated dip domains. This, coupled with many import/export facilities, allows easy incorporation of structural analyses in workflows for 3-D geological modelling. Accordingly, Open Plot Project also candidates as a structural add-on for 3-D geological modelling software.

    The software (for both Windows and Linux O.S., the User Manual, a set of example movies (complementary to the User Manual, and the source code are provided as Supplement. We intend the publication of the source code to set the foundation for free, public software that, hopefully, the structural geologists' community will use, modify, and implement. The creation of additional public controls/tools is strongly encouraged.

  15. Open Plot Project: an open-source toolkit for 3-D structural data analysis

    Directory of Open Access Journals (Sweden)

    S. Tavani

    2010-12-01

    Full Text Available In this work we present the Open Plot Project, a software for structural data analysis including a 3-D environment. This first alpha release represents a stand-alone toolkit for structural data analysis and, due to many import/export facilities and to the presence of a 3-D environment, also candidates as a tool to be incorporated in workflows for 3-D geological modelling.

    The software (for both Windows and Linux O.S., the User Manual, a set of example movies, and the source code are provided as Supplement. It is our purpose that the publication of the source code sets the base for the development of a public and free software that, hopefully, the structural geologists community will use, modify, and implement. The creation of additional public controls/tools is strongly encouraged.

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

    Directory of Open Access Journals (Sweden)

    Dong-Geol Choi

    2017-02-01

    Full Text Available 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.

  17. 2D and 3D crystallization of a bacterial homologue of human vitamin C membrane transport proteins.

    Science.gov (United States)

    Jeckelmann, Jean-Marc; Harder, Daniel; Ucurum, Zöhre; Fotiadis, Dimitrios

    2014-10-01

    Most organisms are able to synthesize vitamin C whereas humans are not. In order to contribute to the elucidation of the molecular working mechanism of vitamin C transport through biological membranes, we cloned, overexpressed, purified, functionally characterized, and 2D- and 3D-crystallized a bacterial protein (UraDp) with 29% of amino acid sequence identity to the human sodium-dependent vitamin C transporter 1 (SVCT1). Ligand-binding experiments by scintillation proximity assay revealed that uracil is a substrate preferably bound to UraDp. For structural analysis, we report on the production of tubular 2D crystals and present a first projection structure of UraDp from negatively stained tubes. On the other hand the successful growth of UraDp 3D crystals and their crystallographic analysis is described. These 3D crystals, which diffract X-rays to 4.2Å resolution, pave the way towards the high-resolution crystal structure of a bacterial homologue with high amino acid sequence identity to human SVCT1.

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

    Science.gov (United States)

    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. Classification of conformational stability of protein mutants from 3D pseudo-folding graph representation of protein sequences using support vector machines.

    Science.gov (United States)

    Fernández, Michael; Caballero, Julio; Fernández, Leyden; Abreu, Jose Ignacio; Acosta, Gianco

    2008-01-01

    This work reports a novel 3D pseudo-folding graph representation of protein sequences for modeling purposes. Amino acids euclidean distances matrices (EDMs) encode primary structural information. Amino Acid Pseudo-Folding 3D Distances Count (AAp3DC) descriptors, calculated from the EDMs of a large data set of 1363 single protein mutants of 64 proteins, were tested for building a classifier for the signs of the change of thermal unfolding Gibbs free energy change (DeltaDeltaG) upon single mutations. An optimum support vector machine (SVM) with a radial basis function (RBF) kernel well recognized stable and unstable mutants with accuracies over 70% in crossvalidation test. To the best of our knowledge, this result for stable mutant recognition is the highest ever reported for a sequence-based predictor with more than 1000 mutants. Furthermore, the model adequately classified mutations associated to diseases of human prion protein and human transthyretin.

  20. 3D multi-layered fibrous cellulose structure using an electrohydrodynamic process for tissue engineering.

    Science.gov (United States)

    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.

  1. Direct-growth carbon nanotubes on 3D structural microelectrodes for electrophysiological recording.

    Science.gov (United States)

    Pan, Alice Ian; Lin, Min-Hsuan; Chung, Hui-Wen; Chen, Hsin; Yeh, Shih-Rung; Chuang, Yung-Jen; Chang, Yen-Chung; Yew, Tri-Rung

    2016-01-01

    A novel 3D carbon nanotube (CNT) microelectrode was developed through direct growth of CNTs on a gold pin-shaped 3D microelectrode at a low temperature (400 °C) for applications in neural and cardiac recording. With an electroplated Ni catalyst layer covering the entire surface of the pin-shaped structure, CNTs were synthesized on a 3D microelectrode by catalytic thermal chemical vapor deposition (CVD). According to the analyses by electrochemical impedance spectroscopy, the impedance of 3D microelectrodes after CNT growth and UV/O3 treatment decreased from 9.3 Ω mm(-2) to 1.2 Ω mm(-2) and the capacitance increased largely from 2.2 mF cm(-2) to 73.3 mF cm(-2). The existence of UVO3-treated CNT led to a large improvement of interfacial capacitance, contributing to the decrease of impedance. The electrophysiological detection capability of this 3D CNT microelectrode was demonstrated by the distinguished P waves, QRS complex and T waves in the electrocardiogram of the zebrafish heart and the action potential recorded from individual rat hippocampal neurons. The compatibility of integration with ICs, high resolution in space, electrophysiological signals, and non-invasive long-term recording suggest that the 3D CNT microelectrode exhibits promising potential for applications in electrophysiological research and clinical trials.

  2. Vision processing for realtime 3-D data acquisition based on coded structured light.

    Science.gov (United States)

    Chen, S Y; Li, Y F; Zhang, Jianwei

    2008-02-01

    Structured light vision systems have been successfully used for accurate measurement of 3-D surfaces in computer vision. However, their applications are mainly limited to scanning stationary objects so far since tens of images have to be captured for recovering one 3-D scene. This paper presents an idea for real-time acquisition of 3-D surface data by a specially coded vision system. To achieve 3-D measurement for a dynamic scene, the data acquisition must be performed with only a single image. A principle of uniquely color-encoded pattern projection is proposed to design a color matrix for improving the reconstruction efficiency. The matrix is produced by a special code sequence and a number of state transitions. A color projector is controlled by a computer to generate the desired color patterns in the scene. The unique indexing of the light codes is crucial here for color projection since it is essential that each light grid be uniquely identified by incorporating local neighborhoods so that 3-D reconstruction can be performed with only local analysis of a single image. A scheme is presented to describe such a vision processing method for fast 3-D data acquisition. Practical experimental performance is provided to analyze the efficiency of the proposed methods.

  3. Modeling 3D soil and sediment distributions for assessing catchment structure and hydrological feedbacks

    Science.gov (United States)

    Maurer, Thomas; Brück, Yasemine; Hinz, Christoph; Gerke, Horst H.

    2015-04-01

    Structural heterogeneity, namely the spatial distribution of soils and sediments (represented by mineral particles), characterizes catchment hydrological behavior. In natural catchments, local geology and the specific geomorphic processes determine the characteristics and spatial distribution of structures. In constructed catchments, structural features are determined primarily by the construction processes and the geological origin of the parent material. Objectives are scenarios of 3D catchment structures in form of complete 3D description of soil hydraulic properties generated from the knowledge of the formation processes. The constructed hydrological catchment 'Hühnerwasser' (Lower Lusatia, Brandenburg, Germany) was used for the calibration and validation of model results due to its well-known conditions. For the modelling of structural features, a structure generator was used to model i) quasi-deterministic sediment distributions using input data from a geological model of the parent material excavation site; ii) sediment distributions that are conditioned to measurement data from soil sampling; and iii) stochastic component sediment distributions. All three approaches allow a randomization within definable limits. Furthermore, the spoil cone / spoil ridge orientation, internal layering, surface compaction and internal spoil cone compaction were modified. These generated structural models were incorporated in a gridded 3D volume model constructed with the GOCAD software. For selected scenarios, the impact of structure variation was assessed by hydrological modelling with HYDRUS 2D/3D software. For that purpose, 3D distributions of soil hydraulic properties were estimated based on generated sediment properties using adapted pedotransfer functions. Results from the hydrological model were compared them to measured discharges from the catchment. The impact of structural feature variation on flow behaviour was analysed by comparing different simulation scenarios

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

    Science.gov (United States)

    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.

  5. High-order finite difference solution for 3D nonlinear wave-structure interaction

    DEFF Research Database (Denmark)

    Ducrozet, Guillaume; Bingham, Harry B.; Engsig-Karup, Allan Peter;

    2010-01-01

    This contribution presents our recent progress on developing an efficient fully-nonlinear potential flow model for simulating 3D wave-wave and wave-structure interaction over arbitrary depths (i.e. in coastal and offshore environment). The model is based on a high-order finite difference scheme...... OceanWave3D presented in [1, 2]. A nonlinear decomposition of the solution into incident and scattered fields is used to increase the efficiency of the wave-structure interaction problem resolution. Application of the method to the diffraction of nonlinear waves around a fixed, bottom mounted circular...

  6. An extremely simple method for fabricating 3D protein microarrays with an anti-fouling background and high protein capacity.

    Science.gov (United States)

    Lin, Zhifeng; Ma, Yuhong; Zhao, Changwen; Chen, Ruichao; Zhu, Xing; Zhang, Lihua; Yan, Xu; Yang, Wantai

    2014-07-21

    Protein microarrays have become vital tools for various applications in biomedicine and bio-analysis during the past decade. The intense requirements for a lower detection limit and industrialization in this area have resulted in a persistent pursuit to fabricate protein microarrays with a low background and high signal intensity via simple methods. Here, we report on an extremely simple strategy to create three-dimensional (3D) protein microarrays with an anti-fouling background and a high protein capacity by photo-induced surface sequential controlled/living graft polymerization developed in our lab. According to this strategy, "dormant" groups of isopropyl thioxanthone semipinacol (ITXSP) were first introduced to a polymeric substrate through ultraviolet (UV)-induced surface abstraction of hydrogen, followed by a coupling reaction. Under visible light irradiation, the ITXSP groups were photolyzed to initiate surface living graft polymerization of poly(ethylene glycol) methyl methacrylate (PEGMMA), thus introducing PEG brushes to the substrate to generate a full anti-fouling background. Due to the living nature of this graft polymerization, there were still ITXSP groups on the chain ends of the PEG brushes. Therefore, by in situ secondary living graft cross-linking copolymerization of glycidyl methacrylate (GMA) and polyethylene glycol diacrylate (PEGDA), we could finally plant height-controllable cylinder microarrays of a 3D PEG network containing reactive epoxy groups onto the PEG brushes. Through a commonly used reaction of amine and epoxy groups, the proteins could readily be covalently immobilized onto the microarrays. This delicate design aims to overcome two universal limitations in protein microarrays: a full anti-fouling background can effectively eliminate noise caused by non-specific absorption and a 3D reactive network provides a larger protein-loading capacity to improve signal intensity. The results of non-specific protein absorption tests

  7. 3D Multiscale Integrated Modeling Approach of Complex Rock Mass Structures

    Directory of Open Access Journals (Sweden)

    Mingchao Li

    2014-01-01

    Full Text Available Based on abundant geological data of different regions and different scales in hydraulic engineering, a new approach of 3D engineering-scale and statistical-scale integrated modeling was put forward, considering the complex relationships among geological structures and discontinuities and hydraulic structures. For engineering-scale geological structures, the 3D rock mass model of the study region was built by the exact match modeling method and the reliability analysis technique. For statistical-scale jointed rock mass, the random network simulation modeling method was realized, including Baecher structure plane model, Monte Carlo simulation, and dynamic check of random discontinuities, and the corresponding software program was developed. Finally, the refined model was reconstructed integrating with the engineering-scale model of rock structures, the statistical-scale model of discontinuities network, and the hydraulic structures model. It has been applied to the practical hydraulic project and offers the model basis for the analysis of hydraulic rock mass structures.

  8. Reduced Dimensionality (4,3)D-hnCOCANH Experiment: An Efficient Backbone Assignment tool for NMR studies of Proteins

    CERN Document Server

    Kumar, Dinesh

    2013-01-01

    Sequence specific resonance assignment and secondary structure determination of proteins form the basis for variety of structural and functional proteomics studies by NMR. In this context, an efficient standalone method for rapid assignment of backbone (1H, 15N, 13Ca and 13C') resonances and secondary structure determination of proteins has been presented here. Compared to currently available strategies used for the purpose, the method employs only a single reduced dimensionality (RD) experiment -(4,3)D-hnCOCANH and exploits the linear combinations of backbone (13Ca and 13C') chemical shifts to achieve a dispersion relatively better compared to those of individual chemical shifts (see the text) for efficient and rapid data analysis. Further, the experiment leads to the spectrum with direct distinction of self (intra-residue) and sequential (inter-residue) carbon correlation peaks; these appear opposite in signs and therefore can easily be discriminated without using an additional complementary experiment. On ...

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

    Science.gov (United States)

    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.

  10. 3D flexible NiTi-braided elastomer composites for smart structure applications

    Science.gov (United States)

    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.

  11. A model of 3D-structure of H+,K+-ATPase catalytic subunit derived by homology modeling

    Institute of Scientific and Technical Information of China (English)

    Dong YAN; Yuan-dong HU; Song LI; Mao-sheng CHENG

    2004-01-01

    AIM: To build a model of 3D-structure of H+, K+-ATPase catalytic subunit for theoretical study and anti-ulcer drug design. METHODS: The model was built on the basis of structural data from the Ca2+-ATPase. Structurally conserved regions were defined by amino acid sequence comparisons, optimum interconnecting loops were selected from the protein databank, and amino (N)- and carboxyl (C)-terminal ends were generated as random coil structures. Applying molecular mechanics method then minimized the model energy. Molecular dynamics technique was used to do further structural optimization. RESULTS: The model of 3D-structure of H+, K+-ATPase was derived. The model is reasonable according to several validation criteria. There were ten transmembrane helices (TM1-TM 10) in the model and inhibitor-binding site was identified on the TM5-8 riched negatively charged residues.CONCLUSION: The 3D-structure model from our study is informative to guide future molecular biology study about H+, K+-ATPase and drug design based on database searching.

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

    Science.gov (United States)

    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.

  13. Automatic segmentation and 3D feature extraction of protein aggregates in Caenorhabditis elegans

    Science.gov (United States)

    Rodrigues, Pedro L.; Moreira, António H. J.; Teixeira-Castro, Andreia; Oliveira, João; Dias, Nuno; Rodrigues, Nuno F.; Vilaça, João L.

    2012-03-01

    In the last years, it has become increasingly clear that neurodegenerative diseases involve protein aggregation, a process often used as disease progression readout and to develop therapeutic strategies. This work presents an image processing tool to automatic segment, classify and quantify these aggregates and the whole 3D body of the nematode Caenorhabditis Elegans. A total of 150 data set images, containing different slices, were captured with a confocal microscope from animals of distinct genetic conditions. Because of the animals' transparency, most of the slices pixels appeared dark, hampering their body volume direct reconstruction. Therefore, for each data set, all slices were stacked in one single 2D image in order to determine a volume approximation. The gradient of this image was input to an anisotropic diffusion algorithm that uses the Tukey's biweight as edge-stopping function. The image histogram median of this outcome was used to dynamically determine a thresholding level, which allows the determination of a smoothed exterior contour of the worm and the medial axis of the worm body from thinning its skeleton. Based on this exterior contour diameter and the medial animal axis, random 3D points were then calculated to produce a volume mesh approximation. The protein aggregations were subsequently segmented based on an iso-value and blended with the resulting volume mesh. The results obtained were consistent with qualitative observations in literature, allowing non-biased, reliable and high throughput protein aggregates quantification. This may lead to a significant improvement on neurodegenerative diseases treatment planning and interventions prevention.

  14. 3D Global Coronal Density Structure and Associated Magnetic Field near Solar Maximum

    Directory of Open Access Journals (Sweden)

    Maxim Kramar

    2016-08-01

    Full Text Available Measurement of the coronal magnetic field is a crucial ingredient in understanding the nature of solar coronal dynamic phenomena at all scales. We employ STEREO/COR1 data obtained near maximum of solar activity in December 2012 (Carrington rotation, CR 2131 to retrieve and analyze the three-dimensional (3D coronal electron density in the range of heights from $1.5$ to $4 R_odot$ using a tomography method and qualitatively deduce structures of the coronal magnetic field. The 3D electron density analysis is complemented by the 3D STEREO/EUVI emissivity in 195 AA band obtained by tomography for the same CR period. We find that the magnetic field configuration during CR 2131 has a tendency to become radially open at heliocentric distances below $sim 2.5 R_odot$. We compared the reconstructed 3D coronal structures over the CR near the solar maximum to the one at deep solar minimum. Results of our 3D density reconstruction will help to constrain solar coronal field models and test the accuracy of the magnetic field approximations for coronal modeling.

  15. 3D Global Coronal Density Structure and Associated Magnetic Field near Solar Maximum

    Science.gov (United States)

    Kramar, Maxim; Airapetian, Vladimir; Lin, Haosheng

    2016-08-01

    Measurement of the coronal magnetic field is a crucial ingredient in understanding the nature of solar coronal dynamic phenomena at all scales. We employ STEREO/COR1 data obtained near maximum of solar activity in December 2012 (Carrington rotation, CR 2131) to retrieve and analyze the three-dimensional (3D) coronal electron density in the range of heights from 1.5 to 4 R_⊙ using a tomography method and qualitatively deduce structures of the coronal magnetic field. The 3D electron density analysis is complemented by the 3D STEREO/EUVI emissivity in 195 Å band obtained by tomography for the same CR period. We find that the magnetic field configuration during CR 2131 has a tendency to become radially open at heliocentric distances below ˜ 2.5 R_⊙. We compared the reconstructed 3D coronal structures over the CR near the solar maximum to the one at deep solar minimum. Results of our 3D density reconstruction will help to constrain solar coronal field models and test the accuracy of the magnetic field approximations for coronal modeling.

  16. 3D Global Coronal Density Structure and Associated Magnetic Field near Solar Maximum

    CERN Document Server

    Kramar, Maxim; Lin, Haosheng

    2016-01-01

    Measurement of the coronal magnetic field is a crucial ingredient in understanding the nature of solar coronal dynamic phenomena at all scales. We employ STEREO/COR1 data obtained near maximum of solar activity in December 2012 (Carrington rotation, CR 2131) to retrieve and analyze the three-dimensional (3D) coronal electron density in the range of heights from $1.5$ to $4\\ \\mathrm{R}_\\odot$ using a tomography method and qualitatively deduce structures of the coronal magnetic field. The 3D electron density analysis is complemented by the 3D STEREO/EUVI emissivity in 195 \\AA \\ band obtained by tomography for the same CR period. We find that the magnetic field configuration during CR 2131 has a tendency to become radially open at heliocentric distances below $\\sim 2.5 \\ \\mathrm{R}_\\odot$. We compared the reconstructed 3D coronal structures over the CR near the solar maximum to the one at deep solar minimum. Results of our 3D density reconstruction will help to constrain solar coronal field models and test the a...

  17. 3D Wide FOV Scanning Measurement System Based on Multiline Structured-Light Sensors

    Directory of Open Access Journals (Sweden)

    He Gao

    2014-03-01

    Full Text Available Structured-light three-dimensional (3D vision measurement is currently one of the most common approaches to obtain 3D surface data. However, the existing structured-light scanning measurement systems are primarily constructed on the basis of single sensor, which inevitably generates three obvious problems: limited measurement range, blind measurement area, and low scanning efficiency. To solve these problems, we developed a novel 3D wide FOV scanning measurement system which adopted two multiline structured-light sensors. Each sensor is composed of a digital CCD camera and three line-structured-light projectors. During the measurement process, the measured object is scanned by the two sensors from two different angles at a certain speed. Consequently, the measurement range is expanded and the blind measurement area is reduced. More importantly, since six light stripes are simultaneously projected on the object surface, the scanning efficiency is greatly improved. The Multiline Structured-light Sensors Scanning Measurement System (MSSS is calibrated on site by a 2D pattern. The experimental results show that the RMS errors of the system for calibration and measurement are less than 0.092 mm and 0.168 mm, respectively, which proves that the MSSS is applicable for obtaining 3D object surface with high efficiency and accuracy.

  18. Predicting 3D structure, flexibility and stability of RNA hairpins in monovalent and divalent ion solutions

    CERN Document Server

    Shi, Ya-Zhou; 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 will further develop the model by improving the implicit-salt electrostatic potential and involving a sequence-dependent coaxial stacking potential to enable the model to simulate RNA 3D structure folding in divalent/monovalent ion solutions. As compared with the experimental data, the present model can predict 3D structures of RNA hairpins with bulge/internal loops (<77nt) from their sequences at the corresponding experimental ion conditions with an overall improved accuracy, and the model also makes reliable predictions for the flexibility of RNA hairpins with bulge loops of different length at extensive divalent/monovalent ion conditions. In addition, the model successfully pred...

  19. Automated Clustering Analysis of Immunoglobulin Sequences in Chronic Lymphocytic Leukemia Based on 3D Structural Descriptors

    DEFF Research Database (Denmark)

    Marcatili, Paolo; Mochament, Konstantinos; Agathangelidis, Andreas

    2016-01-01

    Imunoglobulins (Igs) are crucial for the defense against pathogens, but they are also important in many clinical and biotechnological applications. Their characteristics, and ultimately their function, depend on their three-dimensional (3D) structure; however, the procedures to experimentally det...

  20. Multi-dimensional Seismic Response Analysis of Base-Isolated Frame Structure with 3D Isolator

    Institute of Scientific and Technical Information of China (English)

    Xiong Shishu; Huang Liting; Chen Jinfeng; Su Jingsu

    2005-01-01

    The three-dimensional lead-rubber dish-spring bearing (3DB) is proposed in this paper. The 3DB is composed of lead rubber bearing (LRB) and dish-spring bearing (DSB) with damper in series. The 3DB put forward in this paper is effective in the resolution of difficulties in strong vertical capacity and vertical damping of three-dimensional isolation bearings. It effectively suppresses rocking motions as well. The analytical model and motion equations of multi-dimensional seismic responses of 3D base-isolated frame structures are established. Taking a five-storey frame structure as an example, an extensive simulation analysis is carried out. The results show that the 3D base-isolated structure with the proposed 3DB is effective in 3D isolation; it can reduce seismic responses by 50 % compared to a non-isolated structure. Therefore, the 3D isolation problem in building can be solved easily and effectively with the 3DB proposed in this paper.

  1. 2D vario-scale representations based on real 3D structure

    NARCIS (Netherlands)

    Suba, R.; Meijers, B.M.; Van Oosterom, P.J.M.

    2013-01-01

    This paper focuses on 3D data structures supporting an alternative approach for creating 2D vario-scale maps. The smooth animated zooming functionality have lead us to investigate a volumetric representation of gradually changing vario-scale objects. In this paper, the principle of vario-scale maps

  2. Present-day 3D structural model of the Po Valley basin, Northern Italy

    NARCIS (Netherlands)

    Turrini, C.; Lacombe, O.; Roure, F.

    2014-01-01

    A 3D structural model of the Po Valley basin (Northern Italy) was built by integrating the dataset available from the public domain (DEM, wells, isobath-maps, cross-sections, outcrop-trends).The model shows the complex foredeep-foreland architecture across the basin, from the Moho level to the topog

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

    Directory of Open Access Journals (Sweden)

    Claudia eHänel

    2014-05-01

    Full Text Available The visualization of the progression of brain tissue loss, which occurs in neurodegenerative diseases like corticobasal syndrome (CBS, is an important prerequisite to understand the course and the causes of this neurodegenerative disorder. Common workflows for visual analysis are often based on single 2D sections since in 3D visualizations more internally situated structures may be occluded by structures near the surface. The reduction of dimensions from 3D to 2D allows for an holistic view onto internal and external structures, but results in a loss of spatial information. Here, we present an application with two 3D visualization designs to resolve these challenges. First, in addition to the volume changes, the semi-transparent anatomy is displayed with an anatomical section and cortical areas for spatial orientation. Second, the principle of importance-driven volume rendering is adapted to give an unrestricted line-of-sight to relevant structures by means of a frustum-like cutout. To strengthen the benefits of the 3D visualization, we decided to provide the application next to standard desktop environments in immersive virtual environments with stereoscopic viewing as well. This improves the depth perception in general and in particular for the second design. Thus, the application presented in this work allows for aneasily comprehensible visual analysis of the extent of brain degeneration and the corresponding affected regions.

  4. 3D micro-structures by piezoelectric inkjet printing of gold nanofluids

    KAUST Repository

    Kullmann, Carmen

    2012-04-18

    3D solid and pocketed micro-wires and micro-walls are needed for emerging applications that require fine-scale functional structures in three dimensions, including micro-heaters, micro-reactors and solar cells. To fulfill this demand, 3D micro-structures with high aspect ratios (>50:1) are developed on a low-cost basis that is applicable for mass production with high throughput, also enabling the printing of structures that cannot be manufactured by conventional techniques. Additively patterned 3D gold micro-walls and -wires are grown by piezoelectric inkjet printing of nanofluids, selectively combined with in situ simultaneous laser annealing that can be applied to large-scale bulk production. It is demonstrated how the results of 3D printing depend on the piezoelectric voltage pulse, the substrate heating temperature and the structure height, resulting in the identification of thermal regions of optimal printing for best printing results. Furthermore a parametric analysis of the applied substrate temperature during printing leads to proposed temperature ranges for solid and pocketed micro-wire and micro-wall growth for selected frequency and voltages. © 2012 IOP Publishing Ltd.

  5. Structured light 3D tracking system for measuring motions in PET brain imaging

    DEFF Research Database (Denmark)

    Olesen, Oline Vinter; Jørgensen, Morten Rudkjær; Paulsen, Rasmus Reinhold

    2010-01-01

    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...

  6. A patterned 3D silicon anode fabricated by electrodeposition on a virus-structured current collector

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Xilin; Guo, Juchen; Wang, Chunsheng [Department of Chemical and Biomolecular Engineering, University of Maryland College Park, MD 20742 (United States); Gerasopoulos, Konstantinos; Ghodssi, Reza [Department of Materials Science and Engineering, Institute for Systems Research, Department of Electrical and Computer Engineering, University of Maryland College Park, MD 20742 (United States); Brown, Adam; Culver, James N. [Institute for Bioscience and Biotechology Research, Department of Plant Science and Landscape Architecture, University of Maryland College Park, MD 20742 (United States)

    2011-01-21

    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. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

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

    Science.gov (United States)

    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.

  8. Photonic Band Gaps in 3D Network Structures with Short-range Order

    CERN Document Server

    Liew, Seng Fatt; Noh, Heeso; Schreck, Carl F; Dufresne, Eric R; O'Hern, Corey S; Cao, Hui

    2011-01-01

    We present a systematic study of photonic band gaps (PBGs) in three-dimensional (3D) photonic amorphous structures (PAS) with short-range order. From calculations of the density of optical states (DOS) for PAS with different topologies, we find that tetrahedrally connected dielectric networks produce the largest isotropic PBGs. Local uniformity and tetrahedral order are essential to the formation of PBGs in PAS, in addition to short-range geometric order. This work demonstrates that it is possible to create broad, isotropic PBGs for vector light fields in 3D PAS without long-range order.

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

    Energy Technology Data Exchange (ETDEWEB)

    Avakian, Harut [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Avakian, Harut

    2016-08-01

    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. On the Lagrangian structure of 3D consistent systems of asymmetric quad-equations

    CERN Document Server

    Boll, Raphael

    2011-01-01

    Recently, the first-named author gave a classification of 3D consistent 6-tuples of quad-equations with the tetrahedron property; several novel asymmetric 6-tuples have been found. Due to 3D consistency, these 6-tuples can be extended to discrete integrable systems on Z^m. We establish Lagrangian structures and flip-invariance of the action functional for the class of discrete integrable systems involving equations for which some of the biquadratics are non-degenerate and some are degenerate. This class covers, among others, some of the above mentioned novel systems.

  13. Research of aluminium alloy aerospace structure aperture measurement based on 3D digital speckle correlation method

    Science.gov (United States)

    Bai, Lu; Wang, Hongbo; Zhou, Jiangfan; Yang, Rong; Zhang, Hui

    2014-11-01

    In this paper, the aperture change of the aluminium alloy aerospace structure under real load is researched. Static experiments are carried on which is simulated the load environment of flight course. Compared with the traditional methods, through experiments results, it's proved that 3D digital speckle correlation method has good adaptability and precision on testing aperture change, and it can satisfy measurement on non-contact,real-time 3D deformation or stress concentration. The test results of new method is compared with the traditional method.

  14. Electronic structure of the 3d metals. An investigation by L-shell-photoionisation

    Energy Technology Data Exchange (ETDEWEB)

    Richter, T.S.

    2007-12-03

    The 3d transition metal elements from Sc to Cu have been investigated by both photo electron emission and photo absorption. Experimental spectra in the 2p energy range are discussed based on atomic multiplet models and Hartree- Fock calculations. The samples have been evaporated from an electron bombardment crucible and excited/ionized by monochromatized synchrotron radiation. Fundamental effects and the main interactions which govern the electronic structure of the 3d metal atoms are covered. Common spectral features and trends in the series are discussed as well as the importance of many body electron correlation effects. (orig.)

  15. [High-precision 3D morphology measurement by digital gatling method based on structured light].

    Science.gov (United States)

    Luo, Gang-Yin; Tang, Yu-Guo; Qiao, Pei-Yu; Wang, Bi-Dou; Jia, Zan-Dong; Xu, Zhong

    2012-09-01

    In order to measure the microscopic 3D morphology of the objects with high-precision, a 3D texture measurement system of digital gatling based on structured light was designed, which can calculate the 3D height information with the analytic phase method. First, the authors collected sixteen equal step phase images by the four-step equal step method, and calculated their main value by dividing them into four groups. Then, the authors found the average as the final phase main value. The pretreatment on the fringe was done by the adaptive Wiener filter and wavelet multi-threshold method to eliminate the various effects of noise, projector distortion and CCD camera distortion. Besides, gradient-oriented phase unwrapping algorithm based on multifrequency was introduced to avoid phase discontinuity point in the course phase unwrapping, and it was proven to be effective and stable. Experiments showed that the system's 3D resolution was 2.75 microm, and the high degree accuracy was better than 0.5 microm, when the system was running with the fringe parameter p0 = 22.7 mm(-1). In addition, the system has many advantages such as fast measuring, simple operation and non-contact, which can meet the need of the high precision measurement requirements for the microscopic 3D morphology.

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

    Science.gov (United States)

    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. Topology Optimization Design of 3D Continuum Structure with Reserved Hole Based on Variable Density Method

    Directory of Open Access Journals (Sweden)

    Bai Shiye

    2016-05-01

    Full Text Available An objective function defined by minimum compliance of topology optimization for 3D continuum structure was established to search optimal material distribution constrained by the predetermined volume restriction. Based on the improved SIMP (solid isotropic microstructures with penalization model and the new sensitivity filtering technique, basic iteration equations of 3D finite element analysis were deduced and solved by optimization criterion method. All the above procedures were written in MATLAB programming language, and the topology optimization design examples of 3D continuum structure with reserved hole were examined repeatedly by observing various indexes, including compliance, maximum displacement, and density index. The influence of mesh, penalty factors, and filter radius on the topology results was analyzed. Computational results showed that the finer or coarser the mesh number was, the larger the compliance, maximum displacement, and density index would be. When the filtering radius was larger than 1.0, the topology shape no longer appeared as a chessboard problem, thus suggesting that the presented sensitivity filtering method was valid. The penalty factor should be an integer because iteration steps increased greatly when it is a noninteger. The above modified variable density method could provide technical routes for topology optimization design of more complex 3D continuum structures in the future.

  18. Carbon aerogel with 3-D continuous skeleton and mesopore structure for lithium-ion batteries application

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaoqing, E-mail: yxq-886@163.com [School of Materials and Energy, Guangdong University of Technology, Guangzhou 510006 (China); Huang, Hong [Instrumental Analysis and Research Center, Sun Yat-sen University, Guangzhou 510275 (China); Zhang, Guoqing; Li, Xinxi [School of Materials and Energy, Guangdong University of Technology, Guangzhou 510006 (China); Wu, Dingcai [Materials Science Institute, PCFM Laboratory, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275 (China); Fu, Ruowen, E-mail: cesfrw@mail.sysu.edu.cn [Materials Science Institute, PCFM Laboratory, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275 (China)

    2015-01-15

    Carbon aerogel (CA) with 3-D continuous skeleton and mesopore structure was prepared via a microemulsion-templated sol–gel polymerization method and then used as the anode materials of lithium-ion batteries. It was found that the reversible specific capacity of the as-prepared CAs could stay at about 470 mA h g{sup −1} for 80 cycles, much higher than the theoretical capacity of commercial graphite (372 mAh g{sup −1}). In addition, CA also showed a better rate capacity compared to commercial graphite. The good electrochemical properties could be ascribed to the following three factors: (1) the large BET surface area of 620 m{sup 2} g{sup −1}, which can provide more lithium ion insertion sites, (2) 3-D continuous skeleton of CAs, which favors the transport of the electrons, (3) 3-D continuous mesopore structure with narrow mesopore size distribution and high mesopore ratio of 87.3%, which facilitates the diffusion and transport of the electrolyte and lithium ions. - Highlights: • Carbon aerogel (CA) was prepared via a microemulsion-templated sol–gel method. • The CA presents high surface area, 3D continuous skeleton and mesopore structure. • The reversible capacity of CA is much higher than that of graphite.

  19. Cryo-EM structure of a 3D DNA-origami object

    Science.gov (United States)

    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

  20. seeMotif: exploring and visualizing sequence motifs in 3D structures

    OpenAIRE

    2009-01-01

    Sequence motifs are important in the study of molecular biology. Motif discovery tools efficiently deliver many function related signatures of proteins and largely facilitate sequence annotation. As increasing numbers of motifs are detected experimentally or predicted computationally, characterizing the functional roles of motifs and identifying the potential synergetic relationships between them are important next steps. A good way to investigate novel motifs is to utilize the abundant 3D st...

  1. A Deep Structured Model with Radius-Margin Bound for 3D Human Activity Recognition

    OpenAIRE

    Lin, Liang; Wang, Keze; Zuo, Wangmeng; Wang, Meng; Luo, Jiebo; Zhang, Lei

    2015-01-01

    Understanding human activity is very challenging even with the recently developed 3D/depth sensors. To solve this problem, this work investigates a novel deep structured model, which adaptively decomposes an activity instance into temporal parts using the convolutional neural networks (CNNs). Our model advances the traditional deep learning approaches in two aspects. First, { we incorporate latent temporal structure into the deep model, accounting for large temporal variations of diverse huma...

  2. Three-dimensional (3D) structure model and its parameters for poplar shelterbelts

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The spatial functions of surface area density(vegetative surface area per unit canopy volume) and cubic density(vegetative volume per unit canopy volume) have been used as two three-dimensional(3D) structural descriptors for shelterbelt.The functions were defined by models as a general case.However,sub-models such as surface area,volume,and corresponding distributions were not explicitly defined for poplar trees,which are a dominant woody species in shelterbelts all over China,and this limits applications of the models in China and elsewhere.In order to define and develop these sub-models for shelterbelts,poplar trees were destructively sampled from multiple-row shelterbelts and then were measured for their surface area and volume.Using these measurements,we estimated parameters to define their equations explicitly.Based on the architecture and planting patterns of trees in shelterbelts,the distribution of the surface areas and volumes vertically and across the width for different tree heights were constructed for the three components of trunks,branches and leaves.Incorporating the defined equations into the models,we described the 3D structure of a multiple-row poplar shelterbelt.The results showed that,the spatial change in magnitude of surface area density(0.215-10.131 m2/m3) or cubic density(0.00007-0.04667 m3/m3) in shelterbelts is large and their distributions are not uniform.The assumption for boundary-layer flow modeling efforts that the 3D distribution of shelterbelt structure was uniform is not the case in field.The 3D structure model not only can be used to model the flow field as influenced by each tree component,but also can express the entire aerodynamic characteristics of a shelterbelt.The methodologies and equations that are developed in this study can be applied to estimate the 3D structure of a shelterbelt with a design similar to our studied poplar shelterbelts in terms of species composition and planting patterns.The fitted models can be used to

  3. Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data.

    Science.gov (United States)

    Trieu, Tuan; Cheng, Jianlin

    2014-04-01

    Chromosomes are not positioned randomly within a nucleus, but instead, they adopt preferred spatial conformations to facilitate necessary long-range gene-gene interactions and regulations. Thus, obtaining the 3D shape of chromosomes of a genome is critical for understanding how the genome folds, functions and how its genes interact and are regulated. Here, we describe a method to reconstruct preferred 3D structures of individual chromosomes of the human genome from chromosomal contact data generated by the Hi-C chromosome conformation capturing technique. A novel parameterized objective function was designed for modeling chromosome structures, which was optimized by a gradient descent method to generate chromosomal structural models that could satisfy as many intra-chromosomal contacts as possible. We applied the objective function and the corresponding optimization method to two Hi-C chromosomal data sets of both a healthy and a cancerous human B-cell to construct 3D models of individual chromosomes at resolutions of 1 MB and 200 KB, respectively. The parameters used with the method were calibrated according to an independent fluorescence in situ hybridization experimental data. The structural models generated by our method could satisfy a high percentage of contacts (pairs of loci in interaction) and non-contacts (pairs of loci not in interaction) and were compatible with the known two-compartment organization of human chromatin structures. Furthermore, structural models generated at different resolutions and from randomly permuted data sets were consistent.

  4. Factors Affecting Dimensional Accuracy of 3-D Printed Anatomical Structures Derived from CT Data.

    Science.gov (United States)

    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.

  5. Generation of 3-D surface maps in waste storage silos using a structured light source

    Science.gov (United States)

    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.

  6. Digital 3D Modeling of Whole Garment Based on Structure Illumination

    Institute of Scientific and Technical Information of China (English)

    TAO Jun

    2006-01-01

    With the coming of information age and the development of computer science, digitalization of whole garment is becoming more and more important. The surface of whole garment is sequent and glossy so that it is lack of the texture characteristic which is the key of digital 3D modeling.According to this reason, the structure illumination is steered into a method of this paper. The paper proposes the method by which 3D model of whole garment is created from 2D image sequences directly but not by the common techniques using general CAD model. In the paper the structure illumination is generated by the slide projector and the modeling of whole garment is based on the strict theory of the digital photogrammetry, computer vision and image processing pattern recognition. Because whole garment is lack of the applicable texture for matching, the characteristic texture generated by the structure illumination is added onto the surface of whole garment. After the characteristic texture is extracted from images and is matched well, 3D coordinates of the characteristic texture can be calculated out by the space forward intersection.Then the whole garment model is acquired by connecting all neighbour space points in the TIN and rendering the real texture of whole garment automatically. The 3D modeling method is untouched so that it is nondestructive which is just suitable for the messaline and the clothing. The method of whole garment 3D modeling proposed in the paper is flexible, effective and practical, which is confirmed by the results of the reconstructing experiments.

  7. Optimal Image Stitching for Concrete Bridge Bottom Surfaces Aided by 3d Structure Lines

    Science.gov (United States)

    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.

  8. Pipeline inwall 3D measurement system based on the cross structured light

    Science.gov (United States)

    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.

  9. Fabrication of 3D embedded hollow structures inside polymer dielectric PMMA with femtosecond laser

    Science.gov (United States)

    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.

  10. 3D structure and conductive thermal field of the Upper Rhine Graben

    Science.gov (United States)

    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

  11. 3D printing of layered brain-like structures using peptide modified gellan gum substrates.

    Science.gov (United States)

    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.

  12. X-Ray Nanofocus CT: Visualising Of Internal 3D-Structures With Submicrometer Resolution

    Science.gov (United States)

    Weinekoetter, Christian

    2008-09-01

    High-resolution X-ray Computed Tomography (CT) allows the visualization and failure analysis of the internal micro structure of objects—even if they have complicated 3D-structures where 2D X-ray microscopy would give unclear information. During the past several years, computed tomography has progressed to higher resolution and quicker reconstruction of the 3D-volume. Most recently it even allows a three-dimensional look into the inside of materials with submicron resolution. With the use of nanofocus® tube technology, nanoCT®-systems are pushing forward into application fields that were exclusive to high cost and rare available synchrotron techniques. The study was performed with the new nanotom, a very compact laboratory system which allows the analysis of samples up to 120 mm in diameter and weighing up to 1 kg with exceptional voxel-resolution down to click, this technique will substitute destructive mechanical slicing and cutting in many applications. The initial CT results obtained with the nanotom® demonstrate that it is now possible to analyze the three-dimensional micro structure of materials and small objects with submicrometer resolution. Any internal difference in material, density or porosity within a sample can be visualized and data like distances can be measured. NanoCT® widely expands the spectrum of detectable micro-structures. The nanotom® opens a new dimension of 3D-microanalysis and will replace more destructive methods—saving costs and time per sample inspected.

  13. Low-Cost Impact Detection and Location for Automated Inspections of 3D Metallic Based Structures

    Directory of Open Access Journals (Sweden)

    Carlos Morón

    2015-05-01

    Full Text Available 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.

  14. Low-cost structured-light based 3D capture system design

    Science.gov (United States)

    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.

  15. 3D analysis of vortical structures in an abdominal aortic aneurysm by stereoscopic PIV

    Science.gov (United States)

    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.

  16. 3D Temperature Mapping of Solar Photospheric Fine Structure Using Ca II H Filtergrams

    CERN Document Server

    Henriques, V M J

    2012-01-01

    Context. The wings of the Ca II H and K lines provide excellent photospheric temperature diagnostics. At the Swedish 1-meter Solar Telescope the blue wing of Ca II H is scanned with a narrowband interference filter mounted on a rotation stage. This provides up to 0"10 spatial resolution filtergrams at high cadence that are concurrent with other diagnostics at longer wavelengths. Aims. The aim is to develop observational techniques that provide the photospheric temperature stratification at the highest spatial resolution possible and use those to compare simulations and observations at different heights. Methods. We use filtergrams in the Ca II H blue wing obtained with a tiltable interference filter at the SST. Synthetic observations are produced from 3D HD and 3D MHD numerical simulations and degraded to match the observations. The temperature structure obtained from applying the method to the synthetic data is compared with the known structure in the simulated atmospheres and with observations of an active ...

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

    Science.gov (United States)

    2015-11-17

    of Texas at El Paso, 2014. [19] A. Sihvola, " Electromagnetic Emergence in Metamaterials," in Advances in Electromagnetics of Complex Media and...complex power of radiating elements under electromagnetic source transformation," Microwave and Optical Technology Letters, vol. 53, pp. 1524-1527...AFRL-RW-EG-TP-2015-002 Rapid Prototyping across the Spectrum: RF to Optical 3D Electromagnetic Structures Jeffery W. Allen Monica S. Allen Brett

  18. Modeling of AAR affected structures using the GROW3D FEA program

    Energy Technology Data Exchange (ETDEWEB)

    Curtis, D.D. [Acres International Limited, Niagara Falls, Ontario (Canada)

    1995-12-31

    The objective of this paper is to present a rational and practical methodology for finite element stress analysis of AAR affected structures. The methodology is presented using case history studies which illustrate the practical application of the GROW3D program. GROW3D uses an anisotropic expansion strain function and concrete properties which simulates the following key characteristics of AAR affected concrete (1) concrete growth expansion rates dependent on the stress vectors at each point; (2) concrete growth rate variation due to changes in moisture content and temperature; and (3) time-dependent, enhanced creep behavior. GROW3D has been applied to several hydropower structures and case histories from the Mactaquac Generating Station are presented herein. Mactaquac is selected because extensive instrumentation data before and after remedial measures have been used to calibrate and test the model. The results of analyses of three different structures are given, i.e., the intake, diversion sluiceway and powerhouse. The analysis results are used to identify potential structural problems and the need and timing of remedial measures. The output from GROW3D includes displacement rates, total displacements, global stresses and local factors of safety. The local factors of safety (or strength to stress ratios) are computed for several modes of failure including crushing, cracking, shear and sliding on horizontal construction joints. The analysis results are compared with field measurements which are taken before and after slot cutting. The effects of including the above-mentioned characteristics and other modeling assumptions on the computed results is discussed herein. Finally, a brief discussion on the recent enhancements to the model is given. These enhancements include the implementation of a more rigorous treatment of concrete creep effects.

  19. LB3D: a protein three-dimensional substructure search program based on the lower bound of a root mean square deviation value.

    Science.gov (United States)

    Terashi, Genki; Shibuya, Tetsuo; Takeda-Shitaka, Mayuko

    2012-05-01

    Searching for protein structure-function relationships using three-dimensional (3D) structural coordinates represents a fundamental approach for determining the function of proteins with unknown functions. Since protein structure databases are rapidly growing in size, the development of a fast search method to find similar protein substructures by comparison of protein 3D structures is essential. In this article, we present a novel protein 3D structure search method to find all substructures with root mean square deviations (RMSDs) to the query structure that are lower than a given threshold value. Our new algorithm runs in O(m + N/m(0.5)) time, after O(N log N) preprocessing, where N is the database size and m is the query length. The new method is 1.8-41.6 times faster than the practically best known O(N) algorithm, according to computational experiments using a huge database (i.e., >20,000,000 C-alpha coordinates).

  20. Protection for structures in extreme earthquakes: Full Base Isolation (3-D) by the Swiss Seismafloat System

    Energy Technology Data Exchange (ETDEWEB)

    Staudacher, K.

    1985-02-01

    Full Base Isolation (FBI, 3-D), an antiseismic concept for structures, adds vertical flexibility to horizontal base isolation (HBI, 2-D). Extensive experimental testing at the Swiss Federal Institute of Technology and the University of California, Berkeley, has shown FBI to be a practicable way to reach the final goal of earthquake protection, i.e. elastic behavior of the structural frame in extreme earthquakes. Swiss engineers pioneered base isolation by the construction of the Pestalozzi School at Skopje in 1968. Further development has made Integral Earthquake Protection possible for structures and their contents. (orig.).

  1. Study of macroporous silicon electrochemical etching in 3D structured N type silicon substrates

    Energy Technology Data Exchange (ETDEWEB)

    Kouassi, Sebastien; Gautier, Gael; Desplobain, Sebastien; Ventura, Laurent [Laboratoire de Microelectronique de Puissance, Universite Francois Rabelais Tours, 16 Rue Pierre et Marie Curie, 37071 Tours Cedex 2 (France)

    2011-06-15

    In this paper, the electrochemical etching of 3D n-type substrates is investigated. These types of 3D structures are of interest to increase the active surface of some systems. Our aim is to improve a MEMS (Micro-Electro Mechanical System) micro fuel cell power through total surface enhancement without any modification of the cell footprint. To reach this objective, we perform a gas diffusion layer using localized macro-porous silicon. The porous area total surface is improved through trench formation (before porous silicon etching). This is supposed to allow a better power to surface ratio for manufactured fuel cell. The Figure on the right hand side introduces the aimed MEMS based micro fuel cell. The geometrical parameters of the designed structures and the manufacturing process influence are presented. To perform 3D structures, two types of anisotropic etching techniques have been used, alkaline etching of silicon and deep reactive ion etching (DRIE). Additional steps such as a doping layer have been used to improve the results obtained with the initial micro-fabrication process. (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  2. 3D wind-induced response analysis of a cable-membrane structure

    Institute of Scientific and Technical Information of China (English)

    Jun-jie LUO; Da-jian HAN

    2009-01-01

    Wind loading is a dominant factor for design of a cable-membrane structure. Three orthogonal turbulent components, including the longitudinal, lateral and vertical wind velocities, should be taken into account for the wind loads. In this study, a stochastic 3D coupling wind field model is derived by the spectral representation theory, The coherence functions of the three orthognnal turbulent components are considered in this model. Then the model is applied to generate the three correlated wind turbulent components. After that, formulae are proposed to transform the velocities into wind loads, and to introduce the modified wind pressure force. Finally, a wind-induced time-history response analysis is conducted for a 3D cable-membrane structure. Analytical results indicate that responses induced by the proposed wind load model are 10%--25% larger than those by the con-ventionai uncorrelated model, and that the responses are not quite influenced by the modified wind pressure force. Therefore, we concluded that, in the time-history response analysis, the coherences of the three orthogonal turbulent components are necessary for a 3D cable-membrane structure, but the modified wind pressure force can be ignored.

  3. Mathematical structure of the three-dimensional (3D) Ising model

    Institute of Scientific and Technical Information of China (English)

    Zhang Zhi-Dong

    2013-01-01

    An overview of the mathematical structure of the three-dimensional (3D) Ising model is given from the points of view of topology,algebra,and geometry.By analyzing the relationships among transfer matrices of the 3D Ising model,Reidemeister moves in the knot theory,Yang-Baxter and tetrahedron equations,the following facts are illustrated for the 3D Ising model.1) The complex quaternion basis constructed for the 3D Ising model naturally represents the rotation in a (3+1)-dimensional space-time as a relativistic quantum statistical mechanics model,which is consistent with the 4-fold integrand of the partition function obtained by taking the time average.2) A unitary transformation with a matrix that is a spin representation in 2n·l·o-space corresponds to a rotation in 2n· l· o-space,which serves to smooth all the crossings in the transfer matrices and contributes the non-trivial topological part of the partition function of the 3D Ising model.3)A tetrahedron relationship would ensure the commutativity of the transfer matrices and the integrability of the 3D Ising model,and its existence is guaranteed by the Jordan algebra and the Jordan-von Neumann-Wigner procedures.4) The unitary transformation for smoothing the crossings in the transfer matrices changes the wave functions by complex phases Φx,Φy,and Φz.The relationship with quantum field and gauge theories and the physical significance of the weight factors are discussed in detail.The conjectured exact solution is compared with numerical results,and the singularities at/near infinite temperature are inspected.The analyticity in β =1/(kBT) of both the hard-core and the Ising models has been proved only forβ > 0,not for β =0.Thus the high-temperature series cannot serve as a standard for judging a putative exact solution of the 3D Ising model.

  4. Posture parameters optimization of a structured light 3D angle measuring system

    Directory of Open Access Journals (Sweden)

    Xun DING

    2015-10-01

    Full Text Available To improve the measurement precision of the structured light target angle, this paper studies the relation between the structured light system parameters and measurement accuracy of the angle. Firstly, the main system structure parameters influencing the angle measurement precision are analyzed based on the structured light measurement principle; secondly, simulation research on the laws of how the structured parameters influence the angle measurement precision are conducted, and the optimized range of values of the structured parameters is proposed; finally, the experimental studies show that, the optimized parameters can improve the angle measurement precision effectively, which lays the design foundation for later improvement schemes of the structured light 3D four-wheel alignment instrument.

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

    Science.gov (United States)

    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

  6. 3D measurement method based on combined temporal encoding structured light

    Science.gov (United States)

    Yu, Xiaoyang; Wang, Yang; Yu, Shuang; Cheng, Hao; Sun, Xiaoming; Yu, Shuchun; Chen, Deyun

    2013-10-01

    Three-dimensional (3D) vision measurement technology based on encoding structured light plays an important role and has become the main development trend in the field of 3D non-contact measurement. However, how to synthetically improve measurement speed, accuracy and sampling density is still a difficult problem. Thus in the present work, a novel 3D measurement method based on temporal encoding structured light by combining trapezoidal phase-shifting pattern and cyclic code pattern is proposed. Due to trapezoidal phase-shifting has the advantages of high sampling density and high-speed, the proposed method can maintain these advantages by using cyclic code to expand the range of trapezoidal phase-shifting. In addition, the correction scheme is designed to solve the problem of cycle dislocation. Finally, simulation experimental platform is built with 3ds max and MATLAB. Experimental analyses and results show that, the maximal error is less than 3 mm in the range from 400 mm to 1100 mm, cycle dislocation correction has a good effect.

  7. The first 3-D LaIII-SrII heterometallic complex: Synthesis, structure and luminescent properties

    Science.gov (United States)

    Hong, Zhiwei; Ran, Jingwen; Li, Tao; Chen, Yanmei

    2016-10-01

    The first 3-D LaIII-SrII heterometallic complex, namely [La2Sr(pda)4(H2O)4]n·6nH2O (1, H2pda = pyridine-2,6-dicarboxylic acid), has been successfully synthesized under solvothermal conditions. Single crystal X-ray diffraction analysis reveals that complex 1 features a 3-D porous framework and displays a new topology. The crystal structure can be simplified to a 4,6-connected 3-D network with Schläfli symbol of {34·42·88·9}2{34·42}. The crystals also have been characterized by X-ray powder diffraction, elemental analysis, thermal analysis, and IR spectroscopy. The infrared spectral analysis indicates that complex 1 is a carboxylate coordinated compound, several water molecules exist in the compound. The thermal study shows that there are ten water molecules in the crystal structure. The luminescent property has also been investigated. It shows a blue-purple fluorescence emission.

  8. Characterization of ABS specimens produced via the 3D printing technology for drone structural components

    Science.gov (United States)

    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.

  9. The lithospheric-scale 3D structural configuration of the North Alpine Foreland Basin constrained by gravity modelling and the calculation of the 3D load distribution

    Science.gov (United States)

    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

  10. Benchmarking Close-range Structure from Motion 3D Reconstruction Software under Varying Capturing Conditions

    DEFF Research Database (Denmark)

    Nikolov, Ivan Adriyanov; Madsen, Claus B.

    2016-01-01

    Structure from Motion 3D reconstruction has become widely used in recent years in a number of fields such as industrial surface in- inspection, archeology, cultural heritage preservation and geomapping. A number of software solutions have been released using variations of this technique....... In this paper we analyse the state of the art of these software applications, by comparing the resultant 3D meshes qualitatively and quantitatively. We propose a number of testing scenarios using different lighting conditions, camera positions and image acquisition methods for the best in-depth analysis...... and discuss the results, the overall performance and the problems present in each software. We employ distance and roughness metrics for evaluating the final reconstruction results....

  11. The mesh-matching algorithm: an automatic 3D mesh generator for Finite element structures

    CERN Document Server

    Couteau, B; Lavallee, S; Payan, Yohan; Lavallee, St\\'{e}phane

    2000-01-01

    Several authors have employed Finite Element Analysis (FEA) for stress and strain analysis in orthopaedic biomechanics. Unfortunately, the use of three-dimensional models is time consuming and consequently the number of analysis to be performed is limited. The authors have investigated a new method allowing automatically 3D mesh generation for structures as complex as bone for example. This method called Mesh-Matching (M-M) algorithm generated automatically customized 3D meshes of bones from an already existing model. The M-M algorithm has been used to generate FE models of ten proximal human femora from an initial one which had been experimentally validated. The new meshes seemed to demonstrate satisfying results.

  12. Quantitative electron holographic tomography for the 3D characterisation of semiconductor device structures

    Energy Technology Data Exchange (ETDEWEB)

    Twitchett-Harrison, Alison C. [Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge, CB2 3QZ (United Kingdom)], E-mail: a.harrison@imperial.ac.uk; Yates, Timothy J.V.; Dunin-Borkowski, Rafal E.; Midgley, Paul A. [Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge, CB2 3QZ (United Kingdom)

    2008-10-15

    Electron tomography and electron holography experiments have been combined to investigate the 3D electrostatic potential distribution in semiconductor devices. The experimental procedure for the acquisition and data reconstruction of holographic tilt series of silicon p-n junction specimens is described. A quantitative analysis of the experimental results from specimens of two different thicknesses is presented, revealing the 3D electrostatic potential variations arising from the presence of surfaces and damage generated by focused ion beam (FIB) sample preparation. Close to bulk-like properties are measured in the centre of the tomographic reconstruction of the specimen, revealing higher electrically active dopant concentrations compared to the measurements obtained at the specimen surfaces. A comparison of the experimental results from the different thickness specimens has revealed a 'critical' thickness for this specimen preparation method of 350 nm that is required for this device structure to retain 'bulk'-like properties in the centre of the membrane.

  13. Loading mode dependent effective properties of octet-truss lattice structures using 3D-printing

    Science.gov (United States)

    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.

  14. 3D visualization of deformation structures and potential fluid pathways at the Grimsel Test Site

    Science.gov (United States)

    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

  15. Reconstruction of 3D structure using stochastic methods: morphology and transport properties

    Science.gov (United States)

    Karsanina, Marina; Gerke, Kirill; Čapek, Pavel; Vasilyev, Roman; Korost, Dmitry; Skvortsova, Elena

    2013-04-01

    One of the main factors defining numerous flow phenomena in rocks, soils and other porous media, including fluid and solute movements, is pore structure, e.g., pore sizes and their connectivity. Numerous numerical methods were developed to quantify single and multi-phase flow in such media on microscale. Among most popular ones are: 1) a wide range of finite difference/element/volume solutions of Navier-Stokes equations and its simplifications; 2) lattice-Boltzmann method; 3) pore-network models, among others. Each method has some advantages and shortcomings, so that different research teams usually utilize more than one, depending on the study case. Recent progress in 3D imaging of internal structure, e.g., X-ray tomography, FIB-SEM and confocal microscopy, made it possible to obtain digitized input pore parameters for such models, however, a trade-off between resolution and sample size is usually unavoidable. There are situations then only standard two-dimensional information of porous structure is known due to tomography high cost or resolution limitations. However, physical modeling on microscale requires 3D information. There are three main approaches to reconstruct (using 2D cut(s) or some other limited information/properties) porous media: 1) statistical methods (correlation functions and simulated annealing, multi-point statistics, entropy methods), 2) sequential methods (sphere or other granular packs) and 3) morphological methods. Stochastic reconstructions using correlation functions possess some important advantage - they provide a statistical description of the structure, which is known to have relationships with all physical properties. In addition, this method is more flexible for other applications to characterize porous media. Taking different 3D scans of natural and artificial porous materials (sandstones, soils, shales, ceramics) we choose some 2D cut/s as sources of input correlation functions. Based on different types of correlation functions

  16. 3D Geo-Structures Visualization Education Project (3dgeostructuresvis.ucdavis.edu)

    Science.gov (United States)

    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

  17. A 3D model describing the initial structure of an artificial hydrological catchment

    Science.gov (United States)

    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

  18. Large-scale Magnetic Structure Formation in 3D-MHD Turbulence

    CERN Document Server

    Malapaka, Shiva Kumar

    2013-01-01

    The inverse cascade of magnetic helicity in 3D-MHD turbulence is believed to be one of the processes responsible for large scale magnetic structure formation in astrophysical systems. In this work we present an exhaustive set of high resolution direct numerical simulations (DNS) of both forced and decaying 3D-MHD turbulence, to understand this structure formation process. It is first shown that an inverse cascade of magnetic helicity in small-scale driven turbulence does not necessarily generate coherent large-scale magnetic structures. The observed large-scale magnetic field, in this case, is severely perturbed by magnetic fluctuations generated by the small-scale forcing. In the decaying case, coherent large-scale structure form similar to those observed astronomically. Based on the numerical results the formation of large-scale magnetic structures in some astrophysical systems, is suggested to be the consequence of an initial forcing which imparts the necessary turbulent energy into the system, which, afte...

  19. A preliminary model for 3-D rheological structure of the lithosphere in North China

    Institute of Scientific and Technical Information of China (English)

    ZANG; Shaoxian; (臧绍先); LI; Chang; (李昶); NING; Jieyuan; (宁杰远); WEI; Rongqiang; (魏荣强)

    2003-01-01

    3-D structures of velocity and temperature are obtained using the dataof P-wave velocity and heat flow in North China (105°E-124°E, 30°N-42°N).Taking into account the effect of three main rheological mechanisms, namely friction sliding, brittle fracture and creep in the lithosphere, the 3-D structuresof the rheological strength and viscosity in the lithosphere in North China arecalculated. The results show that the strength and viscosity in the lithospherehave layering characteristics. Under the strain rate of 10-15 s-1, the upper part of the upper crust is in the brittle region and the lower part of the upper crust may be in the ductile region dominated by creep; the middle crust can be inthe brittle region dominated by brittle fracture, or the upper layer of brittlefracture and lower layer of creep ductile; the lower crust almost is in the creep region dominated by creep. In addition, the strength varies horizontally, which has a close relationship with geotectonics. The influence of velocity structure and temperature structure on the rheological structure is discussed and some suggestions to improve the study of lithospheric rheological structure are put forward.

  20. A Porosity Method to Describe Complex 3D-Structures Theory and Application to an Explosion

    Directory of Open Access Journals (Sweden)

    M.-F. Robbe

    2006-01-01

    Full Text Available A theoretical method was developed to be able to describe the influence of structures of complex shape on a transient fluid flow without meshing the structures. Structures are considered as solid pores inside the fluid and act as an obstacle for the flow. The method was specifically adapted to fast transient cases.The porosity method was applied to the simulation of a Hypothetical Core Disruptive Accident in a small-scale replica of a Liquid Metal Fast Breeder Reactor. A 2D-axisymmetrical simulation of the MARS test was performed with the EUROPLEXUS code. Whereas the central internal structures of the mock-up could be described with a classical shell model, the influence of the 3D peripheral structures was taken into account with the porosity method. 

  1. Algorithms for extraction of structural attitudes from 3D outcrop models

    Science.gov (United States)

    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.

  2. Modeling the Impact of Drizzle and 3D Cloud Structure on Remote Sensing of Effective Radius

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  4. Proof of Concept of Integrated Load Measurement in 3D Printed Structures.

    Science.gov (United States)

    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).

  5. Proof of Concept of Integrated Load Measurement in 3D Printed Structures

    Science.gov (United States)

    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

  6. Structural and property studies on metal–organic compounds with 3-D supramolecular network

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qi-Ying; Ma, Ke-Fang; Xiao, Hong-Ping; Li, Xin-Hua; Shi, Qian, E-mail: shiq@wzu.edu.cn

    2014-07-01

    Two carboxylato-bridged allomeric compounds, ([Cu{sub 2}(dbsa){sub 2}(hmt) (H{sub 2}O){sub 4}]{sub 1/2}·2H{sub 2}O){sub n} (1), ([Ni(dbsa)(H{sub 2}O){sub 2}]{sub 1/2}[Ni(dbsa)(hmt)(H{sub 2}O){sub 2}]{sub 1/2}·2H{sub 2}O){sub n} (2) (H{sub 2}dbsa=meso-2,3-dibromosuccinic acid, hmt=hexamethylenetetramine) have been synthesized and characterized by X-ray structral analyses. The metal ions have two kinds of coordination fashion in one unit, and bridged by carboxylate and hmt ligands along with weak interactions existing in the solid structure, forming a 3-D supramolecular network. Variable-temperature magnetic property studies reveal the existence of antiferromagnetic interactions in 1 and 2 with g=2.2, J{sub 1}=−3.5 cm{sup −1}, J{sub 2}=−2.8 cm{sup −1} for 1, and g=2.1, J=−3.5 cm{sup −1} for 2. - Graphical abstract: Variable-temperature magnetic property studies of two 3-D supramolecular compounds reveal the existence of antiferromagnetic interactions between the metal ions, through the effective super-exchange media. - Highlights: • Two 3-D allomeric Cu(II) and Ni(II) metal–organic compounds have been prepared. • The 3-D networks were constructed by coordination bonds, weak interactions and hydrogen bond interactions. • There are antiferromagnetic super-exchange interactions between the metal ions.

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

    Science.gov (United States)

    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 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 areas. Our final 3D Earth model is tested using forward wave simulations of earthquakes (M ≥ 3.7) that were not used during the inversion process. The comparison of observed and synthetic seismograms, calculated by initial and final models, showed significant

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

    Science.gov (United States)

    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

  9. GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.

    Science.gov (United States)

    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/.

  10. Characterization of Power Absorption Response of Periodic 3D Structures to Partially Coherent Fields

    CERN Document Server

    Tihon, Denis; Thomas, Christopher N; Craeye, Christophe

    2016-01-01

    In many applications of absorbing structures it is important to understand their spatial response to incident fields, for example in thermal solar panels, bolometric imaging and controlling radiative heat transfer. In practice, the illuminating field often originates from thermal sources and is only spatially partially coherent when reaching the absorbing device. In this paper, we present a method to fully characterize the way a structure can absorb such partially coherent fields. The method is presented for any 3D material and accounts for the partial coherence and partial polarization of the incident light. This characterization can be achieved numerically using simulation results or experimentally using the Energy Absorption Interferometry (EAI) that has been described previously in the literature. The absorbing structure is characterized through a set of absorbing functions, onto which any partially coherent field can be projected. This set is compact for any structure of finite extent and the absorbing f...

  11. Architectural protein subclasses shape 3-D organization of genomes during lineage commitment

    Science.gov (United States)

    Phillips-Cremins, Jennifer E.; Sauria, Michael E. G.; Sanyal, Amartya; Gerasimova, Tatiana I.; Lajoie, Bryan R.; Bell, Joshua S. K.; Ong, Chin-Tong; Hookway, Tracy A.; Guo, Changying; Sun, Yuhua; Bland, Michael J.; Wagstaff, William; Dalton, Stephen; McDevitt, Todd C.; Sen, Ranjan; Dekker, Job; Taylor, James; Corces, Victor G.

    2013-01-01

    Summary Understanding the topological configurations of chromatin may reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development. Here we generate high-resolution architecture maps across seven genomic loci in embryonic stem cells and neural progenitor cells. We observe a hierarchy of 3-D interactions that undergo marked reorganization at the sub-Mb scale during differentiation. Distinct combinations of CTCF, Mediator, and cohesin show widespread enrichment in looping interactions at different length scales. CTCF/cohesin anchor long-range constitutive interactions that form the topological basis for invariant sub-domains. Conversely, Mediator/cohesin together with pioneer factors bridge shortrange enhancer-promoter interactions within and between larger sub-domains. Knockdown of Smc1 or Med12 in ES cells results in disruption of spatial architecture and down-regulation of genes found in cohesin-mediated interactions. We conclude that cell type-specific chromatin organization occurs at the sub-Mb scale and that architectural proteins shape the genome in hierarchical length scales. PMID:23706625

  12. Grating-based X-ray tomography of 3D food structures

    DEFF Research Database (Denmark)

    Miklos, Rikke; Nielsen, Mikkel Schou; Einarsdottir, Hildur;

    2016-01-01

    A novel grating based X-ray phase-contrast tomographic method has been used to study how partly substitution of meat proteins with two different types of soy proteins affect the structure of the formed protein gel in meat emulsions. The measurements were performed at the Swiss synchrotron radiati...

  13. Structure Theory for Extended Kepler-Coulomb 3D Classical Superintegrable Systems

    Directory of Open Access Journals (Sweden)

    Ernie G. Kalnins

    2012-06-01

    Full Text Available The classical Kepler-Coulomb system in 3 dimensions is well known to be 2nd order superintegrable, with a symmetry algebra that closes polynomially under Poisson brackets. This polynomial closure is typical for 2nd order superintegrable systems in 2D and for 2nd order systems in 3D with nondegenerate (4-parameter potentials. However the degenerate 3-parameter potential for the 3D extended Kepler-Coulomb system (also 2nd order superintegrable is an exception, as its quadratic symmetry algebra doesn't close polynomially. The 3D 4-parameter potential for the extended Kepler-Coulomb system is not even 2nd order superintegrable. However, Verrier and Evans (2008 showed it was 4th order superintegrable, and Tanoudis and Daskaloyannis (2011 showed that in the quantum case, if a second 4th order symmetry is added to the generators, the double commutators in the symmetry algebra close polynomially. Here, based on the Tremblay, Turbiner and Winternitz construction, we consider an infinite class of classical extended Kepler-Coulomb 3- and 4-parameter systems indexed by a pair of rational numbers (k_1,k_2 and reducing to the usual systems when k_1=k_2=1. We show these systems to be superintegrable of arbitrarily high order and work out explicitly the structure of the symmetry algebras determined by the 5 basis generators we have constructed. We demonstrate that the symmetry algebras close rationally; only for systems admitting extra discrete symmetries is polynomial closure achieved. Underlying the structure theory is the existence of raising and lowering constants of the motion, not themselves polynomials in the momenta, that can be employed to construct the polynomial symmetries and their structure relations.

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

    Science.gov (United States)

    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.

  15. Spectral element method for band-structure calculations of 3D phononic crystals

    Science.gov (United States)

    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.

  16. Cross modality registration of video and magnetic tracker data for 3D appearance and structure modeling

    Science.gov (United States)

    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. Interpolation/penalization applied for strength design of 3D thermoelastic structures

    DEFF Research Database (Denmark)

    Pedersen, Pauli; Pedersen, Niels L.

    2012-01-01

    illustrated with examples. In compliance minimization for thermoelastic structures it may be advantageous to decrease the total volume, but for strength maximization it is argued to keep the total permissible volume. Linear interpolation (no penalization) may to a certain extent be argued for 2D thickness...... optimized designs, but for 3D design problems interpolation must be included and not only from the penalization point of view to obtain 0-1 designs. Three interpolation types are presented in a uniform manner, including the well known one parameter penalizations, named SIMP and RAMP. An alternative two...

  18. Active optical system for advanced 3D surface structuring by laser remelting

    Science.gov (United States)

    Pütsch, O.; Temmler, A.; Stollenwerk, J.; Willenborg, E.; Loosen, P.

    2015-03-01

    Structuring by laser remelting enables completely new possibilities for designing surfaces since material is redistributed but not wasted. In addition to technological advantages, cost and time benefits yield from shortened process times, the avoidance of harmful chemicals and the elimination of subsequent finishing steps such as cleaning and polishing. The functional principle requires a completely new optical machine technology that maintains the spatial and temporal superposition and manipulation of three different laser beams emitted from two laser sources of different wavelength. The optical system has already been developed and demonstrated for the processing of flat samples of hot and cold working steel. However, since particularly the structuring of 3D-injection molds represents an application example of high innovation potential, the optical system has to take into account the elliptical beam geometry that occurs when the laser beams irradiate a curved surface. To take full advantage of structuring by remelting for the processing of 3D surfaces, additional optical functionality, called EPS (elliptical pre-shaping) has to be integrated into the existing set-up. The development of the beam shaping devices not only requires the analysis of the mechanisms of the beam projection but also a suitable optical design. Both aspects are discussed in this paper.

  19. Photopolymerization of 3D conductive polypyrrole structures via digital light processing

    Science.gov (United States)

    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. Robotic extrusion processes for direct ink writing of 3D conductive polyaniline structures

    Science.gov (United States)

    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.

  1. Metallic Material Image Segmentation by using 3D Grain Structure Consistency and Intra/Inter-Grain Model Information

    Science.gov (United States)

    2015-01-05

    warping). Often, costly and precisely calibrated special hardware such as stereo cameras, laser scanners , etc. are used to infer the 3D model of the...AFRL-OSR-VA-TR-2015-0015 Metallic Material Image Segmentation by using 3D Grain Structure Consistency Song Wang SOUTH CAROLINA RESEARCH FOUNDATION...Form 298 (Re . 8-98) v Prescribed by ANSI Std. Z39.18 AFOSR Final Performance Report Project Title: Metallic Material Image Segmentation by using 3D

  2. 罗非鱼源无乳链球菌S-核糖基高半胱氨酸酶基因(luxS)的克隆及其推导蛋白的三维结构预测%Cloning of Streptococcus agalactiae luxS gene from tilapia and 3D structure prediction of deduced protein

    Institute of Scientific and Technical Information of China (English)

    马艳平; 李嘉彬; 郝乐; 刘振兴; 冯国清; 周结珊; 柯浩

    2013-01-01

    We have amplified, cloned and determined the sequence of Streptococcus agalactiae luxS gene from Tilapia sp. by PCR. The characteristics of the deduced luxS protein were predicted by ExPAsy software; the 3D structures of luxS and the deduced protein were established and analyzed by SWISS-Model and SwisS-PDBviewer software, respectively. The results indicate that the deduced luxS protein contains conserved active center and Zn2+ binding site, which may affect biofilm formation and regulate virulence factor. The Ramachandram plot shows that the structure of modeled luxS protein is reasonable.%利用PCR技术对罗非鱼源无乳链球菌(Streptococcus agalactiae)S-核糖基高半胱氨酸酶(luxS)基因全长DNA进行了扩增、克隆和序列测定,采用ExPAsy软件包预测了推导蛋白的特性,利用SwisS-Model服务器建立了luxS 三维结构,利用SwisS-PDBviewer软件进行了蛋白质三维结构的分析.预测结果显示,罗非鱼源无乳链球菌luxS推导蛋白包括保守的酶活性中心和锌结合位点,具有影响生物被膜形成、毒力因子调控等特性功能;经拉氏构象图(Ramachandran plot)分析,所构建的luxS的空间结构合理.

  3. Procyon: Constraining Its Temperature Structure with High-Precision Interferometry and 3-D Model Atmospheres

    Science.gov (United States)

    Aufdenberg, J. P.; Ludwig, H.-G.; Kervella, P.

    2004-12-01

    We have fit synthetic visibilities from 3-D (CO5BOLD + PHOENIX) and 1-D (PHOENIX, ATLAS12) model stellar atmospheres for Procyon (F5 IV) to high-precision interferometric data from the VINCI instrument at the VLT Interferometer (K-band) and from the Mark III interferometer (500 nm, 800 nm). These data provide a test of theoretical wavelength-dependent limb-darkening predictions, and therefore Procyon's atmospheric temperature structure. Earlier work (Allende Prieto et al. 2002 ApJ 567, 544) has shown that the temperature structure from a spatially and temporally averaged 3-D hydrodynamical model produces significantly less limb darkening at 500 nm relative to the temperature structure from a 1-D MARCS model atmosphere which uses a mixing-length approximation for convective flux transport. Our direct fits to the interferometric data confirm this prediction, however we find that not all 1-D models fail to reproduce the observations. The key to matching the interferometric data is a shallower temperature gradient than provided by the standard 1-D mixing-length approximation. We find that in addition to our best fitting 3-D hydrodynamical model, a 1-D ATLAS12 model, with an additional free parameter for ``approximate overshooting'', provides the required temperature gradient. We estimate that an interferometric precision better than 0.1% will be required to distinguish between the 3-D model and the ATLAS12 model. This overshooting approximation has been shown to match Solar limb-darkening observations reasonably well (Castelli et al 1997 A&A 324, 432), however published work since using Strömgren photometry of solar-type stars has cast doubt on the importance of overshooting. We have also compared synthetic spectral energy distributions for Procyon to ultraviolet, optical and near-infrared spectrophotometry and find differences from comparisons to Strömgren photometry alone. This work was performed in part contract with the Jet Propulsion Laboratory (JPL) funded by

  4. 3D modeling method for computer animate based on modified weak structured light method

    Science.gov (United States)

    Xiong, Hanwei; Pan, Ming; Zhang, Xiangwei

    2010-11-01

    A simple and affordable 3D scanner is designed in this paper. Three-dimensional digital models are playing an increasingly important role in many fields, such as computer animate, industrial design, artistic design and heritage conservation. For many complex shapes, optical measurement systems are indispensable to acquiring the 3D information. In the field of computer animate, such an optical measurement device is too expensive to be widely adopted, and on the other hand, the precision is not as critical a factor in that situation. In this paper, a new cheap 3D measurement system is implemented based on modified weak structured light, using only a video camera, a light source and a straight stick rotating on a fixed axis. For an ordinary weak structured light configuration, one or two reference planes are required, and the shadows on these planes must be tracked in the scanning process, which destroy the convenience of this method. In the modified system, reference planes are unnecessary, and size range of the scanned objects is expanded widely. A new calibration procedure is also realized for the proposed method, and points cloud is obtained by analyzing the shadow strips on the object. A two-stage ICP algorithm is used to merge the points cloud from different viewpoints to get a full description of the object, and after a series of operations, a NURBS surface model is generated in the end. A complex toy bear is used to verify the efficiency of the method, and errors range from 0.7783mm to 1.4326mm comparing with the ground truth measurement.

  5. Correlative nanoscale 3D imaging of structure and composition in extended objects.

    Directory of Open Access Journals (Sweden)

    Feng Xu

    Full Text Available 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.

  6. Smart three-dimensional lightweight structure triggered from a thin composite sheet via 3D printing technique.

    Science.gov (United States)

    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.

  7. Nanoimprint of a 3D structure on an optical fiber for light wavefront manipulation

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  9. Nanoimprint of a 3D structure on an optical fiber for light wavefront manipulation.

    Science.gov (United States)

    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. Nanoimprint of a 3D structure on an optical fiber for light wavefront manipulation

    CERN Document Server

    Calafiore, Giuseppe; Allen, Frances I; Dhuey, Scott; Sassolini, Simone; Wong, Edward; Lum, Paul; Munechika, Keiko; Cabrini, Stefano

    2016-01-01

    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 excellent lithographic capabilities of the proposed approach as well as the desired optical performance of the imprinted structure. The inexpensive solution presented here should enabl...

  11. The 3D structure of an active region filament as extrapolated from photospheric and chromospheric observations

    CERN Document Server

    Chaouche, L Yelles; Pillet, V Martínez; Moreno-Insertis, F

    2012-01-01

    The 3D structure of an active region (AR) filament is studied using nonlinear force-free field (NLFFF) extrapolations based on simultaneous observations at a photospheric and a chromospheric height. To that end, we used the Si I 10827 \\AA\\ line and the He I 10830 \\AA\\ triplet obtained with the Tenerife Infrared Polarimeter (TIP) at the VTT (Tenerife). The two extrapolations have been carried out independently from each other and their respective spatial domains overlap in a considerable height range. This opens up new possibilities for diagnostics in addition to the usual ones obtained through a single extrapolation from, typically, a photospheric layer. Among those possibilities, this method allows the determination of an average formation height of the He I 10830 \\AA\\ signal of \\approx 2 Mm above the surface of the sun. It allows, as well, to cross-check the obtained 3D magnetic structures in view of verifying a possible deviation from the force- free condition especially at the photosphere. The extrapolati...

  12. Fabrication of 3D nanostructures by multidirectional UV lithography and predictive structural modeling

    Science.gov (United States)

    Kim, Jungkwun; Kim, Cheolbok; Allen, Mark G.; ‘YK' Yoon, Yong-Kyu

    2015-02-01

    This paper presents the fabrication and modeling of three-dimensional (3D) nanostructures by automated multidirectional ultraviolet (UV) lithography, which is a fast, cost-effective, manufacturable fabrication method. Multidirectional UV exposure is performed using a static UV light source equipped with a tilt-rotational substrate holder. A glass substrate with a nanopatterned chrome layer is utilized as both a photomask and a substrate, for which a backside UV exposure scheme is used. For the analytical modeling of the shape of fabricated nanostructures, UV exposure dosage, diffraction and refraction effects, and absorption rate are taken into account. For more accurate process predictive models, a commercially available multiphysics simulation tool is used. The structural shapes predicted from analytical calculation and simulation are compared with the fabricated ones for which various 3D nanoscale test structures are fabricated such as an inclined nanopillar array and a vertical triangular slab. Also, nanostructures with multiple heights are successfully implemented from single layer photoresist by controlling the UV exposure dosage and tilt angles. A tripod embedded horn and a triangular-slab embedded horn are demonstrated.

  13. Orthogonal Range Reporting: Query Lower Bounds, Optimal Structures in 3-d, and Higher Dimensional Improvements

    DEFF Research Database (Denmark)

    Afshani, Peyman; Arge, Lars Allan; Larsen, Kasper Dalgaard

    2010-01-01

    ⌋--1). This is the first known non-trivial higher dimensional orthogonal range reporting query lower bound and it has two important implications. First, it shows that the query bound increases with dimension. Second, in combination with our upper bounds it shows that the optimal query bound increases from Θ(log n + k......Orthogonal range reporting is the problem of storing a set of n points in d-dimensional space, such that the k points in an axis-orthogonal query box can be reported efficiently. While the 2-d version of the problem was completely characterized in the pointer machine model more than two decades ago......, this is not the case in higher dimensions. In this paper we provide a space optimal pointer machine data structure for 3-d orthogonal range reporting that answers queries in O(log n + k) time. Thus we settle the complexity of the problem in 3-d. We use this result to obtain improved structures in higher dimensions...

  14. 3D-Printed Broadband Dielectric Tube Terahertz Waveguide with Anti-Reflection Structure

    Science.gov (United States)

    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.

  15. Observed 3D Structure, Generation, and Dissipation of Oceanic Mesoscale Eddies in the South China Sea

    Science.gov (United States)

    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.

  16. Coupled structure-from-motion and 3D symmetry detection for urban facades

    KAUST Repository

    Ceylan, Duygu

    2014-01-01

    Repeated structures are ubiquitous in urban facades. Such repetitions lead to ambiguity in establishing correspondences across sets of unordered images. A decoupled structure-from-motion reconstruction followed by symmetry detection often produces errors: outputs are either noisy and incomplete, or even worse, appear to be valid but actually have a wrong number of repeated elements.We present an optimization framework for extracting repeated elements in images of urban facades, while simultaneously calibrating the input images and recovering the 3D scene geometry using a graph-based global analysis. We evaluate the robustness of the proposed scheme on a range of challenging examples containing widespread repetitions and nondistinctive features. These image sets are common but cannot be handled well with state-of-the-art methods. We show that the recovered symmetry information along with the 3D geometry enables a range of novel image editing operations that maintain consistency across the images. © 2014 ACM 0730-0301/2014/01-ART3 15.00.

  17. Measuring the 3D shape of high temperature objects using blue sinusoidal structured light

    Science.gov (United States)

    Zhao, Xianling; Liu, Jiansheng; Zhang, Huayu; Wu, Yingchun

    2015-12-01

    The visible light radiated by some high temperature objects (less than 1200 °C) almost lies in the red and infrared waves. It will interfere with structured light projected on a forging surface if phase measurement profilometry (PMP) is used to measure the shapes of objects. In order to obtain a clear deformed pattern image, a 3D measurement method based on blue sinusoidal structured light is proposed in this present work. Moreover, a method for filtering deformed pattern images is presented for correction of the unwrapping phase. Blue sinusoidal phase-shifting fringe pattern images are projected on the surface by a digital light processing (DLP) projector, and then the deformed patterns are captured by a 3-CCD camera. The deformed pattern images are separated into R, G and B color components by the software. The B color images filtered by a low-pass filter are used to calculate the fringe order. Consequently, the 3D shape of a high temperature object is obtained by the unwrapping phase and the calibration parameter matrixes of the DLP projector and 3-CCD camera. The experimental results show that the unwrapping phase is completely corrected with the filtering method by removing the high frequency noise from the first harmonic of the B color images. The measurement system can complete the measurement in a few seconds with a relative error of less than 1 : 1000.

  18. 3D-Printed Broadband Dielectric Tube Terahertz Waveguide with Anti-Reflection Structure

    Science.gov (United States)

    Vogt, Dominik Walter; Leonhardt, Rainer

    2016-07-01

    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. First-principles study on structural stability of 3d transition metal alloying magnesium hydride

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A first-principles plane-wave pseudopotential method based on the density functional theory was used to investigate the energy and electronic structure of magnesium hydride (MgH2) alloyed by 3d transition metal elements. Through calculations of the negative heat formation of magnesium hydride alloyed by X (X denotes 3d transition metal) element, it is found that when a little X (not including Sc) dissolves into magnesium hydride, the structural stability of alloying systems decreases, which indicates that the dehydrogenation properties of MgH2 can be improved. After comparing the densities of states(DOS) and the charge distribution of MgH2 with or without X alloying, it is found that the improvement for the dehydrogenation properties of MgH2 alloyed by X attributes to the fact that the weakened bonding between magnesium and hydrogen is caused by the stronger interactions between X (not including Cu) and hydrogen. The calculation results of the improvement for the dehydrogenation properties of MgH2-X (X=Ti, V, Mn, Fe, Co,Ni, Cu) systems are in agreement with the experimental results. Hence, the dehydrogenation properties of MgH2 are expected to be improved by addition of Cr, Zn alloying elements.

  20. Curvilinear Immersed Boundary Method for Simulating Fluid Structure Interaction with Complex 3D Rigid Bodies.

    Science.gov (United States)

    Borazjani, Iman; Ge, Liang; Sotiropoulos, Fotis

    2008-08-10

    The sharp-interface CURVIB approach of Ge and Sotiropoulos [L. Ge, F. Sotiropoulos, A Numerical Method for Solving the 3D Unsteady Incompressible Navier-Stokes Equations in Curvilinear Domains with Complex Immersed Boundaries, Journal of Computational Physics 225 (2007) 1782-1809] is extended to simulate fluid structure interaction (FSI) problems involving complex 3D rigid bodies undergoing large structural displacements. The FSI solver adopts the partitioned FSI solution approach and both loose and strong coupling strategies are implemented. The interfaces between immersed bodies and the fluid are discretized with a Lagrangian grid and tracked with an explicit front-tracking approach. An efficient ray-tracing algorithm is developed to quickly identify the relationship between the background grid and the moving bodies. Numerical experiments are carried out for two FSI problems: vortex induced vibration of elastically mounted cylinders and flow through a bileaflet mechanical heart valve at physiologic conditions. For both cases the computed results are in excellent agreement with benchmark simulations and experimental measurements. The numerical experiments suggest that both the properties of the structure (mass, geometry) and the local flow conditions can play an important role in determining the stability of the FSI algorithm. Under certain conditions unconditionally unstable iteration schemes result even when strong coupling FSI is employed. For such cases, however, combining the strong-coupling iteration with under-relaxation in conjunction with the Aitken's acceleration technique is shown to effectively resolve the stability problems. A theoretical analysis is presented to explain the findings of the numerical experiments. It is shown that the ratio of the added mass to the mass of the structure as well as the sign of the local time rate of change of the force or moment imparted on the structure by the fluid determine the stability and convergence of the FSI

  1. 2D and 3D reconstruction and geomechanical characterization of kilometre-scale complex folded structures

    Science.gov (United States)

    Zanchi, Andrea; Agliardi, Federico; Crosta, Giovanni B.; Villa, Alberto; Bistacchi, Andrea; Iudica, Gaetano

    2015-04-01

    points based on their normal vector orientations to identify and map bedding and fractures. Combined stereographic analysis of bedding orientations and use of filters allowed the quantification of fold hinge and limb geometries and their 3D reconstruction in GOCAD. Fracture patterns derived from points clouds and field data allowed identifying different geomechanical domains associated to the folded structure. Our results encourage the integrated analysis of high-resolution point clouds and detailed structural and geomechanical field data as inputs to the 3D geometrical reconstruction and modelling of folded rock masses. Validation of virtual outcrop reconstructions through a comparison with field structural measurements suggests that very precise geometrical constraints can be obtained by TLS on geological bodies with complex geometrical features. However, additional constraints on TLS survey layout design are required to optimise the reconstruction and distinction of specific structural elements associated to folding as bedding and fold-related fracture systems.

  2. Structural Color for Additive Manufacturing: 3D-Printed Photonic Crystals from Block Copolymers.

    Science.gov (United States)

    Boyle, Bret M; French, Tracy A; Pearson, Ryan M; McCarthy, Blaine G; Miyake, Garret M

    2017-03-28

    The incorporation of structural color into 3D printed parts is reported, presenting an alternative to the need for pigments or dyes for colored parts produced through additive manufacturing. Thermoplastic build materials composed of dendritic block copolymers were designed, synthesized, and used to additively manufacture plastic parts exhibiting structural color. The reflection properties of the photonic crystals arise from the periodic nanostructure formed through block copolymer self-assembly during polymer processing. The wavelength of reflected light could be tuned across the visible spectrum by synthetically controlling the block copolymer molecular weight and manufacture parts that reflected violet, green, or orange light with the capacity to serve as selective optical filters and light guides.

  3. An automatic 3D CAD model errors detection method of aircraft structural part for NC machining

    Directory of Open Access Journals (Sweden)

    Bo Huang

    2015-10-01

    Full Text Available Feature-based NC machining, which requires high quality of 3D CAD model, is widely used in machining aircraft structural part. However, there has been little research on how to automatically detect the CAD model errors. As a result, the user has to manually check the errors with great effort before NC programming. This paper proposes an automatic CAD model errors detection approach for aircraft structural part. First, the base faces are identified based on the reference directions corresponding to machining coordinate systems. Then, the CAD models are partitioned into multiple local regions based on the base faces. Finally, the CAD model error types are evaluated based on the heuristic rules. A prototype system based on CATIA has been developed to verify the effectiveness of the proposed approach.

  4. 3D Brain Tumors and Internal Brain Structures Segmentation in MR Images

    Directory of Open Access Journals (Sweden)

    P.NARENDRAN

    2012-02-01

    Full Text Available The main topic of this paper is to segment brain tumors, their components (edema and necrosis and internal structures of the brain in 3D MR images. For tumor segmentation we propose a framework that is a combination of region-based and boundary-based paradigms. In this framework, segment the brain using a method adapted for pathological cases and extract some global information on the tumor by symmetry based histogram analysis. We propose a new and original method that combines region and boundary information in two phases: initialization and refinement. The method relies on symmetry-based histogram analysis. The initial segmentation of the tumor is refined relying on boundary information of the image. We use a deformable model which is again constrained by the fused spatial relations of the structure. The method was also evaluated on 10 contrast enhanced T1-weighted images to segment the ventricles, caudate nucleus and thalamus.

  5. Pore - to - Core Modeling of Soil Organic Matter Decomposition in 3D Soil Structures

    Science.gov (United States)

    Falconer, R. E.; Battaia, G.; Baveye, P.; Otten, W.

    2013-12-01

    There is a growing body of literature supporting the need for microbial contributions to be considered explicitly in carbon-climate models. There is also overwhelming evidence that physical protection within aggregates can play a significant role in organic matter dynamics. Yet current models of soil organic matter dynamics divide soil organic matter into conceptual pools with distinct turnover times, assuming that a combination of biochemical and physical properties control decay without explicit description. Albeit robust in their application, such models are not capable to account for changes in soil structure or microbial populations, or accurately predict the effect of wetness or priming. A spatially explicit model is presented that accounts for microbial dynamics and physical processes, permitting consideration of the heterogeneity of the physical and chemical microenvironments at scales relevant for microbes. Exemplified for fungi, we investigate how micro-scale processes manifest at the core scale with particular emphasis on evolution of CO2 and biomass distribution. The microbial model is based upon previous (Falconer et al, 2012) and includes the following processes: uptake, translocation, recycling, enzyme production, growth, spread and respiration. The model is parameterised through a combination of literature data and parameter estimation (Cazelles et al., 2012).The Carbon model comprises two pools, particulate organic matter which through enzymatic activity is converted into dissolved organic matter. The microbial and carbon dynamics occur within a 3D soil structure obtained by X-ray CT. We show that CO2 is affected not only by the amount of Carbon in the soil but also by microbial dynamics, soil structure and the spatial distribution of OM. The same amount of OM can result in substantially different respiration rates, with surprisingly more CO2 with increased clustering of OM. We can explain this from the colony dynamics, production of enzymes and

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

    Science.gov (United States)

    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

  7. MULTIPARAMETER MEASUREMENT FOR RACEWAY GROOVE OF BEARING BASED ON 3D RECONSTRUCTION WITH DIGITAL STRUCTURED LIGHT

    Institute of Scientific and Technical Information of China (English)

    He Tao; Zhong Ming; Li Wei; Zhong Yuning; Shi Tielin

    2005-01-01

    A fast 3D reconstruction method based on structured light to measure various parameters of the raceway groove is presented. Digital parallel grating stripes distributed with sine density are projected onto the raceway groove by a DLP projector, and distorting of stripes is happened on the raceway. Simultaneously, aided by three-step phase-shifting approach, three images covered by different stripes are obtained by a high-resolution CCD camera at the same location, thus a more accuracy local topography can be obtained. And then the bearing is rotated on a high precision computer controlled rotational stage. Three images are also obtained as the former step at next planned location triggered by the motor. After one cycle, all images information is combined through the mosaics. As a result, the 3D information of raceway groove can be gained. Not only geometric properties but also surface flaws can be extracted by software. A preliminary hardware system has been built, with which some geometric parameters have been extracted from reconstructed local topography.

  8. A flexible 3D vision system based on structured light for in-line product inspection

    Science.gov (United States)

    Skotheim, Øystein; Nygaard, Jens Olav; Thielemann, Jens; Vollset, Thor

    2008-02-01

    A flexible and highly configurable 3D vision system targeted for in-line product inspection is presented. The system includes a low cost 3D camera based on structured light and a set of flexible software tools that automate the measurement process. The specification of the measurement tasks is done in a first manual step. The user selects regions of the point cloud to analyze and specifies primitives to be characterized within these regions. After all measurement tasks have been specified, measurements can be carried out on successive parts automatically and without supervision. As a test case, a measurement cell for inspection of a V-shaped car component has been developed. The car component consists of two steel tubes attached to a central hub. Each of the tubes has an additional bushing clamped to its end. A measurement is performed in a few seconds and results in an ordered point cloud with 1.2 million points. The software is configured to fit cylinders to each of the steel tubes as well as to the inside of the bushings of the car part. The size, position and orientation of the fitted cylinders allow us to measure and verify a series of dimensions specified on the CAD drawing of the component with sub-millimetre accuracy.

  9. ISRU 3D printing for habitats and structures on the Moon

    Science.gov (United States)

    Cowley, Aidan

    2016-07-01

    In-situ-resource utilisation (ISRU) in combination with 3D printing may evolve into a key technology for future exploration. Setting up a lunar facility could be made much simpler by using additive manufacturing techniques to build elements from local materials - this would drastically reduce mission mass requirements and act as an excellent demonstrator for ISRU on other planetary bodies. Fabricating structures and components using Lunar regolith is an area of interest for ESA, as evidenced by past successful General Studies Program (GSP) and ongoing technology development studies. In this talk we detail a number of projects looking into the behavior of Lunar regolith simulants, their compositional variants and approaches to sintering such material that are under-way involving EAC, ESTEC and DLR. We report on early studies into utilizing conventional thermal sintering approaches of simulants as well as microwave sintering of these compositions. Both techniques are candidates for developing a 3D printing methodology using Lunar regolith. It is known that the differences in microwave effects between the actual lunar soil and lunar simulants can be readily ascribed to the presence of nanophase metallic Fe, native to Lunar regolith but lacking in simulants. In compostions of simulant with increased Illmenite (FeTiO3) concentrations, we observe improved regolith response to microwave heating, and the readily achieved formation of a glassy melt in ambient atmosphere. The improved response relative to untreated simulant is likely owing to the increased Fe content in the powder mix.

  10. Skeletal camera network embedded structure-from-motion for 3D scene reconstruction from UAV images

    Science.gov (United States)

    Xu, Zhihua; Wu, Lixin; Gerke, Markus; Wang, Ran; Yang, Huachao

    2016-11-01

    Structure-from-Motion (SfM) techniques have been widely used for 3D scene reconstruction from multi-view images. However, due to the large computational costs of SfM methods there is a major challenge in processing highly overlapping images, e.g. images from unmanned aerial vehicles (UAV). This paper embeds a novel skeletal camera network (SCN) into SfM to enable efficient 3D scene reconstruction from a large set of UAV images. First, the flight control data are used within a weighted graph to construct a topologically connected camera network (TCN) to determine the spatial connections between UAV images. Second, the TCN is refined using a novel hierarchical degree bounded maximum spanning tree to generate a SCN, which contains a subset of edges from the TCN and ensures that each image is involved in at least a 3-view configuration. Third, the SCN is embedded into the SfM to produce a novel SCN-SfM method, which allows performing tie-point matching only for the actually connected image pairs. The proposed method was applied in three experiments with images from two fixed-wing UAVs and an octocopter UAV, respectively. In addition, the SCN-SfM method was compared to three other methods for image connectivity determination. The comparison shows a significant reduction in the number of matched images if our method is used, which leads to less computational costs. At the same time the achieved scene completeness and geometric accuracy are comparable.

  11. 3D-quantitative structure-activity relationship study of organophosphate compounds

    Institute of Scientific and Technical Information of China (English)

    ZHAO Jinsong; WANG Bin; DAI Zhaoxia; WANG Xiaodong; KONG Lingren; WANG Liansheng

    2004-01-01

    The biological effects of most organophosphate compounds (OP) are arising by inhibition of the enzyme acetylcholinesterase (AChE). The 3D-quantitative structure-activity relationship (3D-QSAR) on the acute toxicity to housefly (Musca nobulo L.) of 35 dialkyl phenyl phosphate compounds are studied by using comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) methods, and the reaction mechanism between the OP and the AChE are discussed. In contrast to classical QSAR methods, CoMFA and CoMSIA, especially the combination of both approaches, can give more comprehensive and accurate perspectives on the mechanism of the reaction between OP and AChE. The results show that the length of alkyl, and the electronegative of substituent on phenyl of OP have significant effects on the AChE activity, whereas, the hydrophobicity of OP has little influence. The steric and electronic properties of OP have a dominant influence on the reaction between OP and AChE.

  12. 3D building reconstruction from ALS data using unambiguous decomposition into elementary structures

    Science.gov (United States)

    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%.

  13. 3D-Mapping of Dolomitized Structures in Lower Cambrian Phosphorites

    Science.gov (United States)

    Hippler, Dorothee; Stammeier, Jessica A.; Brunner, Roland; Rosc, Jördis; Franz, Gerhard; Dietzel, Martin

    2016-04-01

    Dolomitization is a widespread phenomenon in ancient sedimentary rocks, particularly close to the Precambrian-Cambrian boundary. Dolomite can form in synsedimentary or hydrothermal environments, preferentially via the replacement of solid carbonate precursor phases. Synsedimentary dolomite formation is often associated with microbial activity, such as bacterial sulfate reduction or methanogenesis. In this study, we investigate dolomitic phosphorites from the Lowermost Cambrian Tal Group, Mussoori Syncline, Lesser Himalaya, India, using micro-CT 3D-mapping, in order to unravel the complex diagenetic history of the rocks. The selected sample shows alternating layering of phosphatic mudstones and sparitic dolostone, in which brecciated layers of phosphorite or phosphatic mudstones are immersed in a dolomite-rich matrix. Lamination occurs on a sub-millimetre scale, with lamination sometimes wavy to crinkly. This fabric is interpreted as former microbial mats, providing the environment for early diagenetic phosphatization. Preliminary electron backscatter imaging with scanning microscopy revealed that dolomite crystals often occur in spherical to ellipsoidal structures, typically with a high porosity. This dolomite is associated with botryoidal apatite, organic matter and small amounts of calcite. Micro-CT 3D-mappings reveal that dolomite structures are cigar-shaped, elongated and up to 600 μm long. They are further arranged in a Mikado-like oriented framework spanning a layer thickness of a few millimetres. Analyses of ambient pore space, with similar elongated outlines and filled with organic matter, suggest a potential coherence of ambient pore space and shape of the dolomite structures. Allowing for other associated mineral phases, such as pyrite and silicates, and their spatial distribution, the present approach can be used to unravel distinct diagenetic reaction pathways, and might thus constrain the proxy potential of these Lower Cambrian dolomitic phosphorites

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

    Science.gov (United States)

    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

  15. Aerosol based direct-write micro-additive fabrication method for sub-mm 3D metal-dielectric structures

    Science.gov (United States)

    Rahman, Taibur; Renaud, Luke; Heo, Deuk; Renn, Michael; Panat, Rahul

    2015-10-01

    The fabrication of 3D metal-dielectric structures at sub-mm length scale is highly important in order to realize low-loss passives and GHz wavelength antennas with applications in wearable and Internet-of-Things (IoT) devices. The inherent 2D nature of lithographic processes severely limits the available manufacturing routes to fabricate 3D structures. Further, the lithographic processes are subtractive and require the use of environmentally harmful chemicals. In this letter, we demonstrate an additive manufacturing method to fabricate 3D metal-dielectric structures at sub-mm length scale. A UV curable dielectric is dispensed from an Aerosol Jet system at 10-100 µm length scale and instantaneously cured to build complex 3D shapes at a length scale  <1 mm. A metal nanoparticle ink is then dispensed over the 3D dielectric using a combination of jetting action and tilted dispense head, also using the Aerosol Jet technique and at a length scale 10-100 µm, followed by the nanoparticle sintering. Simulation studies are carried out to demonstrate the feasibility of using such structures as mm-wave antennas. The manufacturing method described in this letter opens up the possibility of fabricating an entirely new class of custom-shaped 3D structures at a sub-mm length scale with potential applications in 3D antennas and passives.

  16. Three-axis distributed fiber optic strain measurement in 3D woven composite structures

    Science.gov (United States)

    Castellucci, Matt; Klute, Sandra; Lally, Evan M.; Froggatt, Mark E.; Lowry, David

    2013-03-01

    Recent advancements in composite materials technologies have broken further from traditional designs and require advanced instrumentation and analysis capabilities. Success or failure is highly dependent on design analysis and manufacturing processes. By monitoring smart structures throughout manufacturing and service life, residual and operational stresses can be assessed and structural integrity maintained. Composite smart structures can be manufactured by integrating fiber optic sensors into existing composite materials processes such as ply layup, filament winding and three-dimensional weaving. In this work optical fiber was integrated into 3D woven composite parts at a commercial woven products manufacturing facility. The fiber was then used to monitor the structures during a VARTM manufacturing process, and subsequent static and dynamic testing. Low cost telecommunications-grade optical fiber acts as the sensor using a high resolution commercial Optical Frequency Domain Reflectometer (OFDR) system providing distributed strain measurement at spatial resolutions as low as 2mm. Strain measurements using the optical fiber sensors are correlated to resistive strain gage measurements during static structural loading.

  17. Quantifying Multiscale Habitat Structural Complexity: A Cost-Effective Framework for Underwater 3D Modelling

    Directory of Open Access Journals (Sweden)

    Renata Ferrari

    2016-02-01

    Full Text Available Coral reef habitat structural complexity influences key ecological processes, ecosystem biodiversity, and resilience. Measuring structural complexity underwater is not trivial and researchers have been searching for accurate and cost-effective methods that can be applied across spatial extents for over 50 years. This study integrated a set of existing multi-view, image-processing algorithms, to accurately compute metrics of structural complexity (e.g., ratio of surface to planar area underwater solely from images. This framework resulted in accurate, high-speed 3D habitat reconstructions at scales ranging from small corals to reef-scapes (10s km2. Structural complexity was accurately quantified from both contemporary and historical image datasets across three spatial scales: (i branching coral colony (Acropora spp.; (ii reef area (400 m2; and (iii reef transect (2 km. At small scales, our method delivered models with <1 mm error over 90% of the surface area, while the accuracy at transect scale was 85.3% ± 6% (CI. Advantages are: no need for an a priori requirement for image size or resolution, no invasive techniques, cost-effectiveness, and utilization of existing imagery taken from off-the-shelf cameras (both monocular or stereo. This remote sensing method can be integrated to reef monitoring and improve our knowledge of key aspects of coral reef dynamics, from reef accretion to habitat provisioning and productivity, by measuring and up-scaling estimates of structural complexity.

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

    Science.gov (United States)

    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.

  19. Three-Axis Distributed Fiber Optic Strain Measurement in 3D Woven Composite Structures

    Science.gov (United States)

    Castellucci, Matt; Klute, Sandra; Lally, Evan M.; Froggatt, Mark E.; Lowry, David

    2013-01-01

    Recent advancements in composite materials technologies have broken further from traditional designs and require advanced instrumentation and analysis capabilities. Success or failure is highly dependent on design analysis and manufacturing processes. By monitoring smart structures throughout manufacturing and service life, residual and operational stresses can be assessed and structural integrity maintained. Composite smart structures can be manufactured by integrating fiber optic sensors into existing composite materials processes such as ply layup, filament winding and three-dimensional weaving. In this work optical fiber was integrated into 3D woven composite parts at a commercial woven products manufacturing facility. The fiber was then used to monitor the structures during a VARTM manufacturing process, and subsequent static and dynamic testing. Low cost telecommunications-grade optical fiber acts as the sensor using a high resolution commercial Optical Frequency Domain Reflectometer (OFDR) system providing distributed strain measurement at spatial resolutions as low as 2mm. Strain measurements using the optical fiber sensors are correlated to resistive strain gage measurements during static structural loading. Keywords: fiber optic, distributed strain sensing, Rayleigh scatter, optical frequency domain reflectometry

  20. A 3D analysis of spatial relationship between geological structure and groundwater profile around Kobe City, Japan: based on ARCGIS 3D Analyst.

    Science.gov (United States)

    Shibahara, A.; Tsukamoto, H.; Kazahaya, K.; Morikawa, N.; Takahashi, M.; Takahashi, H.; Yasuhara, M.; Ohwada, M.; Oyama, Y.; Inamura, A.; Handa, H.; Nakama, J.

    2008-12-01

    Kobe city is located on the northern side of Osaka sedimentary basin, Japan, containing 1,000-2,000 m thick Quaternary sediments. After the Hanshin-Awaji Earthquake (January 17, 1995), a number of geological and geophysical surveys were conducted in this region. Then high-temperature anomaly of groundwater accompanied with high Cl concentration was detected along fault systems in this area. In addition, dissolved He in groundwater showed nearly upper mantle-like 3He/4He ratio, although there were no Quaternary volcanic activities in this region. Some recent studies have assumed that these groundwater profiles are related with geological structure because some faults and joints can function as pathways for groundwater flow, and mantle-derived water can upwell through the fault system to the ground surface. To verify these hypotheses, we established 3D geological and hydrological model around Osaka sedimentary basin. Our primary goal is to analyze spatial relationship between geological structure and groundwater profile. In the study region, a number of geological and hydrological datasets, such as boring log data, seismic profiling data, groundwater chemical profile, were reported. We converted these datasets to meshed data on the GIS, and plotted in the three dimensional space to visualize spatial distribution. Furthermore, we projected seismic profiling data into three dimensional space and calculated distance between faults and sampling points, using Visual Basic for Applications (VBA) scripts. All 3D models are converted into VRML format, and can be used as a versatile dataset on personal computer. This research project has been conducted under the research contract with the Japan Nuclear Energy Safety Organization (JNES).

  1. Structural optimization of 3D-printed synthetic spider webs for high strength

    Science.gov (United States)

    Qin, Zhao; Compton, Brett G.; Lewis, Jennifer A.; Buehler, Markus J.

    2015-05-01

    Spiders spin intricate webs that serve as sophisticated prey-trapping architectures that simultaneously exhibit high strength, elasticity and graceful failure. To determine how web mechanics are controlled by their topological design and material distribution, here we create spider-web mimics composed of elastomeric filaments. Specifically, computational modelling and microscale 3D printing are combined to investigate the mechanical response of elastomeric webs under multiple loading conditions. We find the existence of an asymptotic prey size that leads to a saturated web strength. We identify pathways to design elastomeric material structures with maximum strength, low density and adaptability. We show that the loading type dictates the optimal material distribution, that is, a homogeneous distribution is better for localized loading, while stronger radial threads with weaker spiral threads is better for distributed loading. Our observations reveal that the material distribution within spider webs is dictated by the loading condition, shedding light on their observed architectural variations.

  2. Fast computation of scattering from 3D complex structures by MLFMA

    Institute of Scientific and Technical Information of China (English)

    Hu Jun; Nie Zaiping; Que Xiaofeng; Meng Min

    2008-01-01

    This paper introduces the research work on the extension of multilevel fast multipole algorithm (MLFMA) to 3D complex structures including coating object,thin dielectric sheet,composite dielectric and conductor,cavity.The impedance boundary condition is used for scattering from the object coated by thin lossy material.Instead of volume integral equation,surface integral equation is applied in case of thin dielectric sheet through resistive sheet boundary condition.To realize the fast computation of scattering from composite homogeneous dielectric and conductor,the surface integral equation based on equivalence principle is used.Compared with the traditional volume integral equation,the surface integral equation reduces greatly the number of unknowns.To compute conducting cavity with electrically large aperture,an electric field integral equation is applied.Some numerical results are given to demonstrate the validity and accuracy of the present methods.

  3. Chromospheric heating and structure as determined from high resolution 3D simulations

    CERN Document Server

    Carlsson, Mats; Gudiksen, Boris V

    2010-01-01

    We have performed 3D radiation MHD simulations extending from the convection zone to the corona covering a box 16 Mm$^3$ at 32 km spatial resolution. The simulations show very fine structure in the chromosphere with acoustic shocks interacting with the magnetic field. Magnetic flux concentrations have a temperature lower than the surroundings in the photosphere but higher in the low chromosphere. The heating is there mostly through ohmic dissipation preferentially at the edges of the flux concentrations. The magnetic field is often wound up around the flux concentrations. When acoustic waves travel up along the field this topology leads to swirling motions seen in chromospheric diagnostic lines such as the calcium infrared triplet.

  4. Synthesis, Crystal Structure and Anticancer Activities of Tetrahydropyrido[4,3-d]dihydropyrimidine-2-thiones

    Institute of Scientific and Technical Information of China (English)

    丁丽; 薛思佳; 李静; 肖笛; 王晶; 郝志兵; 庞春成

    2012-01-01

    A new series of tetrahydropyrido[4,3-d]dihydropyrimidine-2-thiones (3a-3x) were designed and synthesized. Their structures were confirmed by 1H NMR, IR, MS and elemental analysis, and the conformation of compound 3j was confirmed by X-ray diffraction. Preliminary bioassays indicated that most of the target compounds presented good antiproliferative activities against leukemic K562 cells, ovarian cancer HO-8910 cells and liver cancer SMMC-7721 cells in vitro. Among them the compounds 3i and 3m afford the best activity, the IC50 of them were 3.22 and 3.65 μg/mL against leukemic K562 cells, respectively, which were lower than the anticancer drug of clini- cal practice 5-FU (IC50 = 8.56μg/mL). Preliminary mechanism of action studies revealed that compound 3i caused DNA fragmentation and activated caspase-3/7 in leukemic K562 cells.

  5. 3D study of the structure of primary crystals in a rheocast Al-Cu alloy

    Energy Technology Data Exchange (ETDEWEB)

    Niroumand, B.; Xia, K. [Melbourne Univ., Parkville, Vic. (Australia). Dept. of Mech. and Manuf. Eng.

    2000-05-15

    An Al-10.25 wt.% Cu alloy was mechanically stirred at 1000 rpm while being cooled to and isothermally held at 619 C for various times before casting. The microstructure of as-cast materials consists of pseudo-particles and pseudo-clusters in two-dimensional (2D) views. Serial sectioning was performed and it was found that pseudo-particles belonging to a pseudo-cluster were connected in three dimensions and a pseudo-cluster was actually a single primary particle. A three dimensional (3-D) model of such a primary particle was constructed from 2D sections which showed the complexity of its structure. It is suggested that the theories based on agglomeration and disagglomeration of particles during rheocasting be re-examined in light of the experimental results. (orig.)

  6. The numerical study of the cavitation-structure interaction around 3D flexible hydrofoil

    Science.gov (United States)

    Shi-liang, Hu; Ying, Chen; Chuan-jing, Lu

    2015-12-01

    The closely coupled approach combined the Finite Volume Method (FVM) solver and the Finite Element Method (FEM) solver is applied to simulation the cavitation-structure interaction of a 3D cantilevered flexible hydrofoil in water tunnel. In the cavitating flow, the elastic hydrofoil would deform or vibrate in bending and twisting mode. And the motion of the foil would affect the characteristics of the cavity and the hydrodynamic load on the foil in turn. With smaller cavitation numbers (σv=2.15), the frequency spectrum of the lift on the foil would contain two frequencies which are associated to the cavity shedding and the first bend frequency of the hydrofoil. With larger cavitation number (σv=2.55), the frequency of the lift is completely dominated by the natural frequency of the foil.

  7. Structural and property studies on metal-organic compounds with 3-D supramolecular network

    Science.gov (United States)

    Zhang, Qi-Ying; Ma, Ke-Fang; Xiao, Hong-Ping; Li, Xin-Hua; Shi, Qian

    2014-07-01

    Two carboxylato-bridged allomeric compounds, {[Cu2(dbsa)2(hmt) (H2O)4]1/2·2H2O}n (1), {[Ni(dbsa)(H2O)2]1/2[Ni(dbsa)(hmt)(H2O)2]1/2·2H2O}n (2) (H2dbsa=meso-2,3-dibromosuccinic acid, hmt=hexamethylenetetramine) have been synthesized and characterized by X-ray structral analyses. The metal ions have two kinds of coordination fashion in one unit, and bridged by carboxylate and hmt ligands along with weak interactions existing in the solid structure, forming a 3-D supramolecular network. Variable-temperature magnetic property studies reveal the existence of antiferromagnetic interactions in 1 and 2 with g=2.2, J1=-3.5 cm-1, J2=-2.8 cm-1 for 1, and g=2.1, J=-3.5 cm-1 for 2.

  8. Ex vivo 3D diffusion tensor imaging and quantification of cardiac laminar structure.

    Science.gov (United States)

    Helm, Patrick A; Tseng, Hsiang-Jer; Younes, Laurent; McVeigh, Elliot R; Winslow, Raimond L

    2005-10-01

    A three-dimensional (3D) diffusion-weighted imaging (DWI) method for measuring cardiac fiber structure at high spatial resolution is presented. The method was applied to the ex vivo reconstruction of the fiber architecture of seven canine hearts. A novel hypothesis-testing method was developed and used to show that distinct populations of secondary and tertiary eigenvalues may be distinguished at reasonable confidence levels (P < or = 0.01) within the canine ventricle. Fiber inclination and sheet angles are reported as a function of transmural depth through the anterior, lateral, and posterior left ventricle (LV) free wall. Within anisotropic regions, two consistent and dominant orientations were identified, supporting published results from histological studies and providing strong evidence that the tertiary eigenvector of the diffusion tensor (DT) defines the sheet normal.

  9. 3D NEAREST NEIGHBOUR SEARCH USING A CLUSTERED HIERARCHICAL TREE STRUCTURE

    Directory of Open Access Journals (Sweden)

    A. Suhaibah

    2016-06-01

    Full Text Available Locating and analysing the location of new stores or outlets is one of the common issues facing retailers and franchisers. This is due to assure that new opening stores are at their strategic location to attract the highest possible number of customers. Spatial information is used to manage, maintain and analyse these store locations. However, since the business of franchising and chain stores in urban areas runs within high rise multi-level buildings, a three-dimensional (3D method is prominently required in order to locate and identify the surrounding information such as at which level of the franchise unit will be located or is the franchise unit located is at the best level for visibility purposes. One of the common used analyses used for retrieving the surrounding information is Nearest Neighbour (NN analysis. It uses a point location and identifies the surrounding neighbours. However, with the immense number of urban datasets, the retrieval and analysis of nearest neighbour information and their efficiency will become more complex and crucial. In this paper, we present a technique to retrieve nearest neighbour information in 3D space using a clustered hierarchical tree structure. Based on our findings, the proposed approach substantially showed an improvement of response time analysis compared to existing approaches of spatial access methods in databases. The query performance was tested using a dataset consisting of 500,000 point locations building and franchising unit. The results are presented in this paper. Another advantage of this structure is that it also offers a minimal overlap and coverage among nodes which can reduce repetitive data entry.

  10. Plasmonic 3D-structures based on silver decorated nanotips for biological sensing

    KAUST Repository

    Coluccio, M. L.

    2015-05-01

    Recent progresses in nanotechnology fabrication gives the opportunity to build highly functional nano-devices. 3D structures based on noble metals or covered by them can be realized down to the nano-scales, obtaining different devices with the functionalities of plasmonic nano-lenses or nano-probes. Here, nano-cones decorated with silver nano-grains were fabricated using advanced nano-fabrication techniques. In fabricating the cones, the angle of the apex was varied over a significant range and, in doing so, different geometries were realized. In depositing the silver nano-particles, the concentration of solution was varied, whereby different growth conditions were realized. The combined effect of tip geometry and growth conditions influences the size and distribution of the silver nano grains. The tips have the ability to guide or control the growth of the grains, in the sense that the nano-particles would preferentially distribute along the cone, and especially at the apex of the cone, with no o minor concentration effects on the substrate. The arrangement of metallic nano-particles into three-dimensional (3D) structures results in a Surface Enhanced Raman Spectroscopy (SERS) device with improved interface with analytes compared to bi-dimensional arrays of metallic nanoparticles. In the future, similar devices may find application in microfluidic devices, and in general in flow chambers, where the system can be inserted as to mimic a a nano-bait, for the recognition of specific biomarkers, or the manipulation and chemical investigation of single cells directly in native environments with good sensitivity, repeatability and selectivity. © 2015 Elsevier Ltd.

  11. Real-time 3D medical structure segmentation using fast evolving active contours

    Science.gov (United States)

    Wang, Xiaotao; Wang, Qiang; Hao, Zhihui; Xu, Kuanhong; Guo, Ping; Ren, Haibing; Jang, Wooyoung; Kim, Jung-bae

    2014-03-01

    Segmentation of 3D medical structures in real-time is an important as well as intractable problem for clinical applications due to the high computation and memory cost. We propose a novel fast evolving active contour model in this paper to reduce the requirements of computation and memory. The basic idea is to evolve the brief represented dynamic contour interface as far as possible per iteration. Our method encodes zero level set via a single unordered list, and evolves the list recursively by adding activated adjacent neighbors to its end, resulting in active parts of the zero level set moves far enough per iteration along with list scanning. To guarantee the robustness of this process, a new approximation of curvature for integer valued level set is proposed as the internal force to penalize the list smoothness and restrain the list continual growth. Besides, list scanning times are also used as an upper hard constraint to control the list growing. Together with the internal force, efficient regional and constrained external forces, whose computations are only performed along the unordered list, are also provided to attract the list toward object boundaries. Specially, our model calculates regional force only in a narrowband outside the zero level set and can efficiently segment multiple regions simultaneously as well as handle the background with multiple components. Compared with state-of-the-art algorithms, our algorithm is one-order of magnitude faster with similar segmentation accuracy and can achieve real-time performance for the segmentation of 3D medical structures on a standard PC.

  12. Generation of Multilayered 3D Structures of HepG2 Cells Using a Bio-printing Technique

    Science.gov (United States)

    Jeon, Hyeryeon; Kang, Kyojin; Park, Su A; Kim, Wan Doo; Paik, Seung Sam; Lee, Sang-Hun; Jeong, Jaemin; Choi, Dongho

    2017-01-01

    Background/Aims Chronic liver disease is a major widespread cause of death, and whole liver transplantation is the only definitive treatment for patients with end-stage liver diseases. However, many problems, including donor shortage, surgical complications and cost, hinder their usage. Recently, tissue-engineering technology provided a potential breakthrough for solving these problems. Three-dimensional (3D) printing technology has been used to mimic tissues and organs suitable for transplantation, but applications for the liver have been rare. Methods A 3D bioprinting system was used to construct 3D printed hepatic structures using alginate. HepG2 cells were cultured on these 3D structures for 3 weeks and examined by fluorescence microscopy, histology and immunohistochemistry. The expression of liver-specific markers was quantified on days 1, 7, 14, and 21. Results The cells grew well on the alginate scaffold, and liver-specific gene expression increased. The cells grew more extensively in 3D culture than two-dimensional culture and exhibited better structural aspects of the liver, indicating that the 3D bioprinting method recapitulates the liver architecture. Conclusions The 3D bioprinting of hepatic structures appears feasible. This technology may become a major tool and provide a bridge between basic science and the clinical challenges for regenerative medicine of the liver. PMID:27559001

  13. Sequence analysis of luxS gene of Haemophilus parasuis and homology modeling of 3D structure of the deduced protein%副猪嗜血杆菌S-核糖基高半胱氨酸酶基因序列分析与推导蛋白三维结构的分子模拟

    Institute of Scientific and Technical Information of China (English)

    马艳平; 张杰; 陈豪泰; 马丽娜; 赵娜; 丁耀忠; 刘文倩; 王猛; 刘永生

    2011-01-01

    利用PCR方法获得副猪嗜血杆菌S-核糖基高半胱氨酸酶(luxS)基因全长DNA,将PCR纯化产物与pMD18-T载体连接并转化E.coil DH5α菌株,重组阳性质粒测序并采用生物信息学软件对所推导的氨基酸序列进行三维结构分析.结果表明,该基因全长510 bp,并与GenBank中登录的其他5株菌株luxS基因完整参考序列进行比较,同源性均在70%以上.用ExPAsy软件包预测了推导蛋白的特性,运用Swiss-PDB viewer软件的SWISS-Model处理器,并利用同源建模的思想建立HPS-luxS的三维结构.拉马钱德兰图证明,构建的luxS蛋白的空间结构是合理的.%Haemophilus parasuis luxS gene was amplified by PCR, the purified PCR product(510 bp) was cloned into pMD18-T vector and transformed into competent cell E.coil DH5α, the positive recombinant plasmid was sequenced.The nucleotide and amino acid sequences were compared with the full-length sequence of the other five referred bacterial strains available on GenBank,identity was higher than 70%.The characteristics of deduced protein were predieted by ExPAsy software.The homology modeling of 3D structure was done by SWISS-Model of Swiss-PDB viewer.The Ramachandram Plot showed that the structure of modeled luxS protein was reasonable.

  14. Limited cross-reactivity among domains of the Plasmodium falciparum clone 3D7 erythrocyte membrane protein 1 family

    DEFF Research Database (Denmark)

    Joergensen, Louise; Turner, Louise; Magistrado, Pamela

    2006-01-01

    The var gene-encoded Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family is responsible for antigenic variation and sequestration of infected erythrocytes during malaria. We have previously grouped the 60 PfEMP1 variants of P. falciparum clone 3D7 into groups A and B/A (category A...... from clone 3D7 by using a competition enzyme-linked immunosorbent assay and a pool of plasma from 63 malaria-exposed Tanzanian individuals. We conclude that naturally acquired antibodies are largely directed toward epitopes varying between different domains with a few, mainly category A, domains...

  15. Oit/Fam3D, a gut secreted protein displaying nutritional status-dependent regulation

    NARCIS (Netherlands)

    Wit, de N.J.W.; IJssenagger, N.; Oosterink, E.; Keshtkar, S.; Hooiveld, G.J.E.J.; Mensink, R.P.; Hammer, S.; Smit, J.W.A.; Muller, M.R.; Meer, van der R.

    2012-01-01

    Oncoprotein-induced transcript 1 (Oit1) was previously identified as a dietary fat-induced gene in the small intestine of C57Bl/6J mice. In this study, we further characterized Oit1 and its human ortholog family with sequence similarity 3, member D (Fam3D), on the messenger RNA as well as the protei

  16. Oit1/Fam3D, a gut-secreted protein displaying nutritional status-dependent regulation

    NARCIS (Netherlands)

    Wit, N.J. de; Ijssennagger, N.; Oosterink, E.; Keshtkar, S.; Hooiveld, G.J.; Mensink, R.P.; Hammer, S.; Smit, J.W.A.; Muller, M.; der Meer, R.

    2012-01-01

    Oncoprotein-induced transcript 1 (Oit1) was previously identified as a dietary fat-induced gene in the small intestine of C57Bl/6J mice. In this study, we further characterized Oit1 and its human ortholog family with sequence similarity 3, member D (Fam3D), on the messenger RNA as well as the protei

  17. 3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes

    NARCIS (Netherlands)

    Ollila, O. H. Samuli; Risselada, H. Jelger; Louhivuori, Martti; Lindahl, Erik; Vattulainen, Ilpo; Marrink, Siewert J.

    2009-01-01

    We calculate full 3D pressure fields for inhomogeneous nanoscale systems using molecular dynamics simulation data. The fields represent systems with increasing level of complexity, ranging from semivesicles and vesicles to membranes characterized by coexistence of two phases, including also a protei

  18. 3D thermography in non-destructive testing of composite structures

    Science.gov (United States)

    Hellstein, Piotr; Szwedo, Mariusz

    2016-12-01

    The combination of 3D scanners and infrared cameras has lead to the introduction of 3D thermography. Such analysis produces results in the form of three-dimensional thermograms, where the temperatures are mapped on a 3D model reconstruction of the inspected object. All work in the field of 3D thermography focused on its utility in passive thermography inspections. The authors propose a new real-time 3D temperature mapping method, which for the first time can be applied to active thermography analyses. All steps required to utilise 3D thermography are discussed, starting from acquisition of three-dimensional and infrared data, going through image processing and scene reconstruction, finishing with thermal projection and ray-tracing visualisation techniques. The application of the developed method was tested during diagnosis of several industrial composite structures—boats, planes and wind turbine blades.

  19. A tetraphenylethylene core-based 3D structure small molecular acceptor enabling efficient non-fullerene organic solar cells.

    Science.gov (United States)

    Liu, Yuhang; Mu, Cheng; Jiang, Kui; Zhao, Jingbo; Li, Yunke; Zhang, Lu; Li, Zhengke; Lai, Joshua Yuk Lin; Hu, Huawei; Ma, Tingxuan; Hu, Rongrong; Yu, Demei; Huang, Xuhui; Tang, Ben Zhong; Yan, He

    2015-02-01

    A tetraphenylethylene core-based small molecular acceptor with a unique 3D molecular structure is developed. Bulk-heterojunction blend films with a small feature size (≈20 nm) are obtained, which lead to non-fullerene organic solar cells (OSCs) with 5.5% power conversion efficiency. The work provides a new molecular design approach to efficient non-fullerene OSCs based on 3D-structured small-molecule acceptors.

  20. 3D structure and formation of hydrothermal vent complexes in the Møre Basin

    Science.gov (United States)

    Kjoberg, Sigurd; Schmiedel, Tobias; Planke, Sverre; Svensen, Henrik H.; Galland, Oliver; Jerram, Dougal A.

    2016-04-01

    The mid-Norwegian Møre margin is regarded as a type example of a volcanic rifted margin, with its formation usually related to the influence of the Icelandic plume activity. The area is characterized by the presence of voluminous basaltic complexes such as extrusive lava sequences, intrusive sills and dikes, and hydrothermal vent complexes within the Møre Basin. Emplacement of hydrothermal vent complexes is accommodated by deformation of the host rock. The edges of igneous intrusions mobilize fluids by heat transfer into the sedimentary host rock (aureoles). Fluid expansion may lead to formation of piercing structures due to upward fluid migration. Hydrothermal vent complexes induce bending of overlying strata, leading to the formation of dome structures at the paleo-surface. These dome structures are important as they indicate the accommodation created for the intrusions by deformation of the upper layers of the stratigraphy, and may form important structures in many volcanic margins. Both the morphological characteristics of the upper part and the underlying feeder-structure (conduit-zone) can be imaged and studied on 3D seismic data. Seismic data from the Tulipan prospect located in the western part of the Møre Basin have been used in this study. The investigation focusses on (1) the vent complex geometries, (2) the induced surface deformation patterns, (3) the relation to the intrusions (heat source), as well as (4) the emplacement depth of the hydrothermal vent complexes. We approach this by doing a detailed 3D seismic interpretation of the Tulipan seismic data cube. The complexes formed during the initial Eocene, and are believed to be a key factor behind the rapid warming event called the Paleocene-Eocene thermal maximum (PETM). The newly derived understanding of age, eruptive deposits, and formation of hydrothermal vent complexes in the Møre Basin enables us to contribute to the general understanding of the igneous plumbing system in volcanic basins and

  1. 3D Modelling of Inaccessible Areas using UAV-based Aerial Photography and Structure from Motion

    Science.gov (United States)

    Obanawa, Hiroyuki; Hayakawa, Yuichi; Gomez, Christopher

    2014-05-01

    In hardly accessible areas, the collection of 3D point-clouds using TLS (Terrestrial Laser Scanner) can be very challenging, while airborne equivalent would not give a correct account of subvertical features and concave geometries like caves. To solve such problem, the authors have experimented an aerial photography based SfM (Structure from Motion) technique on a 'peninsular-rock' surrounded on three sides by the sea at a Pacific coast in eastern Japan. The research was carried out using UAS (Unmanned Aerial System) combined with a commercial small UAV (Unmanned Aerial Vehicle) carrying a compact camera. The UAV is a DJI PHANTOM: the UAV has four rotors (quadcopter), it has a weight of 1000 g, a payload of 400 g and a maximum flight time of 15 minutes. The camera is a GoPro 'HERO3 Black Edition': resolution 12 million pixels; weight 74 g; and 0.5 sec. interval-shot. The 3D model has been constructed by digital photogrammetry using a commercial SfM software, Agisoft PhotoScan Professional®, which can generate sparse and dense point-clouds, from which polygonal models and orthophotographs can be calculated. Using the 'flight-log' and/or GCPs (Ground Control Points), the software can generate digital surface model. As a result, high-resolution aerial orthophotographs and a 3D model were obtained. The results have shown that it was possible to survey the sea cliff and the wave cut-bench, which are unobservable from land side. In details, we could observe the complexity of the sea cliff that is nearly vertical as a whole while slightly overhanging over the thinner base. The wave cut bench is nearly flat and develops extensively at the base of the cliff. Although there are some evidences of small rockfalls at the upper part of the cliff, there is no evidence of very recent activity, because no fallen rock exists on the wave cut bench. This system has several merits: firstly lower cost than the existing measuring methods such as manned-flight survey and aerial laser

  2. Full-hand 3D non-contact scanner using sub-window-based structured light-illumination technique

    Science.gov (United States)

    Yalla, Veeraganesh; Hassebrook, Laurence; Daley, Ray; Boles, Colby; Troy, Mike

    2012-06-01

    Fingerprint identification is a well-regarded and widely accepted modality in the field of biometrics for its high recognition rates. Legacy 2D contact based methods, though highly evolved in terms of technology suffer from certain drawbacks. Being contact based, there are many known issues which affect the recognition rates. Flashscan3D/University of Kentucky (UKY) developed state of the art 3D non-contact fingerprint scanners using different structured light illumination (SLI) techniques namely SLI single Point Of View (POV) and the SLI Subwindowing techniques. Capturing the fingerprints by non-contact means in 3D gives much higher quality fingerprint data which ultimately improves matching rates over a traditional 2D approach. In this paper, we present a full hand 3D non-contact scanner using the SLI Sub-windowing technique. Sample fingerprint data and experimental results for fingerprint matching based on a small sample 3D fingerprint test set are presented.

  3. Combined aerial and terrestrial images for complete 3D documentation of Singosari Temple based on Structure from Motion algorithm

    Science.gov (United States)

    Hidayat, Husnul; Cahyono, A. B.

    2016-11-01

    Singosaritemple is one of cultural heritage building in East Java, Indonesia which was built in 1300s and restorated in 1934-1937. Because of its history and importance, complete documentation of this temple is required. Nowadays with the advent of low cost UAVs combining aerial photography with terrestrial photogrammetry gives more complete data for 3D documentation. This research aims to make complete 3D model of this landmark from aerial and terrestrial photographs with Structure from Motion algorithm. To establish correct scale, position, and orientation, the final 3D model was georeferenced with Ground Control Points in UTM 49S coordinate system. The result shows that all facades, floor, and upper structures can be modeled completely in 3D. In terms of 3D coordinate accuracy, the Root Mean Square Errors (RMSEs) are RMSEx=0,041 m; RMSEy=0,031 m; RMSEz=0,049 m which represent 0.071 m displacement in 3D space. In addition the mean difference of lenght measurements of the object is 0,057 m. With this accuracy, this method can be used to map the site up to 1:237 scale. Although the accuracy level is still in centimeters, the combined aerial and terrestrial photographs with Structure from Motion algorithm can provide complete and visually interesting 3D model.

  4. Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

    Directory of Open Access Journals (Sweden)

    Mihai V. Putz

    2016-07-01

    Full Text Available Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding and quantitative (for predicting mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD as the revived precursor for comparative molecular field analyses (CoMFA and comparative molecular similarity indices analysis (CoMSIA; all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy-methyl]-6-(phenylthiothymine congeners’ (HEPT ligands antiviral activity against Human Immunodeficiency Virus of first type (HIV-1 and new pharmacophores in treating severe genetic disorders (like depression and psychosis, respectively, all involving 3D pharmacophore interactions.

  5. Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

    Science.gov (United States)

    Putz, Mihai V.; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta

    2016-01-01

    Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners’ (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions. PMID:27399692

  6. Electronic structure and local magnetism of 3d-5d impurity substituted CeFe2

    Science.gov (United States)

    Das, Rakesh; Das, G. P.; Srivastava, S. K.

    2016-04-01

    We present here a systematic first-principles study of electronic structure and local magnetic properties of Ce[Fe0.75M0.25]2 compounds, where M is a 3d, 4d or 5d transition or post-transition element, using the generalized gradient approximation of the density functional theory. The d-f band hybridizations existing in CeFe2 get modified by the impurity M in an orderly manner across a period for each impurity series: the hybridization is strongest for the Mn group impurity in the period and gets diminished on either side of it. The weakening of the d-f hybridization strength is also associated with a relative localization of the Ce 4f states with respect to the delocalized 4f states in CeFe2. The above effects are most prominent for 3d impurity series, while for 4d and 5d impurities, the hybridizations and relocalizations are relatively weak due primarily to the relatively extended nature of 4d and 5d wavefunctions. The Ce local moment is found to decrease from the CeFe2 value in proportion to the strength of relocalization, thus following almost the same orderly trend as obeyed by the d-f hybridization. Further, depending on the way the spin-up and spin-down densities of states of an impurity shift relative to the Fermi energy, the impurity local moments are highest for Mn or Fe group, reduce on either side, become zero for Ni to Ga, and are small but negative for V and Ti. The Ce hyperfine field is found to follow the M local moment in a linear fashion, and vice-versa.

  7. Deep structure of the Argentine margin inferred from 3D gravity and temperature modelling, Colorado Basin

    Science.gov (United States)

    Autin, J.; Scheck-Wenderoth, M.; Götze, H.-J.; Reichert, C.; Marchal, D.

    2016-04-01

    Following previous work on the Colorado Basin using a 3D crustal structural model, we now investigate the presence of lower crustal bodies at the base of the crust using 3D lithospheric gravity modelling and calculations of the conductive thermal field. Our first study highlighted two fault directions and depocentres associated with thinned crust (NW-SE in the West and NE-SW at the distal margin). Fault relative chronology argues for two periods of extension: (1) NW-SE faulting and thinning in the western Colorado Basin and (2) NE-SW faulting and thinning related to the continental breakup and formation of the NE-SW-striking volcanic margins of the Atlantic Ocean. In this study, the geometry of modelled high-density Lower Crustal Bodies (LCBs) enables the reproduction of the gravimetric field as well as of the temperature measured in wells down to 4500 m. The modelled LCBs correlate with geological observations: (1) NW-SE LCBs below the deepest depocentres in the West, (2) NE-SW LCBs below the distal margin faults and the seaward dipping reflectors. Thus the proposed poly-phased evolution of the margin could as well correspond to two emplacement phases of the LCBs. The calculated conductive thermal field fits the measured temperatures best if the thermal properties (thermal conductivity and radiogenic heat production) assigned to the LCBs correspond to either high-grade metamorphic rocks or to mafic magmatic intrusions. To explain the possible lithology of the LCBs, we propose that the two successive phases of extension are accompanied by magma supply, emplaced (1) in the thinnest crust below the older NW-SE depocentres, then (2) along the NE-SW continentward boundary of the distal margin and below the volcanic seaward dipping reflectors. The South African conjugate margin records only the second NE-SW event and we discuss hypotheses which could explain these differences between the conjugate margins.

  8. Hollow Cone Electron Imaging for Single Particle 3D Reconstruction of Proteins

    Science.gov (United States)

    Tsai, Chun-Ying; Chang, Yuan-Chih; Lobato, Ivan; van Dyck, Dirk; Chen, Fu-Rong

    2016-06-01

    The main bottlenecks for high-resolution biological imaging in electron microscopy are radiation sensitivity and low contrast. The phase contrast at low spatial frequencies can be enhanced by using a large defocus but this strongly reduces the resolution. Recently, phase plates have been developed to enhance the contrast at small defocus but electrical charging remains a problem. Single particle cryo-electron microscopy is mostly used to minimize the radiation damage and to enhance the resolution of the 3D reconstructions but it requires averaging images of a massive number of individual particles. Here we present a new route to achieve the same goals by hollow cone dark field imaging using thermal diffuse scattered electrons giving about a 4 times contrast increase as compared to bright field imaging. We demonstrate the 3D reconstruction of a stained GroEL particle can yield about 13.5 Å resolution but using a strongly reduced number of images.

  9. 3D Case Studies of Monitoring Dynamic Structural Tests using Long Exposure Imagery

    Science.gov (United States)

    McCarthy, D. M. J.; Chandler, J. H.; Palmeri, A.

    2014-06-01

    Structural health monitoring uses non-destructive testing programmes to detect long-term degradation phenomena in civil engineering structures. Structural testing may also be carried out to assess a structure's integrity following a potentially damaging event. Such investigations are increasingly carried out with vibration techniques, in which the structural response to artificial or natural excitations is recorded and analysed from a number of monitoring locations. Photogrammetry is of particular interest here since a very high number of monitoring locations can be measured using just a few images. To achieve the necessary imaging frequency to capture the vibration, it has been necessary to reduce the image resolution at the cost of spatial measurement accuracy. Even specialist sensors are limited by a compromise between sensor resolution and imaging frequency. To alleviate this compromise, a different approach has been developed and is described in this paper. Instead of using high-speed imaging to capture the instantaneous position at each epoch, long-exposure images are instead used, in which the localised image of the object becomes blurred. The approach has been extended to create 3D displacement vectors for each target point via multiple camera locations, which allows the simultaneous detection of transverse and torsional mode shapes. The proposed approach is frequency invariant allowing monitoring of higher modal frequencies irrespective of a sampling frequency. Since there is no requirement for imaging frequency, a higher image resolution is possible for the most accurate spatial measurement. The results of a small scale laboratory test using off-the-shelf consumer cameras are demonstrated. A larger experiment also demonstrates the scalability of the approach.

  10. Data of evolutionary structure change: 1CCTA-3D0NB [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available ID> A 1CCTA VHWNT-KYGDF ...1CCTA-3D0NB 1CCT 3D0N A B ------WGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHT...SIKEKGKQTRFTNFDLLSLLPPSWDYWTYPGSLTVPPLLESVTWIVLKQPINISSQQLAKFRSLLCTAEGEAAAFLVSNHRPPQPLKGRKVRASFH 0 1CCTEEEEE-GG Hure> ATOM 933 CA VAL A 121 -11.826 4.712 15.895

  11. Data of evolutionary structure change: 3GD5D-3D7SA [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 3GD5D-3D7SA 3GD5 3D7S D A --TRFRPDLLSLDDLDEAQLHALLTLAHQLKRGERVANL...HGKVLGLVFLKASTRTRVSFTVAMYQLGGQVIDL------------EPVRDTARVLGRYVDGLAIRTFAQTELEEYAHYAG-IPVINALTD-HEHPCQVVADLLTIRENFGRLAGLKLAYVGD...ANPLYQKHIISINDLSRDDLNLVLATAAKLKANPQPELLKHKVIASCFFEASTRTRLSFETSMHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMRHPQEGAARLATEFSGNVPVLNAGD...GSNQHPTQTLLDLFTIQETQGRLDNLHVAMVGDLKYGRTVHSLTQALAKFDGNRFYFIAPDALAMPQYILDMLDEK----GIAWSLH.../index> 3GD5 D 3GD5D

  12. Data of evolutionary structure change: 1CCTA-3D0NA [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available A 1CCTA VHWNT-KYGDF ...1CCTA-3D0NA 1CCT 3D0N A A ------WGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHT...SIKEKGKQTRFTNFDLLSLLPPSWDYWTYPGSLTVPPLLESVTWIVLKQPINISSQQLAKFRSLLCTAEGEAAAFLVSNHRPPQPLKGRKVRASFH 0 1CCT...ure>EEEEE-GG Hure> ATOM 933 CA VAL A 121 -11.826 4.712 15

  13. A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction

    Directory of Open Access Journals (Sweden)

    Zaslavskiy Mikhail

    2010-02-01

    Full Text Available Abstract Background Predicting which molecules can bind to a given binding site of a protein with known 3D structure is important to decipher the protein function, and useful in drug design. A classical assumption in structural biology is that proteins with similar 3D structures have related molecular functions, and therefore may bind similar ligands. However, proteins that do not display any overall sequence or structure similarity may also bind similar ligands if they contain similar binding sites. Quantitatively assessing the similarity between binding sites may therefore be useful to propose new ligands for a given pocket, based on those known for similar pockets. Results We propose a new method to quantify the similarity between binding pockets, and explore its relevance for ligand prediction. We represent each pocket by a cloud of atoms, and assess the similarity between two pockets by aligning their atoms in the 3D space and comparing the resulting configurations with a convolution kernel. Pocket alignment and comparison is possible even when the corresponding proteins share no sequence or overall structure similarities. In order to predict ligands for a given target pocket, we compare it to an ensemble of pockets with known ligands to identify the most similar pockets. We discuss two criteria to evaluate the performance of a binding pocket similarity measure in the context of ligand prediction, namely, area under ROC curve (AUC scores and classification based scores. We show that the latter is better suited to evaluate the methods with respect to ligand prediction, and demonstrate the relevance of our new binding site similarity compared to existing similarity measures. Conclusions This study demonstrates the relevance of the proposed method to identify ligands binding to known binding pockets. We also provide a new benchmark for future work in this field. The new method and the benchmark are available at http://cbio.ensmp.fr/paris/.

  14. Ion-beam enhanced etching for the 3D structuration of lithium niobate; Ionenstrahlverstaerktes Aetzen fuer die 3D-Strukturierung von Lithiumniobat

    Energy Technology Data Exchange (ETDEWEB)

    Gischkat, Thomas

    2010-01-12

    The present thesis deals with the usage of the ion-beam enhanced etching (IBEE) for the 3D structuration of lithium niobate (LiNbO{sub 3}).Hereby the approach of the enhancement of the wet-chemical etching rate due to the irradiation with energetic ions is pursued. This method is very success promising for the realization of micro- and nanostructures with perpendicular structural walls as well as small roughnesses. The aim of this thesis consisted therein to form the foundations for the realization of three-dimensional micro- and nanostructures (for instance: Layer systems and photonic crystals) in LiNbO{sub 3} with high optical quality and to demonstrate on selected examples. Conditions for the success of the IBEE structuration technique is first of all the understanding of the defect formation under ion irradiation as well as the radiation-induced structure changes in the crystal and the change of the chemical resistance connected with this. For this the defect formation was studied in dependence on th ion mass, the ion energy, and the irradiation temperature. Thermally induced influences and effects on the radiation damage, as they can occur in intermediate steps in the complex processing, must be known and were studied by means of subsequent temperature treatment. The results from the defect studies were subsequently applied for the fabrication of micro- and nanostructures in LiNbO{sub 3}. Shown is the realization of lateral structure with nearly perpendicular structure walls as well as the realization of thin membranes and slits. The subsequent combination of lateral structuration with the fabrication of thin membranes and slits allowed the three-dimensional structuration of LiNbO{sub 3}. This is exemplarily shown for a microresonator and for a 2D photonic crystal with below lying air slit. [German] Die vorliegende Arbeit beschaeftigt sich mit der Ausnutzung des ionenstrahlverstaerkten Aetzens (IBEE: Ion Beam Enhanced Etching) fuer die 3D-Strukturierung von

  15. 3D Measurement Technology by Structured Light Using Stripe-Edge-Based Gray Code

    Science.gov (United States)

    Wu, H. B.; Chen, Y.; Wu, M. Y.; Guan, C. R.; Yu, X. Y.

    2006-10-01

    The key problem of 3D vision measurement using triangle method based on structured light is to acquiring projecting angle of projecting light accurately. In order to acquire projecting angle thereby determine the corresponding relationship between sampling point and image point, method for encoding and decoding structured light based on stripe edge of Gray code is presented. The method encoded with Gray code stripe and decoded with stripe edge acquired by sub-pixel technology instead of pixel centre, so latter one-bit decoding error was removed. Accuracy of image sampling point location and correspondence between image sampling point and object sampling point achieved sub-pixel degree. In addition, measurement error caused by dividing projecting angle irregularly by even-width encoding stripe was analysed and corrected. Encoding and decoding principle and decoding equations were described. Finally, 3dsmax and Matlab software were used to simulate measurement system and reconstruct measured surface. Indicated by experimental results, measurement error is about 0.05%.

  16. Determining the 3D Subsurface Density Structure of Taurus Littrow Valley Using Apollo 17 Gravity Data

    Science.gov (United States)

    Urbancic, N.; Ghent, R.; Stanley, S,; Johnson, C. L.; Carroll, K. A.; Hatch, D.; Williamson, M. C.; Garry, W. B.; Talwani, M.

    2016-01-01

    Surface gravity surveys can detect subsurface density variations that can reveal subsurface geologic features. In 1972, the Apollo 17 (A17) mission conducted the Traverse Gravimeter Experiment (TGE) using a gravimeter that measured the local gravity field near Taurus Littrow Valley (TLV), located on the south-eastern rim of the Serenitatis basin. TLV is hypothesized to be a basaltfilled radial graben resulting from the impact that formed Mare Serenitatis. It is bounded by both the North and South Massifs (NM and SM) as well as other smaller mountains to the East that are thought to be mainly composed of brecciated highland material. The TGE is the first and only successful gravity survey on the surface of the Moon. Other more recent satellite surveys, such as NASA's Gravity Recovery and Interior Laboratory (GRAIL) mission (2011- 2012), have produced the best global gravity field to date (approx. 13km resolution). However, these satellite surveys are not sensitive enough to detect fine-scale (structures. This underscores the value of the data collected at the surface by A17. In the original analysis of the data a 2D forward-modelling approach was used to derive a thickness of the subsurface basalt layer of 1.0 km by assuming a simple flat-faced rectangular geometry and using densities derived from Apollo lunar samples. We are investigating whether modern 3D modelling techniques in combination with high-resolution topographical and image datasets can reveal additional fine-scale subsurface structure in TLV.

  17. Performance analysis of high quality parallel preconditioners applied to 3D finite element structural analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kolotilina, L.; Nikishin, A.; Yeremin, A. [and others

    1994-12-31

    The solution of large systems of linear equations is a crucial bottleneck when performing 3D finite element analysis of structures. Also, in many cases the reliability and robustness of iterative solution strategies, and their efficiency when exploiting hardware resources, fully determine the scope of industrial applications which can be solved on a particular computer platform. This is especially true for modern vector/parallel supercomputers with large vector length and for modern massively parallel supercomputers. Preconditioned iterative methods have been successfully applied to industrial class finite element analysis of structures. The construction and application of high quality preconditioners constitutes a high percentage of the total solution time. Parallel implementation of high quality preconditioners on such architectures is a formidable challenge. Two common types of existing preconditioners are the implicit preconditioners and the explicit preconditioners. The implicit preconditioners (e.g. incomplete factorizations of several types) are generally high quality but require solution of lower and upper triangular systems of equations per iteration which are difficult to parallelize without deteriorating the convergence rate. The explicit type of preconditionings (e.g. polynomial preconditioners or Jacobi-like preconditioners) require sparse matrix-vector multiplications and can be parallelized but their preconditioning qualities are less than desirable. The authors present results of numerical experiments with Factorized Sparse Approximate Inverses (FSAI) for symmetric positive definite linear systems. These are high quality preconditioners that possess a large resource of parallelism by construction without increasing the serial complexity.

  18. Band structure and spin texture of Bi2Se3 3 d ferromagnetic metal interface

    Science.gov (United States)

    Zhang, Jia; Velev, Julian P.; Dang, Xiaoqian; Tsymbal, Evgeny Y.

    2016-07-01

    The spin-helical surface states in a three-dimensional topological insulator (TI), such as Bi2Se3 , are predicted to have superior efficiency in converting charge current into spin polarization. This property is said to be responsible for the giant spin-orbit torques observed in ferromagnetic metal/TI structures. In this work, using first-principles and model tight-binding calculations, we investigate the interface between the topological insulator Bi2Se3 and 3 d -transition ferromagnetic metals Ni and Co. We find that the difference in the work functions of the topological insulator and the ferromagnetic metals shift the topological surface states down about 0.5 eV below the Fermi energy where the hybridization of these surface states with the metal bands destroys their helical spin structure. The band alignment of Bi2Se3 and Ni (Co) places the Fermi energy far in the conduction band of bulk Bi2Se3 , where the spin of the carriers is aligned with the magnetization in the metal. Our results indicate that the topological surface states are unlikely to be responsible for the huge spin-orbit torque effect observed experimentally in these systems.

  19. Mimicking liver sinusoidal structures and functions using a 3D-configured microfluidic chip.

    Science.gov (United States)

    Du, Yu; Li, Ning; Yang, Hao; Luo, Chunhua; Gong, Yixin; Tong, Chunfang; Gao, Yuxin; Lü, Shouqin; Long, Mian

    2017-02-28

    Physiologically, four major types of hepatic cells - the liver sinusoidal endothelial cells, Kupffer cells, hepatic stellate cells, and hepatocytes - reside inside liver sinusoids and interact with flowing peripheral cells under blood flow. It is hard to mimic an in vivo liver sinusoid due to its complex multiple cell-cell interactions, spatiotemporal construction, and mechanical microenvironment. Here we developed an in vitro liver sinusoid chip by integrating the four types of primary murine hepatic cells into two adjacent fluid channels separated by a porous permeable membrane, replicating liver's key structures and configurations. Each type of cells was identified with its respective markers, and the assembled chip presented the liver-specific unique morphology of fenestration. The flow field in the liver chip was quantitatively analyzed by computational fluid dynamics simulations and particle tracking visualization tests. Intriguingly, co-culture and shear flow enhance albumin secretion independently or cooperatively, while shear flow alone enhances HGF production and CYP450 metabolism. Under lipopolysaccharide (LPS) stimulations, the hepatic cell co-culture facilitated neutrophil recruitment in the liver chip. Thus, this 3D-configured in vitro liver chip integrates the two key factors of shear flow and the four types of primary hepatic cells to replicate key structures, hepatic functions, and primary immune responses and provides a new in vitro model to investigate the short-duration hepatic cellular interactions under a microenvironment mimicking the physiology of a liver.

  20. Synthesis and structure of 3D heterometallic (3d-4f) coordination polymers: {[Ln_2Cu(pydc)_4(H_2O)_6]·2H_2O}_n

    Institute of Scientific and Technical Information of China (English)

    MA JingXin; HUANG XiaoFeng; WEI RuiPing; LIU WeiSheng

    2009-01-01

    Two new 3D heterometallic (3d-4f) coordination polymers {[Ln_2Cu(pydc)_4(H_2O)_6]·2H_2O}_n [Ln = Eu (1) and Gd (2)] have been synthesized by hydrothermal reactions and characterized by elemental analysis, X-ray single-crystal analyses, and IR spectroscopy. X-ray crystal structure analyses show that 1 and 2 possess 3D networks and strong intramolecular hydrogen bonding interactions which was confirmed by thermogravimetric (TG) analysis.

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

    Science.gov (United States)

    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.

  2. Structural evolution of the VMS-hosting Kristineberg area, Sweden – constraints from structural analysis and 3-D-modelling

    Directory of Open Access Journals (Sweden)

    J. Hübert

    2012-10-01

    Full Text Available Structural mapping and 3-D-modelling with constraints from magnetotelluric (MT and reflection seismic investigations have been used to provide a geological synthesis of the geometrically complex Kristineberg area in the western part of the Palaeoproterozoic Skellefte district. The results indicate that, like the south-eastern parts of the Skellefte district, the area was subjected to SSE-NNW transpressional deformation at around 1.87 Ga. The contrasting structural geometries between the Kristineberg and the central Skellefte district areas may be attributed to the termination and splaying of a major ESE-WNW-striking high-strain zone into several branches in the northern part of the Kristineberg area. The transpressional structural signature was preferentially developed within the southern of the two antiformal structures of the area, "the Southern antiform", which exposes the deepest cut through the crust and hosts all the economic volcanogenic massive sulphides (VMS deposits of the area. Partitioning of the SSE-NNW transpression into N–S and E–W components led to formation of a characteristic "flat-steep-flat" geometry defining a highly non-cylindrical hinge of for the Southern antiform. Recognition of the transpressional structural signatures including the "flat-steep-flat" geometry and the distinct pattern of sub-horizontal E–W trending to moderately SW-plunging mineral lineations in the deeper crustal parts of the Kristineberg area is of significance for VMS exploration in both near mine and regional scales. The 3-D-model illustrating the outcomes of this study is available as a 3-D-PDF document through the publication website.

  3. Waves of 3D marine structures slamming at different initial poses in complex wind-wave-flow environments

    Science.gov (United States)

    Zhu, Liang-sheng; Yu, Long-fei

    2016-10-01

    Aimed at the hydrodynamic response for marine structures slamming into water, based on the mechanism analysis to the slamming process, and by combining 3D N-S equation and k- ɛ turbulent kinetic equation with structure fully 6DOF motion equation, a mathematical model for the wind-fluid-solid interaction is established in 3D marine structure slamming wave at free poses and wind-wave-flow complex environments. Compared with the results of physical model test, the numerical results from the slamming wave well correspond with the experimental results. Through the mathematical model, the wave-making issue of 3D marine structure at initial pose falls into water in different complex wind, wave and flow environments is investigated. The research results show that various kinds of natural factors and structure initial poses have different influence on the slamming wave, and there is an obvious rule in this process.

  4. Fabrication, Characterization, And Deformation of 3D Structural Meta-Materials

    Science.gov (United States)

    Montemayor, Lauren C.

    Current technological advances in fabrication methods have provided pathways to creating architected structural meta-materials similar to those found in natural organisms that are structurally robust and lightweight, such as diatoms. Structural meta-materials are materials with mechanical properties that are determined by material properties at various length scales, which range from the material microstructure (nm) to the macro-scale architecture (mum -- mm). It is now possible to exploit material size effect, which emerge at the nanometer length scale, as well as structural effects to tune the material properties and failure mechanisms of small-scale cellular solids, such as nanolattices. This work demonstrates the fabrication and mechanical properties of 3-dimensional hollow nanolattices in both tension and compression. Hollow gold nanolattices loaded in uniaxial compression demonstrate that strength and stiffness vary as a function of geometry and tube wall thickness. Structural effects were explored by increasing the unit cell angle from 30° to 60° while keeping all other parameters constant; material size effects were probed by varying the tube wall thickness, t, from 200nm to 635nm, at a constant relative density and grain size. In-situ uniaxial compression experiments reveal an order-of-magnitude increase in yield stress and modulus in nanolattices with greater lattice angles, and a 150% increase in the yield strength without a concomitant change in modulus in thicker-walled nanolattices for fixed lattice angles. These results imply that independent control of structural and material size effects enables tunability of mechanical properties of 3-dimensional architected meta-materials and highlight the importance of material, geometric, and microstructural effects in small-scale mechanics. This work also explores the flaw tolerance of 3D hollow-tube alumina kagome nanolattices with and without pre-fabricated notches, both in experiment and simulation

  5. Oscillating optical tweezer-based 3-D confocal microrheometer for investigating the intracellular micromechanics and structures

    Science.gov (United States)

    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.

  6. 3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling.

    Science.gov (United States)

    Segura, Joan; Sanchez-Garcia, Ruben; Tabas-Madrid, Daniel; Cuenca-Alba, Jesus; Sorzano, Carlos Oscar S; Carazo, Jose Maria

    2016-02-23

    Electron microscopy (EM) is experiencing a revolution with the advent of a new generation of Direct Electron Detectors, enabling a broad range of large and flexible structures to be resolved well below 1 nm resolution. Although EM techniques are evolving to the point of directly obtaining structural data at near-atomic resolution, for many molecules the attainable resolution might not be enough to propose high-resolution structural models. However, accessing information on atomic coordinates is a necessary step toward a deeper understanding of the molecular mechanisms that allow proteins to perform specific tasks. For that reason, methods for the integration of EM three-dimensional maps with x-ray and NMR structural data are being developed, a modeling task that is normally referred to as fitting, resulting in the so called hybrid models. In this work, we present a novel application-3DIANA-specially targeted to those cases in which the EM map resolution is medium or low and additional experimental structural information is scarce or even lacking. In this way, 3DIANA statistically evaluates proposed/potential contacts between protein domains, presents a complete catalog of both structurally resolved and predicted interacting regions involving these domains and, finally, suggests structural templates to model the interaction between them. The evaluation of the proposed interactions is computed with DIMERO, a new method that scores physical binding sites based on the topology of protein interaction networks, which has recently shown the capability to increase by 200% the number of domain-domain interactions predicted in interactomes as compared to previous approaches. The new application displays the information at a sequence and structural level and is accessible through a web browser or as a Chimera plugin at http://3diana.cnb.csic.es.

  7. Laser Scanning Holographic Lithography for Flexible 3D Fabrication of Multi-Scale Integrated Nano-structures and Optical Biosensors.

    Science.gov (United States)

    Yuan, Liang Leon; Herman, Peter R

    2016-01-01

    Three-dimensional (3D) periodic nanostructures underpin a promising research direction on the frontiers of nanoscience and technology to generate advanced materials for exploiting novel photonic crystal (PC) and nanofluidic functionalities. However, formation of uniform and defect-free 3D periodic structures over large areas that can further integrate into multifunctional devices has remained a major challenge. Here, we introduce a laser scanning holographic method for 3D exposure in thick photoresist that combines the unique advantages of large area 3D holographic interference lithography (HIL) with the flexible patterning of laser direct writing to form both micro- and nano-structures in a single exposure step. Phase mask interference patterns accumulated over multiple overlapping scans are shown to stitch seamlessly and form uniform 3D nanostructure with beam size scaled to small 200 μm diameter. In this way, laser scanning is presented as a facile means to embed 3D PC structure within microfluidic channels for integration into an optofluidic lab-on-chip, demonstrating a new laser HIL writing approach for creating multi-scale integrated microsystems.

  8. Lightweight NiFe2O4 with controllable 3D network structure and enhanced microwave absorbing properties

    Science.gov (United States)

    Wang, Fen; Wang, Xing; Zhu, Jianfeng; Yang, Haibo; Kong, Xingang; Liu, Xiao

    2016-11-01

    3D network structure NiFe2O4 was successfully synthesized by a templated salt precipitation method using PMMA colloid crystal as templates. The morphology, phase composition and microwave absorbing properties of as-prepared samples were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), vector network analyzer (VNA), and so on. The results revealed that the 3D network structure was configurated with smooth spherical walls composed of NiFe2O4 nanocrystals and their pore diameters being in the range of 80–250 nm. The microwave absorption properties of the 3D network structure NiFe2O4 were crucially determined by the special structure. The synergy of intrinsic magnetic loss of magnetic NiFe2O4 and the interfacial polarization enhanced by 3D network structure and the interaction of multiple mechanisms endowed the sample with the feature of strong absorption, broad bandwidth and lightweight. There is more than one valley in the reflection loss curves and the maximum reflection loss is 27.5 dB with a bandwidth of 4 GHz. Moreover, the 3D network structure NiFe2O4 show a greater reflection loss with the same thickness comparing to the ordinary NiFe2O4 nanoparticles, which could achieve the feature of lightweight of the microwave absorbing materials.

  9. Capabilities of 3-D wavelet transforms to detect plume-like structures from seismic tomography

    Science.gov (United States)

    Bergeron, Stephen Y.; Yuen, David A.; Vincent, Alain P.

    2000-10-01

    The wavelet transform methods have been applied to viewing 3-D seismic tomography by casting the transformed quantities into two proxy distributions, E-max, the maximum of the magnitude of the local spectra about a local point and the associated local wavenumber, k-max. Using a stochastic background noise, we test the capability of this procedure in picking up the coherent structures of upper-mantle plumes. Plumes with a Gaussian shape and a characteristic width up to 2250 km have been tested for various amounts of the signal-to-noise ratios (SNR). We have found that plumes can be picked out for SNR as low as 0.08 db and that the optimal plume width for detection is around 1500 km. For plume width ranging between 700 km and 2000 km, the SNR can be lower than 1 db. This length-scale falls within the range for plume-detection based on the signal-to-noise levels associated with the current global tomographical models.

  10. Automated foveola localization in retinal 3D-OCT images using structural support vector machine prediction.

    Science.gov (United States)

    Liu, Yu-Ying; Ishikawa, Hiroshi; Chen, Mei; Wollstein, Gadi; Schuman, Joel S; Rehg, James M

    2012-01-01

    We develop an automated method to determine the foveola location in macular 3D-OCT images in either healthy or pathological conditions. Structural Support Vector Machine (S-SVM) is trained to directly predict the location of the foveola, such that the score at the ground truth position is higher than that at any other position by a margin scaling with the associated localization loss. This S-SVM formulation directly minimizes the empirical risk of localization error, and makes efficient use of all available training data. It deals with the localization problem in a more principled way compared to the conventional binary classifier learning that uses zero-one loss and random sampling of negative examples. A total of 170 scans were collected for the experiment. Our method localized 95.1% of testing scans within the anatomical area of the foveola. Our experimental results show that the proposed method can effectively identify the location of the foveola, facilitating diagnosis around this important landmark.

  11. Qualification of a 3D structured light sensor for a reverse engineering application

    Science.gov (United States)

    Guarato, Alexandre Z.; Loja, Alexandre C.; Pereira, Leonardo P.; Braga, Sergio L.; Trevilato, Thales R. B.

    2016-11-01

    This paper deals with the qualification of a 3D structured light scanning system for an application of reverse engineering of a mechanical part. As this white light scanner is an electro-optical device and based on the principle of optical triangulation, the measurement accuracy is affected by the measured part geometry and its position within the scanning window. The effects of the scan depth and the projected angle, characterizing the surface normal of the measured surface to the scanning point of view, on the measurement of accuracy are not considered in the standard calibration process of manufacturers and have been identified by experiments in the present work. The digitization errors are analyzed and characterized thanks to a measurement protocol based on quality indicators. Theses quality indicators are evaluated thanks to simple calibrated artifacts. The aim of this work is to redefine the ideal relative distance and relative angle for minimizing the digitizing errors in relation to those stated by the manufacturer for a reverse engineering application.

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

    Science.gov (United States)

    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.

  13. A 3D bioprinting system to produce human-scale tissue constructs with structural integrity.

    Science.gov (United States)

    Kang, Hyun-Wook; Lee, Sang Jin; Ko, In Kap; Kengla, Carlos; Yoo, James J; Atala, Anthony

    2016-03-01

    A challenge for tissue engineering is producing three-dimensional (3D), vascularized cellular constructs of clinically relevant size, shape and structural integrity. We present an integrated tissue-organ printer (ITOP) that can fabricate stable, human-scale tissue constructs of any shape. Mechanical stability is achieved by printing cell-laden hydrogels together with biodegradable polymers in integrated patterns and anchored on sacrificial hydrogels. The correct shape of the tissue construct is achieved by representing clinical imaging data as a computer model of the anatomical defect and translating the model into a program that controls the motions of the printer nozzles, which dispense cells to discrete locations. The incorporation of microchannels into the tissue constructs facilitates diffusion of nutrients to printed cells, thereby overcoming the diffusion limit of 100-200 μm for cell survival in engineered tissues. We demonstrate capabilities of the ITOP by fabricating mandible and calvarial bone, cartilage and skeletal muscle. Future development of the ITOP is being directed to the production of tissues for human applications and to the building of more complex tissues and solid organs.

  14. Construction of nitronyl nitroxide-based 3d-4f clusters: structure and magnetism.

    Science.gov (United States)

    Wang, Xiu-Feng; Hu, Peng; Li, Yun-Gai; Li, Li-Cun

    2015-02-01

    Three unprecedented nitronyl nitroxide radical-bridged 3d-4f clusters, [Ln2 Cu2 (hfac)10 (NIT-3py)2 (H2 O)2 ](Ln(III) =Y, Gd, Dy), have been obtained from the self-assembly of Ln(hfac)3 , Cu(hfac)2 , and the radical ligand. The Dy complex shows a slow relaxation of magnetization, representing the first nitronyl nitroxide radical-based 3d-4f cluster with single-molecule magnet behavior.

  15. Cardiac tissue structure. Electric field interactions in polarizing the heart: 3D computer models and applications

    Science.gov (United States)

    Entcheva, Emilia

    1998-11-01

    The goal of this research is to investigate the interactions between the cardiac tissue structure and applied electric fields in producing complex polarization patterns. It is hypothesized that the response of the heart in the conditions of strong electric shocks, as those applied in defibrillation, is dominated by mechanisms involving the cardiac muscle structure perceived as a continuum. Analysis is carried out in three-dimensional models of the heart with detailed fiber architecture. Shock-induced transmembrane potentials are calculated using the bidomain model in its finite element implementation. The major new findings of this study can be summarized as follows: (1) The mechanisms of polarization due to cardiac fiber curvature and fiber rotation are elucidated in three-dimensional ellipsoidal hearts of variable geometry; (2) Results are presented showing that the axis of stimulation and the polarization axis on a whole heart level might differ significantly due to geometric and anisotropic factors; (3) Virtual electrode patterns are demonstrated numerically inside the ventricular wall in internal defibrillation conditions. The role of the tissue-bath interface in shaping the shock-induced polarization is revealed; (4) The generation of 3D phase singularity scrolls by shock-induced intramural virtual electrode patterns is proposed as evidence for a possible new mechanism for the failure to defibrillate. The results of this study emphasize the role of unequal anisotropy in the intra- and extracellular domains, as well as the salient fiber architecture characteristics, such as curvature and transmural rotation, in polarizing the myocardium. Experimental support of the above findings was actively sought and found in recent optical mapping studies using voltage-sensitive dyes. If validated in vivo, these findings would significantly enrich the prevailing concepts about the mechanisms of stimulation and defibrillation of the heart.

  16. Hierarchical micro-lamella-structured 3D porous copper current collector coated with tin for advanced lithium-ion batteries

    Science.gov (United States)

    Park, Hyeji; Um, Ji Hyun; Choi, Hyelim; Yoon, Won-Sub; Sung, Yung-Eun; Choe, Heeman

    2017-03-01

    A Novel 3D porous Sn-Cu architecture is prepared as an anode material for use in an advanced lithium-ion battery. Micro-lamellar-structured 3D porous Cu foam, which is electroless-plated with Sn as an active material, is used as anode current collector. Compared to Sn-coated Cu foil, the 3D Sn-Cu foam exhibits superior Li-ion capacity and stable capacity retention, demonstrating the advantage of 3D porous architecture by preserving its structural integrity. In addition, the effect of heat-treatment after Sn plating is investigated. Sn/Sn6Cu5 and SnO2/Cu10Sn3 were formed on and in the 3D Sn-Cu foam under the heat-treatment at 150 °C and 500 °C, respectively. The development of Cu10Sn3 in the 3D Sn-Cu foam heat-treated at 500 °C can be a key factor for the enhanced cyclic stability because the Cu10Sn3 inactively reacts with Li-ion and alleviates the volume expansion of SnO2 as an inactive matrix.

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

    Directory of Open Access Journals (Sweden)

    Radhakrishna Bettadapura

    2015-10-01

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

  18. 2D and 3D GPR imaging of structural ceilings in historic and existing constructions

    Science.gov (United States)

    Colla, Camilla

    2014-05-01

    GPR applications in civil engineering are to date quite diversified. With respect to civil constructions and monumental buildings, detection of voids, cavities, layering in structural elements, variation of geometry, of moisture content, of materials, areas of decay, defects, cracks have been reported in timber, concrete and masonry elements. Nonetheless, many more fields of investigation remain unexplored. This contribution gives an account of a variety of examples of structural ceilings investigation by GPR radar in reflection mode, either as 2D or 3D data acquisition and visualisation. Ceilings have a pre-eminent role in buildings as they contribute to a good structural behaviour of the construction. Primarily, the following functions can be listed for ceilings: a) they carry vertical dead and live loads on floors and distribute such loads to the vertical walls; b) they oppose to external horizontal forces such as wind loads and earthquakes helping to transfer such forces from the loaded element to the other walls; c) they contribute to create the box skeleton and behaviour of a building, connecting the different load bearing walls and reducing the slenderness and flexural instability of such walls. Therefore, knowing how ceilings are made in specific buildings is of paramount importance for architects and structural engineers. According to the type of building and age of construction, ceilings may present very different solutions and materials. Moreover, in existing constructions, ceilings may have been substituted, modified or strengthened due to material decay or to change of use of the building. These alterations may often go unrecorded in technical documentation or technical drawings may be unavailable. In many cases, the position, orientation and number of the load carrying elements in ceilings may be hidden or not be in sight, due for example to the presence of false ceilings or to technical plants. GPR radar can constitute a very useful tool for

  19. High accuracy tracking of 2D/3D curved line-structures by consecutive cross-section matching

    NARCIS (Netherlands)

    Noordmans, H.J.; Smeulders, A.W.M.

    1998-01-01

    Curved 3D line-structures are found in domains such as angiography, cell biology and material science. This paper describes a new algorithm to track the line-structures with high subvoxel precision. Extra parameters determined for each cross-section are: local intensity, size, orientation and match

  20. Mapping of coma anisotropies to plasma structures of weak comets: a 3-D hybrid simulation study

    Directory of Open Access Journals (Sweden)

    N. Gortsas

    2009-04-01

    Full Text Available The effects of coma anisotropies on the plasma environment of comets have been studied by means of a 3-D hybrid model which treats electrons as a massless, charge-neutralizing fluid, whereas ion dynamics are covered by a kinetic approach. From Earth-based observations as well as from in-situ spacecraft measurements the shape of the coma of many comets is ascertained to be anisotropic. However, most plasma simulation studies deploy a spherically symmetric activity pattern. In this paper anisotropy is studied by considering three different coma shape models. The first model is derived from the Haser model and is characterised by spherically symmetry. This reference model is then compared with two different neutral gas shape models: the dayside restricted model with no nightside activity and a cone shaped model with opening angle of π/2. In all models the integrated surface activity is kept constant. The simulations have been done for the Rosetta target comet 67P/Churyumov-Gerasimenko for two heliocentric distances, 1.30 AU and 3.25 AU. It is found that shock formation processes are modified as a result of increasing spatial confinement. Characteristic plasma structures of comets such as the bow shock, magnetic barrier region and the ion composition boundary exhibit a shift towards the sun. In addition, the cone shaped model leads to a strong increase of the mass-loaded region which in turn leads to a smooth deceleration of the solar wind flow and an increasing degree of mixture between the solar wind and cometary ion species. This creates an additional transport channel of the magnetic field from the magnetic barrier region away which in turn leads to a broadening of this region. In addition, it leads to an ion composition boundary which is only gradually developed.

  1. Imaging of 3-D seismic velocity structure of Southern Sumatra region using double difference tomographic method

    Energy Technology Data Exchange (ETDEWEB)

    Lestari, Titik, E-mail: t2klestari@gmail.com [Meteorological Climatological and Geophysical Agency (MCGA), Jalan Angkasa I No.2 Kemayoran, Jakarta Pusat, 10720 (Indonesia); Faculty of Earth Science and Technology, Bandung Institute of Technology, Jalan Ganesa No.10, Bandung 40132 (Indonesia); Nugraha, Andri Dian, E-mail: nugraha@gf.itb.ac.id [Global Geophysical Research Group, Faculty of Mining and Petroleum Engineering, Bandung Institute of Technology, Jalan Ganesa 10 Bandung 40132 (Indonesia)

    2015-04-24

    Southern Sumatra region has a high level of seismicity due to the influence of the subduction system, Sumatra fault, Mentawai fault and stretching zone activities. The seismic activities of Southern Sumatra region are recorded by Meteorological Climatological and Geophysical Agency (MCGA’s) Seismograph network. In this study, we used earthquake data catalog compiled by MCGA for 3013 events from 10 seismic stations around Southern Sumatra region for time periods of April 2009 – April 2014 in order to invert for the 3-D seismic velocities structure (Vp, Vs, and Vp/Vs ratio). We applied double-difference seismic tomography method (tomoDD) to determine Vp, Vs and Vp/Vs ratio with hypocenter adjustment. For the inversion procedure, we started from the initial 1-D seismic velocity model of AK135 and constant Vp/Vs of 1.73. The synthetic travel time from source to receiver was calculated using ray pseudo-bending technique, while the main tomographic inversion was applied using LSQR method. The resolution model was evaluated using checkerboard test and Derivative Weigh Sum (DWS). Our preliminary results show low Vp and Vs anomalies region along Bukit Barisan which is may be associated with weak zone of Sumatran fault and migration of partial melted material. Low velocity anomalies at 30-50 km depth in the fore arc region may indicated the hydrous material circulation because the slab dehydration. We detected low seismic seismicity in the fore arc region that may be indicated as seismic gap. It is coincides contact zone of high and low velocity anomalies. And two large earthquakes (Jambi and Mentawai) also occurred at the contact of contrast velocity.

  2. Imaging of 3-D seismic velocity structure of Southern Sumatra region using double difference tomographic method

    Science.gov (United States)

    Lestari, Titik; Nugraha, Andri Dian

    2015-04-01

    Southern Sumatra region has a high level of seismicity due to the influence of the subduction system, Sumatra fault, Mentawai fault and stretching zone activities. The seismic activities of Southern Sumatra region are recorded by Meteorological Climatological and Geophysical Agency (MCGA's) Seismograph network. In this study, we used earthquake data catalog compiled by MCGA for 3013 events from 10 seismic stations around Southern Sumatra region for time periods of April 2009 - April 2014 in order to invert for the 3-D seismic velocities structure (Vp, Vs, and Vp/Vs ratio). We applied double-difference seismic tomography method (tomoDD) to determine Vp, Vs and Vp/Vs ratio with hypocenter adjustment. For the inversion procedure, we started from the initial 1-D seismic velocity model of AK135 and constant Vp/Vs of 1.73. The synthetic travel time from source to receiver was calculated using ray pseudo-bending technique, while the main tomographic inversion was applied using LSQR method. The resolution model was evaluated using checkerboard test and Derivative Weigh Sum (DWS). Our preliminary results show low Vp and Vs anomalies region along Bukit Barisan which is may be associated with weak zone of Sumatran fault and migration of partial melted material. Low velocity anomalies at 30-50 km depth in the fore arc region may indicated the hydrous material circulation because the slab dehydration. We detected low seismic seismicity in the fore arc region that may be indicated as seismic gap. It is coincides contact zone of high and low velocity anomalies. And two large earthquakes (Jambi and Mentawai) also occurred at the contact of contrast velocity.

  3. Potential energy curves and electronic structure of 3d transition metal hydrides and their cations.

    Science.gov (United States)

    Goel, Satyender; Masunov, Artëm E

    2008-12-07

    We investigate gas-phase neutral and cationic hydrides formed by 3d transition metals from Sc to Cu with density functional theory (DFT) methods. The performance of two exchange-correlation functionals, Boese-Martin for kinetics (BMK) and Tao-Perdew-Staroverov-Scuseria (TPSS), in predicting bond lengths and energetics, electronic structures, dipole moments, and ionization potentials is evaluated in comparison with available experimental data. To ensure a unique self-consistent field (SCF) solution, we use stability analysis, Fermi smearing, and continuity analysis of the potential energy curves. Broken-symmetry approach was adapted in order to get the qualitatively correct description of the bond dissociation. We found that on average BMK predicted values of dissociation energies and ionization potentials are closer to experiment than those obtained with high level wave function theory methods. This agreement deteriorates quickly when the fraction of the Hartree-Fock exchange in DFT functional is decreased. Natural bond orbital (NBO) population analysis was used to describe the details of chemical bonding in the systems studied. The multireference character in the wave function description of the hydrides is reproduced in broken-symmetry DFT description, as evidenced by NBO analysis. We also propose a new scheme to correct for spin contamination arising in broken-symmetry DFT approach. Unlike conventional schemes, our spin correction is introduced for each spin-polarized electron pair individually and therefore is expected to yield more accurate energy values. We derive an expression to extract the energy of the pure singlet state from the energy of the broken-symmetry DFT description of the low spin state and the energies of the high spin states (pentuplet and two spin-contaminated triplets in the case of two spin-polarized electron pairs). The high spin states are build with canonical natural orbitals and do not require SCF convergence.

  4. A Scalable Multiple Description Scheme for 3D Video Coding Based on the Interlayer Prediction Structure

    Directory of Open Access Journals (Sweden)

    Lorenzo Favalli

    2010-01-01

    Full Text Available The most recent literature indicates multiple description coding (MDC as a promising coding approach to handle the problem of video transmission over unreliable networks with different quality and bandwidth constraints. Furthermore, following recent commercial availability of autostereoscopic 3D displays that allow 3D visual data to be viewed without the use of special headgear or glasses, it is anticipated that the applications of 3D video will increase rapidly in the near future. Moving from the concept of spatial MDC, in this paper we introduce some efficient algorithms to obtain 3D substreams that also exploit some form of scalability. These algorithms are then applied to both coded stereo sequences and to depth image-based rendering (DIBR. In these algorithms, we first generate four 3D subsequences by subsampling, and then two of these subsequences are jointly used to form each of the two descriptions. For each description, one of the original subsequences is predicted from the other one via some scalable algorithms, focusing on the inter layer prediction scheme. The proposed algorithms can be implemented as pre- and postprocessing of the standard H.264/SVC coder that remains fully compatible with any standard coder. The experimental results presented show that these algorithms provide excellent results.

  5. Computational study on 3D structure of L-aspartic acid and L-glutamic acid: molecular descriptors and properties

    Directory of Open Access Journals (Sweden)

    Stefaniu Amalia

    2016-06-01

    Full Text Available The aim of this work is to provide a comprehensive and complex analysis of molecular descriptors and properties of two similar amino acids, L-Aspartic acid and L-Glutamic acid, using a software tool for calculations and properties predictions. As amino acids are model compounds for predicting the physical-chemical properties and behavior of biological, larger molecules as peptides or proteins, researches were focused on providing accurate mechanical calculations using: molecular/mechanical methods. Our study aims to initiate a linear scaling approach, by dividing a large system into small subsystems and performing the calculations for each, individually, then, embedding and correcting the information globally. The calculations were performed on the 3D structure of the studied amino acids that were first generated, as CPK model, and optimized by energy minimization. A comparative assay on their topological, molecular descriptors and properties was conducted, in vacuum and in water, using the Hartree-Fock model and second-order Møller-Plesset perturbation theory MP2 for predicting structure, energy and property calculations with Spartan’14 software. Values of molecular properties such as area, volume, polar surface area, polarizability, ovality, logP, dipole moment, HOMO-LUMO gap, distances and angles between atoms, were obtained. The results have been interpreted in terms of electronic effects of side chain groups, molecular deformability, steric factors and reactivity. This approach can be extended to other amino acids in order to predict protein-ligand interactions, important aspects in drug design studies and protein engineering.

  6. Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D

    Science.gov (United States)

    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

  7. 3D brain atlas reconstructor service--online repository of three-dimensional models of brain structures.

    Science.gov (United States)

    Majka, Piotr; Kowalski, Jakub M; Chlodzinska, Natalia; Wójcik, Daniel K

    2013-10-01

    Brain atlases are important tools of neuroscience. Traditionally prepared in paper book format, more and more commonly they take digital form which extends their utility. To simplify work with different atlases, to lay the ground for developing universal tools which could abstract from the origin of the atlas, efforts are being made to provide common interfaces to these atlases. 3D Brain Atlas Reconstructor service (3dBARs) described here is a repository of digital representations of different brain atlases in CAF format which we recently proposed and a repository of 3D models of brain structures. A graphical front-end is provided for creating and viewing the reconstructed models as well as the underlying 2D atlas data. An application programming interface (API) facilitates programmatic access to the service contents from other websites. From a typical user's point of view, 3dBARs offers an accessible way to mine publicly available atlasing data with a convenient browser based interface, without the need to install extra software. For a developer of services related to brain atlases, 3dBARs supplies mechanisms for enhancing functionality of other software. The policy of the service is to accept new datasets as delivered by interested parties and we work with the researchers who obtain original data to make them available to the neuroscience community at large. The functionality offered by the 3dBARs situates it at the core of present and future general atlasing services tying it strongly to the global atlasing neuroinformatics infrastructure.

  8. Recent Advances in Unconventional Lithography for Challenging 3D Hierarchical Structures and Their Applications

    Directory of Open Access Journals (Sweden)

    Jong Uk Kim

    2016-01-01

    Full Text Available In nanoscience and nanotechnology, nanofabrication is critical. Among the required processes for nanofabrication, lithography is one of core issues. Although conventional photolithography with recent remarkable improvement has contributed to the industry during the past few decades, fabrication of 3-dimensional (3D nanostructure is still challenging. In this review, we summarize recent advances for the construction of 3D nanostructures by unconventional lithography and the combination of two top-down approaches or top-down and bottom-up approaches. We believe that the 3D hierarchical nanostructures described here will have a broad range of applications having adaptable levels of functional integration of precisely controlled nanoarchitectures that are required by not only academia, but also industry.

  9. Introduction of DC line structures into a superconducting microwave 3D cavity

    Energy Technology Data Exchange (ETDEWEB)

    Kong, Wei-Cheng; Deng, Guang-Wei; Li, Shu-Xiao; Li, Hai-Ou; Cao, Gang; Xiao, Ming; Guo, Guo-Ping, E-mail: gpguo@ustc.edu.cn [Key Laboratory of Quantum Information, University of Science and Technology of China, Chinese Academy of Sciences, Hefei 230026, China and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2015-02-15

    We report a technique that can noninvasively add multiple DC wires into a 3D superconducting microwave cavity for electronic devices that require DC electrical terminals. We studied the influence of our DC lines on the cavity performance systematically. We found that the quality factor of the cavity is reduced if any of the components of the electrical wires cross the cavity equipotential planes. Using this technique, we were able to incorporate a quantum dot (QD) device into a 3D cavity. We then controlled and measured the QD transport signal using the DC lines. We have also studied the heating effects of the QD by the microwave photons in the cavity.

  10. A 3D universal structure based on molecular-QCA and CNT technologies

    Science.gov (United States)

    khosroshahy, Milad Bagherian; Daliri, Mahya Sam; Abdoli, Alireza; Navi, Keivan; Bagherzadeh, Nader

    2016-09-01

    This paper presents a novel method for design and implementation of three dimensional (3D) two-layer devices with 1/0 logic values. This method uses carbon nanotube (CNT) technology as well as the molecular quantum cellular automata (MQCA) technology on a graphene substrate. The most significant characteristic of the proposed design, which makes the design unique, is the capability of generating functions in 3D; the proposed method would allow implementation of the designs in a single layer which significantly impacts on reducing the chip area and also greatly facilitates the overall synthesis of the design including placement, routing and reducing the critical path length.

  11. 3D shape measurement of macroscopic objects in digital off-axis holography using structured illumination.

    Science.gov (United States)

    Grosse, Marcus; Buehl, Johannes; Babovsky, Holger; Kiessling, Armin; Kowarschik, Richard

    2010-04-15

    We propose what we believe to be a novel approach to measure the 3D shape of arbitrary diffuse-reflecting macroscopic objects in holographic setups. Using a standard holographic setup, a second CCD and a liquid-crystal-on-silicon spatial light modulator to modulate the object wave, the method yields a dense 3D point cloud of an object or a scene. The calibration process is presented, and first quantitative results of a shape measurement are shown and discussed. Furthermore, a shape measurement of a complex object is displayed to demonstrate its universal use.

  12. 3D P-Wave Velocity Structure of the Deep Galicia Rifted Margin

    Science.gov (United States)

    Bayrakci, Gaye; Minshull, Timothy; Davy, Richard; Sawyer, Dale; Klaeschen, Dirk; Papenberg, Cord; Reston, Timothy; Shillington, Donna; Ranero, Cesar

    2015-04-01

    The combined wide-angle reflection-refraction and multi-channel seismic (MCS) experiment, Galicia 3D, was carried out in 2013 at the Galicia rifted margin in the northeast Atlantic Ocean, west of Spain. The main geological features within the 64 by 20 km (1280 km²) 3D box investigated by the survey are the peridotite ridge (PR), the fault bounded, rotated basement blocks and the S reflector, which has been interpreted to be a low angle detachment fault. 44 short period four-component ocean bottom seismometers and 28 ocean bottom hydrophones were deployed in the 3D box. 3D MCS profiles sampling the whole box were acquired with two airgun arrays of 3300 cu.in. fired alternately every 37.5 m. We present the results from 3D first-arrival time tomography that constrains the P-wave velocity in the 3D box, for the entire depth sampled by reflection data. Results are validated by synthetic tests and by the comparison with Galicia 3D MCS lines. The main outcomes are as follows: 1- The 3.5 km/s iso-velocity contour mimics the top of the acoustic basement observed on MCS profiles. Block bounding faults are imaged as velocity contrasts and basement blocks exhibit 3D topographic variations. 2- On the southern profiles, the top of the PR rises up to 5.5 km depth whereas, 20 km northward, its basement expression (at 6.5 km depth) nearly disappears. 3- The 6.5 km/s iso-velocity contour matches the topography of the S reflector where the latter is visible on MCS profiles. Within a depth interval of 0.6 km (in average), velocities beneath the S reflector increase from 6.5 km/s to 7 km/s, which would correspond to a decrease in the degree of serpentinization from ~45 % to ~30 % if these velocity variations are caused solely by variations in hydration. At the intersections between the block bounding normal faults and the S reflector, this decrease happens over a larger depth interval (> 1 km), suggesting that faults act as conduit for the water flow in the upper mantle.

  13. Preservation of protein fluorescence in embedded human dendritic cells for targeted 3D light and electron microscopy.

    Science.gov (United States)

    Höhn, K; Fuchs, J; Fröber, A; Kirmse, R; Glass, B; Anders-Össwein, M; Walther, P; Kräusslich, H-G; Dietrich, C

    2015-08-01

    In this study, we present a correlative microscopy workflow to combine detailed 3D fluorescence light microscopy data with ultrastructural information gained by 3D focused ion beam assisted scanning electron microscopy. The workflow is based on an optimized high pressure freezing/freeze substitution protocol that preserves good ultrastructural detail along with retaining the fluorescence signal in the resin embedded specimens. Consequently, cellular structures of interest can readily be identified and imaged by state of the art 3D confocal fluorescence microscopy and are precisely referenced with respect to an imprinted coordinate system on the surface of the resin block. This allows precise guidance of the focused ion beam assisted scanning electron microscopy and limits the volume to be imaged to the structure of interest. This, in turn, minimizes the total acquisition time necessary to conduct the time consuming ultrastructural scanning electron microscope imaging while eliminating the risk to miss parts of the target structure. We illustrate the value of this workflow for targeting virus compartments, which are formed in HIV-pulsed mature human dendritic cells.

  14. ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs

    Science.gov (United States)

    Cleves, Ann E.; Jain, Ajay N.

    2017-03-01

    We introduce the ForceGen method for 3D structure generation and conformer elaboration of drug-like small molecules. ForceGen is novel, avoiding use of distance geometry, molecular templates, or simulation-oriented stochastic sampling. The method is primarily driven by the molecular force field, implemented using an extension of MMFF94s and a partial charge estimator based on electronegativity-equalization. The force field is coupled to algorithms for direct sampling of realistic physical movements made by small molecules. Results are presented on a standard benchmark from the Cambridge Crystallographic Database of 480 drug-like small molecules, including full structure generation from SMILES strings. Reproduction of protein-bound crystallographic ligand poses is demonstrated on four carefully curated data sets: the ConfGen Set (667 ligands), the PINC cross-docking benchmark (1062 ligands), a large set of macrocyclic ligands (182 total with typical ring sizes of 12-23 atoms), and a commonly used benchmark for evaluating macrocycle conformer generation (30 ligands total). Results compare favorably to alternative methods, and performance on macrocyclic compounds approaches that observed on non-macrocycles while yielding a roughly 100-fold speed improvement over alternative MD-based methods with comparable performance.

  15. A study of the effects of degraded imagery on tactical 3D model generation using structure-from-motion

    Science.gov (United States)

    Bolick, Leslie; Harguess, Josh

    2016-05-01

    An emerging technology in the realm of airborne intelligence, surveillance, and reconnaissance (ISR) systems is structure-from-motion (SfM), which enables the creation of three-dimensional (3D) point clouds and 3D models from two-dimensional (2D) imagery. There are several existing tools, such as VisualSFM and open source project OpenSfM, to assist in this process, however, it is well-known that pristine imagery is usually required to create meaningful 3D data from the imagery. In military applications, such as the use of unmanned aerial vehicles (UAV) for surveillance operations, imagery is rarely pristine. Therefore, we present an analysis of structure-from-motion packages on imagery that has been degraded in a controlled manner.

  16. Fabrication of scalable and structured tissue engineering scaffolds using water dissolvable sacrificial 3D printed moulds

    DEFF Research Database (Denmark)

    Mohanty, Soumyaranjan; Larsen, Layla Bashir; Trifol Guzman, Jon

    2015-01-01

    One of the major challenges in producing large scale engineered tissue is the lack of ability to create large highly perfused scaffolds in which cells can grow at a high cell density and viability. Here, we explore 3D printed polyvinyl alcohol (PVA) as a sacrificial mould in a polymer casting...

  17. NACr14: A 3D model for the crustal structure of the North American Continent

    NARCIS (Netherlands)

    Tesauro, Magdala; Kaban, Mikhail; Mooney, Walter; Cloetingh, Sierd

    2014-01-01

    Based on the large number of crustal seismic experiments carried out in the last decadeswe create NACr14, a 3D crustal model of the North American continent at a resolution of 1° × 1°. We present maps of thickness and average velocities of the main layers that comprise the North American crystalline

  18. PRONTO3D users` instructions: A transient dynamic code for nonlinear structural analysis

    Energy Technology Data Exchange (ETDEWEB)

    Attaway, S.W.; Mello, F.J.; Heinstein, M.W.; Swegle, J.W.; Ratner, J.A. [Sandia National Labs., Albuquerque, NM (United States); Zadoks, R.I. [Univ. of Texas, El Paso, TX (United States)

    1998-06-01

    This report provides an updated set of users` instructions for PRONTO3D. PRONTO3D is a three-dimensional, transient, solid dynamics code for analyzing large deformations of highly nonlinear materials subjected to extremely high strain rates. This Lagrangian finite element program uses an explicit time integration operator to integrate the equations of motion. Eight-node, uniform strain, hexahedral elements and four-node, quadrilateral, uniform strain shells are used in the finite element formulation. An adaptive time step control algorithm is used to improve stability and performance in plasticity problems. Hourglass distortions can be eliminated without disturbing the finite element solution using either the Flanagan-Belytschko hourglass control scheme or an assumed strain hourglass control scheme. All constitutive models in PRONTO3D are cast in an unrotated configuration defined using the rotation determined from the polar decomposition of the deformation gradient. A robust contact algorithm allows for the impact and interaction of deforming contact surfaces of quite general geometry. The Smooth Particle Hydrodynamics method has been embedded into PRONTO3D using the contact algorithm to couple it with the finite element method.

  19. The structural feasibility of 3D-printing houses using printable polymers

    NARCIS (Netherlands)

    Van der Veen, A.C.; Coenders, J.L.; Veer, F.A.; Nijsse, R.; Houtman, R.; Schonwalder, J.

    2015-01-01

    At this point in time, 3D-printing techniques in general, but especially applied for the building industry, still are in a phase of early experiments. One of the experimental attempts is to print a full-scale, three-story high, house in Amsterdam, using an up scaled version of a FDM-printer that is

  20. Efficient Structure-Aware Selection Techniques for 3D Point Cloud Visualizations with 2DOF Input

    NARCIS (Netherlands)

    Yu, Lingyun; Efstathiou, Konstantinos; Isenberg, Petra; Isenberg, Tobias

    2012-01-01

    Data selection is a fundamental task in visualization because it serves as a pre-requisite to many follow-up interactions. Efficient spatial selection in 3D point cloud datasets consisting of thousands or millions of particles can be particularly challenging. We present two new techniques, TeddySele

  1. Fluoride Bridges as Structure-Directing Motifs in 3d-4f Cluster Chemistry

    DEFF Research Database (Denmark)

    Birk, Torben; Pedersen, Kasper; Thuesen, Christian Aa.

    2012-01-01

    The use of kinetically robust chromium(III) fluorido complexes as synthons for mixed 3d-4f clusters is reported. The tendency toward linear {CrIII–F–LnIII} units dictates the cluster topology. Specifically, we show that reaction of cis-[CrIIIF2(NN)2]NO3 (NN = 1,10-phenanthroline (“phen”) or 2,2′-...

  2. Modelling and analysing 3D buildings with a primal/dual data structure

    NARCIS (Netherlands)

    Boguslawski, P.; Gold, C.; Ledoux, H.

    2011-01-01

    While CityGML permits us to represent 3D city models, its use for applications where spatial analysis and/or real-time modifications are required is limited since at this moment the possibility to store topological relationships between the elements is rather limited and often not exploited. We pres

  3. An Innovative Cell Microincubator for Drug Discovery Based on 3D Silicon Structures

    Directory of Open Access Journals (Sweden)

    Francesca Aredia

    2016-01-01

    Full Text Available We recently employed three-dimensional (3D silicon microstructures (SMSs consisting in arrays of 3 μm-thick silicon walls separated by 50 μm-deep, 5 μm-wide gaps, as microincubators for monitoring the biomechanical properties of tumor cells. They were here applied to investigate the in vitro behavior of HT1080 human fibrosarcoma cells driven to apoptosis by the chemotherapeutic drug Bleomycin. Our results, obtained by fluorescence microscopy, demonstrated that HT1080 cells exhibited a great ability to colonize the narrow gaps. Remarkably, HT1080 cells grown on 3D-SMS, when treated with the DNA damaging agent Bleomycin under conditions leading to apoptosis, tended to shrink, reducing their volume and mimicking the normal behavior of apoptotic cells, and were prone to leave the gaps. Finally, we performed label-free detection of cells adherent to the vertical silicon wall, inside the gap of 3D-SMS, by exploiting optical low coherence reflectometry using infrared, low power radiation. This kind of approach may become a new tool for increasing automation in the drug discovery area. Our results open new perspectives in view of future applications of the 3D-SMS as the core element of a lab-on-a-chip suitable for screening the effect of new molecules potentially able to kill tumor cells.

  4. Structuring Narrative in 3D Digital Game-Based Learning Environments to Support Second Language Acquisition

    Science.gov (United States)

    Neville, David O.

    2010-01-01

    The essay is a conceptual analysis from an instructional design perspective exploring the feasibility of using three-dimensional digital game-based learning (3D-DGBL) environments to assist in second language acquisition (SLA). It examines the shared characteristics of narrative within theories of situated cognition, context-based approaches to…

  5. Structure analysis of solution to equations of quasi 3-D accretion disk model

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    In this paper we discuss the problems contained in the solution to the equations of quasi 3-D accretion disk model, and point out that the angular momentum equation should not be integrated directly. Finally, we develop a criterion of the existence of a disconnected solution to this model.

  6. Robust and Elastic Lunar and Martian Structures from 3D-Printed Regolith Inks

    Science.gov (United States)

    Jakus, Adam E.; Koube, Katie D.; Geisendorfer, Nicholas R.; Shah, Ramille N.

    2017-03-01

    Here, we present a comprehensive approach for creating robust, elastic, designer Lunar and Martian regolith simulant (LRS and MRS, respectively) architectures using ambient condition, extrusion-based 3D-printing of regolith simulant inks. The LRS and MRS powders are characterized by distinct, highly inhomogeneous morphologies and sizes, where LRS powder particles are highly irregular and jagged and MRS powder particles are rough, but primarily rounded. The inks are synthesized via simple mixing of evaporant, surfactant, and plasticizer solvents, polylactic-co-glycolic acid (30% by solids volume), and regolith simulant powders (70% by solids volume). Both LRS and MRS inks exhibit similar rheological and 3D-printing characteristics, and can be 3D-printed at linear deposition rates of 1–150 mm/s using 300 μm to 1.4 cm-diameter nozzles. The resulting LRS and MRS 3D-printed materials exhibit similar, but distinct internal and external microstructures and material porosity (~20–40%). These microstructures contribute to the rubber-like quasi-static and cyclic mechanical properties of both materials, with young’s moduli ranging from 1.8 to 13.2 MPa and extension to failure exceeding 250% over a range of strain rates (10–1‑102 min‑1). Finally, we discuss the potential for LRS and MRS ink components to be reclaimed and recycled, as well as be synthesized in resource-limited, extraterrestrial environments.

  7. 3-D crustal and uppermost mantle structure beneath NE China revealed by ambient noise adjoint tomography

    Science.gov (United States)

    Liu, Yaning; Niu, Fenglin; Chen, Min; Yang, Wencai

    2017-03-01

    We construct a new 3-D shear wave speed model of the crust and the uppermost mantle beneath Northeast China using the ambient noise adjoint tomography method. Without intermediate steps of measuring phase dispersion, the adjoint tomography inverts for shear wave speeds of the crust and uppermost mantle directly from 6-40 s waveforms of Empirical Green's functions (EGFs) of Rayleigh waves, which are derived from interferometry of two years of ambient noise data recorded by the 127 Northeast China Extended Seismic Array stations. With an initial 3-D model derived from traditional asymptotic surface wave tomography method, adjoint tomography refines the 3-D model by iteratively minimizing the frequency-dependent traveltime misfits between EGFs and synthetic Green's functions measured in four period bands: 6-15 s, 10-20 s, 15-30 s, and 20-40 s. Our new model shows shear wave speed anomalies that are spatially correlated with known tectonic units such as the Great Xing'an range and the Changbaishan mountain range. The new model also reveals low wave speed conduits in the mid-lower crust and the uppermost mantle with a wave speed reduction indicative of partial melting beneath the Halaha, Xilinhot-Abaga, and Jingpohu volcanic complexes, suggesting that the Cenozoic volcanism in the area has a deep origin. Overall, the adjoint tomographic images show more vertically continuous velocity anomalies with larger amplitudes due to the consideration of the finite frequency and 3-D effects.

  8. 3D Reconstruction of the Glycocalyx Structure in Mammalian Capillaries using Electron Tomography

    DEFF Research Database (Denmark)

    Arkill, Kp; Neal, Cr; Mantell, Jm;

    2012-01-01

    success (e.g. freeze fracture). A new approach is therefore needed. Here we demonstrate the effectiveness of using the relatively novel electron microscopy technique of 3D electron tomography ontwo differently stained preparations to reveal details of the architecture of the glycocalyx just above...

  9. Theoretical study of relative width of photonic band gap for the 3-D dielectric structure

    Indian Academy of Sciences (India)

    G K Johri; Akhilesh Tiwari; Saumya Saxena; Rajesh Sharma; Kuldeep Srivastava; Manoj Johri

    2002-03-01

    Calculations for the relative width (/0) as a function of refractive index and relative radius of the photonic band gap for the fcc closed packed 3-D dielectric microstructure are reported and comparison of experimental observations and theoretical predictions are given. This work is useful for the understanding of photonic crystals and occurrence of the photonic band gap.

  10. A new structure of 3D