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Sample records for 3d structure prediction

  1. AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures

    PubMed Central

    Zambrano, Rafael; Jamroz, Michal; Szczasiuk, Agata; Pujols, Jordi; Kmiecik, Sebastian; Ventura, Salvador

    2015-01-01

    Protein aggregation underlies an increasing number of disorders and constitutes a major bottleneck in the development of therapeutic proteins. Our present understanding on the molecular determinants of protein aggregation has crystalized in a series of predictive algorithms to identify aggregation-prone sites. A majority of these methods rely only on sequence. Therefore, they find difficulties to predict the aggregation properties of folded globular proteins, where aggregation-prone sites are often not contiguous in sequence or buried inside the native structure. The AGGRESCAN3D (A3D) server overcomes these limitations by taking into account the protein structure and the experimental aggregation propensity scale from the well-established AGGRESCAN method. Using the A3D server, the identified aggregation-prone residues can be virtually mutated to design variants with increased solubility, or to test the impact of pathogenic mutations. Additionally, A3D server enables to take into account the dynamic fluctuations of protein structure in solution, which may influence aggregation propensity. This is possible in A3D Dynamic Mode that exploits the CABS-flex approach for the fast simulations of flexibility of globular proteins. The A3D server can be accessed at http://biocomp.chem.uw.edu.pl/A3D/. PMID:25883144

  2. RNAComposer and RNA 3D structure prediction for nanotechnology.

    PubMed

    Biesiada, Marcin; Pachulska-Wieczorek, Katarzyna; Adamiak, Ryszard W; Purzycka, Katarzyna J

    2016-07-01

    RNAs adopt specific, stable tertiary architectures to perform their activities. Knowledge of RNA tertiary structure is fundamental to understand RNA functions beginning with transcription and ending with turnover. Contrary to advanced RNA secondary structure prediction algorithms, which allow good accuracy when experimental data are integrated into the prediction, tertiary structure prediction of large RNAs still remains a significant challenge. However, the field of RNA tertiary structure prediction is rapidly developing and new computational methods based on different strategies are emerging. RNAComposer is a user-friendly and freely available server for 3D structure prediction of RNA up to 500 nucleotide residues. RNAComposer employs fully automated fragment assembly based on RNA secondary structure specified by the user. Importantly, this method allows incorporation of distance restraints derived from the experimental data to strengthen the 3D predictions. The potential and limitations of RNAComposer are discussed and an application to RNA design for nanotechnology is presented. PMID:27016145

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

    PubMed

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

    2014-07-01

    A new improved hybrid optimization algorithm - PGATS algorithm, which is based on toy off-lattice model, is presented for dealing with three-dimensional protein structure prediction problems. The algorithm combines the particle swarm optimization (PSO), genetic algorithm (GA), and tabu search (TS) algorithms. Otherwise, we also take some different improved strategies. The factor of stochastic disturbance is joined in the particle swarm optimization to improve the search ability; the operations of crossover and mutation that are in the genetic algorithm are changed to a kind of random liner method; at last tabu search algorithm is improved by appending a mutation operator. Through the combination of a variety of strategies and algorithms, the protein structure prediction (PSP) in a 3D off-lattice model is achieved. The PSP problem is an NP-hard problem, but the problem can be attributed to a global optimization problem of multi-extremum and multi-parameters. This is the theoretical principle of the hybrid optimization algorithm that is proposed in this paper. The algorithm combines local search and global search, which overcomes the shortcoming of a single algorithm, giving full play to the advantage of each algorithm. In the current universal standard sequences, Fibonacci sequences and real protein sequences are certified. Experiments show that the proposed new method outperforms single algorithms on the accuracy of calculating the protein sequence energy value, which is proved to be an effective way to predict the structure of proteins. PMID:25069136

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

    PubMed Central

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

    2015-01-01

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

  5. 3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping.

    PubMed

    Lo, Yu-Chen; Senese, Silvia; Damoiseaux, Robert; Torres, Jorge Z

    2016-08-19

    Target identification remains a major challenge for modern drug discovery programs aimed at understanding the molecular mechanisms of drugs. Computational target prediction approaches like 2D chemical similarity searches have been widely used but are limited to structures sharing high chemical similarity. Here, we present a new computational approach called chemical similarity network analysis pull-down 3D (CSNAP3D) that combines 3D chemical similarity metrics and network algorithms for structure-based drug target profiling, ligand deorphanization, and automated identification of scaffold hopping compounds. In conjunction with 2D chemical similarity fingerprints, CSNAP3D achieved a >95% success rate in correctly predicting the drug targets of 206 known drugs. Significant improvement in target prediction was observed for HIV reverse transcriptase (HIVRT) compounds, which consist of diverse scaffold hopping compounds targeting the nucleotidyltransferase binding site. CSNAP3D was further applied to a set of antimitotic compounds identified in a cell-based chemical screen and identified novel small molecules that share a pharmacophore with Taxol and display a Taxol-like mechanism of action, which were validated experimentally using in vitro microtubule polymerization assays and cell-based assays. PMID:27285961

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

    PubMed

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

    2013-09-01

    The problem of protein structure prediction in the hydrophobic-polar (HP) lattice model is the prediction of protein tertiary structure. This problem is usually referred to as the protein folding problem. This paper presents a method for the application of an enhanced hybrid search algorithm to the problem of protein folding prediction, using the three dimensional (3D) HP lattice model. The enhanced hybrid search algorithm is a combination of the particle swarm optimizer (PSO) and tabu search (TS) algorithms. Since the PSO algorithm entraps local minimum in later evolution extremely easily, we combined PSO with the TS algorithm, which has properties of global optimization. Since the technologies of crossover and mutation are applied many times to PSO and TS algorithms, so enhanced hybrid search algorithm is called the MCMPSO-TS (multiple crossover and mutation PSO-TS) algorithm. Experimental results show that the MCMPSO-TS algorithm can find the best solutions so far for the listed benchmarks, which will help comparison with any future paper approach. Moreover, real protein sequences and Fibonacci sequences are verified in the 3D HP lattice model for the first time. Compared with the previous evolutionary algorithms, the new hybrid search algorithm is novel, and can be used effectively to predict 3D protein folding structure. With continuous development and changes in amino acids sequences, the new algorithm will also make a contribution to the study of new protein sequences. PMID:23824509

  7. Molecular Phylogeny and Predicted 3D Structure of Plant beta-D-N-Acetylhexosaminidase

    PubMed Central

    Hossain, Md. Anowar

    2014-01-01

    beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom. PMID:25165734

  8. The deep geothermal potential of Berlin (Germany) - Predictions from 3D structural and thermal modelling

    NASA Astrophysics Data System (ADS)

    Sippel, Judith; Fuchs, Sven; Cacace, Mauro; Kastner, Oliver; Huenges, Ernst; Scheck-Wenderoth, Magdalena

    2013-04-01

    In the light of an aspired reduction of CO2 emissions for Germany's capital Berlin, one possible alternative for meeting the city's growing energy demands lies in deep geothermal energy. To minimise exploration risks, a profound knowledge about the subsurface temperature distribution is indispensable. We present a 3D structural model that is used for thermal modelling and thus correlates calculated subsurface temperatures with geothermally relevant structures in the deep subsurface of Berlin - an ideal base for improving the probability of finding adequate geothermal reservoirs. Berlin is located in the eastern part of the North German Basin which is filled with several thousand metres of Permian to Cenozoic sediments containing hot and water bearing aquifers to potentially be used as hydrothermal reservoirs. To characterise the geological underground, the 3D structural model integrates stratigraphical, petrophysical and well-log based information from local boreholes as well as stratigraphic trends from (seismic data based) regional 3D models. The model differentiates 21 geological units: 17 Permian-Cenozoic sedimentary layers, pre-Permian sediments, upper crust, lower crust and the lithospheric mantle. Based on this 3D geological model complemented by databased lithology-dependent thermal properties, two groups of numerical thermal simulations have been carried out: calculations of the steady-state conductive thermal field and simulations of coupled fluid and heat transport. The 3D thermal models predict large lateral variations in temperatures that are validated by high-precession temperature logs. These variations are mostly caused by three specific geological layers and their physical properties: the Permian Zechstein salt with its markedly high thermal conductivity and strong thickness variation (171-3442 m); the crystalline upper crustal layer with its high radiogenic heat production and decreasing thickness from east to west; and the Tertiary Rupelian

  9. 3D protein structure prediction using Imperialist Competitive algorithm and half sphere exposure prediction.

    PubMed

    Khaji, Erfan; Karami, Masoumeh; Garkani-Nejad, Zahra

    2016-02-21

    Predicting the native structure of proteins based on half-sphere exposure and contact numbers has been studied deeply within recent years. Online predictors of these vectors and secondary structures of amino acids sequences have made it possible to design a function for the folding process. By choosing variant structures and directs for each secondary structure, a random conformation can be generated, and a potential function can then be assigned. Minimizing the potential function utilizing meta-heuristic algorithms is the final step of finding the native structure of a given amino acid sequence. In this work, Imperialist Competitive algorithm was used in order to accelerate the process of minimization. Moreover, we applied an adaptive procedure to apply revolutionary changes. Finally, we considered a more accurate tool for prediction of secondary structure. The results of the computational experiments on standard benchmark show the superiority of the new algorithm over the previous methods with similar potential function. PMID:26718864

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

    PubMed Central

    Kerpedjiev, Peter; Höner zu Siederdissen, Christian; Hofacker, Ivo L.

    2015-01-01

    A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sample tertiary structures given a secondary structure. It strikes a balance between the precision of an all-atom tertiary structure model and the simplicity and effectiveness of a secondary structure representation. It provides a simplified tool for exploring global arrangements of helices and loops within RNA structures. We provide an example of a novel energy function relying only on the positions of stems and loops. We show that coupling our model to this energy function produces predictions as good as or better than the current state of the art tools. We propose that given the wide range of conformational space that needs to be explored, a coarse-grain approach can explore more conformations in less iterations than an all-atom model coupled to a fine-grain energy function. Finally, we emphasize the overarching theme of providing an ensemble of predicted structures, something which our tool excels at, rather than providing a handful of the lowest energy structures. PMID:25904133

  11. mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome.

    PubMed

    Meyer, Michael J; Lapcevic, Ryan; Romero, Alfonso E; Yoon, Mark; Das, Jishnu; Beltrán, Juan Felipe; Mort, Matthew; Stenson, Peter D; Cooper, David N; Paccanaro, Alberto; Yu, Haiyuan

    2016-05-01

    A new algorithm and Web server, mutation3D (http://mutation3d.org), proposes driver genes in cancer by identifying clusters of amino acid substitutions within tertiary protein structures. We demonstrate the feasibility of using a 3D clustering approach to implicate proteins in cancer based on explorations of single proteins using the mutation3D Web interface. On a large scale, we show that clustering with mutation3D is able to separate functional from nonfunctional mutations by analyzing a combination of 8,869 known inherited disease mutations and 2,004 SNPs overlaid together upon the same sets of crystal structures and homology models. Further, we present a systematic analysis of whole-genome and whole-exome cancer datasets to demonstrate that mutation3D identifies many known cancer genes as well as previously underexplored target genes. The mutation3D Web interface allows users to analyze their own mutation data in a variety of popular formats and provides seamless access to explore mutation clusters derived from over 975,000 somatic mutations reported by 6,811 cancer sequencing studies. The mutation3D Web interface is freely available with all major browsers supported. PMID:26841357

  12. Novel 3D bio-macromolecular bilinear descriptors for protein science: Predicting protein structural classes.

    PubMed

    Marrero-Ponce, Yovani; Contreras-Torres, Ernesto; García-Jacas, César R; Barigye, Stephen J; Cubillán, Néstor; Alvarado, Ysaías J

    2015-06-01

    In the present study, we introduce novel 3D protein descriptors based on the bilinear algebraic form in the ℝ(n) space on the coulombic matrix. For the calculation of these descriptors, macromolecular vectors belonging to ℝ(n) space, whose components represent certain amino acid side-chain properties, were used as weighting schemes. Generalization approaches for the calculation of inter-amino acidic residue spatial distances based on Minkowski metrics are proposed. The simple- and double-stochastic schemes were defined as approaches to normalize the coulombic matrix. The local-fragment indices for both amino acid-types and amino acid-groups are presented in order to permit characterizing fragments of interest in proteins. On the other hand, with the objective of taking into account specific interactions among amino acids in global or local indices, geometric and topological cut-offs are defined. To assess the utility of global and local indices a classification model for the prediction of the major four protein structural classes, was built with the Linear Discriminant Analysis (LDA) technique. The developed LDA-model correctly classifies the 92.6% and 92.7% of the proteins on the training and test sets, respectively. The obtained model showed high values of the generalized square correlation coefficient (GC(2)) on both the training and test series. The statistical parameters derived from the internal and external validation procedures demonstrate the robustness, stability and the high predictive power of the proposed model. The performance of the LDA-model demonstrates the capability of the proposed indices not only to codify relevant biochemical information related to the structural classes of proteins, but also to yield suitable interpretability. It is anticipated that the current method will benefit the prediction of other protein attributes or functions. PMID:25843214

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

    PubMed Central

    Hao, Zhikui; Wu, Hangui; Yang, Meiling; Chen, Jianjun; Xi, Limin; Zhao, Weijie; Yu, Jialin; Liu, Jiayang; Liao, Xiangru; Huang, Qingguo

    2016-01-01

    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. PMID:27240345

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

    PubMed

    Hao, Zhikui; Wu, Hangui; Yang, Meiling; Chen, Jianjun; Xi, Limin; Zhao, Weijie; Yu, Jialin; Liu, Jiayang; Liao, Xiangru; Huang, Qingguo

    2016-01-01

    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 Fe(3+), Fe(2+), and Zn(2+) 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. PMID:27240345

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

    PubMed

    Meier, Armin; Söding, Johannes

    2015-10-01

    Homology modeling predicts the 3D structure of a query protein based on the sequence alignment with one or more template proteins of known structure. Its great importance for biological research is owed to its speed, simplicity, reliability and wide applicability, covering more than half of the residues in protein sequence space. Although multiple templates have been shown to generally increase model quality over single templates, the information from multiple templates has so far been combined using empirically motivated, heuristic approaches. We present here a rigorous statistical framework for multi-template homology modeling. First, we find that the query proteins' atomic distance restraints can be accurately described by two-component Gaussian mixtures. This insight allowed us to apply the standard laws of probability theory to combine restraints from multiple templates. Second, we derive theoretically optimal weights to correct for the redundancy among related templates. Third, a heuristic template selection strategy is proposed. We improve the average GDT-ha model quality score by 11% over single template modeling and by 6.5% over a conventional multi-template approach on a set of 1000 query proteins. Robustness with respect to wrong constraints is likewise improved. We have integrated our multi-template modeling approach with the popular MODELLER homology modeling software in our free HHpred server http://toolkit.tuebingen.mpg.de/hhpred and also offer open source software for running MODELLER with the new restraints at https://bitbucket.org/soedinglab/hh-suite. PMID:26496371

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  17. Automated Foveola Localization in Retinal 3D-OCT Images Using Structural Support Vector Machine Prediction

    PubMed Central

    Liu, Yu-Ying; Ishikawa, Hiroshi; Chen, Mei; Wollstein, Gadi; Schuman, Joel S.; Rehg, James M.

    2013-01-01

    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. PMID:23285565

  18. A coarse-grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect

    SciTech Connect

    Shi, Ya-Zhou; Wang, Feng-Hua; Wu, Yuan-Yan; Tan, Zhi-Jie

    2014-09-14

    To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the room/body temperature and high salt (1M NaCl), and thus generally hardly predict the thermodynamics and salt effect. In this study, we propose a coarse-grained model with implicit salt for RNAs to predict 3D structures, stability, and salt effect. Combined with Monte Carlo simulated annealing algorithm and a coarse-grained force field, the model folds 46 tested RNAs (≤45 nt) including pseudoknots into their native-like structures from their sequences, with an overall mean RMSD of 3.5 Å and an overall minimum RMSD of 1.9 Å from the experimental structures. For 30 RNA hairpins, the present model also gives the reliable predictions for the stability and salt effect with the mean deviation ∼ 1.0 °C of melting temperatures, as compared with the extensive experimental data. In addition, the model could provide the ensemble of possible 3D structures for a short RNA at a given temperature/salt condition.

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

    PubMed

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

    2016-04-20

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

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

    PubMed Central

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

    2016-01-01

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

  1. Assessing a novel approach for predicting local 3D protein structures from sequence.

    PubMed

    Benros, Cristina; de Brevern, Alexandre G; Etchebest, Catherine; Hazout, Serge

    2006-03-01

    We developed a novel approach for predicting local protein structure from sequence. It relies on the Hybrid Protein Model (HPM), an unsupervised clustering method we previously developed. This model learns three-dimensional protein fragments encoded into a structural alphabet of 16 protein blocks (PBs). Here, we focused on 11-residue fragments encoded as a series of seven PBs and used HPM to cluster them according to their local similarities. We thus built a library of 120 overlapping prototypes (mean fragments from each cluster), with good three-dimensional local approximation, i.e., a mean accuracy of 1.61 A Calpha root-mean-square distance. Our prediction method is intended to optimize the exploitation of the sequence-structure relations deduced from this library of long protein fragments. This was achieved by setting up a system of 120 experts, each defined by logistic regression to optimize the discrimination from sequence of a given prototype relative to the others. For a target sequence window, the experts computed probabilities of sequence-structure compatibility for the prototypes and ranked them, proposing the top scorers as structural candidates. Predictions were defined as successful when a prototype <2.5 A from the true local structure was found among those proposed. Our strategy yielded a prediction rate of 51.2% for an average of 4.2 candidates per sequence window. We also proposed a confidence index to estimate prediction quality. Our approach predicts from sequence alone and will thus provide valuable information for proteins without structural homologs. Candidates will also contribute to global structure prediction by fragment assembly. PMID:16385557

  2. UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling

    PubMed Central

    Bhattacharya, Debswapna; Cao, Renzhi; Cheng, Jianlin

    2016-01-01

    Motivation: Recent experimental studies have suggested that proteins fold via stepwise assembly of structural units named ‘foldons’ through the process of sequential stabilization. Alongside, latest developments on computational side based on probabilistic modeling have shown promising direction to perform de novo protein conformational sampling from continuous space. However, existing computational approaches for de novo protein structure prediction often randomly sample protein conformational space as opposed to experimentally suggested stepwise sampling. Results: Here, we develop a novel generative, probabilistic model that simultaneously captures local structural preferences of backbone and side chain conformational space of polypeptide chains in a united-residue representation and performs experimentally motivated conditional conformational sampling via stepwise synthesis and assembly of foldon units that minimizes a composite physics and knowledge-based energy function for de novo protein structure prediction. The proposed method, UniCon3D, has been found to (i) sample lower energy conformations with higher accuracy than traditional random sampling in a small benchmark of 6 proteins; (ii) perform comparably with the top five automated methods on 30 difficult target domains from the 11th Critical Assessment of Protein Structure Prediction (CASP) experiment and on 15 difficult target domains from the 10th CASP experiment; and (iii) outperform two state-of-the-art approaches and a baseline counterpart of UniCon3D that performs traditional random sampling for protein modeling aided by predicted residue-residue contacts on 45 targets from the 10th edition of CASP. Availability and Implementation: Source code, executable versions, manuals and example data of UniCon3D for Linux and OSX are freely available to non-commercial users at http://sysbio.rnet.missouri.edu/UniCon3D/. Contact: chengji@missouri.edu Supplementary information: Supplementary data are

  3. High Resolution Prediction of Calcium-Binding Sites in 3D Protein Structures Using FEATURE

    PubMed Central

    2015-01-01

    Metal-binding proteins are ubiquitous in biological systems ranging from enzymes to cell surface receptors. Among the various biologically active metal ions, calcium plays a large role in regulating cellular and physiological changes. With the increasing number of high-quality crystal structures of proteins associated with their metal ion ligands, many groups have built models to identify Ca2+ sites in proteins, utilizing information such as structure, geometry, or homology to do the inference. We present a FEATURE-based approach in building such a model and show that our model is able to discriminate between nonsites and calcium-binding sites with a very high precision of more than 98%. We demonstrate the high specificity of our model by applying it to test sets constructed from other ions. We also introduce an algorithm to convert high scoring regions into specific site predictions and demonstrate the usage by scanning a test set of 91 calcium-binding protein structures (190 calcium sites). The algorithm has a recall of more than 93% on the test set with predictions found within 3 Å of the actual sites. PMID:26226489

  4. A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence.

    PubMed

    Rice, D W; Eisenberg, D

    1997-04-11

    In protein fold recognition, a probe amino acid sequence is compared to a library of representative folds of known structure to identify a structural homolog. In cases where the probe and its homolog have clear sequence similarity, traditional residue substitution matrices have been used to predict the structural similarity. In cases where the probe is sequentially distant from its homolog, we have developed a (7 x 3 x 2 x 7 x 3) 3D-1D substitution matrix (called H3P2), calculated from a database of 119 structural pairs. Members of each pair share a similar fold, but have sequence identity less than 30%. Each probe sequence position is defined by one of seven residue classes and three secondary structure classes. Each homologous fold position is defined by one of seven residue classes, three secondary structure classes, and two burial classes. Thus the matrix is five-dimensional and contains 7 x 3 x 2 x 7 x 3 = 882 elements or 3D-1D scores. The first step in assigning a probe sequence to its homologous fold is the prediction of the three-state (helix, strand, coil) secondary structure of the probe; here we use the profile based neural network prediction of secondary structure (PHD) program. Then a dynamic programming algorithm uses the H3P2 matrix to align the probe sequence with structures in a representative fold library. To test the effectiveness of the H3P2 matrix a challenging, fold class diverse, and cross-validated benchmark assessment is used to compare the H3P2 matrix to the GONNET, PAM250, BLOSUM62 and a secondary structure only substitution matrix. For distantly related sequences the H3P2 matrix detects more homologous structures at higher reliabilities than do these other substitution matrices, based on sensitivity versus specificity plots (or SENS-SPEC plots). The added efficacy of the H3P2 matrix arises from its information on the statistical preferences for various sequence-structure environment combinations from very distantly related proteins. It

  5. 3D-graphite structure

    SciTech Connect

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

    2011-01-15

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

  6. The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists

    NASA Astrophysics Data System (ADS)

    Kalani, M. Yashar S.; Vaidehi, Nagarajan; Hall, Spencer E.; Trabanino, Rene J.; Freddolino, Peter L.; Kalani, Maziyar A.; Floriano, Wely B.; Tak Kam, Victor Wai; Goddard, William A., III

    2004-03-01

    Dopamine neurotransmitter and its receptors play a critical role in the cell signaling process responsible for information transfer in neurons functioning in the nervous system. Development of improved therapeutics for such disorders as Parkinson's disease and schizophrenia would be significantly enhanced with the availability of the 3D structure for the dopamine receptors and of the binding site for dopamine and other agonists and antagonists. We report here the 3D structure of the long isoform of the human D2 dopamine receptor, predicted from primary sequence using first-principles theoretical and computational techniques (i.e., we did not use bioinformatic or experimental 3D structural information in predicting structures). The predicted 3D structure is validated by comparison of the predicted binding site and the relative binding affinities of dopamine, three known dopamine agonists (antiparkinsonian), and seven known antagonists (antipsychotic) in the D2 receptor to experimentally determined values. These structures correctly predict the critical residues for binding dopamine and several antagonists, identified by mutation studies, and give relative binding affinities that correlate well with experiments. The predicted binding site for dopamine and agonists is located between transmembrane (TM) helices 3, 4, 5, and 6, whereas the best antagonists bind to a site involving TM helices 2, 3, 4, 6, and 7 with minimal contacts to TM helix 5. We identify characteristic differences between the binding sites of agonists and antagonists.

  7. Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand- and structure-based approaches.

    PubMed

    Ragno, Rino; Ballante, Flavio; Pirolli, Adele; Wickersham, Richard B; Patsilinakos, Alexandros; Hesse, Stéphanie; Perspicace, Enrico; Kirsch, Gilbert

    2015-08-01

    Vascular endothelial growth factor receptor-2, (VEGFR-2), is a key element in angiogenesis, the process by which new blood vessels are formed, and is thus an important pharmaceutical target. Here, 3-D quantitative structure-activity relationship (3-D QSAR) were used to build a quantitative screening and pharmacophore model of the VEGFR-2 receptors for design of inhibitors with improved activities. Most of available experimental data information has been used as training set to derive optimized and fully cross-validated eight mono-probe and a multi-probe quantitative models. Notable is the use of 262 molecules, aligned following both structure-based and ligand-based protocols, as external test set confirming the 3-D QSAR models' predictive capability and their usefulness in design new VEGFR-2 inhibitors. From a survey on literature, this is the first generation of a wide-ranging computational medicinal chemistry application on VEGFR2 inhibitors. PMID:26194852

  8. Structure based 3D-QSAR studies of Interleukin-2 inhibitors: Comparing the quality and predictivity of 3D-QSAR models obtained from different alignment methods and charge calculations.

    PubMed

    Halim, Sobia Ahsan; Zaheer-ul-Haq

    2015-08-01

    Interleukin-2 is an essential cytokine in an innate immune response, and is a promising drug target for several immunological disorders. In the present study, structure-based 3D-QSAR modeling was carried out via Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Index Analysis (CoMSIA) methods. Six different partial charge calculation methods were used in combination with two different alignment methods to scrutinize their effects on the predictive power of 3D-QSAR models. The best CoMFA and CoMSIA models were obtained with the AM1 charges when used with co-conformer based substructure alignment (CCBSA) method. The obtained models posses excellent correlation coefficient value and also exhibited good predictive power (for CoMFA: q(2)=0.619; r(2)=0.890; r(2)Pred=0.765 and for CoMSIA: q(2)=0.607; r(2)=0.884; r(2)Pred=0.655). The developed models were further validated by using a set of another sixteen compounds as external test set 2 and both models showed strong predictive power with r(2)Pred=>0.8. The contour maps obtained from these models better interpret the structure activity relationship; hence the developed models would help to design and optimize more potent IL-2 inhibitors. The results might have implications for rational design of specific anti-inflammatory compounds with improved affinity and selectivity. PMID:26051521

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

    PubMed

    Dawson, Wayne K; Bujnicki, Janusz M

    2016-04-01

    RNA molecules have key functions in cellular processes beyond being carriers of protein-coding information. These functions are often dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is difficult, which has prompted the development of computational methods for structure prediction from sequence. Recent progress in 3D structure modeling of RNA and emerging approaches for predicting RNA interactions with ions, ligands and proteins have been stimulated by successes in protein 3D structure modeling. PMID:26689764

  10. USM3D Predictions of Supersonic Nozzle Flow

    NASA Technical Reports Server (NTRS)

    Carter, Melissa B.; Elmiligui, Alaa A.; Campbell, Richard L.; Nayani, Sudheer N.

    2014-01-01

    This study focused on the NASA Tetrahedral Unstructured Software System CFD code (USM3D) capability to predict supersonic plume flow. Previous studies, published in 2004 and 2009, investigated USM3D's results versus historical experimental data. This current study continued that comparison however focusing on the use of the volume souring to capture the shear layers and internal shock structure of the plume. This study was conducted using two benchmark axisymmetric supersonic jet experimental data sets. The study showed that with the use of volume sourcing, USM3D was able to capture and model a jet plume's shear layer and internal shock structure.

  11. 3D Structure Prediction of Human β1-Adrenergic Receptor via Threading-Based Homology Modeling for Implications in Structure-Based Drug Designing

    PubMed Central

    Ul-Haq, Zaheer; Saeed, Maria; Halim, Sobia Ahsan; Khan, Waqasuddin

    2015-01-01

    Dilated cardiomyopathy is a disease of left ventricular dysfunction accompanied by impairment of the β1-adrenergic receptor (β1-AR) signal cascade. The disturbed β1-AR function may be based on an elevated sympathetic tone observed in patients with heart failure. Prolonged adrenergic stimulation may induce metabolic and electrophysiological disturbances in the myocardium, resulting in tachyarrhythmia that leads to the development of heart failure in human and sudden death. Hence, β1-AR is considered as a promising drug target but attempts to develop effective and specific drug against this tempting pharmaceutical target is slowed down due to the lack of 3D structure of Homo sapiens β1-AR (hsβADR1). This study encompasses elucidation of 3D structural and physicochemical properties of hsβADR1 via threading-based homology modeling. Furthermore, the docking performance of several docking programs including Surflex-Dock, FRED, and GOLD were validated by re-docking and cross-docking experiments. GOLD and Surflex-Dock performed best in re-docking and cross docking experiments, respectively. Consequently, Surflex-Dock was used to predict the binding modes of four hsβADR1 agonists. This study provides clear understanding of hsβADR1 structure and its binding mechanism, thus help in providing the remedial solutions of cardiovascular, effective treatment of asthma and other diseases caused by malfunctioning of the target protein. PMID:25860348

  12. 3D structure prediction of human β1-adrenergic receptor via threading-based homology modeling for implications in structure-based drug designing.

    PubMed

    Ul-Haq, Zaheer; Saeed, Maria; Halim, Sobia Ahsan; Khan, Waqasuddin

    2015-01-01

    Dilated cardiomyopathy is a disease of left ventricular dysfunction accompanied by impairment of the β1-adrenergic receptor (β1-AR) signal cascade. The disturbed β1-AR function may be based on an elevated sympathetic tone observed in patients with heart failure. Prolonged adrenergic stimulation may induce metabolic and electrophysiological disturbances in the myocardium, resulting in tachyarrhythmia that leads to the development of heart failure in human and sudden death. Hence, β1-AR is considered as a promising drug target but attempts to develop effective and specific drug against this tempting pharmaceutical target is slowed down due to the lack of 3D structure of Homo sapiens β1-AR (hsβADR1). This study encompasses elucidation of 3D structural and physicochemical properties of hsβADR1 via threading-based homology modeling. Furthermore, the docking performance of several docking programs including Surflex-Dock, FRED, and GOLD were validated by re-docking and cross-docking experiments. GOLD and Surflex-Dock performed best in re-docking and cross docking experiments, respectively. Consequently, Surflex-Dock was used to predict the binding modes of four hsβADR1 agonists. This study provides clear understanding of hsβADR1 structure and its binding mechanism, thus help in providing the remedial solutions of cardiovascular, effective treatment of asthma and other diseases caused by malfunctioning of the target protein. PMID:25860348

  13. 3D FSE Cube and VIPR-aTR 3.0 Tesla magnetic resonance imaging predicts canine cranial cruciate ligament structural properties.

    PubMed

    Racette, Molly; Al saleh, Habib; Waller, Kenneth R; Bleedorn, Jason A; McCabe, Ronald P; Vanderby, Ray; Markel, Mark D; Brounts, Sabrina H; Block, Walter F; Muir, Peter

    2016-03-01

    Estimation of cranial cruciate ligament (CrCL) structural properties in client-owned dogs with incipient cruciate rupture would be advantageous. The objective of this study was to determine whether magnetic resonance imaging (MRI) measurement of normal CrCL volume in an ex-vivo canine model predicts structural properties. Stifles from eight dogs underwent 3.0 Tesla 3D MRI. CrCL volume and normalized median grayscale values were determined using 3D Fast Spin Echo (FSE) Cube and Vastly under-sampled Isotropic PRojection (VIPR)-alternative repetition time (aTR) sequences. Stifles were then mechanically tested. After joint laxity testing, CrCL structural properties were determined, including displacement at yield, yield load, load to failure, and stiffness. Yield load and load to failure (R(2)=0.56, P <0.01) were correlated with CrCL volume determined by VIPR-aTR. Yield load was also correlated with CrCL volume determined by 3D FSE Cube (R(2)=0.32, P <0.05). Structural properties were not related to median grayscale values. Joint laxity and CrCL stiffness were not related to MRI parameters, but displacement at yield load was related to CrCL volume for both sequences during testing (R(2)>0.57, P <0.005). In conclusion, 3D MRI offers a predictive method for estimating canine CrCL structural properties. 3D MRI may be useful for monitoring CrCL properties in clinical trials. PMID:26831152

  14. Three-dimensional (3D) structure prediction of the American and African oil-palms β-ketoacyl-[ACP] synthase-II protein by comparative modelling

    PubMed Central

    Wang, Edina; Chinni, Suresh; Bhore, Subhash Janardhan

    2014-01-01

    Background: The fatty-acid profile of the vegetable oils determines its properties and nutritional value. Palm-oil obtained from the African oil-palm [Elaeis guineensis Jacq. (Tenera)] contains 44% palmitic acid (C16:0), but, palm-oil obtained from the American oilpalm [Elaeis oleifera] contains only 25% C16:0. In part, the b-ketoacyl-[ACP] synthase II (KASII) [EC: 2.3.1.179] protein is responsible for the high level of C16:0 in palm-oil derived from the African oil-palm. To understand more about E. guineensis KASII (EgKASII) and E. oleifera KASII (EoKASII) proteins, it is essential to know its structures. Hence, this study was undertaken. Objective: The objective of this study was to predict three-dimensional (3D) structure of EgKASII and EoKASII proteins using molecular modelling tools. Materials and Methods: The amino-acid sequences for KASII proteins were retrieved from the protein database of National Center for Biotechnology Information (NCBI), USA. The 3D structures were predicted for both proteins using homology modelling and ab-initio technique approach of protein structure prediction. The molecular dynamics (MD) simulation was performed to refine the predicted structures. The predicted structure models were evaluated and root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values were calculated. Results: The homology modelling showed that EgKASII and EoKASII proteins are 78% and 74% similar with Streptococcus pneumonia KASII and Brucella melitensis KASII, respectively. The EgKASII and EoKASII structures predicted by using ab-initio technique approach shows 6% and 9% deviation to its structures predicted by homology modelling, respectively. The structure refinement and validation confirmed that the predicted structures are accurate. Conclusion: The 3D structures for EgKASII and EoKASII proteins were predicted. However, further research is essential to understand the interaction of EgKASII and EoKASII proteins with its substrates. PMID

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

    PubMed Central

    Ge, Ping; Zhang, Shaojie

    2015-01-01

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

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

    PubMed

    Ge, Ping; Zhang, Shaojie

    2015-11-16

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

  17. 3D Structured Grid Adaptation

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

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

  18. Structured light field 3D imaging.

    PubMed

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

    2016-09-01

    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. PMID:27607639

  19. FUN3D and CFL3D Computations for the First High Lift Prediction Workshop

    NASA Technical Reports Server (NTRS)

    Park, Michael A.; Lee-Rausch, Elizabeth M.; Rumsey, Christopher L.

    2011-01-01

    Two Reynolds-averaged Navier-Stokes codes were used to compute flow over the NASA Trapezoidal Wing at high lift conditions for the 1st AIAA CFD High Lift Prediction Workshop, held in Chicago in June 2010. The unstructured-grid code FUN3D and the structured-grid code CFL3D were applied to several different grid systems. The effects of code, grid system, turbulence model, viscous term treatment, and brackets were studied. The SST model on this configuration predicted lower lift than the Spalart-Allmaras model at high angles of attack; the Spalart-Allmaras model agreed better with experiment. Neglecting viscous cross-derivative terms caused poorer prediction in the wing tip vortex region. Output-based grid adaptation was applied to the unstructured-grid solutions. The adapted grids better resolved wake structures and reduced flap flow separation, which was also observed in uniform grid refinement studies. Limitations of the adaptation method as well as areas for future improvement were identified.

  20. CFL3D, FUN3d, and NSU3D Contributions to the Fifth Drag Prediction Workshop

    NASA Technical Reports Server (NTRS)

    Park, Michael A.; Laflin, Kelly R.; Chaffin, Mark S.; Powell, Nicholas; Levy, David W.

    2013-01-01

    Results presented at the Fifth Drag Prediction Workshop using CFL3D, FUN3D, and NSU3D are described. These are calculations on the workshop provided grids and drag adapted grids. The NSU3D results have been updated to reflect an improvement to skin friction calculation on skewed grids. FUN3D results generated after the workshop are included for custom participant generated grids and a grid from a previous workshop. Uniform grid refinement at the design condition shows a tight grouping in calculated drag, where the variation in the pressure component of drag is larger than the skin friction component. At this design condition, A fine-grid drag value was predicted with a smaller drag adjoint adapted grid via tetrahedral adaption to a metric and mixed-element subdivision. The buffet study produced larger variation than the design case, which is attributed to large differences in the predicted side-of-body separation extent. Various modeling and discretization approaches had a strong impact on predicted side-of-body separation. This large wing root separation bubble was not observed in wind tunnel tests indicating that more work is necessary in modeling wing root juncture flows to predict experiments.

  1. 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

    PubMed Central

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

    2010-01-01

    An integer linear optimization model is presented to predict residue contacts in β, α + β, and α/β proteins. The total energy of a protein is expressed as sum of a Cα – Cα distance dependent contact energy contribution and a hydrophobic contribution. The model selects contacts that assign lowest energy to the protein structure while 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 β-sheet alignments. These β-sheet alignments are used as constraints for contacts between residues of β-sheets. This model was tested on three independent protein test sets and CASP8 test proteins consisting of β, α + β, α/β proteins and 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 Å and 15.88 Å, 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. PMID:20225257

  2. patGPCR: A Multitemplate Approach for Improving 3D Structure Prediction of Transmembrane Helices of G-Protein-Coupled Receptors

    PubMed Central

    Wu, Hongjie; Lü, Qiang; Quan, Lijun; Qian, Peide; Xia, Xiaoyan

    2013-01-01

    The structures of the seven transmembrane helices of G-protein-coupled receptors are critically involved in many aspects of these receptors, such as receptor stability, ligand docking, and molecular function. Most of the previous multitemplate approaches have built a “super” template with very little merging of aligned fragments from different templates. Here, we present a parallelized multitemplate approach, patGPCR, to predict the 3D structures of transmembrane helices of G-protein-coupled receptors. patGPCR, which employs a bundle-packing related energy function that extends on the RosettaMem energy, parallelizes eight pipelines for transmembrane helix refinement and exchanges the optimized helix structures from multiple templates. We have investigated the performance of patGPCR on a test set containing eight determined G-protein-coupled receptors. The results indicate that patGPCR improves the TM RMSD of the predicted models by 33.64% on average against a single-template method. Compared with other homology approaches, the best models for five of the eight targets built by patGPCR had a lower TM RMSD than that obtained from SWISS-MODEL; patGPCR also showed lower average TM RMSD than single-template and multiple-template MODELLER. PMID:23554839

  3. Predicted 3D-structure of melanopsin, the non-rod, non-cone photopigment of the mammalian circadian clock, from Djungarian hamsters (Phodopus sungorus).

    PubMed

    Hermann, Ralph; Poppe, László; Pilbák, Sarolta; Boden, Carolin; Maurer, Jochen; Weber, Susanne; Lerchl, Alexander

    2005-03-11

    Melanopsin is the photopigment of the retinal ganglion cells, which are involved in the synchronization of the biological clock in the suprachiasmatic nucleus (SCN) of mammals with the exogenous photoperiod. So far, no information about the three-dimensional (3D) structure of melanopsin is available. Here we report the predicted structure based on the protein-coding region of the nucleotide sequence of the gene for melanopsin, originating from isolated mRNA from the eyes of Djungarian hamsters (Phodopus sungorus). The nucleotide sequence shares the largest homologies with melanopsin of mice and rats (each 89%) and humans (84%). Based on the amino-acid sequence, and in comparison with the known structure of bovine rhodopsin, the three-dimensional melanopsin protein structure was modeled by using automated homology modeling approaches that were subsequently refined. Melanopsin consists of highly conserved seven-transmembrane domains and a long cytoplasmatic tail with multiple putative phosphorylation sites. In the binding site of the chromophore, a 11-cis-retinal is likely to be bound to lysine at position 336 as Schiff's base. The modeling results may indicate different photoisomerization within the melanopsin molecule compared with bovine rhodopsin. PMID:15698924

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

    PubMed

    Suyama, M; Matsuo, Y; Nishikawa, K

    1997-01-01

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

  5. Inferential modeling of 3D chromatin structure

    PubMed Central

    Wang, Siyu; Xu, Jinbo; Zeng, Jianyang

    2015-01-01

    For eukaryotic cells, the biological processes involving regulatory DNA elements play an important role in cell cycle. Understanding 3D spatial arrangements of chromosomes and revealing long-range chromatin interactions are critical to decipher these biological processes. In recent years, chromosome conformation capture (3C) related techniques have been developed to measure the interaction frequencies between long-range genome loci, which have provided a great opportunity to decode the 3D organization of the genome. In this paper, we develop a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data. By modeling each chromosome as a polymer chain, we define the conformational energy based on our current knowledge on polymer physics and use it as prior information in the Bayesian framework. We also propose an expectation-maximization (EM) based algorithm to estimate the unknown parameters of the Bayesian model and infer an ensemble of chromatin structures based on interaction frequency data. We have validated our Bayesian inference approach through cross-validation and verified the computed chromatin conformations using the geometric constraints derived from fluorescence in situ hybridization (FISH) experiments. We have further confirmed the inferred chromatin structures using the known genetic interactions derived from other studies in the literature. Our test results have indicated that our Bayesian framework can compute an accurate ensemble of 3D chromatin conformations that best interpret the distance constraints derived from 3C-based data and also agree with other sources of geometric constraints derived from experimental evidence in the previous studies. The source code of our approach can be found in https://github.com/wangsy11/InfMod3DGen. PMID:25690896

  6. 3D high resolution mineral phase distribution and seismic velocity structure of the transition zone: predicted by a full spherical-shell compressible mantle convection model

    NASA Astrophysics Data System (ADS)

    Geenen, T.; Heister, T.; Van Den Berg, A. P.; Jacobs, M.; Bangerth, W.

    2011-12-01

    We present high resolution 3D results of the complex mineral phase distribution in the transition zone obtained by numerical modelling of mantle convection. We extend the work by [Jacobs and van den Berg, 2011] to 3D and illustrate the efficiency of adaptive mesh refinement for capturing the complex spatial distribution and sharp phase transitions as predicted by their model. The underlying thermodynamical model is based on lattice dynamics which allows to predict thermophysical properties and seismic wave speeds for the applied magnesium-endmember olivine-pyroxene mineralogical model. The use of 3D geometry allows more realistic prediction of phase distribution and seismic wave speeds resulting from 3D flow processes involving the Earth's transition zone and more significant comparisons with interpretations from seismic tomography and seismic reflectivity studies aimed at the transition zone. Model results are generated with a recently developed geodynamics modeling application based on dealII (www.dealii.org). We extended this model to incorporate both a general thermodynamic model, represented by P,T space tabulated thermophysical properties, and a solution strategy that allows for compressible flow. When modeling compressible flow in the so called truncated anelastic approximation framework we have to adapt the solver strategy that has been proven by several authors to be highly efficient for incompressible flow to incorporate an extra term in the continuity equation. We present several possible solution strategies and discuss their implication in terms of robustness and computational efficiency.

  7. 3D structure and nuclear targets

    NASA Astrophysics Data System (ADS)

    Dupré, Raphaël; Scopetta, Sergio

    2016-06-01

    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 summarized, in particular novel coincidence measurements at high-luminosity facilities, such as Jefferson Laboratory. Finally the prospects for the next years at future facilities, such as the 12GeV Jefferson Laboratory and the Electron Ion Collider, are presented.

  8. Discovering Structural Regularity in 3D Geometry

    PubMed Central

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

    2010-01-01

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

  9. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.

    PubMed

    Sarver, Michael; Zirbel, Craig L; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B

    2008-01-01

    New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, "Find RNA 3D" (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs whose

  10. Challenges in Lagrangian transport and predictability in 3D flows

    NASA Astrophysics Data System (ADS)

    Branicki, M.; Wiggins, S.; Kirwan, A. D.; Malek-Madani, R.

    2011-12-01

    The interplay between the geometrical theory of dynamical systems and the trajectory-based description of aperiodically time-dependent fluid flows has led to significant advances in understanding the role of chaotic transport in geophysical flows at scales dominated by advection. Lagrangian transport analysis utilizing either the time-dependent geometry of intersecting stable and unstable manifolds of the so-called Distinguished Hyperbolic Trajectories (DHT), or ridges of finite-time Lyapunov exponent fields (LCS), provide a much needed and complementary insight into ephemeral mechanisms responsible for the existence of `leaky' transport barriers and 'leaky' mesoscale eddies. However, to date most oceanic applications have been confined to 2D analysis of near surface regions in 'perfect' flows not accounting for model or measurement error, and with the tacit assumption of negligible vertical velocities. I will systematically address issues concerning the regimes of applicability of two-dimensional analysis in 3D aperiodically time-dependent flows, as well as outstanding challenges in fully 3D Lagrangian transport analysis. Even for perfect horizontal velocities, little is known about the vertical extent of stable/unstable manifolds associated with DHTs and/or other special structures relevant to stratified 3D flows. In particular, their sensitivity to errors in the vertical velocities and data assimilation methods has been little studied. Rigorous results regarding the above issues will be illustrated by revealing and mathematically tractable toy models, as well as examples from a detailed study in an eddy-rich region from the Gulf of Mexico and the Mediterranean. New ways of quantifying the uncertainty in Lagrangian predictions will also be presented.

  11. 3D Structure of Tillage Soils

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  12. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

    PubMed Central

    Sarver, Michael; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B.

    2010-01-01

    New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, “Find RNA 3D” (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs

  13. 3-D structures of planetary nebulae

    NASA Astrophysics Data System (ADS)

    Steffen, W.

    2016-07-01

    Recent advances in the 3-D reconstruction of planetary nebulae are reviewed. We include not only results for 3-D reconstructions, but also the current techniques in terms of general methods and software. In order to obtain more accurate reconstructions, we suggest to extend the widely used assumption of homologous nebula expansion to map spectroscopically measured velocity to position along the line of sight.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  16. Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. A response to the letter by the Cambridge Crystallographic Data Centre.

    PubMed

    Baldi, Pierre

    2011-12-27

    A response is presented to sentiments expressed in "Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response from The Cambridge Crystallographic Data Centre", recently published in the Journal of Chemical Information and Modeling, (1) which may give readers a misleading impression regarding significant impediments to scientific research posed by the CCDC. PMID:22107601

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

    PubMed

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

    2015-07-01

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

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

    PubMed Central

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

    2015-01-01

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

  19. 3D-GNOME: an integrated web service for structural modeling of the 3D genome

    PubMed Central

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

    2016-01-01

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

  20. 3D-GNOME: an integrated web service for structural modeling of the 3D genome.

    PubMed

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

    2016-07-01

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

  1. Predicted residue-residue contacts can help the scoring of 3D models.

    PubMed

    Tress, Michael L; Valencia, Alfonso

    2010-06-01

    During the 7th Critical Assessment of Protein Structure Prediction (CASP7) experiment, it was suggested that the real value of predicted residue-residue contacts might lie in the scoring of 3D model structures. Here, we have carried out a detailed reassessment of the contact predictions made during the recent CASP8 experiment to determine whether predicted contacts might aid in the selection of close-to-native structures or be a useful tool for scoring 3D structural models. We used the contacts predicted by the CASP8 residue-residue contact prediction groups to select models for each target domain submitted to the experiment. We found that the information contained in the predicted residue-residue contacts would probably have helped in the selection of 3D models in the free modeling regime and over the harder comparative modeling targets. Indeed, in many cases, the models selected using just the predicted contacts had better GDT-TS scores than all but the best 3D prediction groups. Despite the well-known low accuracy of residue-residue contact predictions, it is clear that the predictive power of contacts can be useful in 3D model prediction strategies. PMID:20408174

  2. 3D Printing: 3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures.

    PubMed

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

    2015-07-15

    X. Zhao and co-workers develop on page 4035 a new biocompatible hydrogel system that is extremely tough and stretchable and can be 3D printed into complex structures, such as the multilayer mesh shown. Cells encapsulated in the tough and printable hydrogel maintain high viability. 3D-printed structures of the tough hydrogel can sustain high mechanical loads and deformations. PMID:26172844

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    2008-07-01

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

  5. Structure-odor correlations in homologous series of alkanethiols and attempts to predict odor thresholds by 3D-QSAR studies.

    PubMed

    Polster, Johannes; Schieberle, Peter

    2015-02-11

    Homologous series of alkane-1-thiols, alkane-2-thiols, alkane-3-thiols, 2-methylalkane-1-thiols, 2-methylalkane-3-thiols, 2-methylalkane-2-thiols, and alkane-1,ω-dithiols were synthesized to study the influence of structural changes on odor qualities and odor thresholds. In particular, the odor thresholds were strongly influenced by steric effects: In all homologous series a minimum was observed for thiols with five to seven carbon atoms, whereas increasing the chain length led to an exponential increase in the odor threshold. Tertiary alkanethiols revealed clearly lower odor thresholds than found for primary or secondary thiols, whereas neither a second mercapto group in the molecule nor an additional methyl substitution lowered the threshold. To investigate the impact of the SH group, odor thresholds and odor qualities of thiols were compared to those of the corresponding alcohols and (methylthio)alkanes. Replacement of the SH group by an OH group as well as S-methylation of the thiols significantly increased the odor thresholds. By using comparative molecular field analysis, a 3D quantitative structure-activity relationship model was created, which was able to simulate the odor thresholds of alkanethiols in good agreement with the experimental results. NMR and mass spectrometric data for 46 sulfur-containing compounds are additionally supplied. PMID:25608797

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

    NASA Astrophysics Data System (ADS)

    Jaiswal, Neeru; Kishtawal, C. M.

    2016-05-01

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

  7. Patient-Specific Mitral Valve Closure Prediction using 3D Echocardiography

    PubMed Central

    Burlina, Philippe; Sprouse, Chad; Mukherjee, Ryan; DeMenthon, Daniel; Abraham, Theodore

    2013-01-01

    This paper presents an approach to modeling the closure of the mitral valve using patient-specific anatomical information derived from 3D transesophageal echocardiography (3D TEE). Our approach uses physics-based modeling to solve for the stationary configuration of the closed valve structure from the patient-specific open valve structure, which is recovered using a user-in-the-loop, thin-tissue detector segmentation. The method utilizes a tensile shape finding approach based on energy minimization. This method is used to predict the aptitude of the mitral valve leaflets to coapt. We tested the method using ten intraoperative 3D TEE sequences by comparing (a) the closed valve configuration predicted from the segmented open valve, with (b) the segmented closed valve, taken as ground truth. Experiments show promising results, with prediction errors on par with 3D TEE resolution and with good potential for applications in pre-operative planning. PMID:23497987

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

    NASA Astrophysics Data System (ADS)

    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.

  9. Unit cell geometry of 3-D braided structures

    NASA Technical Reports Server (NTRS)

    Du, Guang-Wu; Ko, Frank K.

    1993-01-01

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

  10. Performance prediction for 3D filtering of multichannel images

    NASA Astrophysics Data System (ADS)

    Rubel, Oleksii; Kozhemiakin, Ruslan A.; Abramov, Sergey K.; Lukin, Vladimir V.; Vozel, Benoit; Chehdi, Kacem

    2015-10-01

    Performance of denoising based on discrete cosine transform applied to multichannel remote sensing images corrupted by additive white Gaussian noise is analyzed. Images obtained by satellite Earth Observing-1 (EO-1) mission using hyperspectral imager instrument (Hyperion) that have high input SNR are taken as test images. Denoising performance is characterized by improvement of PSNR. For hard-thresholding 3D DCT-based denoising, simple statistics (probabilities to be less than a certain threshold) are used to predict denoising efficiency using curves fitted into scatterplots. It is shown that the obtained curves (approximations) provide prediction of denoising efficiency with high accuracy. Analysis is carried out for different numbers of channels processed jointly. Universality of prediction for different number of channels is proven.

  11. 3D visualization of middle ear structures

    NASA Astrophysics Data System (ADS)

    Vogel, Uwe; Schmitt, Thomas

    1998-06-01

    The achievement of volume geometry data from middle ear structures and surrounding components performs a necessary supposition for the finite element simulation of the vibrational and transfer characteristics of the ossicular chain. So far those models base on generalized figures and size data from anatomy textbooks or particular manual and one- or two-dimensional distance measurements of single ossicles, mostly obtained by light microscopy, respectively. Therefore the goal of this study is to create a procedure for complete three-dimensional imaging of real middle ear structures (tympanic membrane, ossicles, ligaments) in vitro or even in vivo. The main problems are their microscopic size with relevant structures from 10 micrometer to 5 mm, representing various tissue properties (bone, soft tissue). Additionally, these structures are surrounded by the temporal bone, the most solid bone of the human body. Generally there exist several established diagnostic tools for medical imaging that could be used for geometry data acquisition, e.g., X-ray computed tomography and magnetic resonance imaging. Basically they image different tissue parameters, either bony structures (ossicles), or soft tissue (tympanic membrane, ligaments). But considering this application those standard techniques allow low spatial resolution only, usually in the 0.5 - 1mm range, at least in one spatial direction. Thus particular structures of the middle ear region could even be missed completely because of their spatial location. In vitro there is a way out by collecting three complete data sets, each distinguished by 90 degree rotation of a cube-shaped temporal bone specimen. That allows high-resolution imaging in three orthogonal planes, which essentially supports the three-dimensional interpolation of the unknown elements, starting from the regularly set elements of the cubic grid with an edge extension given by the original two-dimensional matrix. A different approach represents the

  12. Acetylcholinesterase: From 3D Structure to Function

    PubMed Central

    Dvir, Hay; Silman, Israel; Harel, Michal; Rosenberry, Terrone L.; Sussman, Joel L.

    2010-01-01

    By rapid hydrolysis of the neurotransmitter, acetylcholine, acetylcholinesterase terminates neurotransmission at cholinergic synapses. Acetylcholinesterase is a very fast enzyme, functioning at a rate approaching that of a diffusion-controlled reaction. The powerful toxicity of organophosphate poisons is attributed primarily to their potent inhibition of acetylcholinesterase. Acetylcholinesterase inhibitors are utilized in the treatment of various neurological disorders, and are the principal drugs approved thus far by the FDA for management of Alzheimer’s disease. Many organophosphates and carbamates serve as potent insecticides, by selectively inhibiting insect acetylcholinesterase. The determination of the crystal structure of Torpedo californica acetylcholinesterase permitted visualization, for the first time, at atomic resolution, of a binding pocket for acetylcholine. It also allowed identification of the active site of acetylcholinesterase, which, unexpectedly, is located at the bottom of a deep gorge lined largely by aromatic residues. The crystal structure of recombinant human acetylcholinesterase in its apo-state is similar in its overall features to that of the Torpedo enzyme; however, the unique crystal packing reveals a novel peptide sequence which blocks access to the active-site gorge. PMID:20138030

  13. Assist feature printability prediction by 3-D resist profile reconstruction

    NASA Astrophysics Data System (ADS)

    Zheng, Xin; Huang, Jensheng; Chin, Fook; Kazarian, Aram; Kuo, Chun-Chieh

    2012-06-01

    properties may then be used to optimize the printability vs. efficacy of an SRAF either prior to or during an Optical Proximity Correction (OPC) run. The process models that are used during OPC have never been able to reliably predict which SRAFs will print. This appears to be due to the fact that OPC process models are generally created using data that does not include printed subresolution patterns. An enhancement to compact modeling capability to predict Assist Features (AF) printability is developed and discussed. A hypsometric map representing 3-D resist profile was built by applying a first principle approximation to estimate the "energy loss" from the resist top to bottom. Such a 3-D resist profile is an extrapolation of a well calibrated traditional OPC model without any additional information. Assist features are detected at either top of resist (dark field) or bottom of resist (bright field). Such detection can be done by just extracting top or bottom resist models from our 3-D resist model. There is no measurement of assist features needed when we build AF but it can be included if interested but focusing on resist calibration to account for both exposure dosage and focus change sensitivities. This approach significantly increases resist model's capability for predicting printed SRAF accuracy. And we don't need to calibrate an SRAF model in addition to the OPC model. Without increase in computation time, this compact model can draw assist feature contour with real placement and size at any vertical plane. The result is compared and validated with 3-D rigorous modeling as well as SEM images. Since this method does not change any form of compact modeling, it can be integrated into current MBAF solutions without any additional work.

  14. Protein 3D Structure Computed from Evolutionary Sequence Variation

    PubMed Central

    Sheridan, Robert; Hopf, Thomas A.; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

    2011-01-01

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

  15. 3D structures of membrane proteins from genomic sequencing

    PubMed Central

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

    2012-01-01

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

  16. Formal representation of 3D structural geological models

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  17. Capacitance extraction from complex 3D interconnect structures

    SciTech Connect

    Cartwright, D.; Csanak, G.; George, D.; Walker, R.; Kuprat, A.; Dengi, A.; Grobman, W.

    1999-06-01

    A new tool has been developed for calculating the capacitance matrix for complex 3D interconnect structures involving multiple layers of irregularly shaped interconnect, imbedded in different dielectric materials. This method utilizes a new 3D adaptive unstructured grid capability, and a linear finite element algorithm. The capacitance is determined from the minimum in the total system energy as the nodes are varied to minimize the error in the electric field in the dielectric(s).

  18. 3D annotation and manipulation of medical anatomical structures

    NASA Astrophysics Data System (ADS)

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

    2009-02-01

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

  19. 3D Ultrasonic Wave Simulations for Structural Health Monitoring

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

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

  20. Slat Cove Unsteadiness Effect of 3D Flow Structures

    NASA Technical Reports Server (NTRS)

    Choudhari, Meelan M.; Khorrami, Mehdi R.

    2006-01-01

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

  1. Quality Prediction of Asymmetrically Distorted Stereoscopic 3D Images.

    PubMed

    Wang, Jiheng; Rehman, Abdul; Zeng, Kai; Wang, Shiqi; Wang, Zhou

    2015-11-01

    Objective quality assessment of distorted stereoscopic images is a challenging problem, especially when the distortions in the left and right views are asymmetric. Existing studies suggest that simply averaging the quality of the left and right views well predicts the quality of symmetrically distorted stereoscopic images, but generates substantial prediction bias when applied to asymmetrically distorted stereoscopic images. In this paper, we first build a database that contains both single-view and symmetrically and asymmetrically distorted stereoscopic images. We then carry out a subjective test, where we find that the quality prediction bias of the asymmetrically distorted images could lean toward opposite directions (overestimate or underestimate), depending on the distortion types and levels. Our subjective test also suggests that eye dominance effect does not have strong impact on the visual quality decisions of stereoscopic images. Furthermore, we develop an information content and divisive normalization-based pooling scheme that improves upon structural similarity in estimating the quality of single-view images. Finally, we propose a binocular rivalry-inspired multi-scale model to predict the quality of stereoscopic images from that of the single-view images. Our results show that the proposed model, without explicitly identifying image distortion types, successfully eliminates the prediction bias, leading to significantly improved quality prediction of the stereoscopic images. PMID:26087491

  2. Predicted 3D Model of the Rabies Virus Glycoprotein Trimer.

    PubMed

    Fernando, Bastida-González; Yersin, Celaya-Trejo; José, Correa-Basurto; Paola, Zárate-Segura

    2016-01-01

    The RABVG ectodomain is a homotrimer, and trimers are often called spikes. They are responsible for the attachment of the virus through the interaction with nicotinic acetylcholine receptors, neural cell adhesion molecule (NCAM), and the p75 neurotrophin receptor (p75NTR). This makes them relevant in viral pathogenesis. The antigenic structure differs significantly between the trimers and monomers. Surfaces rich in hydrophobic amino acids are important for trimer stabilization in which the C-terminal of the ectodomain plays an important role; to understand these interactions between the G proteins, a mechanistic study of their functions was performed with a molecular model of G protein in its trimeric form. This verified its 3D conformation. The molecular modeling of G protein was performed by a I-TASSER server and was evaluated via a Rachamandran plot and ERRAT program obtained 84.64% and 89.9% of the residues in the favorable regions and overall quality factor, respectively. The molecular dynamics simulations were carried out on RABVG trimer at 310 K. From these theoretical studies, we retrieved the RMSD values from Cα atoms to assess stability. Preliminary model of G protein of rabies virus stable at 12 ns with molecular dynamics was obtained. PMID:27294109

  3. Predicted 3D Model of the Rabies Virus Glycoprotein Trimer

    PubMed Central

    Fernando, Bastida-González; Yersin, Celaya-Trejo; José, Correa-Basurto; Paola, Zárate-Segura

    2016-01-01

    The RABVG ectodomain is a homotrimer, and trimers are often called spikes. They are responsible for the attachment of the virus through the interaction with nicotinic acetylcholine receptors, neural cell adhesion molecule (NCAM), and the p75 neurotrophin receptor (p75NTR). This makes them relevant in viral pathogenesis. The antigenic structure differs significantly between the trimers and monomers. Surfaces rich in hydrophobic amino acids are important for trimer stabilization in which the C-terminal of the ectodomain plays an important role; to understand these interactions between the G proteins, a mechanistic study of their functions was performed with a molecular model of G protein in its trimeric form. This verified its 3D conformation. The molecular modeling of G protein was performed by a I-TASSER server and was evaluated via a Rachamandran plot and ERRAT program obtained 84.64% and 89.9% of the residues in the favorable regions and overall quality factor, respectively. The molecular dynamics simulations were carried out on RABVG trimer at 310 K. From these theoretical studies, we retrieved the RMSD values from Cα atoms to assess stability. Preliminary model of G protein of rabies virus stable at 12 ns with molecular dynamics was obtained. PMID:27294109

  4. Grid-Adapted FUN3D Computations for the Second High Lift Prediction Workshop

    NASA Technical Reports Server (NTRS)

    Lee-Rausch, E. M.; Rumsey, C. L.; Park, M. A.

    2014-01-01

    Contributions of the unstructured Reynolds-averaged Navier-Stokes code FUN3D to the 2nd AIAA CFD High Lift Prediction Workshop are described, and detailed comparisons are made with experimental data. Using workshop-supplied grids, results for the clean wing configuration are compared with results from the structured code CFL3D Using the same turbulence model, both codes compare reasonably well in terms of total forces and moments, and the maximum lift is similarly over-predicted for both codes compared to experiment. By including more representative geometry features such as slat and flap brackets and slat pressure tube bundles, FUN3D captures the general effects of the Reynolds number variation, but under-predicts maximum lift on workshop-supplied grids in comparison with the experimental data, due to excessive separation. However, when output-based, off-body grid adaptation in FUN3D is employed, results improve considerably. In particular, when the geometry includes both brackets and the pressure tube bundles, grid adaptation results in a more accurate prediction of lift near stall in comparison with the wind-tunnel data. Furthermore, a rotation-corrected turbulence model shows improved pressure predictions on the outboard span when using adapted grids.

  5. Designing 3D Structure by 5-7 Kirigami

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    PubMed

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

    2013-07-01

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

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

    PubMed Central

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

    2013-01-01

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

  8. Sydney-Gunnedah-Bowen Basin deep 3D structure

    NASA Astrophysics Data System (ADS)

    Danis, Cara

    2012-01-01

    Studies of the Sydney-Gunnedah-Bowen Basin (SGBB), one of the largest extensional rift sedimentary basins on the east coast of Australia, lack an understanding of the 3D upper crustal structure. Understanding of the subsurface structure is essential for many areas of resource exploration, development and management, as well as scientific research. Geological models provide a way to visualise and investigate the subsurface structure. The integrated regional scale gravity modelling approach, which uses boreholes and seismic data constraints, provides an understanding of the upper crustal structure and allows the development of a 3D geological model which can be used as the architectural framework for many different applications. This work presents a 3D geological model of the SGBB developed for application in high resolution thermal models. It is the culmination of geological surfaces derived from the interpolation of previous regional scale 2D gravity models and numerous borehole records. The model outlines the basement structure of the SGBB and provides information on depth to basement, depth to basal volcanics and thickness of overlying sediments. Through understanding the uncertainties, limitations, confidence and reliability of this model, the 3D geological model can provide the ideal framework for future research.

  9. Instability and Wave Propagation in Structured 3D Composites

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  10. Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

    PubMed Central

    Kristensen, David M; Ward, R Matthew; Lisewski, Andreas Martin; Erdin, Serkan; Chen, Brian Y; Fofanov, Viacheslav Y; Kimmel, Marek; Kavraki, Lydia E; Lichtarge, Olivier

    2008-01-01

    Background Structural genomics projects such as the Protein Structure Initiative (PSI) yield many new structures, but often these have no known molecular functions. One approach to recover this information is to use 3D templates – structure-function motifs that consist of a few functionally critical amino acids and may suggest functional similarity when geometrically matched to other structures. Since experimentally determined functional sites are not common enough to define 3D templates on a large scale, this work tests a computational strategy to select relevant residues for 3D templates. Results Based on evolutionary information and heuristics, an Evolutionary Trace Annotation (ETA) pipeline built templates for 98 enzymes, half taken from the PSI, and sought matches in a non-redundant structure database. On average each template matched 2.7 distinct proteins, of which 2.0 share the first three Enzyme Commission digits as the template's enzyme of origin. In many cases (61%) a single most likely function could be predicted as the annotation with the most matches, and in these cases such a plurality vote identified the correct function with 87% accuracy. ETA was also found to be complementary to sequence homology-based annotations. When matches are required to both geometrically match the 3D template and to be sequence homologs found by BLAST or PSI-BLAST, the annotation accuracy is greater than either method alone, especially in the region of lower sequence identity where homology-based annotations are least reliable. Conclusion These data suggest that knowledge of evolutionarily important residues improves functional annotation among distant enzyme homologs. Since, unlike other 3D template approaches, the ETA method bypasses the need for experimental knowledge of the catalytic mechanism, it should prove a useful, large scale, and general adjunct to combine with other methods to decipher protein function in the structural proteome. PMID:18190718

  11. 3D printed components with ultrasonically arranged microscale structure

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  12. All dispenser printed flexible 3D structured thermoelectric generators

    NASA Astrophysics Data System (ADS)

    Cao, Z.; Shi, J. J.; Torah, R. N.; Tudor, M. J.; Beeby, S. P.

    2015-12-01

    This work presents a vertically fabricated 3D thermoelectric generator (TEG) by dispenser printing on flexible polyimide substrate. This direct-write technology only involves printing of electrodes, thermoelectric active materials and structure material, which needs no masks to transfer the patterns onto the substrate. The dimension for single thermoelectric element is 2 mm × 2 mm × 0.5 mm while the distance between adjacent cubes is 1.2 mm. The polymer structure layer was used to support the electrodes which are printed to connect the top ends of the thermoelectric material and ensure the flexibility as well. The advantages and the limitations of the dispenser printed 3D TEGs will also be evaluated in this paper. The proposed method is potential to be a low-cost and scalable fabrication solution for TEGs.

  13. Advancements in 3D Structural Analysis of Geothermal Systems

    SciTech Connect

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

    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

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

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

  15. 3D reconstruction methods of coronal structures by radio observations

    NASA Astrophysics Data System (ADS)

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

    1992-11-01

    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.

  16. 3D reconstruction methods of coronal structures by radio observations

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

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

    PubMed

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

    2014-09-23

    The multisubunit protein complex, dynactin, is an essential component of the cytoplasmic dynein motor. High-resolution structural work on dynactin and the dynein/dynactin supercomplex has been limited to small subunits and recombinant fragments that do not report fully on either ≈1MDa assembly. In the present study, we used negative-stain electron microscopy and image analysis based on random conical tilt reconstruction to obtain a three-dimensional (3D) structure of native vertebrate dynactin. The 35-nm-long dynactin molecule has a V-shaped shoulder at one end and a flattened tip at the other end, both offset relative to the long axis of the actin-related protein (Arp) backbone. The shoulder projects dramatically away from the Arp filament core in a way that cannot be appreciated in two-dimensional images, which has implications for the mechanism of dynein binding. The 3D structure allows the helical parameters of the entire Arp filament core, which includes the actin capping protein, CP, to be determined for the first time. This structure exhibits near identity to F-actin and can be well fitted into the dynactin envelope. Molecular fitting of modeled CP-Arp polymers into the envelope shows that the filament contains between 7 and 9 Arp protomers and is capped at both ends. In the 7 Arp model, which agrees best with measured Arp stoichiometry and other structural information, actin capping protein (CP) is not present at the distal tip of the structure, unlike what is seen in the other models. The 3D structure suggests a mechanism for dynactin assembly and length specification. PMID:25046383

  18. 3D precision surface measurement by dynamic structured light

    NASA Astrophysics Data System (ADS)

    Franke, Ernest A.; Magee, Michael J.; Mitchell, Joseph N.; Rigney, Michael P.

    2004-02-01

    This paper describes a 3-D imaging technique developed as an internal research project at Southwest Research Institute. The technique is based on an extension of structured light methods in which a projected pattern of parallel lines is rotated over the surface to be measured. A sequence of images is captured and the surface elevation at any location can then be determined from measurements of the temporal pattern, at any point, without considering any other points on the surface. The paper describes techniques for system calibration and surface measurement based on the method of projected quadric shells. Algorithms were developed for image and signal analysis and computer programs were written to calibrate the system and to calculate 3-D coordinates of points on a measured surface. A prototype of the Dynamic Structured Light (DSL) 3-D imaging system was assembled and typical parts were measured. The design procedure was verified and used to implement several different configurations with different measurement volumes and measurement accuracy. A small-parts measurement accuracy of 32 micrometers (.0012") RMS was verified by measuring the surface of a precision-machined plane. Large aircraft control surfaces were measured with a prototype setup that provided .02" depth resolution over a 4" by 8" field of view. Measurement times are typically less than three minutes for 300,000 points. A patent application has been filed.

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

    PubMed Central

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

    2008-01-01

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

  20. 3-D simulation of nanopore structure for DNA sequencing.

    PubMed

    Park, Jun-Mo; Pak, Y Eugene; Chun, Honggu; Lee, Jong-Ho

    2012-07-01

    In this paper, we propose a method for simulating nanopore structure by using conventional 3-D simulation tool to mimic the I-V behavior of the nanopore structure. In the simulation, we use lightly doped silicon for ionic solution where some parameters like electron affinity and dielectric constant are fitted to consider the ionic solution. By using this method, we can simulate the I-V behavior of nanopore structure depending on the location and the size of the sphere shaped silicon oxide which is considered to be an indicator of a DNA base. In addition, we simulate an Ionic Field Effect Transistor (IFET) which has basically the nanopore structure, and show that the simulated curves follow sufficiently the I-V behavior of the measurement data. Therefore, we think it is reasonable to apply parameter modeling mentioned above to simulate nanopore structure. The key idea is to modify electron affinity of silicon which is used to mimic the KCl solution to avoid band bending and depletion inside the nanopore. We could efficiently utilize conventional 3-D simulation tool to simulate the I-V behavior of nanopore structures. PMID:22966538

  1. 3-D lookup: Fast protein structure database searches

    SciTech Connect

    Holm. L.; Sander, C.

    1995-12-31

    There are far fewer classes of three-dimensional protein folds than sequence families but the problem of detecting three-dimensional similarities is NP-complete. We present a novel heuristic for identifying 3-D similarities between a query structure and the database of known protein structures. Many methods for structure alignment use a bottom-up approach, identifying first local matches and then solving a combinatorial problem in building up larger clusters of matching substructures. Here the top-down approach is to start with the global comparison and select a rough superimposition using a fast 3-D lookup of secondary structure motifs. The superimposition is then extended to an alignment of C{sup {alpha}} atoms by an iterative dynamic programming step. An all-against-all comparison of 385-representative proteins (150,000 pair comparisons) took 1 day of computer time on a single R8000 processor. In other words, one query structure is scanned against the database in a matter of minutes. The method is rated at 90% reliability at capturing statistically significant similarities. It is useful as a rapid preprocessor to a comprehensive protein structure database search system.

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

    PubMed

    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. PMID:22113523

  3. Correlative Microscopy for 3D Structural Analysis of Dynamic Interactions

    PubMed Central

    Jun, Sangmi; Zhao, Gongpu; Ning, Jiying; Gibson, Gregory A.; Watkins, Simon C.; Zhang, Peijun

    2013-01-01

    Cryo-electron tomography (cryoET) allows 3D visualization of cellular structures at molecular resolution in a close-to-physiological state1. However, direct visualization of individual viral complexes in their host cellular environment with cryoET is challenging2, due to the infrequent and dynamic nature of viral entry, particularly in the case of HIV-1. While time-lapse live-cell imaging has yielded a great deal of information about many aspects of the life cycle of HIV-13-7, the resolution afforded by live-cell microscopy is limited (~ 200 nm). Our work was aimed at developing a correlation method that permits direct visualization of early events of HIV-1 infection by combining live-cell fluorescent light microscopy, cryo-fluorescent microscopy, and cryoET. In this manner, live-cell and cryo-fluorescent signals can be used to accurately guide the sampling in cryoET. Furthermore, structural information obtained from cryoET can be complemented with the dynamic functional data gained through live-cell imaging of fluorescent labeled target. In this video article, we provide detailed methods and protocols for structural investigation of HIV-1 and host-cell interactions using 3D correlative high-speed live-cell imaging and high-resolution cryoET structural analysis. HeLa cells infected with HIV-1 particles were characterized first by confocal live-cell microscopy, and the region containing the same viral particle was then analyzed by cryo-electron tomography for 3D structural details. The correlation between two sets of imaging data, optical imaging and electron imaging, was achieved using a home-built cryo-fluorescence light microscopy stage. The approach detailed here will be valuable, not only for study of virus-host cell interactions, but also for broader applications in cell biology, such as cell signaling, membrane receptor trafficking, and many other dynamic cellular processes. PMID:23852318

  4. Automatic structural matching of 3D image data

    NASA Astrophysics Data System (ADS)

    Ponomarev, Svjatoslav; Lutsiv, Vadim; Malyshev, Igor

    2015-10-01

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

  5. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

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

  6. Engineering extracellular matrix structure in 3D multiphase tissues

    PubMed Central

    Gillette, Brian M.; Rossen, Ninna S.; Das, Nikkan; Leong, Debra; Wang, Meixin; Dugar, Arushi; Sia, Samuel K.

    2011-01-01

    In native tissues, microscale variations in the extracellular matrix (ECM) structure can drive different cellular behaviors. Although control over ECM structure could prove useful in tissue engineering and in studies of cellular behavior, isotropic 3D matrices poorly replicate variations in local microenvironments. In this paper, we demonstrate a method to engineer local variations in the density and size of collagen fibers throughout 3D tissues. The results showed that, in engineered multiphase tissues, the structures of collagen fibers in both the bulk ECM phases (as measured by mesh size and width of fibers) as well as at tissue interfaces (as measured by density of fibers and thickness of tissue interfaces) could be modulated by varying the collagen concentrations and gelling temperatures. As the method makes use of a previously published technique for tissue bonding, we also confirmed that significant adhesion strength at tissue interfaces was achieved under all conditions tested. Hence, this study demonstrates how collagen fiber structures can be engineered within all regions of a tightly integrated multiphase tissue scaffold by exploiting knowledge of collagen assembly. PMID:21840047

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

    NASA Technical Reports Server (NTRS)

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

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

  10. Using CATH-Gene3D to Analyze the Sequence, Structure, and Function of Proteins.

    PubMed

    Sillitoe, Ian; Lewis, Tony; Orengo, Christine

    2015-01-01

    The CATH database is a classification of protein structures found in the Protein Data Bank (PDB). Protein structures are chopped into individual units of structural domains, and these domains are grouped together into superfamilies if there is sufficient evidence that they have diverged from a common ancestor during the process of evolution. A sister resource, Gene3D, extends this information by scanning sequence profiles of these CATH domain superfamilies against many millions of known proteins to identify related sequences. Thus the combined CATH-Gene3D resource provides confident predictions of the likely structural fold, domain organisation, and evolutionary relatives of these proteins. In addition, this resource incorporates annotations from a large number of external databases such as known enzyme active sites, GO molecular functions, physical interactions, and mutations. This unit details how to access and understand the information contained within the CATH-Gene3D Web pages, the downloadable data files, and the remotely accessible Web services. PMID:26087950

  11. PREDICTING TSUNAMIS GENERATED BY 3D GRANULAR LANDSLIDES

    NASA Astrophysics Data System (ADS)

    Mohammed, F.; Fritz, H. M.

    2009-12-01

    Landslides can trigger tsunamis with locally high amplitudes and runup, which can cause devastating effects in the near field region such as at Lituya Bay (1958), Papua New Guinea (1998) and Java (2006). Tsunamis generated by granular landslides were studied in the three dimensional NEES tsunami wave basin (TWB) at Oregon State University (OSU) based on the generalized Froude similarity. A novel pneumatic landslide generator was deployed to simulate deformable granular landslides with varying geometry and kinematics. Measurement techniques such as particle image velocimetry (PIV), multiple above and underwater video cameras, multiple acoustic transducer arrays (MTA), as well as resistance wave and runup gauges were applied. The wave generation was characterized by an extremely unsteady three phase flow consisting of the slide granulate, water and air entrained into the flow. The landslide deformation during the impact and the subsequent underwater motion was studied by underwater cameras while the MTA provided the shapes of the slide deposits on the basin bottom. The generated waves depend on determined non-dimensional landslide and water body parameters such as the slide Froude number and relative slide shape at impact, among others. The experimental data was used to obtain predictive equations for the wave amplitudes and time periods based on landslide characteristics at impact. The partition between wave crests and troughs departed from equipartition with wave profiles dominated either by a trough or a crest depending on the source. Attenuation functions of the leading wave crest amplitude, the lateral wave runup on the hill slope, the wave length and the time period were obtained to describe the wave behavior in the near field and to quantify the wave amplitude decay away from the landslide source. The measured wave celerity of the leading wave corresponds well to the theoretical approximation of the solitary wave speed while the trailing waves are considerably

  12. Dual multispectral and 3D structured light laparoscope

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  13. Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures.

    PubMed

    Kim, Do-Nyun; Kilchherr, Fabian; Dietz, Hendrik; Bathe, Mark

    2012-04-01

    DNA nanotechnology enables the programmed synthesis of intricate nanometer-scale structures for diverse applications in materials and biological science. Precise control over the 3D solution shape and mechanical flexibility of target designs is important to achieve desired functionality. Because experimental validation of designed nanostructures is time-consuming and cost-intensive, predictive physical models of nanostructure shape and flexibility have the capacity to enhance dramatically the design process. Here, we significantly extend and experimentally validate a computational modeling framework for DNA origami previously presented as CanDo [Castro,C.E., Kilchherr,F., Kim,D.-N., Shiao,E.L., Wauer,T., Wortmann,P., Bathe,M., Dietz,H. (2011) A primer to scaffolded DNA origami. Nat. Meth., 8, 221-229.]. 3D solution shape and flexibility are predicted from basepair connectivity maps now accounting for nicks in the DNA double helix, entropic elasticity of single-stranded DNA, and distant crossovers required to model wireframe structures, in addition to previous modeling (Castro,C.E., et al.) that accounted only for the canonical twist, bend and stretch stiffness of double-helical DNA domains. Systematic experimental validation of nanostructure flexibility mediated by internal crossover density probed using a 32-helix DNA bundle demonstrates for the first time that our model not only predicts the 3D solution shape of complex DNA nanostructures but also their mechanical flexibility. Thus, our model represents an important advance in the quantitative understanding of DNA-based nanostructure shape and flexibility, and we anticipate that this model will increase significantly the number and variety of synthetic nanostructures designed using nucleic acids. PMID:22156372

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

    PubMed

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

    2013-12-01

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

  15. SRB-3D Solid Rocket Booster performance prediction program. Volume 3: Programmer's manual

    NASA Technical Reports Server (NTRS)

    Winkler, J. C.

    1976-01-01

    The programmer's manual for the Modified Solid Rocket Booster Performance Prediction Program (SRB-3D) describes the major control routines of SRB-3D, followed by a super index listing of the program and a cross-reference of the program variables.

  16. 3D Shape and Indirect Appearance by Structured Light Transport.

    PubMed

    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. PMID:27295455

  17. A comparison of 3-D model predictions of Mars' oxygen corona with early MAVEN IUVS observations

    NASA Astrophysics Data System (ADS)

    Lee, Yuni; Combi, Michael R.; Tenishev, Valeriy; Bougher, Stephen W.; Deighan, Justin; Schneider, Nicholas M.; McClintock, William E.; Jakosky, Bruce M.

    2015-11-01

    We have compared our 3-D hot O corona model predictions with the OI 130.4 nm emission detected by Imaging Ultraviolet Spectrograph/Mars Atmosphere and Volatile EvolutioN (IUVS/MAVEN) based completely on our best pre-MAVEN understanding of the 3-D structure of the thermosphere and ionosphere. The model was simulated appropriately for the observational conditions. In addition to dissociative recombination (DR) of O2+, DR of CO2+ is also considered as an important hot O source. The model predictions showed excellent agreement with the transition altitude, the observed altitude variation of density, and the spatial variation of the corona with respect to the Mars-Sun geometry. While previous models predicted escape rates covering a range of nearly 100, the brightness of the modeled hot O densities is a factor of ~1.5 lower than the observations. We discuss possible changes to the model that could come from further analysis of MAVEN measurements and that might close the gap between the modeled and observed brightness.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  19. Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis

    PubMed Central

    Huang, Yan Xin; Bao, Yong Li; Guo, Shu Yan; Wang, Yan; Zhou, Chun Guang; Li, Yu Xin

    2008-01-01

    Background The prediction of conformational B-cell epitopes is one of the most important goals in immunoinformatics. The solution to this problem, even if approximate, would help in designing experiments to precisely map the residues of interaction between an antigen and an antibody. Consequently, this area of research has received considerable attention from immunologists, structural biologists and computational biologists. Phage-displayed random peptide libraries are powerful tools used to obtain mimotopes that are selected by binding to a given monoclonal antibody (mAb) in a similar way to the native epitope. These mimotopes can be considered as functional epitope mimics. Mimotope analysis based methods can predict not only linear but also conformational epitopes and this has been the focus of much research in recent years. Though some algorithms based on mimotope analysis have been proposed, the precise localization of the interaction site mimicked by the mimotopes is still a challenging task. Results In this study, we propose a method for B-cell epitope prediction based on mimotope analysis called Pep-3D-Search. Given the 3D structure of an antigen and a set of mimotopes (or a motif sequence derived from the set of mimotopes), Pep-3D-Search can be used in two modes: mimotope or motif. To evaluate the performance of Pep-3D-Search to predict epitopes from a set of mimotopes, 10 epitopes defined by crystallography were compared with the predicted results from a Pep-3D-Search: the average Matthews correlation oefficient (MCC), sensitivity and precision were 0.1758, 0.3642 and 0.6948. Compared with other available prediction algorithms, Pep-3D-Search showed comparable MCC, specificity and precision, and could provide novel, rational results. To verify the capability of Pep-3D-Search to align a motif sequence to a 3D structure for predicting epitopes, 6 test cases were used. The predictive performance of Pep-3D-Search was demonstrated to be superior to that of other

  20. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

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

  1. 3D Imaging with Structured Illumination for Advanced Security Applications

    SciTech Connect

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

    2015-09-01

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

  2. An Efficient 3D Imaging using Structured Light Systems

    NASA Astrophysics Data System (ADS)

    Lee, Deokwoo

    Structured light 3D surface imaging has been crucial in the fields of image processing and computer vision, particularly in reconstruction, recognition and others. In this dissertation, we propose the approaches to development of an efficient 3D surface imaging system using structured light patterns including reconstruction, recognition and sampling criterion. To achieve an efficient reconstruction system, we address the problem in its many dimensions. In the first, we extract geometric 3D coordinates of an object which is illuminated by a set of concentric circular patterns and reflected to a 2D image plane. The relationship between the original and the deformed shape of the light patterns due to a surface shape provides sufficient 3D coordinates information. In the second, we consider system efficiency. The efficiency, which can be quantified by the size of data, is improved by reducing the number of circular patterns to be projected onto an object of interest. Akin to the Shannon-Nyquist Sampling Theorem, we derive the minimum number of circular patterns which sufficiently represents the target object with no considerable information loss. Specific geometric information (e.g. the highest curvature) of an object is key to deriving the minimum sampling density. In the third, the object, represented using the minimum number of patterns, has incomplete color information (i.e. color information is given a priori along with the curves). An interpolation is carried out to complete the photometric reconstruction. The results can be approximately reconstructed because the minimum number of the patterns may not exactly reconstruct the original object. But the result does not show considerable information loss, and the performance of an approximate reconstruction is evaluated by performing recognition or classification. In an object recognition, we use facial curves which are deformed circular curves (patterns) on a target object. We simply carry out comparison between the

  3. 3D Seismic Imaging over a Potential Collapse Structure

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  4. The 3D structure of Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

    Patsourakos, Spiros

    2016-07-01

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

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

    PubMed Central

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

    2014-01-01

    Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein's atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structure has better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxin protein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broad spectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. The carbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help in understanding the protein folding and function. PMID:24748753

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

    PubMed

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

    2016-07-01

    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. PMID:27095203

  7. Waveform prediction with travel time model LLNL-G3D assessed by Spectral-Element simulation

    NASA Astrophysics Data System (ADS)

    Morency, C.; Simmons, N. A.; Myers, S. C.; Johannesson, G.; Matzel, E.

    2013-12-01

    Seismic monitoring requires accurate prediction of travel times, amplitudes, and whole waveforms. As a first step towards developing a model that is suited to seismic monitoring, LLNL developed the LLNL-G3D P-wave travel time model (Simmons et al., 2012, JGR) to improve seismic event location accuracy. LLNL-G3D fulfills the need to predict travel times from events occurring anywhere in the globe to stations ranging from local to teleseismic distances. Prediction over this distance range requires explicit inclusion of detailed 3-dimensional structure from Earths surface to the core. An open question is how well a model optimized to fit P-wave travel time data can predict waveforms? We begin to address this question by using the P-wave velocities in LLNL-G3D as a proxy for S-wave velocity and density, then performing waveform simulations via the SPECFEM3D_GLOBE spectral-element code. We assess the ability of LLNL-G3D to predict waveforms and draw comparisons to other 3D models available in SPECFEM3D_GLOBE package and widely used in the scientific community. Although we do not expect the P-wave model to perform as well as waveform based models, we view our effort as a first step towards accurate prediction of time times, amplitudes and full waveforms based on a single model. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  8. Binding affinity prediction of novel estrogen receptor ligands using receptor-based 3-D QSAR methods.

    PubMed

    Sippl, Wolfgang

    2002-12-01

    We have recently reported the development of a 3-D QSAR model for estrogen receptor ligands showing a significant correlation between calculated molecular interaction fields and experimentally measured binding affinity. The ligand alignment obtained from docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection procedure, a significant and robust model was obtained (q(2)(LOO)=0.921, SDEP=0.345). To further analyze the robustness and the predictivity of the established model several recently developed estrogen receptor ligands were selected as external test set. An excellent agreement between predicted and experimental binding data was obtained indicated by an external SDEP of 0.531. Two other traditionally used prediction techniques were applied in order to check the performance of the receptor-based 3-D QSAR procedure. The interaction energies calculated on the basis of receptor-ligand complexes were correlated with experimentally observed affinities. Also ligand-based 3-D QSAR models were generated using program FlexS. The interaction energy-based model, as well as the ligand-based 3-D QSAR models yielded models with lower predictivity. The comparison with the interaction energy-based model and with the ligand-based 3-D QSAR models, respectively, indicates that the combination of receptor-based and 3-D QSAR methods is able to improve the quality of prediction. PMID:12413831

  9. 3D Soil Images Structure Quantification using Relative Entropy

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  10. Predicting longshore gradients in longshore transport: the CERC formula compared to Delft3D

    USGS Publications Warehouse

    List, Jeffrey H.; Hanes, Daniel M.; Ruggiero, Peter

    2007-01-01

    The prediction of longshore transport gradients is critical for forecasting shoreline change. We employ simple test cases consisting of shoreface pits at varying distances from the shoreline to compare the longshore transport gradients predicted by the CERC formula against results derived from the process-based model Delft3D. Results show that while in some cases the two approaches give very similar results, in many cases the results diverge greatly. Although neither approach is validated with field data here, the Delft3D-based transport gradients provide much more consistent predictions of erosional and accretionary zones as the pit location varies across the shoreface.

  11. Visualization of 3D ensemble weather forecasts to predict uncertain warm conveyor belt situations

    NASA Astrophysics Data System (ADS)

    Rautenhaus, Marc; Grams, Christian M.; Schäfler, Andreas; Westermann, Rüdiger

    2015-04-01

    We present the application of interactive 3D visualization of ensemble weather predictions to forecasting warm conveyor belt (WCB) situations during aircraft-based atmospheric research campaigns under consideration of uncertainty in the forecast. Based on requirements of the 2012 T-NAWDEX-Falcon campaign, a method based on ensemble Lagrangian particle trajectories has been developed to predict 3D probabilities of the spatial occurrence of WCBs. The method has been integrated into the new open-source 3D ensemble visualization tool Met.3D. The integration facilitates interactive visual exploration of predicted WCB features and derived probabilities in the context of ensemble forecasts from the European Centre for Medium Range Weather Forecasts. To judge forecast uncertainty, Met.3D's interactivity enables the user to compute and visualize ensemble statistical quantities on-demand and to navigate the ensemble members. A new visual analysis method to quantitatively analyse the contribution of ensemble members to a probability region assists the forecaster in interpreting the obtained probabilities. In this presentation, we focus on a case study that illustrates how we envision the use of 3D ensemble visualization for weather forecasting. The case study revisits a forecast case from T-NAWDEX-Falcon and demonstrates the practical application of the proposed uncertainty visualization methods.

  12. Comparison of Computational Aeroacoustics Prediction of Acoustic Transmission Through a 3D Stator With Experiment

    NASA Technical Reports Server (NTRS)

    Hixon, Ray; Envia, Edmane; Dahl, Milo; Sutliff, Daniel L.

    2014-01-01

    In this paper, numerical predictions of acoustic transmission through a 3D stator obtained using the NASA BASS code are compared with experimentally measured data. The influence of vane count and stagger as well as frequency and mode order on the transmission loss is investigated. The data-theory comparisons indicate that BASS can predict all the important trends observed in the experimental data.

  13. Comparison of Computational Aeroacoustics Prediction of Acoustic Transmission Through a 3D Stator with Experiment

    NASA Technical Reports Server (NTRS)

    Hixon, Ray; Envia, Edmane; Dahl, Milo; Sutliff, Daniel

    2014-01-01

    In this paper, numerical predictions of acoustic transmission through a 3D stator obtained using the NASA BASS code are compared with experimentally measured data. The influence of vane count and stagger as well as frequency and mode order on the transmission loss is investigated. The data-theory comparisons indicate that BASS can predict all the important trends observed in the experimental data.

  14. A 3D coupled hydro-mechanical granular model for the prediction of hot tearing formation

    NASA Astrophysics Data System (ADS)

    Sistaninia, M.; Phillion, A. B.; Drezet, J.-M.; Rappaz, M.

    2012-07-01

    A new 3D coupled hydro-mechanical granular model that simulates hot tearing formation in metallic alloys is presented. The hydro-mechanical model consists of four separate 3D modules. (I) The Solidification Module (SM) is used for generating the initial solid-liquid geometry. Based on a Voronoi tessellation of randomly distributed nucleation centers, this module computes solidification within each polyhedron using a finite element based solute diffusion calculation for each element within the tessellation. (II) The Fluid Flow Module (FFM) calculates the solidification shrinkage and deformation-induced pressure drop within the intergranular liquid. (III) The Semi-solid Deformation Module (SDM) is used to simulate deformation of the granular structure via a combined finite element / discrete element method. In this module, deformation of the solid grains is modeled using an elasto-viscoplastic constitutive law. (IV) The Failure Module (FM) is used to simulate crack initiation and propagation with the fracture criterion estimated from the overpressure required to overcome the capillary forces at the liquid-gas interface. The FFM, SDM, and FM are coupled processes since solid deformation, intergranular flow, and crack initiation are deeply linked together. The granular model predictions have been validated against bulk data measured experimentally and calculated with averaging techniques.

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

    NASA Astrophysics Data System (ADS)

    Dong, Jing; Bengtson, Kurt R.; Robinson, Barrett F.; Allebach, Jan P.

    2014-03-01

    Most of the 3D capture products currently in the market are high-end and pricey. They are not targeted for consumers, but rather for research, medical, or industrial usage. Very few aim to provide a solution for home and small business applications. Our goal is to fill in this gap by only using low-cost components to build a 3D capture system that can satisfy the needs of this market segment. In this paper, we present a low-cost 3D capture system based on the structured-light method. The system is built around the HP TopShot LaserJet Pro M275. For our capture device, we use the 8.0 Mpixel camera that is part of the M275. We augment this hardware with two 3M MPro 150 VGA (640 × 480) pocket projectors. We also describe an analytical approach to predicting the achievable resolution of the reconstructed 3D object based on differentials and small signal theory, and an experimental procedure for validating that the system under test meets the specifications for reconstructed object resolution that are predicted by our analytical model. By comparing our experimental measurements from the camera-projector system with the simulation results based on the model for this system, we conclude that our prototype system has been correctly configured and calibrated. We also conclude that with the analytical models, we have an effective means for specifying system parameters to achieve a given target resolution for the reconstructed object.

  16. Ground and Structure Deformation 3d Modelling with a Tin Based Property Model

    NASA Astrophysics Data System (ADS)

    TIAN, T.; Zhang, J.; Jiang, W.

    2013-12-01

    With the development of 3D( three-dimensional) modeling and visualization, more and more 3D tectonics are used to assist the daily work in Engineering Survey, in which the prediction of deformation field in strata and structure induced by underground construction is an essential part. In this research we developed a TIN (Triangulated Irregular Network) based property model for the 3D (three dimensional) visualization of ground deformation filed. By record deformation vector for each nodes, the new model can express the deformation with geometric-deformation-style by drawing each node in its new position and deformation-attribute-distribution-style by drawing each node in the color correspond with its deformation attribute at the same time. Comparing with the volume model based property model, this new property model can provide a more precise geometrical shape for structure objects. Furthermore, by recording only the deformation data of the user-interested 3d surface- such as the ground surface or the underground digging surface, the new property model can save a lot of space, which makes it possible to build the deformation filed model of a much more large scale. To construct the models of deformation filed based on TIN model, the refinement of the network is needed to increase the nodes number, which is necessary to express the deformation filed with a certain resolution. The TIN model refinement is a process of sampling the 3D deformation field values on points on the TIN surface, for which we developed a self-adapting TIN refinement method. By set the parameter of the attribute resolution, this self-adapting method refines the input geometric-expressing TIN model by adding more vertexes and triangles where the 3D deformation filed changing faster. Comparing with the even refinement method, the self-adapting method can generate a refined TIN model with nodes counted less by two thirds. Efficiency Comparison between Self-adapting Refinement Method and Even

  17. Considerations on the Use of 3-D Geophysical Models to Predict Test Ban Monitoring Observables

    SciTech Connect

    Harris, D B; Zucca, J J; McCallen, D B; Pasyanos, M E; Flanagan, M P; Myers, S C; Walter, W R; Rodgers, A J; Harben, P E

    2007-07-09

    The use of 3-D geophysical models to predict nuclear test ban monitoring observables (phase travel times, amplitudes, dispersion, etc.) is widely anticipated to provide improvements in the basic seismic monitoring functions of detection, association, location, discrimination and yield estimation. A number of questions arise when contemplating a transition from 1-D, 2-D and 2.5-D models to constructing and using 3-D models, among them: (1) Can a 3-D geophysical model or a collection of 3-D models provide measurably improved predictions of seismic monitoring observables over existing 1-D models, or 2-D and 2 1/2-D models currently under development? (2) Is a single model that can predict all observables achievable, or must separate models be devised for each observable? How should joint inversion of disparate observable data be performed, if required? (3) What are the options for model representation? Are multi-resolution models essential? How does representation affect the accuracy and speed of observable predictions? (4) How should model uncertainty be estimated, represented and how should it be used? Are stochastic models desirable? (5) What data types should be used to construct the models? What quality control regime should be established? (6) How will 3-D models be used in operations? Will significant improvements in the basic monitoring functions result from the use of 3-D models? Will the calculation of observables through 3-D models be fast enough for real-time use or must a strategy of pre-computation be employed? (7) What are the theoretical limits to 3-D model development (resolution, uncertainty) and performance in predicting monitoring observables? How closely can those limits be approached with projected data availability, station distribution and inverse methods? (8) What priorities should be placed on the acquisition of event ground truth information, deployment of new stations, development of new inverse techniques, exploitation of large

  18. Postprocessing techniques for 3D non-linear structures

    NASA Technical Reports Server (NTRS)

    Gallagher, Richard S.

    1987-01-01

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

  19. Arbitrary and Parallel Nanofabrication of 3D Metal Structures with Polymer Brush Resists.

    PubMed

    Chen, Chaojian; Xie, Zhuang; Wei, Xiaoling; Zheng, Zijian

    2015-12-01

    3D polymer brushes are reported for the first time as ideal resists for the alignment-free nanofabrication of complex 3D metal structures with sub-100 nm lateral resolution and sub-10 nm vertical resolution. Since 3D polymer brushes can be serially fabricated in parallel, this method is effective to generate arbitrary 3D metal structures over a large area at a high throughput. PMID:26439441

  20. Development of a 3D numerical methodology for fast prediction of gun blast induced loading

    NASA Astrophysics Data System (ADS)

    Costa, E.; Lagasco, F.

    2014-05-01

    In this paper, the development of a methodology based on semi-empirical models from the literature to carry out 3D prediction of pressure loading on surfaces adjacent to a weapon system during firing is presented. This loading is consequent to the impact of the blast wave generated by the projectile exiting the muzzle bore. When exceeding a pressure threshold level, loading is potentially capable to induce unwanted damage to nearby hard structures as well as frangible panels or electronic equipment. The implemented model shows the ability to quickly predict the distribution of the blast wave parameters over three-dimensional complex geometry surfaces when the weapon design and emplacement data as well as propellant and projectile characteristics are available. Considering these capabilities, the use of the proposed methodology is envisaged as desirable in the preliminary design phase of the combat system to predict adverse effects and then enable to identify the most appropriate countermeasures. By providing a preliminary but sensitive estimate of the operative environmental loading, this numerical means represents a good alternative to more powerful, but time consuming advanced computational fluid dynamics tools, which use can, thus, be limited to the final phase of the design.

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

    NASA Astrophysics Data System (ADS)

    Gheorghe, Radu; Tchouprakov, Andrei; Sokolov, Roman

    2013-02-01

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

  2. 3-D structure and dynamics of microtubule self-organization

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Ou-Yang, H. Daniel

    2008-03-01

    Laser scanning confocal microscopy was used to study the dynamics of 3D assemblies spontaneously formed in microtubule (MT) solutions. Microtubule solutions prepared by mixing and incubating tubulin in the presence of GTP and Oregon Green conjugated taxol in PM buffer were placed in long, sub-millimeter thin glass cells by the capillary action. Within 24 hours, starting with a uniform distribution, microtubules were found to be gradually separated into a few large ``buckled'' bundles along the long direction, and in the middle plane, of the sample cell. A well-defined wavelength of the buckling sinusoids was around 510 μm. The cross section of these round bundles was approximately 40 μm in diameter and the lengths were several centimeters. Detailed analysis of the 3-D image within the bundles revealed that each bundle seemed to consist of loosely packed MTs. It appeared that MTs were phase separated resulting from attractive interactions between charged MT fibers. The ``buckling'' behavior could be the result of geometrical constraints of the repulsive cell walls and the repulsive interaction between bundles. Detailed 3-D observations of the dynamic evolution of MT assembly could provide insight to the mechanisms of cellular MT organization and phase separation of charged colloidal rods.

  3. Stereoscopic 3D Visual Discomfort Prediction: A Dynamic Accommodation and Vergence Interaction Model.

    PubMed

    Oh, Heeseok; Lee, Sanghoon; Bovik, Alan Conrad

    2016-02-01

    The human visual system perceives 3D depth following sensing via its binocular optical system, a series of massively parallel processing units, and a feedback system that controls the mechanical dynamics of eye movements and the crystalline lens. The process of accommodation (focusing of the crystalline lens) and binocular vergence is controlled simultaneously and symbiotically via cross-coupled communication between the two critical depth computation modalities. The output responses of these two subsystems, which are induced by oculomotor control, are used in the computation of a clear and stable cyclopean 3D image from the input stimuli. These subsystems operate in smooth synchronicity when one is viewing the natural world; however, conflicting responses can occur when viewing stereoscopic 3D (S3D) content on fixed displays, causing physiological discomfort. If such occurrences could be predicted, then they might also be avoided (by modifying the acquisition process) or ameliorated (by changing the relative scene depth). Toward this end, we have developed a dynamic accommodation and vergence interaction (DAVI) model that successfully predicts visual discomfort on S3D images. The DAVI model is based on the phasic and reflex responses of the fast fusional vergence mechanism. Quantitative models of accommodation and vergence mismatches are used to conduct visual discomfort prediction. Other 3D perceptual elements are included in the proposed method, including sharpness limits imposed by the depth of focus and fusion limits implied by Panum's fusional area. The DAVI predictor is created by training a support vector machine on features derived from the proposed model and on recorded subjective assessment results. The experimental results are shown to produce accurate predictions of experienced visual discomfort. PMID:26672036

  4. ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins

    PubMed Central

    Gouet, Patrice; Robert, Xavier; Courcelle, Emmanuel

    2003-01-01

    The fortran program ESPript was created in 1993, to display on a PostScript figure multiple sequence alignments adorned with secondary structure elements. A web server was made available in 1999 and ESPript has been linked to three major web tools: ProDom which identifies protein domains, PredictProtein which predicts secondary structure elements and NPS@ which runs sequence alignment programs. A web server named ENDscript was created in 2002 to facilitate the generation of ESPript figures containing a large amount of information. ENDscript uses programs such as BLAST, Clustal and PHYLODENDRON to work on protein sequences and such as DSSP, CNS and MOLSCRIPT to work on protein coordinates. It enables the creation, from a single Protein Data Bank identifier, of a multiple sequence alignment figure adorned with secondary structure elements of each sequence of known 3D structure. Similar 3D structures are superimposed in turn with the program PROFIT and a final figure is drawn with BOBSCRIPT, which shows sequence and structure conservation along the Cα trace of the query. ESPript and ENDscript are available at http://genopole.toulouse.inra.fr/ESPript. PMID:12824317

  5. Predicting the Electronic Properties of 3D, Million-atom Semiconductor nanostructure Architectures

    SciTech Connect

    Jack Dongarra; Stanimire Tomov

    2012-03-15

    This final report describes the work done by Jack Dongarra (University Distinguished Professor) and Stanimire Tomov (Research Scientist) related to the DOE project entitled Predicting the Electronic Properties of 3D, Million-Atom Semiconductor Nanostructure Architectures. In this project we addressed the mathematical methodology required to calculate the electronic and transport properties of large nanostructures with comparable accuracy and reliability to that of current ab initio methods. This capability is critical for further developing the field, yet it is missing in all the existing computational methods. Additionally, quantitative comparisons with experiments are often needed for a qualitative understanding of the physics, and for guiding the design of new nanostructures. We focused on the mathematical challenges of the project, in particular on solvers and preconditioners for large scale eigenvalue problems that occur in the computation of electronic states of large nanosystems. Usually, the states of interest lie in the interior of the spectrum and their computation poses great difficulties for existing algorithms. The electronic properties of a semiconductor nanostructure architecture can be predicted/determined by computing its band structure. Of particular importance are the 'band edge states' (electronic states near the energy gap) which can be computed from a properly defined interior eigenvalue problem. Our primary mathematics and computational challenge here has been to develop an efficient solution methodology for finding these interior states for very large systems. Our work has produced excellent results in terms of developing both new and extending current state-of-the-art techniques.

  6. Direct observation in 3d of structural crossover in binary hard sphere mixtures

    NASA Astrophysics Data System (ADS)

    Statt, Antonia; Pinchaipat, Rattachai; Turci, Francesco; Evans, Robert; Royall, C. Patrick

    2016-04-01

    For binary fluid mixtures of spherical particles in which the two species are sufficiently different in size, the dominant wavelength of oscillations of the pair correlation functions is predicted to change from roughly the diameter of the large species to that of the small species along a sharp crossover line in the phase diagram [C. Grodon et al., J. Chem. Phys. 121, 7869 (2004)]. Using particle-resolved colloid experiments in 3d we demonstrate that crossover exists and that its location in the phase diagram is in quantitative agreement with the results of both theory and our Monte-Carlo simulations. In contrast with previous work [J. Baumgartl et al., Phys. Rev. Lett. 98, 198303 (2007)], where a correspondence was drawn between crossover and percolation of both species, in our 3d study we find that structural crossover is unrelated to percolation.

  7. 3D Reconstruction of virtual colon structures from colonoscopy images.

    PubMed

    Hong, DongHo; Tavanapong, Wallapak; Wong, Johnny; Oh, JungHwan; de Groen, Piet C

    2014-01-01

    This paper presents the first fully automated reconstruction technique of 3D virtual colon segments from individual colonoscopy images. It is the basis of new software applications that may offer great benefits for improving quality of care for colonoscopy patients. For example, a 3D map of the areas inspected and uninspected during colonoscopy can be shown on request of the endoscopist during the procedure. The endoscopist may revisit the suggested uninspected areas to reduce the chance of missing polyps that reside in these areas. The percentage of the colon surface seen by the endoscopist can be used as a coarse objective indicator of the quality of the procedure. The derived virtual colon models can be stored for post-procedure training of new endoscopists to teach navigation techniques that result in a higher level of procedure quality. Our technique does not require a prior CT scan of the colon or any global positioning device. Our experiments on endoscopy images of an Olympus synthetic colon model reveal encouraging results with small average reconstruction errors (4.1 mm for the fold depths and 12.1 mm for the fold circumferences). PMID:24225230

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

    NASA Technical Reports Server (NTRS)

    Riggs, H. R.

    2000-01-01

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

  9. 3D structure and conductive thermal field of the Upper Rhine Graben

    NASA Astrophysics Data System (ADS)

    Freymark, Jessica; Sippel, Judith; Scheck-Wenderoth, Magdalena; Bär, Kristian; Stiller, Manfred; Fritsche, Johann-Gerhard; Kracht, Matthias

    2016-04-01

    The Upper Rhine Graben (URG) was formed as part of the European Cenozoic Rift System in a complex extensional setting. At present-day, it has a large socioeconomic relevance as it provides a great potential for geothermal energy production in Germany and France. For the utilisation of this energy resource it is crucial to understand the structure and the observed temperature anomalies in the rift basin. In the framework of the EU-funded "IMAGE" project (Integrated Methods for Advanced Geothermal Exploration), we apply a data-driven numerical modelling approach to quantify the processes and properties controlling the spatial distribution of subsurface temperatures. Typically, reservoir-scale numerical models are developed for predictions on the subsurface hydrothermal conditions and for reducing the risk of drilling non-productive geothermal wells. One major problem related to such models is setting appropriate boundary conditions that define, for instance, how much heat enters the reservoir from greater depths. Therefore, we first build a regional lithospheric-scale 3D structural model, which covers not only the entire URG but also adjacent geological features like the Black Forest and the Vosges Mountains. In particular, we use a multidisciplinary dataset (e.g. well data, seismic reflection data, existing structural models, gravity) to construct the geometries of the sediments, the crust and the lithospheric mantle that control the spatial distribution of thermal conductivity and radiogenic heat production and hence temperatures. By applying a data-based and lithology-dependent parameterisation of this lithospheric-scale 3D structural model and a 3D finite element method, we calculate the steady-state conductive thermal field for the entire region. Available measured temperatures (down to depths of up to 5 km) are considered to validate the 3D thermal model. We present major characteristics of the lithospheric-scale 3D structural model and results of the 3D

  10. Computer modeling of 3D structures of cytochrome P450s.

    PubMed

    Chang, Y T; Stiffelman, O B; Loew, G H

    1996-01-01

    The understanding of structure-function relationship of enzymes requires detailed information of their three-dimensional structure. Protein structure determination by X-ray and NMR methods, the two most frequently used experimental procedures, are often difficult and time-consuming. Thus computer modeling of protein structures has become an increasingly active and attractive option for obtaining predictive models of three-dimensional protein structures. Specifically, for the ubiquitous metabolizing heme proteins, the cytochrome P450s, the X-ray structures of four isozymes of bacterial origin, P450cam, P450terp, P450BM-3 and P450eryF have now been determined. However, attempts to obtain the structure of mammalian forms by experimental means have thus far not been successful. Thus, there have been numerous attempts to construct models of mammalian P450s using homology modeling methods in which the known structures have been used to various extents and in various strategies to build models of P450 isozymes. In this paper, we review these efforts and then describe a strategy for structure building and assessment of 3D models of P450s recently developed in our laboratory that corrects many of the weaknesses in the previous procedures. The results are 3D models that for the first time are stable to unconstrained molecular dynamics simulations. The use of this method is demonstrated by the construction and validation of a 3D model for rabbit liver microsomal P450 isozyme 2B4, responsible for the oxidative metabolism of diverse xenobiotics including widely used inhalation anesthetics. Using this 2B4 model, the substrate access channel, substrate binding site and plausible surface regions for binding with P450 redox partners were identified. PMID:9010606

  11. 3D Printing: 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles (Adv. Mater. 19/2016).

    PubMed

    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. PMID:27167030

  12. Triangular framework mesh generation of 3D geological structure

    NASA Astrophysics Data System (ADS)

    Meng, Xianhai; Zhou, Kun; Li, Jigang; Yang, Qin

    2013-03-01

    The dynamic simulation of oil migration and accumulation is an important issue on the research of petroleum exploration, and it is a numerical simulation process with special requirement on the framework mesh of 3D geological models, which means that the mesh should have same geometry and topology relation near the intersected part of geological surfaces. In this paper, basing on the conforming Delaunay triangulation algorithm to construct mesh of individual geological stratum or fault, a novel link-Delaunay-triangulation method is presented to achieve the geometric and topological consistency in the intersected line between two surfaces, also with the analysis of termination of our algorithm. Finally, some examples of the geological framework mesh are provided and the experimental result proved that the algorithm's effectiveness in engineering practice.

  13. Prediction of parallel NIKE3D performance on the KSR1 system

    SciTech Connect

    Su, P.S.; Zacharia, T.; Fulton, R.E.

    1995-05-01

    Finite element method is one of the bases for numerical solutions to engineering problems. Complex engineering problems using finite element analysis typically imply excessively large computational time. Parallel supercomputers have the potential for significantly increasing calculation speeds in order to meet these computational requirements. This paper predicts parallel NIKE3D performance on the Kendall Square Research (KSR1) system. The first part of the prediction is based on the implementation of parallel Cholesky (U{sup T}DU) matrix decomposition algorithm through actual computations on the KSRI multiprocessor system, with 64 processors, at Oak Ridge National Laboratory. The other predictions are based on actual computations for parallel element matrix generation, parallel global stiffness matrix assembly, and parallel forward/backward substitution on the BBN TC2000 multiprocessor system at Lawrence Livermore National Laboratory. The preliminary results indicate that parallel NIKE3D performance can be attractive under local/shared-memory multiprocessor system environments.

  14. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers.

    PubMed

    Mao, Yiqi; Yu, Kai; Isakov, Michael S; Wu, Jiangtao; Dunn, Martin L; Jerry Qi, H

    2015-01-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations. PMID:26346202

  15. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

    PubMed Central

    Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.

    2015-01-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations. PMID:26346202

  16. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

    NASA Astrophysics Data System (ADS)

    Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.

    2015-09-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations.

  17. Image quality improvement for a 3D structure exhibiting multiple 2D patterns and its implementation.

    PubMed

    Hirayama, Ryuji; Nakayama, Hirotaka; Shiraki, Atsushi; Kakue, Takashi; Shimobaba, Tomoyoshi; Ito, Tomoyoshi

    2016-04-01

    A three-dimensional (3D) structure designed by our proposed algorithm can simultaneously exhibit multiple two-dimensional patterns. The 3D structure provides multiple patterns having directional characteristics by distributing the effects of the artefacts. In this study, we proposed an iterative algorithm to improve the image quality of the exhibited patterns and have verified the effectiveness of the proposed algorithm using numerical simulations. Moreover, we fabricated different 3D glass structures (an octagonal prism, a cube and a sphere) using the proposed algorithm. All 3D structures exhibit four patterns, and different patterns can be observed depending on the viewing direction. PMID:27137021

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  19. Type II solar radio bursts predicted by 3-D MHD CME and kinetic radio emission simulations

    NASA Astrophysics Data System (ADS)

    Schmidt, J. M.; Cairns, Iver H.

    2014-01-01

    Impending space weather events at Earth are often signaled by type II solar radio bursts. These bursts are generated upstream of shock waves driven by coronal mass ejections (CMEs) that move away from the Sun. We combine elaborate three-dimensional (3-D) magnetohydrodynamic predictions of realistic CMEs near the Sun with a recent analytic kinetic radiation theory in order to simulate two type II bursts. Magnetograms of the Sun are used to reconstruct initial solar magnetic and active region fields for the modeling. STEREO spacecraft data are used to dimension the flux rope of the initial CME, launched into an empirical data-driven corona and solar wind. We demonstrate impressive accuracy in time, frequency, and intensity for the two type II bursts observed by the Wind spacecraft on 15 February 2011 and 7 March 2012. Propagation of the simulated CME-driven shocks through coronal plasmas containing preexisting density and magnetic field structures that stem from the coronal setup and CME initiation closely reproduce the isolated islands of type II emission observed. These islands form because of a competition between the growth of the radio source due to spherical expansion and a fragmentation of the radio source due to increasingly radial fields in the nose region of the shock and interactions with streamers in the flank regions of the shock. Our study provides strong support for this theory for type II bursts and implies that the physical processes involved are understood. It also supports a near-term capability to predict and track these events for space weather predictions.

  20. Source Methodology for Turbofan Noise Prediction (SOURCE3D Technical Documentation)

    NASA Technical Reports Server (NTRS)

    Meyer, Harold D.

    1999-01-01

    This report provides the analytical documentation for the SOURCE3D Rotor Wake/Stator Interaction Code. It derives the equations for the rotor scattering coefficients and stator source vector and scattering coefficients that are needed for use in the TFANS (Theoretical Fan Noise Design/Prediction System). SOURCE3D treats the rotor and stator as isolated source elements. TFANS uses this information, along with scattering coefficients for inlet and exit elements, and provides complete noise solutions for turbofan engines. SOURCE3D is composed of a collection of FORTRAN programs that have been obtained by extending the approach of the earlier V072 Rotor Wake/Stator Interaction Code. Similar to V072, it treats the rotor and stator as a collection of blades and vanes having zero thickness and camber contained in an infinite, hardwall annular duct. SOURCE3D adds important features to the V072 capability-a rotor element, swirl flow and vorticity waves, actuator disks for flow turning, and combined rotor/actuator disk and stator/actuator disk elements. These items allow reflections from the rotor, frequency scattering, and mode trapping, thus providing more complete noise predictions than previously. The code has been thoroughly verified through comparison with D.B. Hanson's CUP2D two- dimensional code using a narrow annulus test case.

  1. Analysis of simple 2-D and 3-D metal structures subjected to fragment impact

    NASA Technical Reports Server (NTRS)

    Witmer, E. A.; Stagliano, T. R.; Spilker, R. L.; Rodal, J. J. A.

    1977-01-01

    Theoretical methods were developed for predicting the large-deflection elastic-plastic transient structural responses of metal containment or deflector (C/D) structures to cope with rotor burst fragment impact attack. For two-dimensional C/D structures both, finite element and finite difference analysis methods were employed to analyze structural response produced by either prescribed transient loads or fragment impact. For the latter category, two time-wise step-by-step analysis procedures were devised to predict the structural responses resulting from a succession of fragment impacts: the collision force method (CFM) which utilizes an approximate prediction of the force applied to the attacked structure during fragment impact, and the collision imparted velocity method (CIVM) in which the impact-induced velocity increment acquired by a region of the impacted structure near the impact point is computed. The merits and limitations of these approaches are discussed. For the analysis of 3-d responses of C/D structures, only the CIVM approach was investigated.

  2. FUN3D Analyses in Support of the First Aeroelastic Prediction Workshop

    NASA Technical Reports Server (NTRS)

    Chwalowski, Pawel; Heeg, Jennifer; Wieseman, Carol D.; Florance, Jennifer P.

    2013-01-01

    This paper presents the computational aeroelastic results generated in support of the first Aeroelastic Prediction Workshop for the Benchmark Supercritical Wing (BSCW) and the HIgh REynolds Number AeroStructural Dynamics (HIRENASD) configurations and compares them to the experimental data. The computational results are obtained using FUN3D, an unstructured grid Reynolds-averaged Navier-Stokes solver developed at NASA Langley Research Center. The analysis results for both configurations include aerodynamic coefficients and surface pressures obtained for steady-state or static aeroelastic equilibrium (BSCW and HIRENASD, respectively) and for unsteady flow due to a pitching wing (BSCW) or modally-excited wing (HIRENASD). Frequency response functions of the pressure coefficients with respect to displacement are computed and compared with the experimental data. For the BSCW, the shock location is computed aft of the experimentally-located shock position. The pressure distribution upstream of this shock is in excellent agreement with the experimental data, but the pressure downstream of the shock in the separated flow region does not match as well. For HIRENASD, very good agreement between the numerical results and the experimental data is observed at the mid-span wing locations.

  3. A 3-D Vortex Code for Parachute Flow Predictions: VIPAR Version 1.0

    SciTech Connect

    STRICKLAND, JAMES H.; HOMICZ, GREGORY F.; PORTER, VICKI L.; GOSSLER, ALBERT A.

    2002-07-01

    This report describes a 3-D fluid mechanics code for predicting flow past bluff bodies whose surfaces can be assumed to be made up of shell elements that are simply connected. Version 1.0 of the VIPAR code (Vortex Inflation PARachute code) is described herein. This version contains several first order algorithms that we are in the process of replacing with higher order ones. These enhancements will appear in the next version of VIPAR. The present code contains a motion generator that can be used to produce a large class of rigid body motions. The present code has also been fully coupled to a structural dynamics code in which the geometry undergoes large time dependent deformations. Initial surface geometry is generated from triangular shell elements using a code such as Patran and is written into an ExodusII database file for subsequent input into VIPAR. Surface and wake variable information is output into two ExodusII files that can be post processed and viewed using software such as EnSight{trademark}.

  4. 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles.

    PubMed

    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. PMID:26992060

  5. 3D Modeling of Branching Structures for Anatomical Instruction

    PubMed Central

    Mattingly, William A.; Chariker, Julia H.; Paris, Richard; Chang, Dar-jen; Pani, John R.

    2015-01-01

    Branching tubular structures are prevalent in many different organic and synthetic settings. From trees and vegetation in nature, to vascular structures throughout human and animal biology, these structures are always candidates for new methods of graphical and visual expression. We present a modeling tool for the creation and interactive modification of these structures. Parameters such as thickness and position of branching structures can be modified, while geometric constraints ensure that the resulting mesh will have an accurate anatomical structure by not having inconsistent geometry. We apply this method to the creation of accurate representations of the different types of retinal cells in the human eye. This method allows a user to quickly produce anatomically accurate structures with low polygon counts that are suitable for rendering at interactive rates on commodity computers and mobile devices. PMID:27087764

  6. Effects of 3D random correlated velocity perturbations on predicted ground motions

    USGS Publications Warehouse

    Hartzell, S.; Harmsen, S.; Frankel, A.

    2010-01-01

    Three-dimensional, finite-difference simulations of a realistic finite-fault rupture on the southern Hayward fault are used to evaluate the effects of random, correlated velocity perturbations on predicted ground motions. Velocity perturbations are added to a three-dimensional (3D) regional seismic velocity model of the San Francisco Bay Area using a 3D von Karman random medium. Velocity correlation lengths of 5 and 10 km and standard deviations in the velocity of 5% and 10% are considered. The results show that significant deviations in predicted ground velocities are seen in the calculated frequency range (≤1 Hz) for standard deviations in velocity of 5% to 10%. These results have implications for the practical limits on the accuracy of scenario ground-motion calculations and on retrieval of source parameters using higher-frequency, strong-motion data.

  7. UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation

    PubMed Central

    Zhu, Jinhao; Wei, Bryan; Yuan, Yuan; Mi, Yongli

    2009-01-01

    A user-friendly software system, UNIQUIMER 3D, was developed to design DNA structures for nanotechnology applications. It consists of 3D visualization, internal energy minimization, sequence generation and construction of motif array simulations (2D tiles and 3D lattices) functionalities. The system can be used to check structural deformation and design errors under scaled-up conditions. UNIQUIMER 3D has been tested on the design of both existing motifs (holiday junction, 4 × 4 tile, double crossover, DNA tetrahedron, DNA cube, etc.) and nonexisting motifs (soccer ball). The results demonstrated UNIQUIMER 3D's capability in designing large complex structures. We also designed a de novo sequence generation algorithm. UNIQUIMER 3D was developed for the Windows environment and is provided free of charge to the nonprofit research institutions. PMID:19228709

  8. Prediction of the 3D structure for the rat urotensin II receptor and comparison of the antagonist binding sites and binding selectivity between human and rat from atomistic simulations

    PubMed Central

    Kim, Soo-Kyung; Li, Youyong; Park, Changmoon; Abrol, Ravinder

    2012-01-01

    Urotensin-II (U-II) has been shown to be the most potent mammalian vasoconstrictor known.[1, 2] Thus a U-II antagonist might be of therapeutic value in a number of cardiovascular disorders.[3] However, interspecies variability of several nonpeptidic ligands complicates the interpretation of in vivo studies of such antagonists in pre-clinical animal models of disease. Thus compound ACT058362 is a selective antagonist for human U-II receptor (hUT2R) with a reported Kd ~ 4 nM in a molecular binding assay, but it is reported to bind weakly to rat UT2R (rUT2R), with Kd ~ 1,500 nM.[4] In contrast, the arylsulphonamide SB706375 is a selective antagonist against both hUT2R (Kd: ~ 9 nM) and rUT2R (Kd: ~ 21 nM).[3] To understand the species selectivity of the UT2R, we investigated the binding site of ACT058362 and SB706375 complex with both hUT2R and rUT2R to explain the dramatic (~ 400-fold) lower affinity of ACT058362 for rUT2R and the similar (~10 nM) affinity of SB706375 for both UT2R. These studies.used MembStruk and MSCDock to predict the UT2R structure and the binding site for ACT058362 and SB706375. Based on binding energy, we found two binding modes each with D1303.32 as the crucial anchoring point. We predict that ACT058362 (an aryl-amine-aryl or ANA ligand) binds in the TM 3456 region while we predict that SB706375 (an aryl-aryl-amine or AAN ligand) binds in the TM 1237 region. These predicted sites explain the known differences in binding the ANA ligand to rat and human while explaining the similar binding of the AAN compound to rat and human. Moreover the predictions explain currently available SAR data. To further validate the predicted binding site of these ligands to hUT2R and rUT2R, we propose several mutations that would help define the structural origins of differential responses of UT2R among species potentially indicating novel UT2R antagonists with cross-species high affinity. PMID:20683923

  9. 3D Crustal Structure and 3D-b-value in AbuDabbab Seismogenic Source, Northern Red Sea.

    NASA Astrophysics Data System (ADS)

    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

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

    PubMed Central

    Pei, Jimin; Grishin, Nick V.

    2015-01-01

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

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

    PubMed

    Pei, Jimin; Grishin, Nick V

    2014-01-01

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

  12. GMOL: An Interactive Tool for 3D Genome Structure Visualization.

    PubMed

    Nowotny, Jackson; Wells, Avery; Oluwadare, Oluwatosin; Xu, Lingfei; Cao, Renzhi; Trieu, Tuan; He, Chenfeng; Cheng, Jianlin

    2016-01-01

    It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there still exists a shortage of tools dedicated to visualizing the genome. Creating a tool that can accurately visualize the genome can aid researchers by highlighting structural relationships that may not be obvious when examining the sequence information alone. Here we present a desktop application, known as GMOL, designed to effectively visualize genome structures so that researchers may better analyze genomic data. GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences. Users can also interactively manipulate and measure the whole genome structure and extract static images and machine-readable data files in PDB format from the multi-scale structure. By using GMOL researchers will be able to better understand and analyze genome structure models and the impact their structural relations have on genome activity and DNA function. PMID:26868282

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

    PubMed

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

    2016-07-01

    The importance of elucidating the three dimensional structures of RNA molecules is becoming increasingly clear. However, traditional protein structural techniques such as NMR and X-ray crystallography have several important drawbacks when probing long RNA molecules. Single molecule Förster resonance energy transfer (smFRET) has emerged as a useful alternative as it allows native sequences to be probed in physiological conditions and allows multiple conformations to be probed simultaneously. This review serves to describe the method of generating a three dimensional RNA structure from smFRET data from the biochemical probing of the secondary structure to the computational refinement of the final model. PMID:26853327

  14. Micro-structured materials and mechanical cues in 3D collagen gels.

    PubMed

    Phillips, James B; Brown, Robert

    2011-01-01

    Collagen gels provide a versatile and widely used substrate for three-dimensional (3D) cell culture. Here we describe how cell-seeded Type-I collagen gels can be adapted to provide powerful 3D models to support a wide range of research applications where cell/substrate alignment, density, stiffness/compliance, and strain are critical factors. In their fully hydrated form, rectangular collagen gels can be tethered such that endogenous forces generated as resident cells attach to and remodel the fibrillar collagen network can align the substrate in a controllable, predictable, and quantifiable manner. By removing water from collagen gels (plastic compression), their density increases towards that of body tissues, facilitating the engineering of a range of biomimetic constructs with controllable mechanical properties. This dense collagen can be used in combination with other components to achieve a range of functional properties from controlled perfusion, or tensile/compressive strength to new micro-structures. Detailed methodology is provided for the assembly of a range of 3D collagen materials including tethered aligned hydrogels and plastic compressed constructs. A range of techniques for analysing cell behaviour within these models, including microscopy and molecular analyses are described. These systems therefore provide a highly controllable mechanical and chemical micro-environment for investigating a wide range of cellular responses. PMID:21042973

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  16. Determining 3-D motion and structure from image sequences

    NASA Technical Reports Server (NTRS)

    Huang, T. S.

    1982-01-01

    A method of determining three-dimensional motion and structure from two image frames is presented. The method requires eight point correspondences between the two frames, from which motion and structure parameters are determined by solving a set of eight linear equations and a singular value decomposition of a 3x3 matrix. It is shown that the solution thus obtained is unique.

  17. The 3D Structure of the Galactic Bulge

    NASA Astrophysics Data System (ADS)

    Zoccali, Manuela; Valenti, Elena

    2016-06-01

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

  18. Sensitivity of power and RMS delay spread predictions of a 3D indoor ray tracing model.

    PubMed

    Liu, Zhong-Yu; Guo, Li-Xin; Li, Chang-Long; Wang, Qiang; Zhao, Zhen-Wei

    2016-06-13

    This study investigates the sensitivity of a three-dimensional (3D) indoor ray tracing (RT) model for the use of the uniform theory of diffraction and geometrical optics in radio channel characterizations of indoor environments. Under complex indoor environments, RT-based predictions require detailed and accurate databases of indoor object layouts and the electrical characteristics of such environments. The aim of this study is to assist in selecting the appropriate level of accuracy required in indoor databases to achieve good trade-offs between database costs and prediction accuracy. This study focuses on the effects of errors in indoor environments on prediction results. In studying the effects of inaccuracies in geometry information (indoor object layout) on power coverage prediction, two types of artificial erroneous indoor maps are used. Moreover, a systematic analysis is performed by comparing the predictions with erroneous indoor maps and those with the original indoor map. Subsequently, the influence of random errors on RMS delay spread results is investigated. Given the effect of electrical parameters on the accuracy of the predicted results of the 3D RT model, the relative permittivity and conductivity of different fractions of an indoor environment are set with different values. Five types of computer simulations are considered, and for each type, the received power and RMS delay spread under the same circumstances are simulated with the RT model. PMID:27410335

  19. TBIEM3D: A Computer Program for Predicting Ducted Fan Engine Noise. Version 1.1

    NASA Technical Reports Server (NTRS)

    Dunn, M. H.

    1997-01-01

    This document describes the usage of the ducted fan noise prediction program TBIEM3D (Thin duct - Boundary Integral Equation Method - 3 Dimensional). A scattering approach is adopted in which the acoustic pressure field is split into known incident and unknown scattered parts. The scattering of fan-generated noise by a finite length circular cylinder in a uniform flow field is considered. The fan noise is modeled by a collection of spinning point thrust dipoles. The program, based on a Boundary Integral Equation Method (BIEM), calculates circumferential modal coefficients of the acoustic pressure at user-specified field locations. The duct interior can be of the hard wall type or lined. The duct liner is axisymmetric, locally reactive, and can be uniform or axially segmented. TBIEM3D is written in the FORTRAN programming language. Input to TBIEM3D is minimal and consists of geometric and kinematic parameters. Discretization and numerical parameters are determined automatically by the code. Several examples are presented to demonstrate TBIEM3D capabilities.

  20. 3D visualization of deformation structures and potential fluid pathways at the Grimsel Test Site

    NASA Astrophysics Data System (ADS)

    Schneeberger, Raphael; Kober, Florian; Berger, Alfons; Spillmann, Thomas; Herwegh, Marco

    2015-04-01

    each other, water flow is high. Our 3D structural model allows the recognition of such intersections in 3D space and the prediction of their spatial extent. The structural model developed with the introduction of the locally known hydraulic permeabilities and in combination with the results of on-going hydrochemical investigations will allow to estimate the location of the recently active water pathways. References Wehrens, P., Baumberger, R., Berger, A., & Herwegh, M. (in prep.). How is strain localized in a mid-crustal basement section? Spatial distribution of deformation in the Aar massif (Switzerland).

  1. Geothermal Project Den Haag - 3-D models for temperature prediction and reservoir characterization

    NASA Astrophysics Data System (ADS)

    Mottaghy, D.; Pechnig, R.; Willemsen, G.; Simmelink, H. J.; Vandeweijer, V.

    2009-04-01

    In the framework of the "Den Haag Zuidwest" geothermal district heating system a deep geothermal installation is projected. The target horizon of the planned doublet is the "Delft sandstone" which has been extensively explored for oil- and gas reservoirs in the last century. In the target area, this upper Jurassic sandstone layer is found at a depth of about 2300 m with an average thickness of about 50 m. The study presented here focuses on the prediction of reservoir temperatures and production behavior which is crucial for planning a deep geothermal installation. In the first phase, the main objective was to find out whether there is a significant influence of the 3-dimensional structures of anticlines and synclines on the temperature field, which could cause formation temperatures deviating from the predicted extrapolated temperature data from oil and gas exploration wells. To this end a regional model was set up as a basis for steady state numerical simulations. Since representative input parameters are decisive for reliable model results, all available information was compiled: a) the subsurface geometry, depth and thickness of the stratigraphic layers known from seismic data sets 2) borehole geophysical data and c) geological and petrographical information from exploration wells. In addition 50 cuttings samples were taken from two selected key wells in order to provide direct information on thermal properties of the underlying strata. Thermal conductivity and rock matrix density were measured in the laboratory. These data were combined with a petrophysical log analysis (Gamma Ray, Sonic, Density and Resistivity), which resulted in continuous profiles of porosity, effective thermal conductivity and radiogenetic heat production. These profiles allowed to asses in detail the variability of the petrophysical properties with depth and to check for lateral changes between the wells. All this data entered the numerical simulations which were performed by a 3-D

  2. 3D Thermoelectric Structures Derived from a New Mixed Micromachining Process

    NASA Astrophysics Data System (ADS)

    Du, Chen-Hsun; Lee, Chengkuo

    2000-12-01

    This paper proposes an innovative 3D thermoelectric structure which significantly reduce the componet size without deterioration of sensor performance. Based on complementary metal-oxide-semiconductor (CMOS) transistor compatible process, this 3D thermoelectric structure is demonstrated and fabricated by combining front-side silicon anisotropic wet etching and aluminum sacrificial layer etching technique. The voltage responsivity of derived 3D thermoelectric structure with 180× 180 μm2 pixel size can be as high as 190 V/W in vacuum. This new thermoelectric structure shows its potential to be an excellent pixel structure of infrared sensor array for infrared recognition applications.

  3. LV motion tracking from 3D echocardiography using textural and structural information.

    PubMed

    Myronenko, Andriy; Song, Xubo; Sahn, David J

    2007-01-01

    Automated motion reconstruction of the left ventricle (LV) from 3D echocardiography provides insight into myocardium architecture and function. Low image quality and artifacts make 3D ultrasound image processing a challenging problem. We introduce a LV tracking method, which combines textural and structural information to overcome the image quality limitations. Our method automatically reconstructs the motion of the LV contour (endocardium and epicardium) from a sequence of 3D ultrasound images. PMID:18044597

  4. Delineation of nuclear structures in 3D multicellular systems

    2013-09-13

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

  5. Cookoff Response of PBXN-109: Material Characterization and ALE3D Thermal Predictions

    SciTech Connect

    McClelland, M A; Tran, T D; Cunningham, B J; Weese, R K; Maienschein, J L

    2001-05-29

    Materials properties measurements are made for the RDX-based explosive, PBXN-109, and initial ALE3D model predictions are given for the cookoff temperature in a U.S. Navy test. This work is part of an effort in the U.S. Navy and Department of Energy (DOE) laboratories to understand the thermal explosion behavior of this material. Benchmark cookoff experiments are being performed by the U.S. Navy to validate DOE materials models and computer codes. The ALE3D computer code can model the coupled thermal, mechanical, and chemical behavior of heating, ignition, and explosion in cookoff tests. In our application, a standard three-step step model is selected for the chemical kinetics. The strength behavior of the solid constituents is represented by a Steinberg-Guinan model while polynomial and gamma-law expressions are used for the Equation Of State (EOS) for the solid and gas species, respectively. Materials characterization measurements are given for thermal expansion, heat capacity, shear modulus, bulk modulus, and One-Dimensional-Time-to-Explosion (ODTX). These measurements and those of the other project participants are used to determine parameters in the ALE3D chemical, mechanical, and thermal models. Time-dependent, two-dimensional results are given for the temperature and material expansion. The results show predicted cookoff temperatures slightly higher than the measured values.

  6. Cookoff Response of PBXN-109: Material Characterization and ALE3D Thermal Predictions

    SciTech Connect

    McClelland, M A; Tran, T D; Cunningham, B J; Weese, R K; Maienschein, J L

    2001-08-21

    Materials properties measurements are made for the RDX-based explosive, PBXN-109, and initial ALE3D model predictions are given for the cookoff temperature in a U.S. Navy test. This work is part of an effort in the U.S. Navy and Department of Energy (DOE) laboratories to understand the thermal explosion behavior of this material. Benchmark cookoff experiments are being performed by the U.S. Navy to validate DOE materials models and computer codes. The ALE3D computer code can model the coupled thermal, mechanical, and chemical behavior of heating, ignition, and explosion in cookoff tests. In our application, a standard three-step step model is selected for the chemical kinetics. The strength behavior of the solid constituents is represented by a Steinberg-Guinan model while polynomial and gamma-law expressions are used for the Equation Of State (EOS) for the solid and gas species, respectively. Materials characterization measurements are given for thermal expansion, heat capacity, shear modulus, bulk modulus, and One-Dimensional-Time-to-Explosion (ODTX). These measurements and those of the other project participants are used to determine parameters in the ALE3D chemical, mechanical, and thermal models. Time-dependent, two-dimensional results are given for the temperature and material expansion. The results show predicted cookoff temperatures slightly higher than the measured values.

  7. TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants.

    PubMed

    Tung, Chun-Wei; Lin, Ying-Chi; Chang, Hsun-Shuo; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng

    2014-01-01

    The rich indigenous and endemic plants in Taiwan serve as a resourceful bank for biologically active phytochemicals. Based on our TIPdb database curating bioactive phytochemicals from Taiwan indigenous plants, this study presents a three-dimensional (3D) chemical structure database named TIPdb-3D to support the discovery of novel pharmacologically active compounds. The Merck Molecular Force Field (MMFF94) was used to generate 3D structures of phytochemicals in TIPdb. The 3D structures could facilitate the analysis of 3D quantitative structure-activity relationship, the exploration of chemical space and the identification of potential pharmacologically active compounds using protein-ligand docking. Database URL: http://cwtung.kmu.edu.tw/tipdb. PMID:24930145

  8. 5D Modelling: An Efficient Approach for Creating Spatiotemporal Predictive 3D Maps of Large-Scale Cultural Resources

    NASA Astrophysics Data System (ADS)

    Doulamis, A.; Doulamis, N.; Ioannidis, C.; Chrysouli, C.; Grammalidis, N.; Dimitropoulos, K.; Potsiou, C.; Stathopoulou, E.-K.; Ioannides, M.

    2015-08-01

    Outdoor large-scale cultural sites are mostly sensitive to environmental, natural and human made factors, implying an imminent need for a spatio-temporal assessment to identify regions of potential cultural interest (material degradation, structuring, conservation). On the other hand, in Cultural Heritage research quite different actors are involved (archaeologists, curators, conservators, simple users) each of diverse needs. All these statements advocate that a 5D modelling (3D geometry plus time plus levels of details) is ideally required for preservation and assessment of outdoor large scale cultural sites, which is currently implemented as a simple aggregation of 3D digital models at different time and levels of details. The main bottleneck of such an approach is its complexity, making 5D modelling impossible to be validated in real life conditions. In this paper, a cost effective and affordable framework for 5D modelling is proposed based on a spatial-temporal dependent aggregation of 3D digital models, by incorporating a predictive assessment procedure to indicate which regions (surfaces) of an object should be reconstructed at higher levels of details at next time instances and which at lower ones. In this way, dynamic change history maps are created, indicating spatial probabilities of regions needed further 3D modelling at forthcoming instances. Using these maps, predictive assessment can be made, that is, to localize surfaces within the objects where a high accuracy reconstruction process needs to be activated at the forthcoming time instances. The proposed 5D Digital Cultural Heritage Model (5D-DCHM) is implemented using open interoperable standards based on the CityGML framework, which also allows the description of additional semantic metadata information. Visualization aspects are also supported to allow easy manipulation, interaction and representation of the 5D-DCHM geometry and the respective semantic information. The open source 3DCity

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

    NASA Astrophysics Data System (ADS)

    Wang, Jianwei; Zhang, Yong

    2016-04-01

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

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

    PubMed Central

    Wang, Jianwei; Zhang, Yong

    2016-01-01

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

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

    PubMed

    Wang, Jianwei; Zhang, Yong

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Eiríksson, E. R.; Wilm, J.; Pedersen, D. B.; Aanæs, H.

    2016-04-01

    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 measure is the established VDI/VDE 2634 (Part 2) guideline using precision made calibration artifacts. Experiments are performed on our own structured light setup, consisting of two cameras and a projector. We place our focus on the influence of calibration design parameters, the calibration procedure and encoding strategy and present our findings. Finally, we compare our setup to a state of the art metrology grade commercial scanner. Our results show that comparable, and in some cases better, results can be obtained using the parameter settings determined in this study.

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

    PubMed

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

    2016-08-01

    PRO: tein S: tructure A: nnotation T: ool-plus (ProSAT(+)) is a new web server for mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure. ProSAT(+) incorporates many of the features of the preceding ProSAT and ProSAT2 tools but also provides new options for the visualization and sharing of protein annotations. Data are extracted from the UniProt KnowledgeBase, the RCSB PDB and the PDBe SIFTS resource, and visualization is performed using JSmol. User-defined sequence annotations can be added directly to the URL, thus enabling visualization and easy data sharing. ProSAT(+) is available at http://prosat.h-its.org. PMID:27284084

  14. A fast and accurate method to predict 2D and 3D aerodynamic boundary layer flows

    NASA Astrophysics Data System (ADS)

    Bijleveld, H. A.; Veldman, A. E. P.

    2014-12-01

    A quasi-simultaneous interaction method is applied to predict 2D and 3D aerodynamic flows. This method is suitable for offshore wind turbine design software as it is a very accurate and computationally reasonably cheap method. This study shows the results for a NACA 0012 airfoil. The two applied solvers converge to the experimental values when the grid is refined. We also show that in separation the eigenvalues remain positive thus avoiding the Goldstein singularity at separation. In 3D we show a flow over a dent in which separation occurs. A rotating flat plat is used to show the applicability of the method for rotating flows. The shown capabilities of the method indicate that the quasi-simultaneous interaction method is suitable for design methods for offshore wind turbine blades.

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

    1999-11-22

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

  16. 3D Printing for Spacecraft Multi-Functional Structures

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  17. Designing self-assembling 3D structures of microcapsules

    NASA Astrophysics Data System (ADS)

    Li, Like; Shum, Henry; Shklyaev, Oleg; Yashin, Victor; Balazs, Anna

    Self-assembly of complex, three-dimensional structures is commonly achieved by biological cells but difficult to realize in synthetic systems with micron-scale or larger components. Some previous modeling studies have considered only the planar self-assembly of microcapsules on a substrate. In this work, nanoparticles released from the capsules bind to the substrate and to the shells of nearby capsules. The non-uniform nanoparticle deposition on a capsule's surface leads to adhesion gradients, which drive the capsules to effectively ``climb'' on top of one another and self-organize in the vertical direction. We determine conditions that favor this structural organization. In particular, we study how the vertical structuring depends on the background fluid flow, the topography of the microcapsules and the underlying surface, the capsule-capsule interaction and that between the capsules and the substrate. The findings can provide design rules for the autonomous creation of novel nanocomposites, where the layers are formed from nanoparticle-containing and nanoparticle-decorated microcapsules.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  20. TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants

    PubMed Central

    Tung, Chun-Wei; Lin, Ying-Chi; Chang, Hsun-Shuo; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng

    2014-01-01

    The rich indigenous and endemic plants in Taiwan serve as a resourceful bank for biologically active phytochemicals. Based on our TIPdb database curating bioactive phytochemicals from Taiwan indigenous plants, this study presents a three-dimensional (3D) chemical structure database named TIPdb-3D to support the discovery of novel pharmacologically active compounds. The Merck Molecular Force Field (MMFF94) was used to generate 3D structures of phytochemicals in TIPdb. The 3D structures could facilitate the analysis of 3D quantitative structure–activity relationship, the exploration of chemical space and the identification of potential pharmacologically active compounds using protein–ligand docking. Database URL: http://cwtung.kmu.edu.tw/tipdb. PMID:24930145

  1. Formation of 3D structures in a volumetric photocurable material via a holographic method

    NASA Astrophysics Data System (ADS)

    Vorzobova, N. D.; Bulgakova, V. G.; Veselov, V. O.

    2015-12-01

    The principle of forming 3D polymer structures is considered, based on the display of the 3D intensity distribution of radiation formed by a hologram in the bulk of a photocurable material. The conditions are determined for limiting the cure depth and reproducing the projected wavefront configuration.

  2. Dirac cones in artificial structures of 3d transitional-metals doped Mg-Al spinels

    NASA Astrophysics Data System (ADS)

    Lu, Yuan; Feng, Min; Shao, Bin; Zuo, Xu

    2014-05-01

    Motivated by recent theoretical predications for Dirac cone in two-dimensional (2D) triangular lattice [H. Ishizuka, Phys. Rev. Lett. 109, 237207 (2012)], first-principles studies are performed to predict Dirac cones in artificial structures of 3d transitional-metals (TM = Ti, V, Cr, Mn, Fe, Co, Ni, and Cu) doped Mg-Al spinels. In investigated artificial structures, TM dopants substitute specific positions of the B sub-lattice in Mg-Al spinel, and form a quasi-2D triangular lattice in the a-b plane. Calculated results illustrate the existence of the spin-polarized Dirac cones formed in d-wave bands at (around) the K-point in the momentum space. The study provides a promising route for engineering Dirac physics in condensed matters.

  3. Dirac cones in artificial structures of 3d transitional-metals doped Mg-Al spinels

    SciTech Connect

    Lu, Yuan; Zuo, Xu; Feng, Min; Shao, Bin

    2014-05-07

    Motivated by recent theoretical predications for Dirac cone in two-dimensional (2D) triangular lattice [H. Ishizuka, Phys. Rev. Lett. 109, 237207 (2012)], first-principles studies are performed to predict Dirac cones in artificial structures of 3d transitional-metals (TM = Ti, V, Cr, Mn, Fe, Co, Ni, and Cu) doped Mg-Al spinels. In investigated artificial structures, TM dopants substitute specific positions of the B sub-lattice in Mg-Al spinel, and form a quasi-2D triangular lattice in the a-b plane. Calculated results illustrate the existence of the spin-polarized Dirac cones formed in d-wave bands at (around) the K-point in the momentum space. The study provides a promising route for engineering Dirac physics in condensed matters.

  4. 3D stochastic inversion of potential field data using structural geologic constraints

    NASA Astrophysics Data System (ADS)

    Shamsipour, Pejman; Schetselaar, Ernst; Bellefleur, Gilles; Marcotte, Denis

    2014-12-01

    We introduce a new method to include structural orientation constraints into potential field inversion using a stochastic framework. The method considers known geological interfaces and planar orientation data such as stratification estimated from seismic surveys or drill hole information. Integrating prior geological information into inversion methods can effectively reduce ambiguity and improve inversion results. The presented approach uses cokriging prediction with derivatives. The method is applied to two synthetic models to demonstrate its suitability for 3D inversion of potential field data. The method is also applied to the inversion of gravity data collected over the Lalor volcanogenic massive sulfide deposit at Snow Lake, Central Manitoba, Canada. The results show that using a structurally-constrained inversion leads to a better-resolved solution.

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

    PubMed

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

    2016-03-01

    Two-dimensional-three-dimensional (2D-3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which makes it difficult to obtain the correct solution of 2D-3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34±1.94mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets. PMID:26824922

  6. 3D Structured Grid Generation Codes for Turbomachinery

    NASA Technical Reports Server (NTRS)

    Loellbach, James; Tsung, Fu-Lin

    1999-01-01

    This report describes the research tasks during the past year. The research was mainly in the area of computational grid generation in support of CFD analyses of turbomachinery components. In addition to the grid generation work, a numerical simulation was obtained for the flow through a centrifugal gas compressor using an unstructured Navier-Stokes solver. Other tasks involved many different turbomachinery component analyses. These analyses were performed for NASA projects or for industrial applications. The work includes both centrifugal and axial machines, single and multiple blade rows, and steady and unsteady analyses. Over the past five years, a set of structured grid generation codes were developed that allow grids to be obtained fairly quickly for the large majority of configurations we encounter. These codes do not comprise a generalized grid generation package; they are noninteractive codes specifically designed for turbomachinery blade row geometries. But because of this limited scope, the codes are small, fast, and portable, and they can be run in the batch mode on small workstations. During the past year, these programs were used to generate computational grids were modified for a wide variety of configurations. In particular, the codes or wrote supplementary codes to improve our grid generation capabilities for multiple blade row configurations. This involves generating separate grids for each blade row, and then making them match and overlap by a few grid points at their common interface so that fluid properties are communicated across the interface. Unsteady rotor/stator analyses were performed for an axial turbine, a centrifugal compressor, and a centrifugal pump. Steady-state single-blade-row analyses were made for a study of blade sweep in transonic compressors. There was also cooperation on the application of an unstructured Navier-Stokes solver for turbomachinery flow simulations. In particular, the unstructured solver was used to analyze the

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

    NASA Astrophysics Data System (ADS)

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

    2010-02-01

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

  8. Micro- and macroturbulence predictions from CO5BOLD 3D stellar atmospheres .

    NASA Astrophysics Data System (ADS)

    Steffen, M.; Caffau, E.; Ludwig, H.-G.

    We present an overview of the current status of our efforts to derive the microturbulence and macroturbulence parameters (xi_mic and xi_mac) from the CIFIST grid of CO5BOLD 3D model atmospheres as a function of the basic stellar parameters T_{eff}, log g, and [M/H]. The latest results for the Sun and Procyon show that the derived microturbulence parameter depends significantly on the numerical resolution of the underlying 3D simulation, confirming that `low-resolution' models tend to underestimate the true value of xi_mic . Extending the investigation to 12 further simulations with different T_{eff}, log g, and [M/H], we obtain a first impression of the predicted trend of xi_mic over the Hertzsprung-Russell diagram: in agreement with empirical evidence, microturbulence increases towards higher effective temperature and lower gravity. The metallicity dependence of xi_mic must be interpreted with care, since it also reflects the deviation between the 1D and 3D photospheric temperature stratifications that increases systematically towards lower [M/H].

  9. The mantle wedge's transient 3-D flow regime and thermal structure

    NASA Astrophysics Data System (ADS)

    Davies, D. R.; Le Voci, G.; Goes, S.; Kramer, S. C.; Wilson, C. R.

    2016-01-01

    Arc volcanism, volatile cycling, mineralization, and continental crust formation are likely regulated by the mantle wedge's flow regime and thermal structure. Wedge flow is often assumed to follow a regular corner-flow pattern. However, studies that incorporate a hydrated rheology and thermal buoyancy predict internal small-scale-convection (SSC). Here, we systematically explore mantle-wedge dynamics in 3-D simulations. We find that longitudinal "Richter-rolls" of SSC (with trench-perpendicular axes) commonly occur if wedge hydration reduces viscosities to Pa s, although transient transverse rolls (with trench-parallel axes) can dominate at viscosities of Pa s. Rolls below the arc and back arc differ. Subarc rolls have similar trench-parallel and trench-perpendicular dimensions of 100-150 km and evolve on a 1-5 Myr time-scale. Subback-arc instabilities, on the other hand, coalesce into elongated sheets, usually with a preferential trench-perpendicular alignment, display a wavelength of 150-400 km and vary on a 5-10 Myr time scale. The modulating influence of subback-arc ridges on the subarc system increases with stronger wedge hydration, higher subduction velocity, and thicker upper plates. We find that trench-parallel averages of wedge velocities and temperature are consistent with those predicted in 2-D models. However, lithospheric thinning through SSC is somewhat enhanced in 3-D, thus expanding hydrous melting regions and shifting dehydration boundaries. Subarc Richter-rolls generate time-dependent trench-parallel temperature variations of up to K, which exceed the transient 50-100 K variations predicted in 2-D and may contribute to arc-volcano spacing and the variable seismic velocity structures imaged beneath some arcs.

  10. 3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

  12. Sensitivity of an MT Array to 3D Structure Outside the Array Footprint

    NASA Astrophysics Data System (ADS)

    Booker, J. R.; Mackie, R. L.; Burd, A. I.; Pomposiello, M. C.; Favetto, A. B.

    2015-12-01

    Standard data collection strategy in magnetotellurics (MT) is to deploy a profile or array of sites that spans the target of interest. There is no expectation that structure can be imaged outside the area covered by sites. We have inverted two MT arrays for 3D structure under Argentina. The two arrays do not overlap, but serendipitously the 3D model for the northern array overlaps the position of a prominent 3D deep conductive structure seen in the inversion of the southern array. To our surprise this deep southern feature is also imaged by the northern array even though it is well outside the footprint of the northern array. It therefore appears that typical intuition about one's ability to image structure outside the span of the sites is not always true. We present model studies to demonstrate why this is so and under what conditions one can expect a 3D array to be capable of imaging structure outside the array.

  13. Comparison of Different 2D and 3D-QSAR Methods on Activity Prediction of Histamine H3 Receptor Antagonists.

    PubMed

    Dastmalchi, Siavoush; Hamzeh-Mivehroud, Maryam; Asadpour-Zeynali, Karim

    2012-01-01

    Histamine H3 receptor subtype has been the target of several recent drug development programs. Quantitative structure-activity relationship (QSAR) methods are used to predict the pharmaceutically relevant properties of drug candidates whenever it is applicable. The aim of this study was to compare the predictive powers of three different QSAR techniques, namely, multiple linear regression (MLR), artificial neural network (ANN), and HASL as a 3D QSAR method, in predicting the receptor binding affinities of arylbenzofuran histamine H3 receptor antagonists. Genetic algorithm coupled partial least square as well as stepwise multiple regression methods were used to select a number of calculated molecular descriptors to be used in MLR and ANN-based QSAR studies. Using the leave-group-out cross-validation technique, the performances of the MLR and ANN methods were evaluated. The calculated values for the mean absolute percentage error (MAPE), ranging from 2.9 to 3.6, and standard deviation of error of prediction (SDEP), ranging from 0.31 to 0.36, for both MLR and ANN methods were statistically comparable, indicating that both methods perform equally well in predicting the binding affinities of the studied compounds toward the H3 receptors. On the other hand, the results from 3D-QSAR studies using HASL method were not as good as those obtained by 2D methods. It can be concluded that simple traditional approaches such as MLR method can be as reliable as those of more advanced and sophisticated methods like ANN and 3D-QSAR analyses. PMID:25317190

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  15. 3D structure of individual nanocrystals in solution by electron microscopy

    NASA Astrophysics Data System (ADS)

    Park, Jungwon; Elmlund, Hans; Ercius, Peter; Yuk, Jong Min; Limmer, David T.; Chen, Qian; Kim, Kwanpyo; Han, Sang Hoon; Weitz, David A.; Zettl, A.; Alivisatos, A. Paul

    2015-07-01

    Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.

  16. 3D Printers Can Provide an Added Dimension for Teaching Structure-Energy Relationships

    ERIC Educational Resources Information Center

    Blauch, David N.; Carroll, Felix A.

    2014-01-01

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

  17. Object-adaptive depth compensated inter prediction for depth video coding in 3D video system

    NASA Astrophysics Data System (ADS)

    Kang, Min-Koo; Lee, Jaejoon; Lim, Ilsoon; Ho, Yo-Sung

    2011-01-01

    Nowadays, the 3D video system using the MVD (multi-view video plus depth) data format is being actively studied. The system has many advantages with respect to virtual view synthesis such as an auto-stereoscopic functionality, but compression of huge input data remains a problem. Therefore, efficient 3D data compression is extremely important in the system, and problems of low temporal consistency and viewpoint correlation should be resolved for efficient depth video coding. In this paper, we propose an object-adaptive depth compensated inter prediction method to resolve the problems where object-adaptive mean-depth difference between a current block, to be coded, and a reference block are compensated during inter prediction. In addition, unique properties of depth video are exploited to reduce side information required for signaling decoder to conduct the same process. To evaluate the coding performance, we have implemented the proposed method into MVC (multiview video coding) reference software, JMVC 8.2. Experimental results have demonstrated that our proposed method is especially efficient for depth videos estimated by DERS (depth estimation reference software) discussed in the MPEG 3DV coding group. The coding gain was up to 11.69% bit-saving, and it was even increased when we evaluated it on synthesized views of virtual viewpoints.

  18. FUN3D Analyses in Support of the Second Aeroelastic Prediction Workshop

    NASA Technical Reports Server (NTRS)

    Chwalowski, Pawel; Heeg, Jennifer

    2016-01-01

    This paper presents the computational aeroelastic results generated in support of the second Aeroelastic Prediction Workshop for the Benchmark Supercritical Wing (BSCW) configurations and compares them to the experimental data. The computational results are obtained using FUN3D, an unstructured grid Reynolds- Averaged Navier-Stokes solver developed at NASA Langley Research Center. The analysis results include aerodynamic coefficients and surface pressures obtained for steady-state, static aeroelastic equilibrium, and unsteady flow due to a pitching wing or flutter prediction. Frequency response functions of the pressure coefficients with respect to the angular displacement are computed and compared with the experimental data. The effects of spatial and temporal convergence on the computational results are examined.

  19. Prediction of 3D chip formation in the facing cutting with lathe machine using FEM

    NASA Astrophysics Data System (ADS)

    Prasetyo, Yudhi; Tauviqirrahman, Mohamad; Rusnaldy

    2016-04-01

    This paper presents the prediction of the chip formation at the machining process using a lathe machine in a more specific way focusing on facing cutting (face turning). The main purpose is to propose a new approach to predict the chip formation with the variation of the cutting directions i.e., the backward and forward direction. In addition, the interaction between stress analysis and chip formation on cutting process was also investigated. The simulations were conducted using three dimensional (3D) finite element method based on ABAQUS software with aluminum and high speed steel (HSS) as the workpiece and the tool materials, respectively. The simulation result showed that the chip resulted using a backward direction depicts a better formation than that using a conventional (forward) direction.

  20. Self-Assembled 3D Ordered Macroporous Structures for Tissue Engineering Scaffolds

    NASA Astrophysics Data System (ADS)

    Juan, Wen-Tau; Chung, Kuo-Yuan; Mishra, Narayan; Lin, Keng-Hui

    2008-03-01

    A simple, inexpensive and fast microfluidic method to fabricate three-dimensional ordered macroporous gel is demonstrated using alginate as the scaffold material. The microfluidic device consists of two concentric micropipettes where one is nested inside the other. Nitrogen gas and aqueous alginate solution with Pluronic F127 are pumped through the inner and the outer channel respectively. Under appropriate conditions, bubbles of a uniform size are generated within the device at few thousand Hz. We show the control over bubble size by the gas pressure and quantitatively predict the size dependence from the geometry of fluidic device. Monodisperse bubbles are collected and self-assemble into crystal structures as wet foam. The alginate solution between bubbles is crosslinked by divalent calcium ions and turns into 3D ordered macroporous gel where the pores are highly interconnected. The pore size can be directly controlled by the bubble size which ranges from few tens microns to few millimeters. This technique promises a versatile and robust way to make 3D ordered tissue engineering scaffolds.

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

    PubMed

    McLeod, J A; Buling, A; Green, R J; Boyko, T D; Skorikov, N A; Kurmaev, E Z; Neumann, M; Finkelstein, L D; Ni, N; Thaler, A; Bud'ko, S L; Canfield, P C; Moewes, A

    2012-05-30

    The electronic structure of BaFe(2)As(2) 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 3d(10) shell. These findings help shed light on why superconductivity can occur in BaFe(2)As(2) doped with Co and Ni but not Cu. PMID:22534111

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

    SciTech Connect

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

    2012-04-25

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

  3. Towards 3D and Multilayer Electromagnetic Metamaterials Structures in the THz Range

    NASA Astrophysics Data System (ADS)

    Casse, B. D. F.; Moser, H. O.; Lee, J. W.; Inglis, S.; Bahou, M.; Jian, L. K.

    2007-03-01

    V. G. Veselago predicted that left-handed materials would exhibit a plethora of unusual effects such as a negative index of refraction as used in Snell's law, a reverse Doppler and Cerenkov effect. This novel class of materials, following Pendry's recipes, can potentially restore evanescent waves to focus subwavelength details in an image. Micron-size electromagnetic metamaterials (EM^3) structures which exist so far were produced and characterized as single layer structures. Furthermore the structures were produced with a low yield. In the first part of the talk, we will present techniques for producing copious amount of EM^3 chips via the LIGA process using Synchrotron radiation and demonstrate assembly of the first multilayer THz EM^3 structures. The planar micro- or nanoEM^3 produced so far are also highly anisotropic. Recently, we proposed schemes to produce more isotropic structures, within the same matrix, via tilted X-ray exposures that were introduced in the LIGA process years ago. In the second part of the talk, we will show the results of microfabrication of nearly 3D EM^3 structures for the THz range.

  4. Using self-similarity compensation for improving inter-layer prediction in scalable 3D holoscopic video coding

    NASA Astrophysics Data System (ADS)

    Conti, Caroline; Nunes, Paulo; Ducla Soares, Luís.

    2013-09-01

    Holoscopic imaging, also known as integral imaging, has been recently attracting the attention of the research community, as a promising glassless 3D technology due to its ability to create a more realistic depth illusion than the current stereoscopic or multiview solutions. However, in order to gradually introduce this technology into the consumer market and to efficiently deliver 3D holoscopic content to end-users, backward compatibility with legacy displays is essential. Consequently, to enable 3D holoscopic content to be delivered and presented on legacy displays, a display scalable 3D holoscopic coding approach is required. Hence, this paper presents a display scalable architecture for 3D holoscopic video coding with a three-layer approach, where each layer represents a different level of display scalability: Layer 0 - a single 2D view; Layer 1 - 3D stereo or multiview; and Layer 2 - the full 3D holoscopic content. In this context, a prediction method is proposed, which combines inter-layer prediction, aiming to exploit the existing redundancy between the multiview and the 3D holoscopic layers, with self-similarity compensated prediction (previously proposed by the authors for non-scalable 3D holoscopic video coding), aiming to exploit the spatial redundancy inherent to the 3D holoscopic enhancement layer. Experimental results show that the proposed combined prediction can improve significantly the rate-distortion performance of scalable 3D holoscopic video coding with respect to the authors' previously proposed solutions, where only inter-layer or only self-similarity prediction is used.

  5. 3D choroid neovascularization growth prediction based on reaction-diffusion model

    NASA Astrophysics Data System (ADS)

    Zhu, Shuxia; Chen, Xinjian; Shi, Fei; Xiang, Dehui; Zhu, Weifang; Chen, Haoyu

    2016-03-01

    Choroid neovascularization (CNV) is a kind of pathology from the choroid and CNV-related disease is one important cause of vision loss. It is desirable to predict the CNV growth rate so that appropriate treatment can be planned. In this paper, we seek to find a method to predict the growth of CNV based on 3D longitudinal Optical Coherence Tomography (OCT) images. A reaction-diffusion model is proposed for prediction. The method consists of four phases: pre-processing, meshing, CNV growth modeling and prediction. We not only apply the reaction-diffusion model to the disease region, but also take the surrounding tissues into consideration including outer retinal layer, inner retinal layer and choroid layer. The diffusion in these tissues is considered as isotropic. The finite-element-method (FEM) is used to solve the partial differential equations (PDE) in the diffusion model. The curve of CNV growth with treatment are fitted and then we can predict the CNV status in a future time point. The preliminary results demonstrated that our proposed method is accurate and the validity and feasibility of our model is obvious.

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

    SciTech Connect

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

    2004-04-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

    Zhang, Fengxiang; Low, Hong Yee

    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. PMID:21832645

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

    NASA Astrophysics Data System (ADS)

    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

  10. Regional structural styles in the northeast Netherlands as expressed on 3-D data

    SciTech Connect

    Goeyenbier, H. )

    1993-09-01

    The northeast Netherlands areas is a highly prospective gas province, containing the Groningen gas field and a multitude of smaller fields. Some 40 three-dimensional (3-D) seismic surveys have been acquired over the last 10 yr. covering a major part of this 15,000-km[sup 2] area. These surveys have been combined for the first time on a Landmark workstation to produce time, depth, and horizon attribute maps from six important (overburden and reservoir) levels: base Tertiary, base Chalk, base Cretaceous, base Jurassic, top Zechstein and base Zechstein. The structural history was reconstructed by analyzing isopach maps of the various units in combination with dip extractions along the mapped horizons to outline the active fault trends. Isopach maps of the Tertiary, Chalk, and Lower Cretaceous sediments reveal the salt movement during this interval with depocenters in the Lauwerszee trough as a result of salt withdrawal and salt diapirism in the areas of structural weakness near existing fault trends. The dip maps at the base of these units show the en-echelon fault pattern and the presence of crestal collapse systems above the salt domes. A comparison between base Cretaceous and base Chalk isopach maps also highlights the presence of inverted Lower Cretaceous basins. By comparing the overburden fault trends with the pre-Zechstein pattern, late faults can be separated from older trends, which has helped the prediction of sealing faults. The regional 3-D data provide a powerful and unambiguous tool to unravel the structural history in the northeast Netherlands.

  11. Self-Discovery of Structural Geology Concepts using Interactive 3D Visualization

    NASA Astrophysics Data System (ADS)

    Billen, M. I.; Saunders, J.

    2010-12-01

    Mastering structural geology concepts that depend on understanding three-dimensional (3D) geometries and imagining relationships among unseen subsurface structures are fundamental skills for geologists. Traditionally these skills are developed first, through use of 2D drawings of 3D structures that can be difficult to decipher or 3D physical block models that show only a limited set of relationships on the surfaces of the blocks, followed by application and testing of concepts in field settings. We hypothesize that this learning process can be improved by providing repeated opportunities to evaluate and explore synthetic 3D structures using interactive 3D visualization software. We present laboratory modules designed for undergraduate structural geology curriculum using a self-discovery approach to teach concepts such as: the Rule of V’s, structure separation versus fault slip, and the more general dependence of structural exposure on surface topography. The laboratory modules are structured to allow students to discover and articulate each concept from observations of synthetic data both on traditional maps and using the volume visualization software 3DVisualizer. Modules lead students through exploration of data (e.g., a dipping layered structure exposed in ridge-valley topography or obliquely offset across a fault) by allowing them to interactively view (rotate, pan, zoom) the exposure of structures on topographic surfaces and to toggle on/off the full 3D structure as a transparent colored volume. This tool allows student to easily visually understand the relationships between, for example a dipping structure and its exposure on valley walls, as well as how the structure extends beneath the surface. Using this method gives students more opportunities to build a mental library of previously-seen relationships from which to draw-on when applying concepts in the field setting. These laboratory modules, the data and software are freely available from KeckCAVES.

  12. Liner Optimization Studies Using the Ducted Fan Noise Prediction Code TBIEM3D

    NASA Technical Reports Server (NTRS)

    Dunn, M. H.; Farassat, F.

    1998-01-01

    In this paper we demonstrate the usefulness of the ducted fan noise prediction code TBIEM3D as a liner optimization design tool. Boundary conditions on the interior duct wall allow for hard walls or a locally reacting liner with axially segmented, circumferentially uniform impedance. Two liner optimization studies are considered in which farfield noise attenuation due to the presence of a liner is maximized by adjusting the liner impedance. In the first example, the dependence of optimal liner impedance on frequency and liner length is examined. Results show that both the optimal impedance and attenuation levels are significantly influenced by liner length and frequency. In the second example, TBIEM3D is used to compare radiated sound pressure levels between optimal and non-optimal liner cases at conditions designed to simulate take-off. It is shown that significant noise reduction is achieved for most of the sound field by selecting the optimal or near optimal liner impedance. Our results also indicate that there is relatively large region of the impedance plane over which optimal or near optimal liner behavior is attainable. This is an important conclusion for the designer since there are variations in liner characteristics due to manufacturing imprecisions.

  13. ALE3D Model Predictions and Experimental Analysis of the Cookoff Response of Comp B*

    SciTech Connect

    Maienschein, J L; McClelland, M A; Wardell, J F; Reaugh, J E; Nichols, A L; Tran, T D

    2003-11-24

    ALE3D simulations are presented for the thermal explosion of Comp B (RDX,TNT) in a Scaled Thermal Explosion Experiment (STEX). Candidate models and numerical strategies are being tested using the ALE3D code which simulates the coupled thermal, mechanical, and chemical behavior during heating, ignition, and explosion. The mechanical behavior of the solid constituents is represented by a Steinberg-Guinan model while polynomial and gamma-law expressions are used for the equation of state of the solid and gas species, respectively. A gamma-law model is employed for the air in gaps, and a mixed material model is used for the interface between air and explosive. A three-step chemical kinetics model is used for each of the RDX and TNT reaction sequences during the heating and ignition phases, and a pressure-dependent deflagration model is employed during the rapid expansion. Parameters for the three-step kinetics model are specified using measurements of the One-Dimensional-Time-to-Explosion (ODTX), while measurements for burn rate are employed to determine parameters in the burn front model. We compare model predictions to measurements for temperature fields, ignition temperature, and tube wall strain during the heating, ignition, and explosive phases.

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

    NASA Technical Reports Server (NTRS)

    Lietzke, Susan E; Barnes, Cindy L.

    1998-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

    In this paper, a method of vascular structure identification in intraoperative 3D Contrast-Enhanced Ultrasound (CEUS) data is presented. Ultrasound imaging is commonly used in brain tumor surgery to investigate in real time the current status of cerebral structures. The use of an ultrasound contrast agent enables to highlight tumor tissue, but also surrounding blood vessels. However, these structures can be used as landmarks to estimate and correct the brain shift. This work proposes an alternative method for extracting small vascular segments close to the tumor as landmark. The patient image dataset involved in brain tumor operations includes preoperative contrast T1MR (cT1MR) data and 3D intraoperative contrast enhanced ultrasound data acquired before (3D-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. PMID:27070610

  17. i3Drefine Software for Protein 3D Structure Refinement and Its Assessment in CASP10

    PubMed Central

    Bhattacharya, Debswapna; Cheng, Jianlin

    2013-01-01

    Protein structure refinement refers to the process of improving the qualities of protein structures during structure modeling processes to bring them closer to their native states. Structure refinement has been drawing increasing attention in the community-wide Critical Assessment of techniques for Protein Structure prediction (CASP) experiments since its addition in 8th CASP experiment. During the 9th and recently concluded 10th CASP experiments, a consistent growth in number of refinement targets and participating groups has been witnessed. Yet, protein structure refinement still remains a largely unsolved problem with majority of participating groups in CASP refinement category failed to consistently improve the quality of structures issued for refinement. In order to alleviate this need, we developed a completely automated and computationally efficient protein 3D structure refinement method, i3Drefine, based on an iterative and highly convergent energy minimization algorithm with a powerful all-atom composite physics and knowledge-based force fields and hydrogen bonding (HB) network optimization technique. In the recent community-wide blind experiment, CASP10, i3Drefine (as ‘MULTICOM-CONSTRUCT’) was ranked as the best method in the server section as per the official assessment of CASP10 experiment. Here we provide the community with free access to i3Drefine software and systematically analyse the performance of i3Drefine in strict blind mode on the refinement targets issued in CASP10 refinement category and compare with other state-of-the-art refinement methods participating in CASP10. Our analysis demonstrates that i3Drefine is only fully-automated server participating in CASP10 exhibiting consistent improvement over the initial structures in both global and local structural quality metrics. Executable version of i3Drefine is freely available at http://protein.rnet.missouri.edu/i3drefine/. PMID:23894517

  18. Metal nanoparticle direct inkjet printing for low-temperature 3D micro metal structure fabrication

    NASA Astrophysics Data System (ADS)

    Ko, Seung Hwan; Chung, Jaewon; Hotz, Nico; Nam, Koo Hyun; Grigoropoulos, Costas P.

    2010-12-01

    Inkjet printing of functional materials is a key technology toward ultra-low-cost, large-area electronics. We demonstrate low-temperature 3D micro metal structure fabrication by direct inkjet printing of metal nanoparticles (NPs) as a versatile, direct 3D metal structuring approach representing an alternative to conventional vacuum deposition and photolithographic methods. Metal NP ink was inkjet-printed to exploit the large melting temperature drop of the nanomaterial and the ease of the NP ink formulation. Parametric studies on the basic conditions for stable 3D inkjet printing of NP ink were carried out. Furthermore, diverse 3D metal microstructures, including micro metal pillar arrays, helices, zigzag and micro bridges were demonstrated and electrical characterization was performed. Since the process requires low temperature, it carries substantial potential for fabrication of electronics on a plastic substrate.

  19. Mantle wedge flow pattern and thermal structure in Northeast Japan: Effects of oblique subduction and 3-D slab geometry

    NASA Astrophysics Data System (ADS)

    Wada, Ikuko; He, Jiangheng; Hasegawa, Akira; Nakajima, Junichi

    2015-09-01

    We develop a 3-D thermal model for the Northeast Japan subduction margin, using a realistic slab geometry for the subducting Pacific plate, and investigate the effects of oblique subduction and 3-D slab geometry on the mantle wedge flow pattern and the thermal structure. In the Tohoku region, the mantle wedge flow pattern is nearly two-dimensional resulting in a thermal structure similar to those obtained by a 2-D model, owing to the simple slab geometry and subduction nearly perpendicular to the margin. However, in Hokkaido, oblique subduction leads to 3-D mantle wedge flow with northerly inflow and west-northwestward outflow and also results in lower temperatures in the shallow part of the mantle wedge than in Tohoku due to lower sinking rate of the slab. Between Hokkaido and Tohoku, the slab has a hinge-like shape due to a relatively sharp change in the dip direction. In this hinge zone, northerly mantle inflow from Hokkaido and westerly mantle inflow from Tohoku converge, discouraging inflow from northwest and resulting in a cooler mantle wedge. The model-predicted mantle wedge flow patterns are consistent with observed seismic anisotropy and may explain the orientations of volcanic cross-chains. The predicted 3-D thermal structure correlates well with the along-arc variations in the location of the frontal arc volcanoes and help to provide new insights into the surface heat flow pattern and the down-dip extent of interplate earthquakes.

  20. A combined fuzzy-neural network model for non-linear prediction of 3-D rendering workload in grid computing.

    PubMed

    Doulamis, Nikolaos D; Doulamis, Anastasios D; Panagakis, Athanasios; Dolkas, Konstantinos; Varvarigou, Theodora A; Varvarigos, Emmanuel

    2004-04-01

    Implementation of a commercial application to a grid infrastructure introduces new challenges in managing the quality-of-service (QoS) requirements, most stem from the fact that negotiation on QoS between the user and the service provider should strictly be satisfied. An interesting commercial application with a wide impact on a variety of fields, which can benefit from the computational grid technologies, is three-dimensional (3-D) rendering. In order to implement, however, 3-D rendering to a grid infrastructure, we should develop appropriate scheduling and resource allocation mechanisms so that the negotiated (QoS) requirements are met. Efficient scheduling schemes require modeling and prediction of rendering workload. In this paper workload prediction is addressed based on a combined fuzzy classification and neural network model. Initially, appropriate descriptors are extracted to represent the synthetic world. The descriptors are obtained by parsing RIB formatted files, which provides a general structure for describing computer-generated images. Fuzzy classification is used for organizing rendering descriptor so that a reliable representation is accomplished which increases the prediction accuracy. Neural network performs workload prediction by modeling the nonlinear input-output relationship between rendering descriptors and the respective computational complexity. To increase prediction accuracy, a constructive algorithm is adopted in this paper to train the neural network so that network weights and size are simultaneously estimated. Then, a grid scheduler scheme is proposed to estimate the queuing order that the tasks should be executed and the most appopriate processor assignment so that the demanded QoS are satisfied as much as possible. A fair scheduling policy is considered as the most appropriate. Experimental results on a real grid infrastructure are presented to illustrate the efficiency of the proposed workload prediction--scheduling algorithm

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

    PubMed

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

    2010-09-27

    A novel method for fabrication of 2D and 3D metal nanoparticle structures and arrays is proposed. This technique is based on laser-induced transfer of molten metal nanodroplets from thin metal films. Metal nanoparticles are produced by solidification of these nanodroplets. The size of the transferred nanoparticles can be controllably changed in the range from 180 nm to 1500 nm. Several examples of complex 2D and 3D microstructures generated form gold nanoparticles are demonstrated. PMID:20941016

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

    NASA Astrophysics Data System (ADS)

    Cook, Kevin; Leon-Saval, Sergio; Canning, John; Reid, Zane; Hossain, Md. Arafat; Peng, Gang-Ding

    2015-09-01

    We report the first optical fibre drawn from a 3D-printed preform. An air-structured polymer preform is printed using a modified butadiene plastic called Bendlay as opposed to the more-common Acrylonitrile Butadiene Styrene (ABS). The preform is subsequently drawn to fibre form at a relatively low temperature of 160 °C and maintains its air-structured cladding holes. Such ability to freely-design and 3D-print complex preform structures, such as photonic bandgap and photonic crystal structures, opens up an exciting new front in optical fibre fabrication.

  3. Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

    PubMed Central

    Li, Wenyuan; Kalhor, Reza; Dai, Chao; Hao, Shengli; Gong, Ke; Zhou, Yonggang; Li, Haochen; Zhou, Xianghong Jasmine; Le Gros, Mark A.; Larabell, Carolyn A.; Chen, Lin; Alber, Frank

    2016-01-01

    Conformation capture technologies (e.g., Hi-C) chart physical interactions between chromatin regions on a genome-wide scale. However, the structural variability of the genome between cells poses a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range and interchromosomal interactions. Here, we present a probabilistic approach for deconvoluting Hi-C data into a model population of distinct diploid 3D genome structures, which facilitates the detection of chromatin interactions likely to co-occur in individual cells. Our approach incorporates the stochastic nature of chromosome conformations and allows a detailed analysis of alternative chromatin structure states. For example, we predict and experimentally confirm the presence of large centromere clusters with distinct chromosome compositions varying between individual cells. The stability of these clusters varies greatly with their chromosome identities. We show that these chromosome-specific clusters can play a key role in the overall chromosome positioning in the nucleus and stabilizing specific chromatin interactions. By explicitly considering genome structural variability, our population-based method provides an important tool for revealing novel insights into the key factors shaping the spatial genome organization. PMID:26951677

  4. High-coverage stable structures of 3d transition metal intercalated bilayer graphene.

    PubMed

    Liao, Ji-Hai; Zhao, Yu-Jun; Tang, Jia-Jun; Yang, Xiao-Bao; Xu, Hu

    2016-06-01

    Alkali-metal intercalated graphite and graphene have been intensively studied for decades, where alkali-metal atoms are found to form ordered structures at the hollow sites of hexagonal carbon rings. Using first-principles calculations, we have predicted various stable structures of high-coverage 3d transition metal (TM) intercalated bilayer graphene (BLG) stabilized by the strain. Specifically, with reference to the bulk metal, Sc and Ti can form stable TM-intercalated BLG without strain, while the stabilization of Fe, Co, and Ni intercalated BLG requires the biaxial strain of over 7%. Under the biaxial strain ranging from 0% to 10%, there are four ordered sandwich structures for Sc with the coverage of 0.25, 0.571, 0.684, and 0.75, in which the Sc atoms are all distributed homogenously instead of locating at the hollow sites. According to the phase diagram, a homogenous configuration of C8Ti3C8 with the coverage of 0.75 and another inhomogeneous structure with the coverage of 0.692 were found. The electronic and magnetic properties as a function of strain were also analyzed to indicate that the strain was important for the stabilities of the high-coverage TM-intercalated BLG. PMID:27167998

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

    PubMed Central

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

    2015-01-01

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

  6. 3D quantification of microclimate volume in layered clothing for the prediction of clothing insulation.

    PubMed

    Lee, Yejin; Hong, Kyunghi; Hong, Sung-Ae

    2007-05-01

    Garment fit and resultant air volume is a crucial factor in thermal insulation, and yet, it has been difficult to quantify the air volume of clothing microclimate and relate it to the thermal insulation value just using the information on the size of clothing pattern without actual 3D volume measurement in wear condition. As earlier methods for the computation of air volume in clothing microclimate, vacuum over suit and circumference model have been used. However, these methods have inevitable disadvantages in terms of cost or accuracy due to the limitations of measurement equipment. In this paper, the phase-shifting moiré topography was introduced as one of the 3D scanning tools to measure the air volume of clothing microclimate quantitatively. The purpose of this research is to adopt a non-contact image scanning technology, phase-shifting moiré topography, to ascertain relationship between air volume and insulation value of layered clothing systems in wear situations where the 2D fabric creates new conditions in 3D spaces. The insulation of vests over shirts as a layered clothing system was measured with a thermal manikin in the environmental condition of 20 degrees C, 65% RH and air velocity of 0.79 m/s. As the pattern size increased, the insulation of the clothing system was increased. But beyond a certain limit, the insulation started to decrease due to convection and ventilation, which is more apparent when only the vest was worn over the torso of manikin. The relationship between clothing air volume and insulation was difficult to predict with a single vest due to the extreme openings which induced active ventilation. But when the vest was worn over the shirt, the effects of thickness of the fabrics on insulation were less pronounced compared with that of air volume. In conclusion, phase-shifting moiré topography was one of the efficient and accurate ways of quantifying air volume and its distribution across the clothing microclimate. It is also noted

  7. 3D hand motion trajectory prediction from EEG mu and beta bandpower.

    PubMed

    Korik, A; Sosnik, R; Siddique, N; Coyle, D

    2016-01-01

    A motion trajectory prediction (MTP) - based brain-computer interface (BCI) aims to reconstruct the three-dimensional (3D) trajectory of upper limb movement using electroencephalography (EEG). The most common MTP BCI employs a time series of bandpass-filtered EEG potentials (referred to here as the potential time-series, PTS, model) for reconstructing the trajectory of a 3D limb movement using multiple linear regression. These studies report the best accuracy when a 0.5-2Hz bandpass filter is applied to the EEG. In the present study, we show that spatiotemporal power distribution of theta (4-8Hz), mu (8-12Hz), and beta (12-28Hz) bands are more robust for movement trajectory decoding when the standard PTS approach is replaced with time-varying bandpower values of a specified EEG band, ie, with a bandpower time-series (BTS) model. A comprehensive analysis comprising of three subjects performing pointing movements with the dominant right arm toward six targets is presented. Our results show that the BTS model produces significantly higher MTP accuracy (R~0.45) compared to the standard PTS model (R~0.2). In the case of the BTS model, the highest accuracy was achieved across the three subjects typically in the mu (8-12Hz) and low-beta (12-18Hz) bands. Additionally, we highlight a limitation of the commonly used PTS model and illustrate how this model may be suboptimal for decoding motion trajectory relevant information. Although our results, showing that the mu and beta bands are prominent for MTP, are not in line with other MTP studies, they are consistent with the extensive literature on classical multiclass sensorimotor rhythm-based BCI studies (classification of limbs as opposed to motion trajectory prediction), which report the best accuracy of imagined limb movement classification using power values of mu and beta frequency bands. The methods proposed here provide a positive step toward noninvasive decoding of imagined 3D hand movements for movement-free BCIs

  8. A finite element analysis of a 3D auxetic textile structure for composite reinforcement

    NASA Astrophysics Data System (ADS)

    Ge, Zhaoyang; Hu, Hong; Liu, Yanping

    2013-08-01

    This paper reports the finite element analysis of an innovative 3D auxetic textile structure consisting of three yarn systems (weft, warp and stitch yarns). Different from conventional 3D textile structures, the proposed structure exhibits an auxetic behaviour under compression and can be used as a reinforcement to manufacture auxetic composites. The geometry of the structure is first described. Then a 3D finite element model is established using ANSYS software and validated by the experimental results. The deformation process of the structure at different compression strains is demonstrated, and the validated finite element model is finally used to simulate the auxetic behaviour of the structure with different structural parameters and yarn properties. The results show that the auxetic behaviour of the proposed structure increases with increasing compression strain, and all the structural parameters and yarn properties have significant effects on the auxetic behaviour of the structure. It is expected that the study could provide a better understanding of 3D auxetic textile structures and could promote their application in auxetic composites.

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

    PubMed Central

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

    2003-01-01

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

  10. FEM-Based 3-D Tumor Growth Prediction for Kidney Tumor

    PubMed Central

    Chen, Xinjian; Summers, Ronald

    2012-01-01

    It is important to predict the tumor growth so that appropriate treatment can be planned in the early stage. In this letter, we propose a finite-element method (FEM)-based 3-D tumor growth prediction system using longitudinal kidney tumor images. To the best of our knowledge, this is the first kidney tumor growth prediction system. The kidney tissues are classified into three types: renal cortex, renal medulla, and renal pelvis. The reaction–diffusion model is applied as the tumor growth model. Different diffusion properties are considered in the model: the diffusion for renal medulla is considered as anisotropic, while those of renal cortex and renal pelvis are considered as isotropic. The FEM is employed to solve the diffusion model. Themodel parameters are estimated by the optimization of an objective function of overlap accuracy using a hybrid optimization parallel search package. The proposed method was tested on two longitudinal studies with seven time points on five tumors. The average true positive volume fraction and false positive volume fraction on all tumors is 91.4% and 4.0%, respectively. The experimental results showed the feasibility and efficacy of the proposed method. PMID:21342810

  11. Temperature predictions for geothermal exploration - a lithospheric-scale 3D approach applied to the northern Upper Rhine Graben

    NASA Astrophysics Data System (ADS)

    Freymark, Jessica; Sippel, Judith; Scheck-Wenderoth, Magdalena; Bär, Kristian; Fritsche, Johann-Gerhard; Kracht, Matthias; Stiller, Manfred

    2015-04-01

    The Upper Rhine Graben and its prolongation, the Hessian depression, were formed as part of the European Cenozoic Rift System in a complex extensional to transtensional setting. At present-day, the Upper Rhine Graben is one of the regions in Germany that are well suitable for deep geothermal exploitation. In the framework of the EU-funded project "IMAGE" (Integrated Methods for Advanced Geothermal Exploration) we aim to contribute to the development of an integrated and multidisciplinary approach for the exploration of geothermal reservoirs by understanding the processes and properties controlling the spatial distribution of key parameters such as the underground temperature. 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. To understand the deep thermal field of the northern Upper Rhine Graben in the federal state of Hessen, we first develop a 3D structural model that differentiates the main geological units of the lithosphere including the shallow sedimentary fill. This model allows to solve the steady-state conductive heat equation and understand the first-order controlling factors of the regional thermal field. We present the database (e.g. seismic reflection data) and the methodological workflow (involving, e.g., 3D gravity modelling) that were used to develop the lithospheric-scale 3D structural model. Furthermore, we show how certain features of the structural model such as thickness variations of the radiogenic-heat-producing crystalline crust control the temperature distribution in the subsurface.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  13. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography

    PubMed Central

    Ishikawa, Takashi

    2013-01-01

    Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex. PMID:27493552

  14. 3-D seismic velocity and attenuation structures in the geothermal field

    SciTech Connect

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

    2013-09-09

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

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

    PubMed

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

    2016-04-28

    Inspired by the structural color from the multilayer nanophotonic structures in Morpho butterfly wing scales, 3D lamellae layers in dielectric polymers (polymethyl methacrylate, PMMA) with n ∼ 1.5 were designed and fabricated by standard top-down electron beam lithography with one-step exposure followed by an alternating development/dissolution process of PMMA/LOR (lift-off resist) multilayers. This work offers direct proof of the structural blue/green color via lithographically-replicated PMMA/air multilayers, analogous to those in real Morpho butterfly wings. The success of nanolithography in this work for the 3D lamellae structures in dielectric polymers not only enables us to gain deeper insight into the mysterious blue color of the Morpho butterfly wings, but also breaks through the bottleneck in technical development toward broad applications in gas/liquid sensors, 3D meta-materials, coloring media, and infrared imaging devices, etc. PMID:27087577

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

    NASA Astrophysics Data System (ADS)

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

    2009-01-01

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

  17. Simulation of the 3-D Evolution of Electron Scale Magnetic Reconnection - Motivated by Laboratory Experiments Predictions for MMS

    NASA Astrophysics Data System (ADS)

    Buechner, J.; Jain, N.; Sharma, A.

    2013-12-01

    The four s/c of the Magnetospheric Multiscale (MMS) mission, to be launched in 2014, will use the Earth's magnetosphere as a laboratory to study the microphysics of three fundamental plasma processes. One of them is magnetic reconnection, an essentially multi-scale process. While laboratory experiments and past theoretical investigations have shown that important processes necessary to understand magnetic reconnection take place at electron scales the MMS mission for the first time will be able to resolve these scales by in space observations. For the measurement strategy of MMS it is important to make specific predictions of the behavior of current sheets with a thickness of the order of the electron skin depth which play an important role in the evolution of collisionless magnetic reconnection. Since these processes are highly nonlinear and non-local numerical simulation is needed to specify the current sheet evolution. Here we present new results about the nonlinear evolution of electron-scale current sheets starting from the linear stage and using 3-D electron-magnetohydrodynamic (EMHD) simulations. The growth rates of the simulated instabilities compared well with the growth rates obtained from linear theory. Mechanisms and conditions of the formation of flux ropes and of current filamentation will be discussed in comparison with the results of fully kinetic simulations. In 3D the X- and O-point configurations of the magnetic field formed in reconnection planes alternate along the out-of-reconnection-plane direction with the wavelength of the unstable mode. In the presence of multiple reconnection sites, the out-of-plane magnetic field can develop nested structure of quadrupoles in reconnection planes, similar to the 2-D case, but now with variations in the out-of-plane direction. The structures of the electron flow and magnetic field in 3-D simulations will be compared with those in 2-D simulations to discriminate the essentially 3D features. We also discuss

  18. 3D printing of weft knitted textile based structures by selective laser sintering of nylon powder

    NASA Astrophysics Data System (ADS)

    Beecroft, M.

    2016-07-01

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

  19. Characterizing 3D Structure of Convective Momentum Transport Associated with the MJO Based on Contemporary Reanalyses

    NASA Astrophysics Data System (ADS)

    Oh, J.; Jiang, X.; Waliser, D. E.; Moncrieff, M. W.; Johnson, R. H.

    2013-12-01

    As one of the most prominent tropical atmospheric variability modes, the Madden-Julian Oscillation (MJO) exerts profound influences on global weather and climate, and serves as a critical predictability source for extend-range forecast. While credible representation of the MJO still represents a great challenge for current general circulation models (GCMs), previous studies on the vertical structure of the MJO have largely focused on collective impacts from multi-scale convective systems on thermodynamic properties of the MJO. Most recently, limited observational studies and idealized modeling work suggested that convective momentum transport (CMT) could also play an important role in interpreting the observed MJO features. In this study, the 3D CMT structure associated with the MJO is examined by analyzing model output from three recent high-quality reanalysis systems, including NOAA's Climate Forecast System Reanalysis (CFSR), NASA's Modern Era Retrospective-analysis for Research and Applications (MERRA), and ECMWF-the Year of Tropical Convection (YOTC) reanalysis. Consistent with previous cloud-resolving model study, a well-organized three-layer vertical structure in the CMT associated with the MJO is also discerned based on reanalyses. The result suggests that CMT tends to intensify the MJO circulation, particularly in the lower troposphere. Relative roles of meso-scale systems (MCS) and synoptic waves in contributing the total CMT profiles of the MJO will also be explored. Differences in CMT profiles in these several reanalysis models will be discussed.

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

    PubMed Central

    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

  1. Chemical Structure-Biological Activity Models for Pharmacophores' 3D-Interactions.

    PubMed

    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

  2. Studies of coupled cavity LINAC (CCL) accelerating structures with 3-D codes

    SciTech Connect

    Spalek, G.

    2000-08-01

    The cw CCL being designed for the Accelerator Production of Tritium (APT) project accelerates protons from 96 MeV to 211 MeV. It consists of 99 segments each containing up to seven accelerating cavities. Segments are coupled by intersegment coupling cavities and grouped into supermodules. The design method needs to address not only basic cavity sizing for a given coupling and pi/2 mode frequency, but also the effects of high power densities on the cavity frequency, mechanical stresses, and the structure's stop band during operation. On the APT project, 3-D RF (Ansoft Corp.'s HFSS) and coupled RF/structural (Ansys Inc.'s ANSYS) codes are being used. to develop tools to address the above issues and guide cooling channel design. The code's predictions are being checked against available low power Aluminum models. Stop band behavior under power will be checked once the tools are extended to CCDTL structures that have been tested at high power. A summary of calculations made to date and agreement with measured results will be presented.

  3. Drag Prediction for the NASA CRM Wing-Body-Tail Using CFL3D and OVERFLOW on an Overset Mesh

    NASA Technical Reports Server (NTRS)

    Sclafani, Anthony J.; DeHaan, Mark A.; Vassberg, John C.; Rumsey, Christopher L.; Pulliam, Thomas H.

    2010-01-01

    In response to the fourth AIAA CFD Drag Prediction Workshop (DPW-IV), the NASA Common Research Model (CRM) wing-body and wing-body-tail configurations are analyzed using the Reynolds-averaged Navier-Stokes (RANS) flow solvers CFL3D and OVERFLOW. Two families of structured, overset grids are built for DPW-IV. Grid Family 1 (GF1) consists of a coarse (7.2 million), medium (16.9 million), fine (56.5 million), and extra-fine (189.4 million) mesh. Grid Family 2 (GF2) is an extension of the first and includes a superfine (714.2 million) and an ultra-fine (2.4 billion) mesh. The medium grid anchors both families with an established build process for accurate cruise drag prediction studies. This base mesh is coarsened and enhanced to form a set of parametrically equivalent grids that increase in size by a factor of roughly 3.4 from one level to the next denser level. Both CFL3D and OVERFLOW are run on GF1 using a consistent numerical approach. Additional OVERFLOW runs are made to study effects of differencing scheme and turbulence model on GF1 and to obtain results for GF2. All CFD results are post-processed using Richardson extrapolation, and approximate grid-converged values of drag are compared. The medium grid is also used to compute a trimmed drag polar for both codes.

  4. Acquisition of 3d Information for Vanished Structure by Using Only AN Ancient Picture

    NASA Astrophysics Data System (ADS)

    Kunii, Y.; Sakamoto, R.

    2016-06-01

    In order to acquire 3D information for reconstruction of vanished historical structure, grasp of 3D shape of such structure was attempted by using an ancient picture. Generally, 3D information of a structure is acquired by photogrammetric theory which requires two or more pictures. This paper clarifies that the geometrical information of the structure was obtained only from an ancient picture, and 3D information was acquired. This kind of method was applied for an ancient picture of the Old Imperial Theatre. The Old Imperial Theatre in the picture is constituted by two-point perspective. Therefore, estimated value of focal length of camera, length of camera to the Old Imperial Theatre and some parameters were calculated by estimation of field angle, using body height as an index of length and some geometrical information. Consequently, 3D coordinate of 120 measurement points on the surface of the Old Imperial Theatre were calculated respectively, and 3DCG modeling of the Old Imperial Theatre was realized.

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

    PubMed

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

    2016-03-01

    3D printing is of great interest for tissue engineering scaffolds due to the ability to form complex geometries and control internal structures, including porosity and pore size. The porous structure of scaffolds plays an important role in cell ingrowth and nutrition infusion. Although the internal porosity and pore size of 3D printed scaffolds have been frequently studied, the surface porosity and pore size, which are critical for cell infiltration and mass transport, have not been investigated. The surface geometry can differ considerably from the internal scaffold structure depending on the 3D printing process. It is vital to be able to control the surface geometry of scaffolds as well as the internal structure to fabricate optimal architectures. This work presents a method to control the surface porosity and pore size of 3D printed scaffolds. Six scaffold designs have been printed with surface porosities ranging from 3% to 21%. We have characterised the overall scaffold porosity and surface porosity using optical microscopy and microCT. It has been found that surface porosity has a significant impact on cell infiltration and proliferation. In addition, the porosity of the surface has been found to have an effect on mechanical properties and on the forces required to penetrate the scaffold with a surgical suturing needle. To the authors' knowledge, this study is the first to investigate the surface geometry of extrusion-based 3D printed scaffolds and demonstrates the importance of surface geometry in cell infiltration and clinical manipulation. PMID:26930179

  6. 3D OCT imaging in clinical settings: toward quantitative measurements of retinal structures

    NASA Astrophysics Data System (ADS)

    Zawadzki, Robert J.; Fuller, Alfred R.; Zhao, Mingtao; Wiley, David F.; Choi, Stacey S.; Bower, Bradley A.; Hamann, Bernd; Izatt, Joseph A.; Werner, John S.

    2006-02-01

    The acquisition speed of current FD-OCT (Fourier Domain - Optical Coherence Tomography) instruments allows rapid screening of three-dimensional (3D) volumes of human retinas in clinical settings. To take advantage of this ability requires software used by physicians to be capable of displaying and accessing volumetric data as well as supporting post processing in order to access important quantitative information such as thickness maps and segmented volumes. We describe our clinical FD-OCT system used to acquire 3D data from the human retina over the macula and optic nerve head. B-scans are registered to remove motion artifacts and post-processed with customized 3D visualization and analysis software. Our analysis software includes standard 3D visualization techniques along with a machine learning support vector machine (SVM) algorithm that allows a user to semi-automatically segment different retinal structures and layers. Our program makes possible measurements of the retinal layer thickness as well as volumes of structures of interest, despite the presence of noise and structural deformations associated with retinal pathology. Our software has been tested successfully in clinical settings for its efficacy in assessing 3D retinal structures in healthy as well as diseased cases. Our tool facilitates diagnosis and treatment monitoring of retinal diseases.

  7. Structural response to 3D simulated earthquake motions in San Bernardino Valley

    USGS Publications Warehouse

    Safak, E.; Frankel, A.

    1994-01-01

    Structural repsonse to one- and three-dimensional (3D) simulated motions in San Bernardino Valley from a hypothetical earthquake along the San Andreas fault with moment magnitude 6.5 and rupture length of 30km is investigated. The results show that the ground motions and the structural response vary dramatically with the type of simulation and the location. -from Authors

  8. 3D Travel Time Prediction for Earthquake Location - An Assessment of Methods and Models

    NASA Astrophysics Data System (ADS)

    Begnaud, M. L.; Ballard, S.; Rowe, C. A.; Young, C. J.; Steck, L.; Hipp, J. R.

    2009-12-01

    We have selected several crustal and mantle 3D models to test for travel-time prediction in a global event location context. Included are the ak135, DoE Unified, Sun et al. (2004) and MITP08 models, among others. Using the recently published tesselated 3D global ray tracing algorithm of Ballard et al., we compare and contrast our travel-time predictions through these obtained models for a set of ~500 Ground Truth (GT) 5 or better events, most of which are chemical or nuclear explosions. We explore the degree of travel-time misfit that can be expected when integrating rays through a model using a different method, or different parameterization, from that which generated the model. For instance, we compare the effect of dynamic ray tracing vs. fixed rays through a mantle tomographic model that was generated by inverting travel-time residuals for pre-calculated, fixed rays in the 1D radial AK135 model. We examine the success of these models for not only teleseismic P arrivals but also Pn and Pg. We explore the geographic biases observed for each phase and the trade-offs encountered when models are integrated. We find that our GT travel times are best predicted through any model when the calculation is perfomed using methods as close as possible to those used in generation of the model, as expected. Such considerations as Earth ellipticity correction and fixed ray vs. dynamic ray tracing need to be applied appropriately for a fair evaluation. Models available to the community are thus of little practical use for global location unless their methods of derivation are also provided, although they may independently provide enlightening images of tectonic features. We conclude that towards our development of a seamless, global model and locator, existing models may best serve as starting models for a global inversion using a single, consistent ray tracing and travel-time calculation approach; thus we view our evaluation of available models as a search for the best starting

  9. The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture.

    PubMed

    Markaki, Yolanda; Smeets, Daniel; Fiedler, Susanne; Schmid, Volker J; Schermelleh, Lothar; Cremer, Thomas; Cremer, Marion

    2012-05-01

    Three-dimensional structured illumination microscopy (3D-SIM) has opened up new possibilities to study nuclear architecture at the ultrastructural level down to the ~100 nm range. We present first results and assess the potential using 3D-SIM in combination with 3D fluorescence in situ hybridization (3D-FISH) for the topographical analysis of defined nuclear targets. Our study also deals with the concern that artifacts produced by FISH may counteract the gain in resolution. We address the topography of DAPI-stained DNA in nuclei before and after 3D-FISH, nuclear pores and the lamina, chromosome territories, chromatin domains, and individual gene loci. We also look at the replication patterns of chromocenters and the topographical relationship of Xist-RNA within the inactive X-territory. These examples demonstrate that an appropriately adapted 3D-FISH/3D-SIM approach preserves key characteristics of the nuclear ultrastructure and that the gain in information obtained by 3D-SIM yields new insights into the functional nuclear organization. PMID:22508100

  10. 3D Markov Process for Traffic Flow Prediction in Real-Time.

    PubMed

    Ko, Eunjeong; Ahn, Jinyoung; Kim, Eun Yi

    2016-01-01

    Recently, the correct estimation of traffic flow has begun to be considered an essential component in intelligent transportation systems. In this paper, a new statistical method to predict traffic flows using time series analyses and geometric correlations is proposed. The novelty of the proposed method is two-fold: (1) a 3D heat map is designed to describe the traffic conditions between roads, which can effectively represent the correlations between spatially- and temporally-adjacent traffic states; and (2) the relationship between the adjacent roads on the spatiotemporal domain is represented by cliques in MRF and the clique parameters are obtained by example-based learning. In order to assess the validity of the proposed method, it is tested using data from expressway traffic that are provided by the Korean Expressway Corporation, and the performance of the proposed method is compared with existing approaches. The results demonstrate that the proposed method can predict traffic conditions with an accuracy of 85%, and this accuracy can be improved further. PMID:26821025

  11. An objective method for 3D quality prediction using visual annoyance and acceptability level

    NASA Astrophysics Data System (ADS)

    Khaustova, Darya; Fournier, Jérôme; Wyckens, Emmanuel; Le Meur, Olivier

    2015-03-01

    This study proposes a new objective metric for video quality assessment. It predicts the impact of technical quality parameters relevant to visual discomfort on human perception. The proposed metric is based on a 3-level color scale: (1) Green - not annoying, (2) Orange - annoying but acceptable, (3) Red - not acceptable. Therefore, each color category reflects viewers' judgment based on stimulus acceptability and induced visual annoyance. The boundary between the "Green" and "Orange" categories defines the visual annoyance threshold, while the boundary between the "Orange" and "Red" categories defines the acceptability threshold. Once the technical quality parameters are measured, they are compared to perceptual thresholds. Such comparison allows estimating the quality of the 3D video sequence. Besides, the proposed metric is adjustable to service or production requirements by changing the percentage of acceptability and/or visual annoyance. The performance of the metric is evaluated in a subjective experiment that uses three stereoscopic scenes. Five view asymmetries with four degradation levels were introduced into initial test content. The results demonstrate high correlations between subjective scores and objective predictions for all view asymmetries.

  12. 3D Markov Process for Traffic Flow Prediction in Real-Time

    PubMed Central

    Ko, Eunjeong; Ahn, Jinyoung; Kim, Eun Yi

    2016-01-01

    Recently, the correct estimation of traffic flow has begun to be considered an essential component in intelligent transportation systems. In this paper, a new statistical method to predict traffic flows using time series analyses and geometric correlations is proposed. The novelty of the proposed method is two-fold: (1) a 3D heat map is designed to describe the traffic conditions between roads, which can effectively represent the correlations between spatially- and temporally-adjacent traffic states; and (2) the relationship between the adjacent roads on the spatiotemporal domain is represented by cliques in MRF and the clique parameters are obtained by example-based learning. In order to assess the validity of the proposed method, it is tested using data from expressway traffic that are provided by the Korean Expressway Corporation, and the performance of the proposed method is compared with existing approaches. The results demonstrate that the proposed method can predict traffic conditions with an accuracy of 85%, and this accuracy can be improved further. PMID:26821025

  13. 3D topography of biologic tissue by multiview imaging and structured light illumination

    NASA Astrophysics Data System (ADS)

    Liu, Peng; Zhang, Shiwu; Xu, Ronald

    2014-02-01

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

  14. Advanced methods for 3-D inelastic structural analysis for hot engine structures

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.

    1989-01-01

    Three-dimensional Inelastic Analysis Methods are described. These methods were incorporated into a series of new computer codes embodying a progression of mathematical models (mechanics of materials, specialty finite element, boundary element) for streamlined analysis of hot engine structures such as: (1) combustor liners, (2) turbine blades, and (3) turbine vanes. These models address the effects of high temperatures and thermal/mechanical loadings on the local (stress/strain) and global (displacements, frequencies, amplitudes, buckling) structural behavior of the three respective components. The methods and the three computer codes, referred to as MOMM (Mechanics Of Materials Model), MHOST (MARC-Hot Section Technology), and BEST3D (Boundary Element Stress Technology), have been developed and are briefly described.

  15. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae’s Colliding Winds Using 3D Prints of Smoothed Particle Hydrodynamics Simulations

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

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

    PubMed

    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. PMID:26588673

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

    NASA Astrophysics Data System (ADS)

    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

  18. 2D and 3D X-Ray Structural Microscopy Using Submicron-Resolution Laue Microdiffraction

    SciTech Connect

    Budai, John D.; Yang, Wenge; Larson, Bennett C.; Tischler, Jonathan Z.; Liu, Wenjun; Ice, Gene E.

    2010-11-10

    We have developed a scanning, polychromatic x-ray microscopy technique with submicron spatial resolution at the Advanced Photon Source. In this technique, white undulator radiation is focused to submicron diameter using elliptical mirrors. Laue diffraction patterns scattered from the sample are collected with an area detector and then analyzed to obtain the local crystal structure, lattice orientation, and strain tensor. These new microdiffraction capabilities have enabled both 2D and 3D structural studies of materials on mesoscopic length-scales of tenths-to-hundreds of microns. For thin samples such as deposited films, 2D structural maps are obtained by step-scanning the area of interest. For example, 2D x-ray microscopy has been applied in studies of the epitaxial growth of oxide films. For bulk samples, a 3D differential-aperture x-ray microscopy technique has been developed that yields the full diffraction information from each submicron volume element. The capabilities of 3D x-ray microscopy are demonstrated here with measurements of grain orientations and grain boundary motion in polycrystalline aluminum during 3D thermal grain growth. X-ray microscopy provides the needed, direct link between the experimentally measured 3D microstructural evolution and the results of theory and modeling of materials processes on mesoscopic length scales.

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

    DOEpatents

    Zemla, Adam T.

    2011-09-20

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

  20. Mixed-Mode Fracture and Fatigue Analysis of Cracked 3D Complex Structures using a 3D SGBEM-FEM Alternating Method

    NASA Astrophysics Data System (ADS)

    Bhavanam, Sharada

    The aim of this thesis is to numerically evaluate the mixed-mode Stress Intensity Factors (SIFs) of complex 3D structural geometries with arbitrary 3D cracks using the Symmetric Galerkin Boundary Element Method-Finite Element Method (SGBEM-FEM) Alternating Method. Various structural geometries with different loading scenarios and crack configurations were examined in this thesis to understand the behavior and trends of the mixed-mode SIFs as well as the fatigue life for these complex structural geometries. Although some 3D structures have empirical and numerical solutions that are readily available in the open literature, some do not; therefore this thesis presents the results of fracture and fatigue analyses of these 3D complex structures using the SGBEM-FEM Alternating Method to serve as reference for future studies. Furthermore, there are advantages of using the SGBEM-FEM Alternating Method compared to traditional FEM methods. For example, the fatigue-crack-growth and fatigue life can be better estimated for a structure because different fatigue models (i.e. Walker, Paris, and NASGRO) can be used within the same framework of the SGBEM-FEM Alternating Method. The FEM (un-cracked structure)/BEM(crack model) meshes are modeled independently, which speeds up the computation process and reduces the cost of human labor. A simple coarse mesh can be used for all fracture and fatigue analyses of complex structures. In this thesis, simple coarse meshes were used for 3D complex structures, which were below 5000 elements as compared to traditional FEM, which require meshes where the elements range on the order of ˜250,000 to ˜106 and sometimes even more than that.

  1. Band structure and spin texture of Bi2Se3 3 d ferromagnetic metal interface

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed Central

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-01-01

    Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3 Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided. PMID:23796504

  3. Anomalously low amplitude of S waves produced by the 3D structures in the lower mantle

    NASA Astrophysics Data System (ADS)

    To, Akiko; Capdeville, Yann; Romanowicz, Barbara

    2016-07-01

    Direct S and Sdiff phases with anomalously low amplitudes are recorded for the earthquakes in Papua New Guinea by seismographs in northern America. According to the prediction by a standard 1D model, the amplitudes are the lowest at stations in southern California, at a distance and azimuth of around 95° and 55°, respectively, from the earthquake. The amplitude anomaly is more prominent at frequencies higher than 0.03 Hz. We checked and ruled out the possibility of the anomalies appearing because of the errors in the focal mechanism used in the reference synthetic waveform calculations. The observed anomaly distribution changes drastically with a relatively small shift in the location of the earthquake. The observations indicate that the amplitude reduction is likely due to the 3D shear velocity (Vs) structure, which deflects the wave energy away from the original ray paths. Moreover, some previous studies suggested that some of the S and Sdiff phases in our dataset are followed by a prominent postcursor and show a large travel time delay, which was explained by placing a large ultra-low velocity zone (ULVZ) located on the core-mantle boundary southwest of Hawaii. In this study, we evaluated the extent of amplitude anomalies that can be explained by the lower mantle structures in the existing models, including the previously proposed ULVZ. In addition, we modified and tested some models and searched for the possible causes of low amplitudes. Full 3D synthetic waveforms were calculated and compared with the observations. Our results show that while the existing models explain the trends of the observed amplitude anomalies, the size of such anomalies remain under-predicted especially at large distances. Adding a low velocity zone, which is spatially larger and has less Vs reduction than ULVZ, on the southwest side of ULVZ, contributes to explain the low amplitudes observed at distances larger than 100° from the earthquake. The newly proposed low velocity zone

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

    NASA Astrophysics Data System (ADS)

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

    2004-05-01

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

  5. 3D flexible NiTi-braided elastomer composites for smart structure applications

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Simutė, S.; Fichtner, A.

    2015-12-01

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

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

    PubMed Central

    Jacob, J. Augustin; Kumar, N. Senthil

    2015-01-01

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

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

    PubMed

    Jacob, J Augustin; Kumar, N Senthil

    2015-01-01

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

  9. Pore-scale intermittent velocity structure underpinning anomalous transport through 3-D porous media

    NASA Astrophysics Data System (ADS)

    Kang, Peter K.; Anna, Pietro; Nunes, Joao P.; Bijeljic, Branko; Blunt, Martin J.; Juanes, Ruben

    2014-09-01

    We study the nature of non-Fickian particle transport in 3-D porous media by simulating fluid flow in the intricate pore space of real rock. We solve the full Navier-Stokes equations at the same resolution as the 3-D micro-CT (computed tomography) image of the rock sample and simulate particle transport along the streamlines of the velocity field. We find that transport at the pore scale is markedly anomalous: longitudinal spreading is superdiffusive, while transverse spreading is subdiffusive. We demonstrate that this anomalous behavior originates from the intermittent structure of the velocity field at the pore scale, which in turn emanates from the interplay between velocity heterogeneity and velocity correlation. Finally, we propose a continuous time random walk model that honors this intermittent structure at the pore scale and captures the anomalous 3-D transport behavior at the macroscale.

  10. Element-specific X-ray phase tomography of 3D structures at the nanoscale.

    PubMed

    Donnelly, Claire; Guizar-Sicairos, Manuel; Scagnoli, Valerio; Holler, Mirko; Huthwelker, Thomas; Menzel, Andreas; Vartiainen, Ismo; Müller, Elisabeth; Kirk, Eugenie; Gliga, Sebastian; Raabe, Jörg; Heyderman, Laura J

    2015-03-20

    Recent advances in fabrication techniques to create mesoscopic 3D structures have led to significant developments in a variety of fields including biology, photonics, and magnetism. Further progress in these areas benefits from their full quantitative and structural characterization. We present resonant ptychographic tomography, combining quantitative hard x-ray phase imaging and resonant elastic scattering to achieve ab initio element-specific 3D characterization of a cobalt-coated artificial buckyball polymer scaffold at the nanoscale. By performing ptychographic x-ray tomography at and far from the Co K edge, we are able to locate and quantify the Co layer in our sample to a 3D spatial resolution of 25 nm. With a quantitative determination of the electron density we can determine that the Co layer is oxidized, which is confirmed with microfluorescence experiments. PMID:25839287

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

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  12. 3D watershed-based segmentation of internal structures within MR brain images

    NASA Astrophysics Data System (ADS)

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

    2000-06-01

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

  13. 3D shape shearography with integrated structured light projection for strain inspection of curved objects

    NASA Astrophysics Data System (ADS)

    Anisimov, Andrei G.; Groves, Roger M.

    2015-05-01

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

  14. RNAssess--a web server for quality assessment of RNA 3D structures.

    PubMed

    Lukasiak, Piotr; Antczak, Maciej; Ratajczak, Tomasz; Szachniuk, Marta; Popenda, Mariusz; Adamiak, Ryszard W; Blazewicz, Jacek

    2015-07-01

    Nowadays, various methodologies can be applied to model RNA 3D structure. Thus, the plausible quality assessment of 3D models has a fundamental impact on the progress of structural bioinformatics. Here, we present RNAssess server, a novel tool dedicated to visual evaluation of RNA 3D models in the context of the known reference structure for a wide range of accuracy levels (from atomic to the whole molecule perspective). The proposed server is based on the concept of local neighborhood, defined as a set of atoms observed within a sphere localized around a central atom of a particular residue. A distinctive feature of our server is the ability to perform simultaneous visual analysis of the model-reference structure coherence. RNAssess supports the quality assessment through delivering both static and interactive visualizations that allows an easy identification of native-like models and/or chosen structural regions of the analyzed molecule. A combination of results provided by RNAssess allows us to rank analyzed models. RNAssess offers new route to a fast and efficient 3D model evaluation suitable for the RNA-Puzzles challenge. The proposed automated tool is implemented as a free and open to all users web server with an user-friendly interface and can be accessed at: http://rnassess.cs.put.poznan.pl/. PMID:26068469

  15. 3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography

    PubMed Central

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

    2015-01-01

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions. PMID:25940394

  16. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    SciTech Connect

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

    2015-05-05

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

  17. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGESBeta

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

    2015-05-05

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

  18. A reduced-coordinate approach to modeling RNA 3-D structures

    SciTech Connect

    Tung, Chang-Shung

    1997-09-01

    With the realization of RNA molecules capable of performing very specific functions (e.g., catalytic RNAs and RNAs that bind ligand with affinity and specificity of an anti-body) and contrary to the traditional view that structure of RNA molecules being functionally passive, it has become clear that studying the 3-dimensional (3-D) folding of RNA molecules is a very important task. In the absence of sufficient number of experimentally determined RNA structures available up-to-date, folding of RNA structures computationally provides an alternative approach in studying the 3-D structure of RNA molecules. We have developed a computational approach for folding RNA 3-D structures. The method is conceptually simple and general. It consists of two major components. The first being the arrangement of all helices in space. Once the helices are positioned and oriented in space, structures of the connecting loops are modeled and inserted between the helices. Any number of structural constraints derived either experimentally or theoretically can be used to guide the folding processes. A conformational sampling approach is developed with structural equilibration using the Metropolis Monte Carlo simulation. The lengths of various loop sizes (ranging from 1 base to 7 bases) are calculated based on a set of RNA structures deposited in PDB as well as a set of loop structures constructed using our method. The validity of using the averaged loop lengths of the connecting loops as distance constraints for arranging the helices in space is studied.

  19. Ocular surface temperature: a 3D FEM prediction using bioheat equation.

    PubMed

    Ng, E Y K; Ooi, E H

    2007-06-01

    Computational and mathematical human eye models from previous studies which were constructed in two-dimensions (2D) did not give a precise representation of the actual human eye. This work is an extension from an earlier published work on the 2D model. In this paper, a 3D FEM model of the human eye is simulated for the steady state temperature distribution during normal condition and during electromagnetic (EM) wave radiation. Results show a discrepancy of 0.49% for a normal condition as opposed to 1.9% of a 2D model when compared to experimental results from open literatures. Investigations on the EM wave radiations found an average power absorption density of 15,151 and 22,145 Wm(-3) for the 750 and 1500 MHz radiation, respectively. A peak temperature of 38.18( composite function)C was predicted for the 750 MHz radiation while 41.19( composite function)C was computed for the 1500 MHz radiation. These temperatures are in reasonable agreement with the simulated results computed by another report in the past. PMID:17034781

  20. About the automated pattern creation of 3D jacquard double needle bed warp knitted structures

    NASA Astrophysics Data System (ADS)

    Renkens, W.; Kyosev, Y.

    2016-07-01

    Three dimensional structures can be produced on jacquard warp knitting machines with double needle bed. This work presents theoretical considerations about the modelling and simulation of these structures. After that a method is described, how to obtain production parameters from the simulation data. The analysis demonstrates, that the automated pattern creation of 3D structures is not always possible and not all mathematical solutions of the problem can be knittable.

  1. What spherically symmetric viscosity structure produces the same PGR as a realistic 3D Earth?

    NASA Astrophysics Data System (ADS)

    Paulson, A.; Zhong, S.; Wahr, J.

    2003-04-01

    Observations of isostatic adjustment of the earth's surface due to transient loading provide important constraints on the mantle viscosity structure. However, most studies of this response have assumed a spherically symmetric (1D) earth. This study is motivated by the following question: when a one-dimensional viscosity model is derived from post-glacial rebound (PGR) observations, how does this 1D structure correspond to the three-dimensional structure of the earth? Using the 3D spherical finite element software CitcomSVE [Zhong et al., 2002], we are able to compute the earth's response to realistic glacial loading when the earth has a truly 3D viscosity structure. The loading is provided by the ICE-3G deglaciation history [Tushingham &Peltier, 1991]. The 3D viscosity structure is constructed by first selecting a priori a radial average viscosity (for example, ( 1021 \\: {Pa \\cdot s}) in the upper mantle and (2 × 1021 \\: {Pa \\cdot s}) in the lower mantle). The lateral variations about this radial structure are derived from seismic shear-velocity tomography models by converting velocities to temperature, then temperature to viscosity. The seismic tomography models used are S20RTS [Ritsema et al., 1999] and NA00 [Van der Lee, 2002]. From the computed isostatic response, we measure typical PGR observables: relative sea level change (RSLC) and (dot{J2}). These measurements are then treated as synthetic data, and we search for 1D (radially stratified) viscosity models, forced with the same glaciation history, that will best fit these synthetic PGR observations. We find that for sites near the center of a large glacial load (e.g., southern Hudson Bay), a local average of the 3D viscosity structure provides a reasonable 1D proxy. For sites along the periphery of the glacial load (e.g., Boston), it is much more difficult to find a 1D model that can reproduce the 3D observations. We also approach the problem by running an ensemble of 1D viscosity models, and finding

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

    NASA Astrophysics Data System (ADS)

    Zhang, Zhi-Dong

    2013-03-01

    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 varphix, varphiy, and varphiz. 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 for β > 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.

  3. Modelling and analysing 3D buildings with a primal/dual data structure

    NASA Astrophysics Data System (ADS)

    Boguslawski, Pawel; Gold, Christopher M.; Ledoux, Hugo

    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 present in this paper a new topological data structure, the dual half-edge (DHE), which permits us to represent the topology of 3D buildings (including their interiors) and of the surrounding terrain. It is based on the idea of simultaneously storing a graph in 3D space and its dual graph, and to link the two. We propose Euler-type operators for incrementally constructing 3D models (for adding individual edges, faces and volumes to the model while updating the dual structure simultaneously), and we also propose navigation operators to move from a given point to all the connected planes or polyhedra for example. The DHE also permits us to store attributes to any element. We have implemented the DHE and have tested it with different CityGML models. Our technique allows us to handle important query types, for example finding the nearest exterior exit to a given room, as in disaster management planning. As the structure is locally modifiable the model may be adapted whenever a particular pathway is no longer available. The proposed DHE structure adds significant analytic value to the increasingly popular CityGML model.

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

    ERIC Educational Resources Information Center

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

    2010-01-01

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

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

    SciTech Connect

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

    2009-03-10

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

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

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    Meng, Hui; Hussain, Fazle

    1991-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

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

    SciTech Connect

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

    2010-11-09

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

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

    NASA Astrophysics Data System (ADS)

    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.

  11. Simulation of unsteady state performance of a secondary air system by the 1D-3D-Structure coupled method

    NASA Astrophysics Data System (ADS)

    Wu, Hong; Li, Peng; Li, Yulong

    2016-02-01

    This paper describes the calculation method for unsteady state conditions in the secondary air systems in gas turbines. The 1D-3D-Structure coupled method was applied. A 1D code was used to model the standard components that have typical geometric characteristics. Their flow and heat transfer were described by empirical correlations based on experimental data or CFD calculations. A 3D code was used to model the non-standard components that cannot be described by typical geometric languages, while a finite element analysis was carried out to compute the structural deformation and heat conduction at certain important positions. These codes were coupled through their interfaces. Thus, the changes in heat transfer and structure and their interactions caused by exterior disturbances can be reflected. The results of the coupling method in an unsteady state showed an apparent deviation from the existing data, while the results in the steady state were highly consistent with the existing data. The difference in the results in the unsteady state was caused primarily by structural deformation that cannot be predicted by the 1D method. Thus, in order to obtain the unsteady state performance of a secondary air system more accurately and efficiently, the 1D-3D-Structure coupled method should be used.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

    Zenou, M; Sa'ar, A; Kotler, Z

    2015-01-01

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

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

    PubMed Central

    Zenou, M.; Sa’ar, A.; Kotler, Z.

    2015-01-01

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

  16. 3D shape measurement of shoeprint impression with structured illumination and fringe pattern analysis

    NASA Astrophysics Data System (ADS)

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

    2002-06-01

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

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

    NASA Astrophysics Data System (ADS)

    Zenou, M.; Sa'Ar, A.; Kotler, Z.

    2015-11-01

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

  18. GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes

    PubMed Central

    2014-01-01

    Background Interpretation of binding modes of protein–small ligand complexes from 3D structure data is essential for understanding selective ligand recognition by proteins. It is often performed by visual inspection and sometimes largely depends on a priori knowledge about typical interactions such as hydrogen bonds and π-π stacking. Because it can introduce some biases due to scientists’ subjective perspectives, more objective viewpoints considering a wide range of interactions are required. Description In this paper, we present a web server for analyzing protein–small ligand interactions on the basis of patterns of atomic contacts, or “interaction patterns” obtained from the statistical analyses of 3D structures of protein–ligand complexes in our previous study. This server can guide visual inspection by providing information about interaction patterns for each atomic contact in 3D structures. Users can visually investigate what atomic contacts in user-specified 3D structures of protein–small ligand complexes are statistically overrepresented. This server consists of two main components: “Complex Analyzer”, and “Pattern Viewer”. The former provides a 3D structure viewer with annotations of interacting amino acid residues, ligand atoms, and interacting pairs of these. In the annotations of interacting pairs, assignment to an interaction pattern of each contact and statistical preferences of the patterns are presented. The “Pattern Viewer” provides details of each interaction pattern. Users can see visual representations of probability density functions of interactions, and a list of protein–ligand complexes showing similar interactions. Conclusions Users can interactively analyze protein–small ligand binding modes with statistically determined interaction patterns rather than relying on a priori knowledge of the users, by using our new web server named GIANT that is freely available at http://giant.hgc.jp/. PMID:24423161

  19. Modeling tumor/polyp/lesion structure in 3D for computer-aided diagnosis in colonoscopy

    NASA Astrophysics Data System (ADS)

    Chen, Chao-I.; Sargent, Dusty; Wang, Yuan-Fang

    2010-02-01

    We describe a software system for building three-dimensional (3D) models from colonoscopic videos. The system is end-to-end in the sense that it takes as input raw image frames-shot during a colon exam-and produces the 3D structure of objects of interest (OOI), such as tumors, polyps, and lesions. We use the structure-from-motion (SfM) approach in computer vision which analyzes an image sequence in which camera's position and aim vary relative to the OOI. The varying pose of the camera relative to the OOI induces the motion-parallax effect which allows 3D depth of the OOI to be inferred. Unlike the traditional SfM system pipeline, our software system contains many check-and-balance mechanisms to ensure robustness, and the analysis from earlier stages of the pipeline is used to guide the later processing stages to better handle challenging medical data. The constructed 3D models allow the pathology (growth and change in both structure and appearance) to be monitored over time.

  20. EK3D: an E. coli K antigen 3-dimensional structure database

    PubMed Central

    Kunduru, Bharathi Reddy; Nair, Sanjana Anilkumar; Rathinavelan, Thenmalarchelvi

    2016-01-01

    A very high rate of multidrug resistance (MDR) seen among Gram-negative bacteria such as Escherichia, Klebsiella, Salmonella, Shigella, etc. is a major threat to public health and safety. One of the major virulent determinants of Gram-negative bacteria is capsular polysaccharide or K antigen located on the bacterial outer membrane surface, which is a potential drug & vaccine target. It plays a key role in host–pathogen interactions as well as host immune evasion and thus, mandates detailed structural information. Nonetheless, acquiring structural information of K antigens is not straightforward due to their innate enormous conformational flexibility. Here, we have developed a manually curated database of K antigens corresponding to various E. coli serotypes, which differ from each other in their monosaccharide composition, linkage between the monosaccharides and their stereoisomeric forms. Subsequently, we have modeled their 3D structures and developed an organized repository, namely EK3D that can be accessed through www.iith.ac.in/EK3D/. Such a database would facilitate the development of antibacterial drugs to combat E. coli infections as it has evolved resistance against 2 major drugs namely, third-generation cephalosporins and fluoroquinolones. EK3D also enables the generation of polymeric K antigens of varying lengths and thus, provides comprehensive information about E. coli K antigens. PMID:26615200

  1. Fabrication of 3D microfluidic structures inside glass by femtosecond laser micromachining

    NASA Astrophysics Data System (ADS)

    Sugioka, Koji; Cheng, Ya

    2014-01-01

    Femtosecond lasers have opened up new avenues in materials processing due to their unique characteristics of ultrashort pulse widths and extremely high peak intensities. One of the most important features of femtosecond laser processing is that a femtosecond laser beam can induce strong absorption in even transparent materials due to nonlinear multiphoton absorption. This makes it possible to directly create three-dimensional (3D) microfluidic structures in glass that are of great use for fabrication of biochips. For fabrication of the 3D microfluidic structures, two technical approaches are being attempted. One of them employs femtosecond laser-induced internal modification of glass followed by wet chemical etching using an acid solution (Femtosecond laser-assisted wet chemical etching), while the other one performs femtosecond laser 3D ablation of the glass in distilled water (liquid-assisted femtosecond laser drilling). This paper provides a review on these two techniques for fabrication of 3D micro and nanofluidic structures in glass based on our development and experimental results.

  2. Parametric estimation of 3D tubular structures for diffuse optical tomography

    PubMed Central

    Larusson, Fridrik; Anderson, Pamela G.; Rosenberg, Elizabeth; Kilmer, Misha E.; Sassaroli, Angelo; Fantini, Sergio; Miller, Eric L.

    2013-01-01

    We explore the use of diffuse optical tomography (DOT) for the recovery of 3D tubular shapes representing vascular structures in breast tissue. Using a parametric level set method (PaLS) our method incorporates the connectedness of vascular structures in breast tissue to reconstruct shape and absorption values from severely limited data sets. The approach is based on a decomposition of the unknown structure into a series of two dimensional slices. Using a simplified physical model that ignores 3D effects of the complete structure, we develop a novel inter-slice regularization strategy to obtain global regularity. We report on simulated and experimental reconstructions using realistic optical contrasts where our method provides a more accurate estimate compared to an unregularized approach and a pixel based reconstruction. PMID:23411913

  3. Image enhancement and segmentation of fluid-filled structures in 3D ultrasound images

    NASA Astrophysics Data System (ADS)

    Chalana, Vikram; Dudycha, Stephen; McMorrow, Gerald

    2003-05-01

    Segmentation of fluid-filled structures, such as the urinary bladder, from three-dimensional ultrasound images is necessary for measuring their volume. This paper describes a system for image enhancement, segmentation and volume measurement of fluid-filled structures on 3D ultrasound images. The system was applied for the measurement of urinary bladder volume. Results show an average error of less than 10% in the estimation of the total bladder volume.

  4. 3D scanning of internal structure in gel engineering materials with visual scanning microscopic light scattering

    NASA Astrophysics Data System (ADS)

    Watanabe, Yosuke; Gong, Jing; Masato, Makino; Kabir, M. Hasnat; Furukawa, Hidemitsu

    2014-04-01

    The 3D printing technology, causing much attention from the beginning of 2013, will be possibly an alternative method to fabricate the biological soft tissues. Recently our group of Yamagata University has developed the world-first 3D Gel Printer to fabricate the complicated gel-materials with high-strength and biocompatibility. However, there are no 3D scanners that collect the data from the internal structure of complicated gel objects such as eye lens. It means that a new system for scanning the internal structure is needed now. In this study, firstly, we have tried to investigate the gel network of synthetic and biological gel with scanning microscopic light scattering (SMILS). We calculated the Young's modulus of synthetic gels with the SMILS and with the tensile test, and precisely compared the results between them. The temperature dependences of the inside structure and the transparency are observed in the pig crystalline lens. The quantitative analysis indicates the importance of the internal structure of real object. Secondary, we show the new system named Gel-scanner that can provide the 2-dimentional data of the internal structure. From examining our findings, the scanning of internal structure will enable us to expect physical properties of the real object. We convince that the gelscanner will play major role in the various fields.

  5. Analysis of the rupture process of the 1995 Kobe earthquake using a 3D velocity structure

    NASA Astrophysics Data System (ADS)

    Guo, Yujia; Koketsu, Kazuki; Ohno, Taichi

    2013-12-01

    A notable feature of the 1995 Kobe (Hyogo-ken Nanbu) earthquake is that violent ground motions occurred in a narrow zone. Previous studies have shown that the origin of such motions can be explained by the 3D velocity structure in this zone. This indicates not only that the 3D velocity structure significantly affects strong ground motions, but also that we should consider its effects in order to determine accurately the rupture process of the earthquake. Therefore, we have performed a joint source inversion of strong-motion, geodetic, and teleseismic data, where 3D Green's functions were calculated for strong-motion and geodetic data in the Osaka basin. Our source model estimates the total seismic moment to be about 2.1 × 1019 N m and the maximum slip reaches 2.9 m near the hypocenter. Although the locations of large slips are similar to those reported by Yoshida et al. (1996), there are quantitative differences between our results and their results due to the differences between the 3D and 1D Green's functions. We have also confirmed that our source model realized a better fit to the strong motion observations, and a similar fit as Yoshida et al. (1996) to the observed static displacements.

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

    PubMed

    Ogden, Kent M; Aslan, Can; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Soman, Pranav

    2015-12-01

    Additive manufacturing and bio-printing, with the potential for direct fabrication of complex patient-specific anatomies derived from medical scan data, are having an ever-increasing impact on the practice of medicine. Anatomic structures are typically derived from CT or MRI scans, and there are multiple steps in the model derivation process that influence the geometric accuracy of the printed constructs. In this work, we compare the dimensional accuracy of 3-D printed constructs of an L1 vertebra derived from CT data for an ex vivo cadaver T-L spine with the original vertebra. Processing of segmented structures using binary median filters and various surface extraction algorithms is evaluated for the effect on model dimensions. We investigate the effects of changing CT reconstruction kernels by scanning simple geometric objects and measuring the impact on the derived model dimensions. We also investigate if there are significant differences between physical and virtual model measurements. The 3-D models were printed using a commercial 3-D printer, the Replicator 2 (MakerBot, Brooklyn, NY) using polylactic acid (PLA) filament. We found that changing parameters during the scan reconstruction, segmentation, filtering, and surface extraction steps will have an effect on the dimensions of the final model. These effects need to be quantified for specific situations that rely on the accuracy of 3-D printed models used in medicine or tissue engineering applications. PMID:25982877

  7. 3D interactive model of lumbar spinal structures of anesthetic interest.

    PubMed

    Prats-Galino, Alberto; Reina, Miguel A; Mavar Haramija, Marija; Puigdellivol-Sánchez, Anna; Juanes Méndez, Juan A; De Andrés, José A

    2015-03-01

    A 3D model of lumbar structures of anesthetic interest was reconstructed from human magnetic resonance (MR) images and embedded in a Portable Document Format (PDF) file, which can be opened by freely available software and used offline. The MR images were analyzed using a specific 3D software platform for biomedical data. Models generated from manually delimited volumes of interest and selected MR images were exported to Virtual Reality Modeling Language format and were presented in a PDF document containing JavaScript-based functions. The 3D file and the corresponding instructions and license files can be downloaded freely at http://diposit.ub.edu/dspace/handle/2445/44844?locale=en. The 3D PDF interactive file includes reconstructions of the L3-L5 vertebrae, intervertebral disks, ligaments, epidural and foraminal fat, dural sac and nerve root cuffs, sensory and motor nerve roots of the cauda equina, and anesthetic approaches (epidural medial, spinal paramedial, and selective nerve root paths); it also includes a predefined sequential educational presentation. Zoom, 360° rotation, selective visualization, and transparency graduation of each structure and clipping functions are available. Familiarization requires no specialized informatics knowledge. The ease with which the document can be used could make it valuable for anatomical and anesthetic teaching and demonstration of patient information. PMID:25352014

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

    NASA Technical Reports Server (NTRS)

    Burks, B. L.; Rowe, J. C.; Dinkins, M. A.; Christensen, B.; Selleck, C.; Jacoboski, D.; Markus, R.

    1992-01-01

    Surface contours inside the large waste storage tanks typical of the Department of Energy (DOE) complex are, in general, highly irregular. In addition to pipes and other pieces of equipment in the tanks, the surfaces may have features such as mounds, fissures, crystalline structures, and mixed solid and liquid forms. Prior to remediation activities, it will be necessary to characterize the waste to determine the most effective remediation approaches. Surface contour data will be required both prior to and during remediation. The use is described of a structured light source to generate 3-D surface contour maps of the interior of waste storage silos at the Feed Materials Production Center at Fernald, OH. The landscape inside these large waste storage tanks bears a strong resemblance to some of the landscapes that might be encountered during lunar or planetary exploration. Hence, these terrestrial 3-D mapping techniques may be directly applicable to extraterrestrial exploration. In further development, it will be demonstrated that these 3-D data can be used for robotic task planning just as 3-D surface contour data of a satellite could be used to plan maintenance tasks for a space-based servicing robot.

  9. The degree of π electron delocalization and the formation of 3D-extensible sandwich structures.

    PubMed

    Wang, Xiang; Wang, Qiang; Yuan, Caixia; Zhao, Xue-Feng; Li, Jia-Jia; Li, Debao; Wu, Yan-Bo; Wang, Xiaotai

    2016-04-28

    DFT B3LYP/6-31G(d) calculations were performed to examine the feasibility of graphene-like C42H18 and starbenzene C6(BeH)6 (SBz) polymers as ligands of 3D-extensible sandwich compounds (3D-ESCs) with uninterrupted sandwich arrays. The results revealed that sandwich compounds with three or more C42H18 ligands were not feasible. The possible reason may be the localization of π electrons on certain C6 hexagons due to π-metal interactions, which makes the whole ligand lose its electronic structure basis (higher degree of π electron delocalization) to maintain the planar structure. For comparison, with the aid of benzene (Bz) molecules, the SBz polymers can be feasible ligands for designing 3D-ESCs because the C-Be interactions in individual SBz are largely ionic, which will deter the π electrons on one C6 ring from connecting to those on neighbouring C6 rings. This means that high degree of π electron delocalization is not necessary for maintaining the planarity of SBz polymers. Such a locally delocalized π electron structure is desirable for the ligands of 3D-ESCs. Remarkably, the formation of a sandwich compound with SBz is thermodynamically more favourable than that found for bis(Bz)chromium. The assembly of 3D-ESCs is largely exothermic, which will facilitate future experimental synthesis. The different variation trends on the HOMO-LUMO gaps in different directions (relative to the sandwich axes) suggest that they can be developed to form directional conductors or semiconductors, which may be useful in the production of electronic devices. PMID:27004750

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

    NASA Astrophysics Data System (ADS)

    Liu, Yahui; Yao, Jian; Liu, Kang; Lu, Xiaohu; Xia, Menghan

    2016-06-01

    Crack detection for bridge bottom surfaces via remote sensing techniques is undergoing a revolution in the last few years. For such applications, a large amount of images, acquired with high-resolution industrial cameras close to the bottom surfaces with some mobile platform, are required to be stitched into a wide-view single composite image. The conventional idea of stitching a panorama with the affine model or the homographic model always suffers a series of serious problems due to poor texture and out-of-focus blurring introduced by depth of field. In this paper, we present a novel method to seamlessly stitch these images aided by 3D structure lines of bridge bottom surfaces, which are extracted from 3D camera data. First, we propose to initially align each image in geometry based on its rough position and orientation acquired with both a laser range finder (LRF) and a high-precision incremental encoder, and these images are divided into several groups with the rough position and orientation data. Secondly, the 3D structure lines of bridge bottom surfaces are extracted from the 3D cloud points acquired with 3D cameras, which impose additional strong constraints on geometrical alignment of structure lines in adjacent images to perform a position and orientation optimization in each group to increase the local consistency. Thirdly, a homographic refinement between groups is applied to increase the global consistency. Finally, we apply a multi-band blending algorithm to generate a large-view single composite image as seamlessly as possible, which greatly eliminates both the luminance differences and the color deviations between images and further conceals image parallax. Experimental results on a set of representative images acquired from real bridge bottom surfaces illustrate the superiority of our proposed approaches.

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

    NASA Astrophysics Data System (ADS)

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

    Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other structures. Proteopedia ( http://www.proteopedia.org ) presents 3D biomolecule structures in a broadly accessible manner to a diverse scientific audience through easy-to-use molecular visualization tools integrated into a wiki environment that anyone with a user account can edit. We describe recent advances in the web resource in the areas of content and software. In terms of content, we describe a large growth in user-added content as well as improvements in automatically-generated content for all PDB entry pages in the resource. In terms of software, we describe new features ranging from the capability to create pages hidden from public view to the capability to export pages for offline viewing. New software features also include an improved file-handling system and availability of biological assemblies of protein structures alongside their asymmetric units.

  12. Finding the displacement of wood structure in heritage building by 3D laser scanner

    NASA Astrophysics Data System (ADS)

    Lee, M. C.; Tsai, Y. L.; Wang, R. Z.; Lin, M. L.

    2015-08-01

    Heritage buildings are highly prone to long term damage from the microclimate, scourge and vandalism, which can result in damaged materials, structures, painting and cultural heritage items. This study will focus on finding the displacement of wood structural members through the use of a 3D laser scanner and the 4D concept of time. The results will compare the scans from different periods to find the difference (if any) in the structural member position. Wood structures usually consist of numerous wood members connected to form the structure. However, these members can be damaged in various ways such as physical mechanisms, chemical reactions, and biological corrosion. When damage to the wood structure occurs, the structural displacement can be affected, and if affected severely, can lead to a building collapse. Monitoring of the structural displacement is the best way to discover damage immediately and to preserve the heritage building. However, the Cultural Heritage Preservation Law in Taiwan prohibits the installation of monitoring instruments (e.g strain gauge, accelerometer) in historic structures (heritage buildings). Scanning the wood structure with 3D lasers is the most non-intrusive method and quickly achieves displacement through visualization. The displacement scan results can be compared with different periods and different members to analyze the severity of damage. Once the 3D scanner is installed, the whole building is scanned, and point clouds created to build the visual building model. The structural displacement can be checked via the building model and the differences are measured between each member to find the high risk damaged areas or members with large displacement. Early detection of structural damage is the most effective way means of preservation.

  13. Joint inversion of 3D crustal structure with ambient noise and earthquake body wave travel time

    NASA Astrophysics Data System (ADS)

    Li, Z.; Ni, S.; Chong, J.; Wang, X.

    2012-12-01

    Surface wave tomography based on the noise correlation function of seismic ambient noise has been widely used in studies of crustal and mantle structure . However, the periods of surface wave dispersions in the ambient noise tomography are typically less than 40 s, which limits its resolution on the lower crust. Travel times of earthquake body waves, such as Sg and SmS, could provide additional constraints to the crustal structure, especially to the lower crust due to the ray paths of SmS traveling through the lower crust twice. Here, we proposed a joint inversion method for 3D crustal structure with ambient noise and earthquake body wave travel time data, with the goal of providing better constraints and resolutions on the whole crust. We constructed the linear equations for joint inversion of crustal S velocity structure with the surface wave dispersion and body wave travel time data, and solved the equations with LSQR algorithm. Different weighting and damping factors, together with smoothing constraints, are adopted for surface wave dispersion and body wave travel time data to fit both dataset simultaneously. Synthetics experiments showed that the joint inversion could resolve the crust structure better than sole tomography of ambient noise or body wave travel time. We conducted the joint inversion around the Yangtze block in the eastern China. Rayleigh wave dispersions are extracted from the seismic ambient noise tomography by Zheng et al (2011) in this area. The body waves (e.g., Sg, SmS, Sn) are coherent to be identified and their travel times are measured with accuracy from high quality waveforms of some recent local earthquakes in this area. In order to minimize the travel time uncertainties, the focal depth and epicenter of these local earthquakes were resolved by depth phases and temporary aftershock observations. The result from joint inversion suggests that the crustal velocity structure, especially the lower crust, was well improved, which not only

  14. Verification and validation of ShipMo3D ship motion predictions in the time and frequency domains

    NASA Astrophysics Data System (ADS)

    McTaggart, Kevin A.

    2011-03-01

    This paper compares frequency domain and time domain predictions from the ShipMo3D ship motion library with observed motions from model tests and sea trials. ShipMo3D evaluates hull radiation and diffraction forces using the frequency domain Green function for zero forward speed, which is a suitable approach for ships travelling at moderate speed (e.g., Froude numbers up to 0.4). Numerical predictions give generally good agreement with experiments. Frequency domain and linear time domain predictions are almost identical. Evaluation of nonlinear buoyancy and incident wave forces using the instantaneous wetted hull surface gives no improvement in numerical predictions. Consistent prediction of roll motions remains a challenge for seakeeping codes due to the associated viscous effects.

  15. Topological evolutionary computing in the optimal design of 2D and 3D structures

    NASA Astrophysics Data System (ADS)

    Burczynski, T.; Poteralski, A.; Szczepanik, M.

    2007-10-01

    An application of evolutionary algorithms and the finite-element method to the topology optimization of 2D structures (plane stress, bending plates, and shells) and 3D structures is described. The basis of the topological evolutionary optimization is the direct control of the density material distribution (or thickness for 2D structures) by the evolutionary algorithm. The structures are optimized for stress, mass, and compliance criteria. The numerical examples demonstrate that this method is an effective technique for solving problems in computer-aided optimal design.

  16. Effect of 3-D viscoelastic structure on post-seismic relaxation from the 2004 M = 9.2 Sumatra earthquake

    USGS Publications Warehouse

    Pollitz, F.; Banerjee, P.; Grijalva, K.; Nagarajan, B.; Burgmann, R.

    2008-01-01

    The 2004 M=9.2 Sumatra-Andaman earthquake profoundly altered the state of stress in a large volume surrounding the ???1400 km long rupture. Induced mantle flow fields and coupled surface deformation are sensitive to the 3-D rheology structure. To predict the post-seismic motions from this earthquake, relaxation of a 3-D spherical viscoelastic earth model is simulated using the theory of coupled normal modes. The quasi-static deformation basis set and solution on the 3-D model is constructed using: a spherically stratified viscoelastic earth model with a linear stress-strain relation; an aspherical perturbation in viscoelastic structure; a 'static'mode basis set consisting of Earth's spheroidal and toroidal free oscillations; a "viscoelastic" mode basis set; and interaction kernels that describe the coupling among viscoelastic and static modes. Application to the 2004 Sumatra-Andaman earthquake illustrates the profound modification of the post-seismic flow field at depth by a slab structure and similarly large effects on the near-field post-seismic deformation field at Earth's surface. Comparison with post-seismic GPS observations illustrates the extent to which viscoelastic relaxation contributes to the regional post-seismic deformation. ?? Journal compilation ?? 2008 RAS.

  17. 3D printing of layered brain-like structures using peptide modified gellan gum substrates.

    PubMed

    Lozano, Rodrigo; Stevens, Leo; Thompson, Brianna C; Gilmore, Kerry J; Gorkin, Robert; Stewart, Elise M; in het Panhuis, Marc; Romero-Ortega, Mario; Wallace, Gordon G

    2015-10-01

    The brain is an enormously complex organ structured into various regions of layered tissue. Researchers have attempted to study the brain by modeling the architecture using two dimensional (2D) in vitro cell culturing methods. While those platforms attempt to mimic the in vivo environment, they do not truly resemble the three dimensional (3D) microstructure of neuronal tissues. Development of an accurate in vitro model of the brain remains a significant obstacle to our understanding of the functioning of the brain at the tissue or organ level. To address these obstacles, we demonstrate a new method to bioprint 3D brain-like structures consisting of discrete layers of primary neural cells encapsulated in hydrogels. Brain-like structures were constructed using a bio-ink consisting of a novel peptide-modified biopolymer, gellan gum-RGD (RGD-GG), combined with primary cortical neurons. The ink was optimized for a modified reactive printing process and developed for use in traditional cell culturing facilities without the need for extensive bioprinting equipment. Furthermore the peptide modification of the gellan gum hydrogel was found to have a profound positive effect on primary cell proliferation and network formation. The neural cell viability combined with the support of neural network formation demonstrated the cell supportive nature of the matrix. The facile ability to form discrete cell-containing layers validates the application of this novel printing technique to form complex, layered and viable 3D cell structures. These brain-like structures offer the opportunity to reproduce more accurate 3D in vitro microstructures with applications ranging from cell behavior studies to improving our understanding of brain injuries and neurodegenerative diseases. PMID:26231917

  18. Low-cost impact detection and location for automated inspections of 3D metallic based structures.

    PubMed

    Morón, Carlos; Portilla, Marina P; Somolinos, José A; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

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

    PubMed Central

    Morón, Carlos; Portilla, Marina P.; Somolinos, José A.; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  20. LigandBox: A database for 3D structures of chemical compounds

    PubMed Central

    Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

    2013-01-01

    A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

  1. Sequence-based identification of 3D structural modules in RNA with RMDetect.

    PubMed

    Cruz, José Almeida; Westhof, Eric

    2011-06-01

    Structural RNA modules, sets of ordered non-Watson-Crick base pairs embedded between Watson-Crick pairs, have central roles as architectural organizers and sites of ligand binding in RNA molecules, and are recurrently observed in RNA families throughout the phylogeny. Here we describe a computational tool, RNA three-dimensional (3D) modules detection, or RMDetect, for identifying known 3D structural modules in single and multiple RNA sequences in the absence of any other information. Currently, four modules can be searched for: G-bulge loop, kink-turn, C-loop and tandem-GA loop. In control test sequences we found all of the known modules with a false discovery rate of 0.23. Scanning through 1,444 publicly available alignments, we identified 21 yet unreported modules and 141 known modules. RMDetect can be used to refine RNA 2D structure, assemble RNA 3D models, and search and annotate structured RNAs in genomic data. PMID:21552257

  2. Experimentation of structured light and stereo vision for underwater 3D reconstruction

    NASA Astrophysics Data System (ADS)

    Bruno, F.; Bianco, G.; Muzzupappa, M.; Barone, S.; Razionale, A. V.

    Current research on underwater 3D imaging methods is mainly addressing long range applications like seafloor mapping or surveys of archeological sites and shipwrecks. Recently, there is an increasing need for more accessible and precise close-range 3D acquisition technologies in some application fields like, for example, monitoring the growth of coral reefs or reconstructing underwater archaeological pieces that in most cases cannot be recovered from the seabed. This paper presents the first results of a research project that aims to investigate the possibility of using active optical techniques for the whole-field 3D reconstructions in an underwater environment. In this work we have tested an optical technique, frequently used for in air acquisition, based on the projection of structured lighting patterns acquired by a stereo vision system. We describe the experimental setup used for the underwater tests, which were conducted in a water tank with different turbidity conditions. The tests have evidenced that the quality of 3D reconstruction is acceptable even with high turbidity values, despite the heavy presence of scattering and absorption effects.

  3. Local backbone structure prediction of proteins.

    PubMed

    de Brevern, Alexandre G; Benros, Cristina; Gautier, Romain; Valadié, Héléne; Hazout, Serge; Etchebest, Catherine

    2004-01-01

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

  4. Determination and validation of mTOR kinase-domain 3D structure by homology modeling

    PubMed Central

    Lakhlili, Wiame; Chevé, Gwénaël; Yasri, Abdelaziz; Ibrahimi, Azeddine

    2015-01-01

    The AKT/mammalian target of rapamycin (mTOR) pathway is considered as one of the commonly activated and deregulated signaling pathways in human cancer. mTOR is associated with other proteins in two molecular complexes: mTOR complex 1/Raptor and the mTOR complex 2/Rictor. Using the crystal structure of the related lipid kinase PI3Kγ, we built a model of the catalytic region of mTOR. The modeling of the three-dimensional (3D) structure of the mTOR was performed by homology modeling program SWISS-MODEL. The quality and validation of the obtained model were performed using PROCHECK and PROVE softwares. The overall stereochemical property of the protein was assessed by the Ramachandran plot. The model validation was also done by docking of known inhibitors. In this paper, we describe and validate a 3D model for the mTOR catalytic site. PMID:26257525

  5. Utilizing in-situ resources and 3D printing structures for a manned Mars mission

    NASA Astrophysics Data System (ADS)

    Kading, Benjamin; Straub, Jeremy

    2015-02-01

    This paper presents a manned Mars mission, which is based on the use of in-situ resources for the fabrication of structures. First, it provides an overview of the two-phase mission. In phase one, robotic construction units prepare a functional base for phase-two human habitation. Then, it describes a set of prospective structures that can be created utilizing additive manufacturing (commonly known as 3D printing) techniques and in situ materials. Next, the technological advancements required to allow this type of mission are considered and their feasibility is discussed. Specific focus is given to the topics of basalt 3D printing and the maintenance of the pressure environment. The process of the construction of the base is also discussed. Finally the proposed approach is analyzed through comparison to prior missions, before concluding.

  6. Topology optimization of 3D structures with design-dependent loads

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Liu, Shu-Tian; Zhang, Xiong

    2010-10-01

    Topology optimization of continuum structures with design-dependent loads has long been a challenge. In this paper, the topology optimization of 3D structures subjected to design-dependent loads is investigated. A boundary search scheme is proposed for 3D problems, by means of which the load surface can be identified effectively and efficiently, and the difficulties arising in other approaches can be overcome. The load surfaces are made up of the boundaries of finite elements and the loads can be directly applied to corresponding element nodes, which leads to great convenience in the application of this method. Finally, the effectiveness and efficiency of the proposed method is validated by several numerical examples.

  7. 3D structural analysis of proteins using electrostatic surfaces based on image segmentation

    PubMed Central

    Vlachakis, Dimitrios; Champeris Tsaniras, Spyridon; Tsiliki, Georgia; Megalooikonomou, Vasileios; Kossida, Sophia

    2016-01-01

    Herein, we present a novel strategy to analyse and characterize proteins using protein molecular electro-static surfaces. Our approach starts by calculating a series of distinct molecular surfaces for each protein that are subsequently flattened out, thus reducing 3D information noise. RGB images are appropriately scaled by means of standard image processing techniques whilst retaining the weight information of each protein’s molecular electrostatic surface. Then homogeneous areas in the protein surface are estimated based on unsupervised clustering of the 3D images, while performing similarity searches. This is a computationally fast approach, which efficiently highlights interesting structural areas among a group of proteins. Multiple protein electrostatic surfaces can be combined together and in conjunction with their processed images, they can provide the starting material for protein structural similarity and molecular docking experiments.

  8. 3D reconstruction of internal structure of animal body using near-infrared light

    NASA Astrophysics Data System (ADS)

    Tran, Trung Nghia; Yamamoto, Kohei; Namita, Takeshi; Kato, Yuji; Shimizu, Koichi

    2014-03-01

    To realize three-dimensional (3D) optical imaging of the internal structure of animal body, we have developed a new technique to reconstruct CT images from two-dimensional (2D) transillumination images. In transillumination imaging, the image is blurred due to the strong scattering in the tissue. We had developed a scattering suppression technique using the point spread function (PSF) for a fluorescent light source in the body. In this study, we have newly proposed a technique to apply this PSF for a light source to the image of unknown light-absorbing structure. The effectiveness of the proposed technique was examined in the experiments with a model phantom and a mouse. In the phantom experiment, the absorbers were placed in the tissue-equivalent medium to simulate the light-absorbing organs in mouse body. Near-infrared light was illuminated from one side of the phantom and the image was recorded with CMOS camera from another side. Using the proposed techniques, the scattering effect was efficiently suppressed and the absorbing structure can be visualized in the 2D transillumination image. Using the 2D images obtained in many different orientations, we could reconstruct the 3D image. In the mouse experiment, an anesthetized mouse was held in an acrylic cylindrical holder. We can visualize the internal organs such as kidneys through mouse's abdomen using the proposed technique. The 3D image of the kidneys and a part of the liver were reconstructed. Through these experimental studies, the feasibility of practical 3D imaging of the internal light-absorbing structure of a small animal was verified.

  9. A theoretical study of the structure and stability of borohydride on 3d transition metals

    NASA Astrophysics Data System (ADS)

    Arevalo, Ryan Lacdao; Escaño, Mary Clare Sison; Gyenge, Elod; Kasai, Hideaki

    2012-12-01

    The adsorption of borohydride on 3d transition metals (Cr, Mn, Fe, Co, Ni and Cu) was studied using first principles calculations within spin-polarized density functional theory. Magnetic effect on the stability of borohydride is noted. Molecular adsorption is favorable on Co, Ni and Cu, which is characterized by the strong s-dzz hybridization of the adsorbate-substrate states. Dissociated adsorption structure yielding one or two H adatom fragments on the surface is observed for Cr, Mn and Fe.

  10. Assessment of the isostatic state and the load distribution of the European Molasse basin by means of lithospheric-scale 3D structural and 3D gravity modelling

    NASA Astrophysics Data System (ADS)

    Przybycin, Anna M.; Scheck-Wenderoth, Magdalena; Schneider, Michael

    2015-07-01

    The European Molasse basin is a foreland basin situated at the northern front of the European Alps and has formed as a consequence of the Euro-Adriatic continental collision since the Tertiary. Today, it is underlain by Mesozoic sedimentary successions on top of a Paleozoic crust. To investigate the deep structure, the isostatic state, as well as the load distribution in the basin and the adjacent Alpine area, we constructed a lithospheric-scale 3D structural model by implementing available surface, well and seismic data. Subsequently, the structure of the model was constrained by means of 3D gravity modelling. Complementary, the isostatic state has been assessed based on the calculation of the 3D load distribution. Our results show that the Molasse basin is not in isostatic equilibrium and that the gravity field of the area is strongly controlled by the configuration of the crystalline crust. Furthermore, we show that the area is influenced by significant lateral load variations down to a depth of -150 km, which are considerably larger than commonly assumed for this level. Furthermore, our results allow a first-order assessment of the minimum compensating horizontal stress required to prevent gravitational collapse.

  11. Characterizing Woody Vegetation Spectral and Structural Parameters with a 3-D Scene Model

    NASA Astrophysics Data System (ADS)

    Qin, W.; Yang, L.

    2004-05-01

    Quantification of structural and biophysical parameters of woody vegetation is of great significance in understanding vegetation condition, dynamics and functionality. Such information over a landscape scale is crucial for global and regional land cover characterization, global carbon-cycle research, forest resource inventories, and fire fuel estimation. While great efforts and progress have been made in mapping general land cover types over large area, at present, the ability to quantify regional woody vegetation structural and biophysical parameters is limited. One approach to address this research issue is through an integration of physically based 3-D scene model with multiangle and multispectral remote sensing data and in-situ measurements. The first step of this work is to model woody vegetation structure and its radiation regime using a physically based 3-D scene model and field data, before a robust operational algorithm can be developed for retrieval of important woody vegetation structural/biophysical parameters. In this study, we use an advanced 3-D scene model recently developed by Qin and Gerstl (2000), based on L-systems and radiosity theories. This 3-D scene model has been successfully applied to semi-arid shrubland to study structure and radiation regime at a regional scale. We apply this 3-D scene model to a more complicated and heterogeneous forest environment dominated by deciduous and coniferous trees. The data used in this study are from a field campaign conducted by NASA in a portion of the Superior National Forest (SNF) near Ely, Minnesota during the summers of 1983 and 1984, and supplement data collected during our revisit to the same area of SNF in summer of 2003. The model is first validated with reflectance measurements at different scales (ground observations, helicopter, aircraft, and satellite). Then its ability to characterize the structural and spectral parameters of the forest scene is evaluated. Based on the results from this study

  12. Dynamic Characteristics of a Model and Prototype for 3D-RC Structure

    NASA Astrophysics Data System (ADS)

    Moniuddin, Md. Khaja; Vasanthalakshmi, G.; Chethan, K.; Babu, R. Ramesh

    2016-06-01

    Infill walls provide durable and economical partitions that have relatively excellent thermal and sound insulation with high fire resistance. Monolithic infilled walls are provided within RC structures without being analyzed as a combination of concrete and brick elements, although in reality they act as a single unit during earthquakes. The performance of such structures during earthquakes has proved to be superior in comparison to bare frames in terms of stiffness, strength and energy dissipation. To know the dynamic characteristics of monolithic infill wall panels and masonry infill, modal, response spectrum and time history analyses have been carried out on a model and prototype of a 3D RC structure for a comparative study.

  13. A geometric pore-scale model for predicting the permeability of 3D flow through fibrous porous media

    NASA Astrophysics Data System (ADS)

    Woudberg, Sonia

    2012-05-01

    A geometric pore-scale model, based on rectangular geometry, is used to quantify the fluid-solid interaction in fibrous porous media in order to predict the permeability. The analytical modeling procedure is based on sound physical principles. Permeability predictions are presented for flow parallel and perpendicular to the axes of unidirectional fibres. In the latter case maximum possible staggering is introduced. A weighted average is performed to obtain the permeability prediction for 3D flow through fibrous porous media. Effects such as pore blockage at very low porosities and developing flow are incorporated into the predictive equations for the permeability to provide a model that is applicable over the entire porosity range. The resulting 3D model leads to satisfactory agreement with other three-dimensional models and data from the literature.

  14. 3-D Structure of the Slave and Rae Cratons Provides Clues to Their Construction

    NASA Astrophysics Data System (ADS)

    Snyder, D. B.

    2013-12-01

    Deep geologic structures within cratons that make up continental cores were long neglected. Recently acquired geophysical data from large observational arrays and geochemical data resulting from exploration for diamond has now made possible co-registration of large-scale (400-km depth), truly 3-dimensional data sets. P-waves, surface waves and magnetotelluric observations provide 3-D wavespeed and conductivity models. Multi-azimuthal receiver functions map seismic discontinuity surfaces in 3-D. Xenolith suites erupted in kimberlites provide rock samples at key lithospheric depths, albeit at sparsely distributed locations. These multi-disciplinary models are becoming available for several key cratons worldwide; here the deep structure of the Slave and Rae cratons of the Canadian Shield is described. Lithospheric layers with tapered, wedge-shaped margins are common. Slave craton layers are sub-horizontal and indicate construction of the craton core at 2.7 Ga by underthrusting and flat stacking of lithosphere. The central Rae craton has predominantly dipping discontinuities that indicate construction at 1.9 Ga by thrusting similar to that observed in crustal ';thick-skinned' fold-and-thrust belts. 3-D mapping of conductivity and metasomatism, the latter via mineral recrystallization and resetting of isotopic ages, overprints primary structures in both cratons. Distribution of more conductivitve mantle suggests that assumed causative pervasive metasomatism occurs at 100-200 km depths with ';chimneys' reaching to shallower depths, typically in locations where kimberlites or mineralization has occurred.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  16. SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures

    PubMed Central

    Nadzirin, Nurul; Gardiner, Eleanor J.; Willett, Peter; Artymiuk, Peter J.; Firdaus-Raih, Mohd

    2012-01-01

    Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function. In contrast, a 3D pattern of interest can be searched for existing occurrences in available PDB structures using ASSAM. Both programs are freely accessible without any login requirement. SPRITE is available at http://mfrlab.org/grafss/sprite/ while ASSAM can be accessed at http://mfrlab.org/grafss/assam/. PMID:22573174

  17. Integration of nano-scale components and supports in micromachined 3D silicon structures

    NASA Astrophysics Data System (ADS)

    Song, J.; Azimi, S.; Y Dang, Z.; Breese, M. B. H.

    2014-04-01

    We have developed a process for the three-dimensional (3D) machining of p-type silicon on a micro- and nano-scale using high-energy ion beam irradiation with one or more energies and fluences, followed by electrochemical anodization in hydrofluoric acid. We present a study of the dependence of our fabricated structures on irradiating ion energies, fluences, geometries and wafer resistivity. All these factors determine whether the micro- and nano-scale features are properly connected to the supports in the 3D silicon structures. If wrongly chosen, any of these factors may cause a breakage at the connection through localized over-etching. Under optimum irradiation and anodization conditions, free-standing patterned membranes can be fabricated with feature dimensions of 100 nm over areas of many square millimeters. This investigation is based on silicon structures but is relevant to any electro-assisted etching process for 3D fabrication, paving the way for achieving free-standing silicon photonics, mechanical resonators and micro-/nano-electromechanical systems.

  18. 3D Axon structure extraction and analysis in confocal fluorescence microscopy images.

    PubMed

    Zhang, Yong; Zhou, Xiaobo; Lu, Ju; Lichtman, Jeff; Adjeroh, Donald; Wong, Stephen T C

    2008-08-01

    The morphological properties of axons, such as their branching patterns and oriented structures, are of great interest for biologists in the study of the synaptic connectivity of neurons. In these studies, researchers use triple immunofluorescent confocal microscopy to record morphological changes of neuronal processes. Three-dimensional (3D) microscopy image analysis is then required to extract morphological features of the neuronal structures. In this article, we propose a highly automated 3D centerline extraction tool to assist in this task. For this project, the most difficult part is that some axons are overlapping such that the boundaries distinguishing them are barely visible. Our approach combines a 3D dynamic programming (DP) technique and marker-controlled watershed algorithm to solve this problem. The approach consists of tracking and updating along the navigation directions of multiple axons simultaneously. The experimental results show that the proposed method can rapidly and accurately extract multiple axon centerlines and can handle complicated axon structures such as cross-over sections and overlapping objects. PMID:18336075

  19. Minimizing camera-eye optical aberrations during the 3D reconstruction of retinal structures

    NASA Astrophysics Data System (ADS)

    Aldana-Iuit, Javier; Martinez-Perez, M. Elena; Espinosa-Romero, Arturo; Diaz-Uribe, Rufino

    2010-05-01

    3D reconstruction of blood vessels is a powerful visualization tool for physicians, since it allows them to refer to qualitative representation of their subject of study. In this paper we propose a 3D reconstruction method of retinal vessels from fundus images. The reconstruction method propose herein uses images of the same retinal structure in epipolar geometry. Images are preprocessed by RISA system for segmenting blood vessels and obtaining feature points for correspondences. The correspondence points process is solved using correlation. The LMedS analysis and Graph Transformation Matching algorithm are used for outliers suppression. Camera projection matrices are computed with the normalized eight point algorithm. Finally, we retrieve 3D position of the retinal tree points by linear triangulation. In order to increase the power of visualization, 3D tree skeletons are represented by surfaces via generalized cylinders whose radius correspond to morphological measurements obtained by RISA. In this paper the complete calibration process including the fundus camera and the optical properties of the eye, the so called camera-eye system is proposed. On one hand, the internal parameters of the fundus camera are obtained by classical algorithms using a reference pattern. On the other hand, we minimize the undesirable efects of the aberrations induced by the eyeball optical system assuming that contact enlarging lens corrects astigmatism, spherical and coma aberrations are reduced changing the aperture size and eye refractive errors are suppressed adjusting camera focus during image acquisition. Evaluation of two self-calibration proposals and results of 3D blood vessel surface reconstruction are presented.

  20. Novel 3D bismuth-based coordination polymers: Synthesis, structure, and second harmonic generation properties

    SciTech Connect

    Wibowo, Arief C.; Smith, Mark D.; Yeon, Jeongho; Halasyamani, P. Shiv; Loye, Hans-Conrad zur

    2012-11-15

    Two new 3D bismuth containing coordination polymers are reported along with their single crystal structures and SHG properties. Compound 1: Bi{sub 2}O{sub 2}(pydc) (pydc=pyridine-2, 5-dicarboxylate), crystallizes in the monoclinic, polar space group, P2{sub 1} (a=9.6479(9) A, b=4.2349(4) A, c=11.9615(11) A, {beta}=109.587(1) Degree-Sign ), which contains Bi{sub 2}O{sub 2} chains that are connected into a 3D structure via the pydc ligands. Compound 2: Bi{sub 4}Na{sub 4}(1R3S-cam){sub 8}(EtOH){sub 3.1}(H{sub 2}O){sub 3.4} (1R3S cam=1R3S-camphoric acid) crystallizes in the monoclinic, polar space group, P2{sub 1} (a=19.0855(7) A, b=13.7706(5) A, c=19.2429(7) A, {beta}=90.701(1) Degree-Sign ) and is a true 3D coordination polymer. These are two example of SHG compounds prepared using unsymmetric ligands (compound 1) or chiral ligands (compound 2), together with metals that often exhibit stereochemically-active lone pairs, such as Bi{sup 3+}, a synthetic approach that resulted in polar, non-centrosymmetric, 3D metal-organic coordination polymer. - Graphical Abstract: Structures of two new, polar, 3D Bismuth(III)-based coordination polymers: Bi{sub 2}O{sub 2}(pydc) (compound 1), and Bi{sub 4}Na{sub 4}(1R3S-cam){sub 8}(EtOH){sub 3.1}(H{sub 2}O){sub 3.4} (compound 2). Highlights: Black-Right-Pointing-Pointer New, polar, 3D Bismuth(III)-based coordination polymers. Black-Right-Pointing-Pointer First polar bismuth-based coordination polymers synthesized via a 'hybrid' strategy. Black-Right-Pointing-Pointer Combination of stereochemically-active lone pairs and unsymmetrical or chiral ligands. Black-Right-Pointing-Pointer Synthesis of class C-SHG materials based on Kurtz-Perry categories.

  1. GeoCube: A 3D mineral resources quantitative prediction and assessment system

    NASA Astrophysics Data System (ADS)

    Li, Ruixi; Wang, Gongwen; Carranza, Emmanuel John Muico

    2016-04-01

    This paper introduces a software system (GeoCube) for three dimensional (3D) extraction and integration of exploration criteria from spatial data. The software system contains four key modules: (1) Import and Export, supporting many formats from commercial 3D geological modeling software and offering various export options; (2) pre-process, containing basic statistics and fractal/multi-fractal methods (concentration-volume (C-V) fractal method) for extraction of exploration criteria from spatial data (i.e., separation of geological, geochemical and geophysical anomalies from background values in 3D space); (3) assessment, supporting five data-driven integration methods (viz., information entropy, logistic regression, ordinary weights of evidence, weighted weights of evidence, boost weights of evidence) for integration of exploration criteria; and (4) post-process, for classifying integration outcomes into several levels based on mineralization potentiality. The Nanihu Mo (W) camp (5.0 km×4.0 km×2.7 km) of the Luanchuan region was used as a case study. The results show that GeoCube can enhance the use of 3D geological modeling to store, retrieve, process, display, analyze and integrate exploration criteria. Furthermore, it was found that the ordinary weights of evidence, boost weights of evidence and logistic regression methods showed superior performance as integration tools for exploration targeting in this case study.

  2. 3-D Radar Imaging Reveals Deep Structures and Buried Craters Within the Martian Polar Caps

    NASA Astrophysics Data System (ADS)

    Putzig, N. E.; Foss, F. J., II; Campbell, B. A.; Phillips, R. J.; Smith, I. B.

    2015-12-01

    We use Shallow Radar (SHARAD) observations on thousands of orbital passes by the Mars Reconnaissance Orbiter to produce fully imaged 3-D data volumes encompassing both polar ice caps of Mars. Greatly clarifying the view of subsurface features, a completed volume for Planum Boreum provides new constraints on the nature and timing of emplacement of the northern polar deposits and their relationship to climate. The standard method of mapping subsurface features with single-pass 2-D radargrams has been very fruitful (see Brothers et al. 2015, JGR 120 in press, and references therein), but a full assessment of internal structures has been hindered by interfering off-nadir echoes from spiral troughs and other variable topography prevalent on both caps. By assembling the SHARAD radargrams into a volume and applying a 3-D imaging process (migration) borrowed from seismic processing techniques, we enhance the signal-to-noise ratio while repositioning the echoes to their proper locations, thereby unraveling the interference. As part of the process, we correct ionospheric distortions and delays of the radar echoes (Campbell et al. 2014, IEEE GRSL 11 #3). Interfaces painstakingly mapped in radargrams (e.g., the basal-unit surface, a buried chasma) are clearly visible in the 3-D volume, and new features are revealed. Structures may now be mapped through trough-rich regions, including a widespread sequence that provides corroborative evidence of recent ice ages (Smith et al. 2015, LPSC XLVI #2574). Distinctive radar signatures associated with known, partially buried craters also occur elsewhere in the volume but without surface expression. Presumably, these are fully buried craters that may provide a new means to estimate the age of the deposits. Preliminary work for Planum Australe demonstrates that the 3-D processing currently underway will illuminate deep structures that are broadly obfuscated in 2-D radargrams by a shallow scatterer (Campbell et al. 2015, LPSC XLVI #2366).

  3. 3-D Waveguide Effects of Topographical Structural Variation on Full Waveform Propagation: 3-D Finite Difference Modeling Comparisons with Field Data From Yuma Proving Ground, Arizona

    NASA Astrophysics Data System (ADS)

    Anderson, T. S.; Miller, R.; Greenfield, R.; Fisk, D.

    2002-12-01

    The propagation of seismic waves through regions of complex topography is not thoroughly understood. Surface waves, are of particular interest, as they are large in amplitude and can characterize the source depth, magnitude, and frequency content. The amplitude and frequency content of seismic waves that propagate in regions with large topographical variations are affected by both the scattering and blockage of the wave energy. The ability to predict the 3-d scattering due to topography will improve the understanding of both regional scale surface wave magnitudes, and refine surface wave discriminants as well as at the local scale (<2 km ) where it will aid in the development of rule of thumb guide lines for array sensor placement for real time sensing technologies. Ideally, when validating the numerical accuracy of a propagation model against field data, the input geologic parameters would be known and thus eliminates geology as a source of error in the calculation. In March of 2001, Kansas Geological Survey (KGS) performed a detailed seismic site characterization at the Smart Weapons Test Range, Yuma Proving Ground, Arizona. The result of the KGS characterization study is a high-resolution 3-d model that is used in our seismic simulations. The velocities Vs, Vp are calculated by tomography and refraction, attenuation coefficients estimated from the surface wave and from p-waves and are provided in a model with attributes resolved in 3-d to 0.5 meters. In the present work, we present comparisons of synthetic data with seismic data collected at the Smart Weapons Test Range to benchmark the accuracy achieved in simulating 3-d wave propagation in the vicinity of a topographical anomaly (trench). Synthetic seismograms are generated using a 3-d 8th order staggered grid visco-elastic finite difference code that accounts for topography. The geologic model is based on the Yuma site characterization. The size of these calculations required use of the DoD High Performance

  4. A 3-D numerical study of pinhole diffraction to predict the accuracy of EUV point diffraction interferometry

    SciTech Connect

    Goldberg, K.A. |; Tejnil, E.; Bokor, J. |

    1995-12-01

    A 3-D electromagnetic field simulation is used to model the propagation of extreme ultraviolet (EUV), 13-nm, light through sub-1500 {Angstrom} dia pinholes in a highly absorptive medium. Deviations of the diffracted wavefront phase from an ideal sphere are studied within 0.1 numerical aperture, to predict the accuracy of EUV point diffraction interferometersused in at-wavelength testing of nearly diffraction-limited EUV optical systems. Aberration magnitudes are studied for various 3-D pinhole models, including cylindrical and conical pinhole bores.

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

    PubMed

    Mrozek, Dariusz; Brożek, Miłosz; Małysiak-Mrozek, Bożena

    2014-02-01

    Searching for similar 3D protein structures is one of the primary processes employed in the field of structural bioinformatics. However, the computational complexity of this process means that it is constantly necessary to search for new methods that can perform such a process faster and more efficiently. Finding molecular substructures that complex protein structures have in common is still a challenging task, especially when entire databases containing tens or even hundreds of thousands of protein structures must be scanned. Graphics processing units (GPUs) and general purpose graphics processing units (GPGPUs) can perform many time-consuming and computationally demanding processes much more quickly than a classical CPU can. In this paper, we describe the GPU-based implementation of the CASSERT algorithm for 3D protein structure similarity searching. This algorithm is based on the two-phase alignment of protein structures when matching fragments of the compared proteins. The GPU (GeForce GTX 560Ti: 384 cores, 2GB RAM) implementation of CASSERT ("GPU-CASSERT") parallelizes both alignment phases and yields an average 180-fold increase in speed over its CPU-based, single-core implementation on an Intel Xeon E5620 (2.40GHz, 4 cores). In this paper, we show that massive parallelization of the 3D structure similarity search process on many-core GPU devices can reduce the execution time of the process, allowing it to be performed in real time. GPU-CASSERT is available at: http://zti.polsl.pl/dmrozek/science/gpucassert/cassert.htm. PMID:24481593

  6. Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities

    PubMed Central

    Dai, Chao; Li, Wenyuan; Tjong, Harianto; Hao, Shengli; Zhou, Yonggang; Li, Qingjiao; Chen, Lin; Zhu, Bing; Alber, Frank; Jasmine Zhou, Xianghong

    2016-01-01

    Three-dimensional (3D) genome structures vary from cell to cell even in an isogenic sample. Unlike protein structures, genome structures are highly plastic, posing a significant challenge for structure-function mapping. Here we report an approach to comprehensively identify 3D chromatin clusters that each occurs frequently across a population of genome structures, either deconvoluted from ensemble-averaged Hi-C data or from a collection of single-cell Hi-C data. Applying our method to a population of genome structures (at the macrodomain resolution) of lymphoblastoid cells, we identify an atlas of stable inter-chromosomal chromatin clusters. A large number of these clusters are enriched in binding of specific regulatory factors and are therefore defined as ‘Regulatory Communities.' We reveal two major factors, centromere clustering and transcription factor binding, which significantly stabilize such communities. Finally, we show that the regulatory communities differ substantially from cell to cell, indicating that expression variability could be impacted by genome structures. PMID:27240697

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  8. Optimizing radioimmunotherapy by matching dose distribution with tumor structure using 3D reconstructions of serial images.

    PubMed

    Flynn, A A; Pedley, R B; Green, A J; Boxer, G M; Boden, R; Begent, R H

    2001-10-01

    The biological effect of radioimmunotherapy (RIT) is most commonly assessed in terms of the absorbed radiation dose. In tumor, conventional dosimetry methods assume a uniform radionuclide and calculate a mean dose throughout the tumor. However, the vasculature of solid tumors tends to be highly irregular and the systemic delivery of antibodies is therefore heterogeneous. Tumor-specific antibodies preferentially localize in the viable, radiosensitive parts of the tumor whereas non-specific antibodies can penetrate into the necrosis where the dose is wasted. As a result, the observed biological effect can be very different to the predicted effect from conventional dose estimates. The purpose of this study is to assess the potential for optimizing the biological effect of RIT by matching the dose-distribution with tumor structure through the selection of appropriate antibodies and radionuclides. Storage phosphor plate technology was used to acquire images of the antibody distribution in serial tumor sections. Images of the distributions of a trivalent (TFM), bivalent (A5B7-IgG), monovalent (MFE-23) and a non-specific antibody (MOPC) were obtained. These images were registered with corresponding images showing tumor morphology. Serial images were reconstructed to form 3D maps of the antibody distribution and tumor structure. Convolution of the image of antibody distribution with beta dose point kernals generated dose-rate distributions for 14C, 131I and 90Y. These were statistically compared with the tumor structure. The highest correlation was obtained for the multivalent antibodies combined with 131I, due to specific retention in viable areas of tumor coupled with the fact that much of the dose was deposted locally. With decreasing avidity the correlation also decreased and with the non-specific antibody this correlation was negative, indicating higher concentrations in the necrotic regions. In conclusion, the dose distribution can be optimized in tumor by selecting

  9. 3D measurement method based on combined temporal encoding structured light

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    Ferro, Carlo Giovanni; Brischetto, Salvatore; Torre, Roberto; Maggiore, Paolo

    2016-07-01

    The Fused Deposition Modelling (FDM) technology is widely used in rapid prototyping. 3D printers for home desktop applications are usually employed to make non-structural objects. When the mechanical stresses are not excessive, this technology can also be successfully employed to produce structural objects, not only in prototyping stage but also in the realization of series pieces. The innovative idea of the present work is the application of this technology, implemented in a desktop 3D printer, to the realization of components for aeronautical use, especially for unmanned aerial systems. For this purpose, the paper is devoted to the statistical study of the performance of a desktop 3D printer to understand how the process performs and which are the boundary limits of acceptance. Mechanical and geometrical properties of ABS (Acrylonitrile Butadiene Styrene) specimens, such as tensile strength and stiffness, have been evaluated. ASTM638 type specimens have been used. A capability analysis has been applied for both mechanical and dimensional performances. Statistically stable limits have been determined using experimentally collected data.

  11. An unprecedented 3D POM-Ag architecture with intertwined and homological helical structures.

    PubMed

    Sha, Jing-Quan; Li, Meng-Ting; Sun, Jing-Wen; Zhang, Yu-Nan; Yan, Peng-Fei; Li, Guang-Ming

    2013-06-01

    A new hybrid compound, Na[Ag6(pyttz)2(H2O)][PMo12O40] (pyttz = 3-(pyrid-3-yl)-5-(1H-1,2,4-triazol-3-yl)-1,2,4-triazolyl), has been hydrothermally synthesized and structurally characterized by routine techniques. X-ray diffraction analysis reveals that the title compound is constructed by the 2D Ag-pyttz coordination polymer and 3D Ag-POM architecture with helix. A fascinating structural feature is the assembling fashion of the right- and left-helical chain, namely, the helical chains with different orientations are intertwined with each other forming intertwined double helical layers along the c-axis, and the identical left- or right-handed helical chains are fused together in a hand-by-hand mode generating another homological helical layer along the a-axis. As a result, these helical layers intersect each other obtaining an unprecedented 3D POM-Ag inorganic architecture. Note that the 3D framework with a helix constructed by POMs and metal ions has never been observed up to date. Additionally, its photocatalytic degradation of RhB was also investigated. PMID:23558903

  12. Micro-CT for the quantification of 3D voids within damaged structures

    SciTech Connect

    Patterson, Brian M; Hamilton, Christopher E; Cerreta, Ellen K; Dennis - Koller, Darcie; Bronkhorst, C. A.; Hansen, B. L.

    2011-01-26

    Micro X-ray Computed Tomography (MXCT) is widely used in the materials community to examine the internal structure of materials for voids and cracks due to damage or casting, or other defects. Most research in this area focuses on the qualitative aspect of the image, simply answering; Are there voids present? Here we present an ongoing study of the quantified incipient spall voids in Cu with different grain sizes, using a gas gun with various velocities. Data analysis packages for MXCT are just now becoming able to dimensionally measure and produce statistics on the voids-present. In order to make the size of the features in the 3D image quantifiable, the question, how many radiographs are required to render the object dimensionally accurate in 3D, must be answered. A series of data sets has been coUected, varying the number of radiographs collected in order to determine the appropriate number required.

  13. Shape optimization of 3D continuum structures via force approximation techniques

    NASA Technical Reports Server (NTRS)

    Vanderplaats, Garret N.; Kodiyalam, Srinivas

    1988-01-01

    The existing need to develop methods whereby the shape design efficiency can be improved through the use of high quality approximation methods is addressed. An efficient approximation method for stress constraints in 3D shape design problems is proposed based on expanding the nodal forces in Taylor series with respect to shape variations. The significance of this new method is shown through elementary beam theory calculations and via numerical computations using 3D solid finite elements. Numerical examples including the classical cantilever beam structure and realistic automotive parts like the engine connecting rod are designed for optimum shape using the proposed method. The numerical results obtained from these methods are compared with other published results, to assess the efficiency and the convergence rate of the proposed method.

  14. Field structure of collapsing wave packets in 3D strong Langmuir turbulence

    NASA Technical Reports Server (NTRS)

    Newman, D. L.; Robinson, P. A.; Goldman, M. V.

    1989-01-01

    A simple model is constructed for the electric fields in the collapsing wave packets found in 3D simulations of driven and damped isotropic strong Langmuir turbulence. This model, based on a spherical-harmonic decomposition of the electrostatic potential, accounts for the distribution of wave-packet shapes observed in the simulations, particularly the predominance of oblate wave packets. In contrast with predictions for undamped and undriven subsonic collapse of scalar fields, oblate vector-field wave packets do not flatten during collapse but, instead, remain approximately self-similar and rigid.

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

    NASA Astrophysics Data System (ADS)

    Przybycin, Anna M.; Scheck-Wenderoth, Magdalena; Schneider, Michael

    2014-05-01

    The North Alpine Foreland Basin is situated in the northern front of the European Alps and extends over parts of France, Switzerland, Germany and Austria. It formed as a wedge shaped depression since the Tertiary in consequence of the Euro - Adriatic continental collision and the Alpine orogeny. The basin is filled with clastic sediments, the Molasse, originating from erosional processes of the Alps and underlain by Mesozoic sedimentary successions and a Paleozoic crystalline crust. For our study we have focused on the German part of the basin. To investigate the deep structure, the isostatic state and the load distribution of this region we have constructed a 3D structural model of the basin and the Alpine area using available depth and thickness maps, regional scale 3D structural models as well as seismic and well data for the sedimentary part. The crust (from the top Paleozoic down to the Moho (Grad et al. 2008)) has been considered as two-parted with a lighter upper crust and a denser lower crust; the partition has been calculated following the approach of isostatic equilibrium of Pratt (1855). By implementing a seismic Lithosphere-Asthenosphere-Boundary (LAB) (Tesauro 2009) the crustal scale model has been extended to the lithospheric-scale. The layer geometry and the assigned bulk densities of this starting model have been constrained by means of 3D gravity modelling (BGI, 2012). Afterwards the 3D load distribution has been calculated using a 3D finite element method. Our results show that the North Alpine Foreland Basin is not isostatically balanced and that the configuration of the crystalline crust strongly controls the gravity field in this area. Furthermore, our results show that the basin area is influenced by varying lateral load differences down to a depth of more than 150 km what allows a first order statement of the required compensating horizontal stress needed to prevent gravitational collapse of the system. BGI (2012). The International

  16. Determining the 3-D structure and motion of objects using a scanning laser range sensor

    NASA Technical Reports Server (NTRS)

    Nandhakumar, N.; Smith, Philip W.

    1993-01-01

    In order for the EVAHR robot to autonomously track and grasp objects, its vision system must be able to determine the 3-D structure and motion of an object from a sequence of sensory images. This task is accomplished by the use of a laser radar range sensor which provides dense range maps of the scene. Unfortunately, the currently available laser radar range cameras use a sequential scanning approach which complicates image analysis. Although many algorithms have been developed for recognizing objects from range images, none are suited for use with single beam, scanning, time-of-flight sensors because all previous algorithms assume instantaneous acquisition of the entire image. This assumption is invalid since the EVAHR robot is equipped with a sequential scanning laser range sensor. If an object is moving while being imaged by the device, the apparent structure of the object can be significantly distorted due to the significant non-zero delay time between sampling each image pixel. If an estimate of the motion of the object can be determined, this distortion can be eliminated; but, this leads to the motion-structure paradox - most existing algorithms for 3-D motion estimation use the structure of objects to parameterize their motions. The goal of this research is to design a rigid-body motion recovery technique which overcomes this limitation. The method being developed is an iterative, linear, feature-based approach which uses the non-zero image acquisition time constraint to accurately recover the motion parameters from the distorted structure of the 3-D range maps. Once the motion parameters are determined, the structural distortion in the range images is corrected.

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

    NASA Astrophysics Data System (ADS)

    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

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

    NASA Astrophysics Data System (ADS)

    Challapalli, Adithya

    Cellular materials, often called lattice materials, are increasingly receiving attention for their ultralight structures with high specific strength, excellent impact absorption, acoustic insulation, heat dissipation media and compact heat exchangers. In alignment with emerging additive manufacturing (AM) technology, realization of the structural applications of the lattice materials appears to be becoming faster. Considering the direction dependent material properties of the products with AM, by directionally dependent printing resolution, effective moduli of lattice structures appear to be directionally dependent. In this paper, a constitutive model of a lattice structure, which is an octet-truss with a base material having an orthotropic material property considering AM is developed. In a case study, polyjet based 3D printing material having an orthotropic property with a 9% difference in the principal direction provides difference in the axial and shear moduli in the octet-truss by 2.3 and 4.6%. Experimental validation for the effective properties of a 3D printed octet-truss is done for uniaxial tension and compression test. The theoretical value based on the micro-buckling of truss member are used to estimate the failure strength. Modulus value appears a little overestimate compared with the experiment. Finite element (FE) simulations for uniaxial compression and tension of octettruss lattice materials are conducted. New effective properties for the octet-truss lattice structure are developed considering the observed behavior of the octet-truss structure under macroscopic compression and tension trough simulations.

  19. The "lnc" between 3D chromatin structure and X chromosome inactivation.

    PubMed

    Pandya-Jones, Amy; Plath, Kathrin

    2016-08-01

    The long non-coding RNA Xist directs a remarkable instance of developmentally regulated, epigenetic change known as X Chromosome Inactivation (XCI). By spreading in cis across the X chromosome from which it is expressed, Xist RNA facilitates the creation of a heritably silent, heterochromatic nuclear territory that displays a three-dimensional structure distinct from that of the active X chromosome. How Xist RNA attaches to and propagates across a chromosome and its influence over the three-dimensional (3D) structure of the inactive X are aspects of XCI that have remained largely unclear. Here, we discuss studies that have made significant contributions towards answering these open questions. PMID:27062886

  20. A 3D moisture-stress FEM analysis for time dependent problems in timber structures

    NASA Astrophysics Data System (ADS)

    Fortino, Stefania; Mirianon, Florian; Toratti, Tomi

    2009-11-01

    This paper presents a 3D moisture-stress numerical analysis for timber structures under variable humidity and load conditions. An orthotropic viscoelastic-mechanosorptive material model is specialized on the basis of previous models. Both the constitutive model and the equations needed to describe the moisture flow across the structure are implemented into user subroutines of the Abaqus finite element code and a coupled moisture-stress analysis is performed for several types of mechanical loads and moisture changes. The presented computational approach is validated by analyzing some wood tests described in the literature and comparing the computational results with the reported experimental data.

  1. The “lnc” between 3D Chromatin Structure and X Chromosome Inactivation

    PubMed Central

    Pandya-Jones, Amy; Plath, Kathrin

    2016-01-01

    The long non-coding RNA Xist directs a remarkable instance of developmentally regulated, epigenetic change known as X Chromosome Inactivation (XCI). By spreading in cis across the X chromosome from which it is expressed, Xist RNA facilities the creation of a heritably silent, heterochromatic nuclear territory that displays a three-dimensional structure distinct from that of the active X chromosome. How Xist RNA attaches to and propagates across a chromosome and its influence over the three-dimensional (3D) structure of the inactive X are aspects of XCI that have remained largely unclear. Here, we discuss studies that have made significant contributions towards answering these open questions. PMID:27062886

  2. Prognostic breast cancer signature identified from 3D culture model accurately predicts clinical outcome across independent datasets

    SciTech Connect

    Martin, Katherine J.; Patrick, Denis R.; Bissell, Mina J.; Fournier, Marcia V.

    2008-10-20

    One of the major tenets in breast cancer research is that early detection is vital for patient survival by increasing treatment options. To that end, we have previously used a novel unsupervised approach to identify a set of genes whose expression predicts prognosis of breast cancer patients. The predictive genes were selected in a well-defined three dimensional (3D) cell culture model of non-malignant human mammary epithelial cell morphogenesis as down-regulated during breast epithelial cell acinar formation and cell cycle arrest. Here we examine the ability of this gene signature (3D-signature) to predict prognosis in three independent breast cancer microarray datasets having 295, 286, and 118 samples, respectively. Our results show that the 3D-signature accurately predicts prognosis in three unrelated patient datasets. At 10 years, the probability of positive outcome was 52, 51, and 47 percent in the group with a poor-prognosis signature and 91, 75, and 71 percent in the group with a good-prognosis signature for the three datasets, respectively (Kaplan-Meier survival analysis, p<0.05). Hazard ratios for poor outcome were 5.5 (95% CI 3.0 to 12.2, p<0.0001), 2.4 (95% CI 1.6 to 3.6, p<0.0001) and 1.9 (95% CI 1.1 to 3.2, p = 0.016) and remained significant for the two larger datasets when corrected for estrogen receptor (ER) status. Hence the 3D-signature accurately predicts breast cancer outcome in both ER-positive and ER-negative tumors, though individual genes differed in their prognostic ability in the two subtypes. Genes that were prognostic in ER+ patients are AURKA, CEP55, RRM2, EPHA2, FGFBP1, and VRK1, while genes prognostic in ER patients include ACTB, FOXM1 and SERPINE2 (Kaplan-Meier p<0.05). Multivariable Cox regression analysis in the largest dataset showed that the 3D-signature was a strong independent factor in predicting breast cancer outcome. The 3D-signature accurately predicts breast cancer outcome across multiple datasets and holds prognostic

  3. ALE3D Model Predictions and Materials Characterization for the Cookoff Response of PBXN-109

    SciTech Connect

    McClelland, M A; Maienschein, J L; Nichols, A L; Wardell, J F; Atwood, A I; Curran, P O

    2002-03-19

    ALE3D simulations are presented for the thermal explosion of PBXN-109 (RDX, AI, HTPB, DOA) in support of an effort by the U. S. Navy and Department of Energy (DOE) to validate computational models. The U.S. Navy is performing benchmark tests for the slow cookoff of PBXN-109 in a sealed tube. Candidate models are being tested using the ALE3D code, which can simulate the coupled thermal, mechanical, and chemical behavior during heating, ignition, and explosion. The strength behavior of the solid constituents is represented by a Steinberg-Guinan model while polynomial and gamma-law expressions are used for the Equation Of State (EOS) for the solid and gas species, respectively. A void model is employed to represent the air in gaps. ALE3D model 'parameters are specified using measurements of thermal and mechanical properties including thermal expansion, heat capacity, shear modulus, and bulk modulus. A standard three-step chemical kinetics model is used during the thermal ramp, and a pressure-dependent burn front model is employed during the rapid expansion. Parameters for the three-step kinetics model are specified using measurements of the One-Dimensional-Time-to-Explosion (ODTX), while measurements for burn rate of pristine and thermally damaged material are employed to determine parameters in the burn front model. Results are given for calculations in which heating, ignition, and explosion are modeled in a single simulation. We compare model results to measurements for the cookoff temperature and tube wall strain.

  4. Modeling, Prediction, and Reduction of 3D Crosstalk in Circular Polarized Stereoscopic LCDs.

    PubMed

    Zeng, Menglin; Robinson, Alan E; Nguyen, Truong Q

    2015-12-01

    Crosstalk, which is the incomplete separation between the left and right views in 3D displays, induces ghosting and causes difficulty of the eyes to fuse the stereo image for depth perception. Circularly polarized (CP) liquid crystal display (LCD) is one of the main-stream consumer 3D displays with the prospering of 3D movies and gamings. The polarizing system including the patterned retarder is one of the major causes of crosstalk in CP LCD. The contributions of this paper are the modeling of the polarizing system of CP LCD, and a crosstalk reduction method that efficiently cancels crosstalk and preserves image contrast. For the modeling, the practical orientation of the polarized glasses (PG) is considered. In addition, this paper calculates the rotation of the light-propagation coordinate for the Stokes vector as light propagates from LCD to PG, and this calculation is missing in the previous works when applying Mueller calculus. The proposed crosstalk reduction method is formulated as a linear programming problem, which can be easily solved. In addition, we propose excluding the highly textured areas in the input images to further preserve image contrast in crosstalk reduction. PMID:26259220

  5. 3D Geo-Structures Visualization Education Project (3dgeostructuresvis.ucdavis.edu)

    NASA Astrophysics Data System (ADS)

    Billen, M. I.

    2014-12-01

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

  6. Simulating Seismic Wave Propagation in 3-D Structure: A Case Study For Istanbul City

    NASA Astrophysics Data System (ADS)

    Yelkenci, Seda; Aktar, Mustafa

    2013-04-01

    Investigation of the wave propagation around the Marmara Sea, in particular for the city of Istanbul is critical because this target area is identified as one of the megacities with the highest seismic risk in the world. This study makes an attempt for creating an integrated 3D seismic/geologic model and precise understanding of 3-D wave propagation in the city of Istanbul. The approach is based on generating synthetic seismograms using realistic velocity structures as well as accurate location, focal mechanism and source parameters of reference earthquakes. The modarate size reference earthquakes occured in the Marmara Sea and were recorded by the National Seismic Network of Turkey as well as the network of Istanbul Early Warning and Rapid Response System. The seismograms are simulated by means of a 3-D finite difference method operated on parallel processing environment. In the content of creating a robust velocity model; 1D velocity models which are derived fom previous crustal studies of Marmara region such as refraction seismic and receiver functions have been conducted firstly for depths greater than 1km. Velocity structure in shallower part of the study region is then derived from recent geophysical and geotechnical surveys. To construct 3-D model from the obtained 1-D model data, a variety of interpolation methods are considered. According to the observations on amplitude and arrival time based on comparison of simulated seismograms, the considered velocity model is refined the way that S delay times are compensated. Another important task of this work is an application of the finite difference method to estimate three-dimensional seismic responses for a specified basin structure including soft sediments with low shear velocities in respect of the surrounded area in the Asian part of Istanbul. The analysis performed both in the time and frequency domain, helps in understanding of the comprehensive wave propagation characteristics and the distribution of

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-05-01

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

  9. The internal geometry of salt structures - A first look using 3D seismic data from the Zechstein of the Netherlands

    NASA Astrophysics Data System (ADS)

    Van Gent, Heijn; Urai, Janos L.; de Keijzer, Martin

    2011-03-01

    We present a first look at the large-scale, complexly folded and faulted internal structure of Zechstein salt bodies in NW Europe using 3D reflection seismic reflection data from two surveys on the Groningen High and the Cleaver Bank High. We focus on a relatively brittle, folded and boudinaged, claystone-carbonate-anhydrite layer (the Z3 stringer) enclosed in ductile salt. A first classification of the structures is presented and compared with observations from salt mines and analogue and numerical models. Z3 stringers not only are reservoirs for hydrocarbons but can also present a serious drilling problem in some areas. Results of this study could provide the basis for better prediction of zones of drilling problems. More generally, the techniques presented here can be used to predict the internal structure of salt bodies, to estimate the geometry of economic deposits of all kinds and locate zones suitable for storage caverns. Structures observed include an extensive network of zones with increased thickness of the stringer. These we infer to have formed by early diagenesis, karstification, gravitational sliding and associated local sedimentation. Later, this template was deformed into large-scale folds and boudins during salt tectonics. Salt flow was rarely plane strain, producing complex fold and boudin geometries. Deformation was further complicated by the stronger zones of increased thickness, which led to strongly non-cylindrical structures. We present some indications that the thicker zones also influence the locations of later suprasalt structures, suggesting a feedback between the early internal evolution of this salt giant and later salt tectonics. This study opens the possibility to study the internal structure of the Zechstein and other salt giants in 3D using this technique, exposing a previously poorly known structure which is comparable in size and complexity to the internal parts of some orogens.

  10. Color influence on accuracy of 3D scanners based on structured light

    NASA Astrophysics Data System (ADS)

    Voisin, Sophie; Page, David L.; Foufou, Sebti; Truchetet, Frédéric; Abidi, Mongi A.

    2006-02-01

    The characterization of commercial 3D scanners allows acquiring precise and useful data. The accuracy of range and, more recently, color for 3D scanners is usually studied separately, but when the 3D scanner is based on structured light with a color coding pattern, color influence on range accuracy should be investigated. The commercial product that we have tested has the particularity that it can acquire data under ambient light instead of a controlled environment as it is with most available scanners. Therefore, based on related work in the literature and on experiments we have done on a variety of standard illuminants, we have designed an interesting setup to control illuminant interference. Basically, the setup consists of acquiring the well-known Macbeth ColorChecker under a controlled environment and also ambient daylight. The results have shown variations with respect to the color. We have performed several statistical studies to show how the range results evolve with respect to the RGB and the HSV channels. In addition, a systematic noise error has also been identified. This noise depends on the object color. A subset of colors shows strong noise errors while other colors have minimal or even no systematic error under the same illuminant.

  11. PACS-based interface for 3D anatomical structure visualization and surgical planning

    NASA Astrophysics Data System (ADS)

    Koehl, Christophe; Soler, Luc; Marescaux, Jacques

    2002-05-01

    The interpretation of radiological image is routine but it remains a rather difficult task for physicians. It requires complex mental processes, that permit translation from 2D slices into 3D localization and volume determination of visible diseases. An easier and more extensive visualization and exploitation of medical images can be reached through the use of computer-based systems that provide real help from patient admission to post-operative followup. In this way, we have developed a 3D visualization interface linked to a PACS database that allows manipulation and interaction on virtual organs delineated from CT-scan or MRI. This software provides the 3D real-time surface rendering of anatomical structures, an accurate evaluation of volumes and distances and the improvement of radiological image analysis and exam annotation through a negatoscope tool. It also provides a tool for surgical planning allowing the positioning of an interactive laparoscopic instrument and the organ resection. The software system could revolutionize the field of computerized imaging technology. Indeed, it provides a handy and portable tool for pre-operative and intra-operative analysis of anatomy and pathology in various medical fields. This constitutes the first step of the future development of augmented reality and surgical simulation systems.

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

    NASA Technical Reports Server (NTRS)

    Platnick, Steven; Zinner, Tobias; Ackerman, S.

    2008-01-01

    Remote sensing of cloud particle size with passive sensors like MODIS is an important tool for cloud microphysical studies. As a measure of the radiatively relevant droplet size, effective radius can be retrieved with different combinations of visible through shortwave infrared channels. MODIS observations sometimes show significantly larger effective radii in marine boundary layer cloud fields derived from the 1.6 and 2.1 pm channel observations than for 3.7 pm retrievals. Possible explanations range from 3D radiative transport effects and sub-pixel cloud inhomogeneity to the impact of drizzle formation on the droplet distribution. To investigate the potential influence of these factors, we use LES boundary layer cloud simulations in combination with 3D Monte Carlo simulations of MODIS observations. LES simulations of warm cloud spectral microphysics for cases of marine stratus and broken stratocumulus, each for two different values of cloud condensation nuclei density, produce cloud structures comprising droplet size distributions with and without drizzle size drops. In this study, synthetic MODIS observations generated from 3D radiative transport simulations that consider the full droplet size distribution will be generated for each scene. The operational MODIS effective radius retrievals will then be applied to the simulated reflectances and the results compared with the LES microphysics.

  13. Integration of 3D Structure from Disparity into Biological Motion Perception Independent of Depth Awareness

    PubMed Central

    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. PMID:24586622

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

    NASA Astrophysics Data System (ADS)

    Duelis Viana, Camila; Endlein, Arthur; Ademar da Cruz Campanha, Ginaldo; Henrique Grohmann, Carlos

    2016-05-01

    The acquisition of geological attitudes on rock cuts using traditional field compass survey can be a time consuming, dangerous, or even impossible task depending on the conditions and location of outcrops. The importance of this type of data in rock-mass classifications and structural geology has led to the development of new techniques, in which the application of photogrammetric 3D digital models has had an increasing use. In this paper we present two algorithms for extraction of attitudes of geological discontinuities from virtual outcrop models: ply2atti and scanline, implemented with the Python programming language. The ply2atti algorithm allows for the virtual sampling of planar discontinuities appearing on the 3D model as individual exposed surfaces, while the scanline algorithm allows the sampling of discontinuities (surfaces and traces) along a virtual scanline. Application to digital models of a simplified test setup and a rock cut demonstrated a good correlation between the surveys undertaken using traditional field compass reading and virtual sampling on 3D digital models.

  15. Tensor decomposition in electronic structure calculations on 3D Cartesian grids

    SciTech Connect

    Khoromskij, B.N. Khoromskaia, V.; Chinnamsetty, S.R.; Flad, H.-J.

    2009-09-01

    In this paper, we investigate a novel approach based on the combination of Tucker-type and canonical tensor decomposition techniques for the efficient numerical approximation of functions and operators in electronic structure calculations. In particular, we study applicability of tensor approximations for the numerical solution of Hartree-Fock and Kohn-Sham equations on 3D Cartesian grids. We show that the orthogonal Tucker-type tensor approximation of electron density and Hartree potential of simple molecules leads to low tensor rank representations. This enables an efficient tensor-product convolution scheme for the computation of the Hartree potential using a collocation-type approximation via piecewise constant basis functions on a uniform nxnxn grid. Combined with the Richardson extrapolation, our approach exhibits O(h{sup 3}) convergence in the grid-size h=O(n{sup -1}). Moreover, this requires O(3rn+r{sup 3}) storage, where r denotes the Tucker rank of the electron density with r=O(logn), almost uniformly in n. For example, calculations of the Coulomb matrix and the Hartree-Fock energy for the CH{sub 4} molecule, with a pseudopotential on the C atom, achieved accuracies of the order of 10{sup -6} hartree with a grid-size n of several hundreds. Since the tensor-product convolution in 3D is performed via 1D convolution transforms, our scheme markedly outperforms the 3D-FFT in both the computing time and storage requirements.

  16. Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure.

    PubMed

    Tokheim, Collin; Bhattacharya, Rohit; Niknafs, Noushin; Gygax, Derek M; Kim, Rick; Ryan, Michael; Masica, David L; Karchin, Rachel

    2016-07-01

    The impact of somatic missense mutation on cancer etiology and progression is often difficult to interpret. One common approach for assessing the contribution of missense mutations in carcinogenesis is to identify genes mutated with statistically nonrandom frequencies. Even given the large number of sequenced cancer samples currently available, this approach remains underpowered to detect drivers, particularly in less studied cancer types. Alternative statistical and bioinformatic approaches are needed. One approach to increase power is to focus on localized regions of increased missense mutation density or hotspot regions, rather than a whole gene or protein domain. Detecting missense mutation hotspot regions in three-dimensional (3D) protein structure may also be beneficial because linear sequence alone does not fully describe the biologically relevant organization of codons. Here, we present a novel and statistically rigorous algorithm for detecting missense mutation hotspot regions in 3D protein structures. We analyzed approximately 3 × 10(5) mutations from The Cancer Genome Atlas (TCGA) and identified 216 tumor-type-specific hotspot regions. In addition to experimentally determined protein structures, we considered high-quality structural models, which increase genomic coverage from approximately 5,000 to more than 15,000 genes. We provide new evidence that 3D mutation analysis has unique advantages. It enables discovery of hotspot regions in many more genes than previously shown and increases sensitivity to hotspot regions in tumor suppressor genes (TSG). Although hotspot regions have long been known to exist in both TSGs and oncogenes, we provide the first report that they have different characteristic properties in the two types of driver genes. We show how cancer researchers can use our results to link 3D protein structure and the biologic functions of missense mutations in cancer, and to generate testable hypotheses about driver mechanisms. Our results

  17. Influence of pre-existing salt structures in the 3D pattern of multilayer folding

    NASA Astrophysics Data System (ADS)

    Fernandez, Naiara; Kaus, Boris J. P.; Collignon, Marine

    2014-05-01

    Upward movement of the Precambrian Hormuz salt in the Fars region of the Zagros is supposed to have started as early as Late Cretaceous. The Late Cretaceous - Tertiary deformation events that lead to the folding of the sedimentary cover in this area would have therefore, enhance the upward salt movement by squeezing the pre-existing salt structures. How these salt diapirs evolve under such compressive events has already been previously addressed using analogue models (e.g. Callot et al. 2012). The same authors observed that pre-existing salt structures control the size and geometry of folds in sandbox models. Our previous work has shown that 3D folding instability gives rise to a wide variety of fold shapes (e.g. from dome shape structures to long en echelon or straight anticlines), resulting of the interactions between growing fold segments. The three dimensional growth of these folds, the wavelength and the lateral propagation, is itself controlled by physical parameters. However, the existence of initial weak zones such as pre-existing salt plugs within the sedimentary cover can affect the development of such folds by localizing part of the deformation. In this study we have used numerical modeling to investigate how the fold pattern in 3D multilayer folding is affected by pre-existing salt structures. High-resolution 3D folding simulations (with and without pre-existing salt structures) were performed with the parallel code LaMEM. Cylindrically shaped diapirs with different diameters and heights have been added to a multilayer folding setup. The use of a finite element based landscape evolution model (both erosion and sedimentation) allows for initially buried salt diapirs to be exposed at the surface during folding evolution. Acknowledgements Funding was provided by the European Research Council under the European Community's Seventh Framework program (FP7/2007-2013) ERC Grant agreement #258830. 3D simulations are performed in the IBM Blue Gene/Q JUQUEEN

  18. Experimental Investigation of the Near Wall Flow Structure of a Low Reynolds Number 3-D Turbulent Boundary Layer

    NASA Technical Reports Server (NTRS)

    Fleming, J. L.; Simpson, R. L.

    1997-01-01

    Laser Doppler velocimetry (LDV) measurements and hydrogen bubble flow visualization techniques were used to examine the near-wall flow structure of 2D and 3D turbulent boundary layers (TBLs) over a range of low Reynolds numbers. The goals of this research were (1) an increased understanding of the flow physics in the near wall region of turbulent boundary layers,(2) to observe and quantify differences between 2D and 3D TBL flow structures, and (3) to document Reynolds number effects for 3D TBLs. The LDV data have provided results detailing the turbulence structure of the 2D and 3D TBLs. These results include mean Reynolds stress distributions, flow skewing results, and U and V spectra. Effects of Reynolds number for the 3D flow were also examined. Comparison to results with the same 3D flow geometry but at a significantly higher Reynolds number provided unique insight into the structure of 3D TBLs. While the 3D mean and fluctuating velocities were found to be highly dependent on Reynolds number, a previously defined shear stress parameter was discovered to be invariant with Reynolds number. The hydrogen bubble technique was used as a flow visualization tool to examine the near-wall flow structure of 2D and 3D TBLs. Both the quantitative and qualitative results displayed larger turbulent fluctuations with more highly concentrated vorticity regions for the 2D flow.

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

    SciTech Connect

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

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  1. The 3D geological model of the Eastern Romania tectonics and structure

    NASA Astrophysics Data System (ADS)

    Necula, Nicusor; Sorin Baciu, Dorin; Niculita, Mihai; Dumitriu, Tony-Cristian

    2016-04-01

    3D geologic modelling is a modern tool which allow the conceptualization of geologic relations in an interactive environment, strengthening the ability to understand and present tectonic and structural geologic models. We integrated the data available in the literature (wells, maps, cross-sections) for the geological structure of the Eastern Romania, comprising the Eastern Carpathians Orogen and its foreland. The subducting East European plate generated the Eastern Carphatians thrusts. Under the Eastern Carpathians, beside East European plate, the Tornquist-Teysseire zone is caught. East European Craton (Proterozoic), Scythian Platform (Paleozoic), North Dobrogean Orogen (Paleozoic) and Moesian Platform (Paleozoic), all neighbor Tornquist-Teysseire zone (Paleozoic), playing the role of foreland for the Eastern Carpathian Orogen. The Eastern Carphatians Orogen has two flysch belts, the Inner Carpathian called Dacides formed in Cretacic deformations and the Outer Carpathian called Moldavides and formed in Late Badenian to Sarmatian deformations. The modelling was performed in Midland Valley's Move software. The boundaries of all the structural units presented above were modelled, together with the faults which are represented on the various osurces used. The created 3D geological model is seen as a tool to better understand and represent the tectonic and structural model of the Eastern ROmania and will also allow a better quantification of the relations between geology and landforms in Eastern Romania.

  2. 3-D seismic improves structural mapping of a gas storage reservoir (Paris basin)

    SciTech Connect

    Huguet, F. ); Pinson, C. )

    1993-09-01

    In the Paris basin, anticlinal structures with closure of no more than 80 m and surface area of a few km[sup 2] are used for underground gas storage. At Soings-en-Sologne, a three-dimensional (3-D) survey (13 km[sup 2]) was carried out over such a structure to establish its exact geometry and to detail its fault network. Various reflectors were picked automatically on the migrated data: the top of the Kimmeridgian, the top of the Bathoinian and the base of the Hettangian close to the top of the reservoir. The isochron maps were converted into depth using data from 12 wells. Horizon attributes (amplitude, dip, and azimuth) were used to reconstruct the fault's pattern with much greater accuracy than that supplied by interpretation from previous two-dimensional seismic. The Triassic and the Jurassic are affected by two systems of conjugate faults (N10-N110, inherited from the Hercynian basement and N30-N120). Alternating clay and limestone are the cause of numerous structural disharmonies, particularly on both sides of the Bathonian. Ridges associated with N30-N120 faults suggest compressive movements contemporaneous with the tertiary events. The northern structure in Soings-en-Sologne thus appear to be the result of polyphased tectonics. Its closure (25 m), which is associated either with dips or faults, is described in detail by 3-D seismic, permitting more accurate forecast of the volume available for gas storage.

  3. Error analysis for creating 3D face templates based on cylindrical quad-tree structure

    NASA Astrophysics Data System (ADS)

    Gutfeter, Weronika

    2015-09-01

    Development of new biometric algorithms is parallel to advances in technology of sensing devices. Some of the limitations of the current face recognition systems may be eliminated by integrating 3D sensors into these systems. Depth sensing devices can capture a spatial structure of the face in addition to the texture and color. This kind of data is yet usually very voluminous and requires large amount of computer resources for being processed (face scans obtained with typical depth cameras contain more than 150 000 points per face). That is why defining efficient data structures for processing spatial images is crucial for further development of 3D face recognition methods. The concept described in this work fulfills the aforementioned demands. Modification of the quad-tree structure was chosen because it can be easily transformed into less dimensional data structures and maintains spatial relations between data points. We are able to interpret data stored in the tree as a pyramid of features which allow us to analyze face images using coarse-to-fine strategy, often exploited in biometric recognition systems.

  4. Comparative 3D Genome Structure Analysis of the Fission and the Budding Yeast

    PubMed Central

    Gong, Ke; Tjong, Harianto; Zhou, Xianghong Jasmine; Alber, Frank

    2015-01-01

    We studied the 3D structural organization of the fission yeast genome, which emerges from the tethering of heterochromatic regions in otherwise randomly configured chromosomes represented as flexible polymer chains in an nuclear environment. This model is sufficient to explain in a statistical manner many experimentally determined distinctive features of the fission yeast genome, including chromatin interaction patterns from Hi-C experiments and the co-locations of functionally related and co-expressed genes, such as genes expressed by Pol-III. Our findings demonstrate that some previously described structure-function correlations can be explained as a consequence of random chromatin collisions driven by a few geometric constraints (mainly due to centromere-SPB and telomere-NE tethering) combined with the specific gene locations in the chromosome sequence. We also performed a comparative analysis between the fission and budding yeast genome structures, for which we previously detected a similar organizing principle. However, due to the different chromosome sizes and numbers, substantial differences are observed in the 3D structural genome organization between the two species, most notably in the nuclear locations of orthologous genes, and the extent of nuclear territories for genes and chromosomes. However, despite those differences, remarkably, functional similarities are maintained, which is evident when comparing spatial clustering of functionally related genes in both yeasts. Functionally related genes show a similar spatial clustering behavior in both yeasts, even though their nuclear locations are largely different between the yeast species. PMID:25799503

  5. Linear-Time Protein 3-D Structure Searching with Insertions and Deletions

    NASA Astrophysics Data System (ADS)

    Shibuya, Tetsuo; Jansson, Jesper; Sadakane, Kunihiko

    It becomes more and more important to search for similar structures from molecular 3-D structure databases in the structural biology of the post genomic era. Two molecules are said to be similar if the RMSD (root mean square deviation) of the two molecules is less than or equal to some given constant bound. In this paper, we consider an important, fundamental problem of finding all the similar substructures from 3-D structure databases of chain molecules (such as proteins), with consideration of indels (i.e., insertions and deletions). The problem has been believed to be very difficult, but its computational difficulty has not been well known. In this paper, we first show that the same problem in arbitrary dimension is NP-hard. Moreover, we also propose a new algorithm that dramatically improves the average-case time complexity for the problem, in case the number of indels k is bounded by some constant. Our algorithm solves the above problem in average O(N) time, while the time complexity of the best known algorithm was O(Nm k + 1), for a query of size m and a database of size N.

  6. MHD Modeling in Complex 3D Geometries: Towards Predictive Simulation of SIHI Current Drive

    NASA Astrophysics Data System (ADS)

    Hansen, Christopher James

    The HIT-SI experiment studies Steady Inductive Helicity Injection (SIHI) for the purpose of forming and sustaining a spheromak plasma. A spheromak is formed in a nearly axisymmetric flux conserver, with a bow tie cross section, by means of two semi-toroidal injectors. The plasma-facing surfaces of the device, which are made of copper for its low resistivity, are covered in an insulating coating in order to operate in a purely inductive manner. Following formation, the spheromak flux and current are increased during a quiescent period marked by a decrease in the global mode activity. A proposed mechanism, Imposed Dynamo Current Drive (IDCD), is expected to be responsible for this phase of quiescent current drive. Due to the geometric complexity of the experiment, previous numerical modeling efforts have used a simplified geometry that excludes the injector volumes from the simulated domain. The effect of helicity injection is then modeled by boundary conditions on this reduced plasma volume. The work presented here has explored and developed more complete computational models of the HIT-SI device. This work is separated into 3 distinct but complementary areas: 1) Development of a 3D MHD equilibrium code that can incorporate the non-axisymmetric injector fields present in HIT-SI and investigation of equilibria of interest during spheromak sustainment. 2) A 2D axisymmetric MHD equilibrium code that was used to explore reduced order models for mean-field evolution using equations derived from IDCD theory including coupling to 3D equilibria. 3) A 3D time-dependent non-linear MHD code that is capable of modeling the entire plasma volume including dynamics within the injectors. Although HIT-SI was the motivation for, and experiment studied in this research, the tools and methods developed are general --- allowing their application to a broad range of magnetic confinement experiments. These tools constitute a significant advance for modeling plasma dynamics in devices with

  7. Prediction of car cabin environment by means of 1D and 3D cabin model

    NASA Astrophysics Data System (ADS)

    Fišer, J.; Pokorný, J.; Jícha, M.

    2012-04-01

    Thermal comfort and also reduction of energy requirements of air-conditioning system in vehicle cabins are currently very intensively investigated and up-to-date issues. The article deals with two approaches of modelling of car cabin environment; the first model was created in simulation language Modelica (typical 1D approach without cabin geometry) and the second one was created in specialized software Theseus-FE (3D approach with cabin geometry). Performance and capabilities of this tools are demonstrated on the example of the car cabin and the results from simulations are compared with the results from the real car cabin climate chamber measurements.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Kalnins, Ernie G.; Miller, Willard, Jr.

    2012-06-01

    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 a! n infinite class of classical extended Kepler-Coulomb 3- and 4-parameter systems indexed by a pair of rational numbers (k1,k2) and reducing to the usual systems when k1=k2=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.

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

    NASA Astrophysics Data System (ADS)

    Sargent, Dusty; Chen, Chao-I.; Wang, Yuan-Fang

    2010-02-01

    The paper reports a fully-automated, cross-modality sensor data registration scheme between video and magnetic tracker data. This registration scheme is intended for use in computerized imaging systems to model the appearance, structure, and dimension of human anatomy in three dimensions (3D) from endoscopic videos, particularly colonoscopic videos, for cancer research and clinical practices. The proposed cross-modality calibration procedure operates this way: Before a colonoscopic procedure, the surgeon inserts a magnetic tracker into the working channel of the endoscope or otherwise fixes the tracker's position on the scope. The surgeon then maneuvers the scope-tracker assembly to view a checkerboard calibration pattern from a few different viewpoints for a few seconds. The calibration procedure is then completed, and the relative pose (translation and rotation) between the reference frames of the magnetic tracker and the scope is determined. During the colonoscopic procedure, the readings from the magnetic tracker are used to automatically deduce the pose (both position and orientation) of the scope's reference frame over time, without complicated image analysis. Knowing the scope movement over time then allows us to infer the 3D appearance and structure of the organs and tissues in the scene. While there are other well-established mechanisms for inferring the movement of the camera (scope) from images, they are often sensitive to mistakes in image analysis, error accumulation, and structure deformation. The proposed method using a magnetic tracker to establish the camera motion parameters thus provides a robust and efficient alternative for 3D model construction. Furthermore, the calibration procedure does not require special training nor use expensive calibration equipment (except for a camera calibration pattern-a checkerboard pattern-that can be printed on any laser or inkjet printer).

  11. 3D velocity structure of upper crust beneath NW Bohemia/Vogtland

    NASA Astrophysics Data System (ADS)

    Javad Fallahi, Mohammad; Mousavi, Sima; Korn, Michael; Sens-Schönfelder, Christoph; Bauer, Klaus; Rößler, Dirk

    2013-04-01

    The 3D structure of the upper crust beneath west Bohemia/Vogtland region, analyzed with travel time tomography and ambient noise surface wave tomography using existing data. This region is characterized by a series of phenomena like occurrence of repeated earthquake swarms, surface exhalation, CO2 enriched fluids, mofettes, mineral springs and enhanced heat flow, and has been proposed as an excellent location for an ICDP drilling project targeted to a better understanding of the crust in an active magmatic environment. We performed a 3D tomography using P-and S-wave travel times of local earthquakes and explosions. The data set were taken from permanent and temporary seismic networks in Germany and Czech Republic from 2000 to 2010, as well as active seismic experiments like Celebration 2000 and quarry blasts. After picking P and S wave arrival times, 399 events which were recorded by 9 or more stations and azimuthal gap<160° were selected for inversion. A simultaneous inversion of P and S wave 1D velocity models together with relocations of hypocenters and station corrections was performed. The obtained minimum 1D velocity model was used as starting model for the 3D Vp and Vp/Vs velocity models. P and S wave travel time tomography employs damped least-square method and ray tracing by pseudo-bending algorithm. For model parametrization different cell node spacings have been tested to evaluate the resolution in each node. Synthetic checkerboard tests have been done to check the structural resolution. Then Vp and Vp/Vs in the preferred 3D grid model have been determined. Earthquakes locations in iteration process change till the hypocenter adjustments and travel time residuals become smaller than the defined threshold criteria. Finally the analysis of the resolution depicts the well resolved features for interpretation. We observed lower Vp/Vs ratio in depth of 5-10 km close to the foci of earthquake swarms and higher Vp/Vs ratio is observed in Saxoturingian zone and

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

    NASA Astrophysics Data System (ADS)

    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 <500 nm (<0.5 microns). It is the first 180 kV nanofocus® computed tomography system in the world which is tailored specifically to the highest-resolution applications in the fields of material science, micro electronics, geology and biology. Therefore it is particularly suitable for nanoCT-examinations e.g. of synthetic materials, metals, ceramics, composite materials, mineral and organic samples. There are a few physical effects influencing the CT quality, such as beam-hardening within the sample or ring-artefacts, which can not be completely avoided. To optimize the quality of high resolution 3D volumes, the nanotom® includes a variety of effective software tools to reduce ring-artefacts and correct beam hardenings or drift effects which occurred during data acquisition. The resulting CT volume data set can be displayed in various ways, for example by virtual slicing and sectional views in any direction of the volume. By the fact that this requires only a mouse click, this technique will substitute destructive mechanical slicing and cutting in many applications. The initial CT results obtained with the

  13. 3D structural model of the North Alpine Foreland Basin, Bavarian Part

    NASA Astrophysics Data System (ADS)

    Przybycin, Anna M.; Scheck-Wenderoth, Magdalena; Schneider, Michael

    2013-04-01

    The continental collision of Europe and Africa leads to the rise of the European Alps, which gave way to the formation of the North Alpine Foreland Basin, also referred to as the Molasse Basin, since the Tertiary. This typically wedge formed "foredeep" basin is filled with predominantly clastic sediments originating from erosional processes of the Alps which overly a southward dipping Mesozoic and Paleozoic succession. With our project we want to contribute to the understanding of the structure and subsequently of the thermal configuration of the Molasse Basin and its underlying deposits on a basin wide scale. We constructed a 3D structural model of the basin down to the crust-mantle-boundary, beginning with the Bavarian part. Therefore we used an approach of already existing local to midscale 2D and 3D structural models (e.g. Lüschen et al. 2006) as well as surface maps, seismic, well and gravity data. This 3D structural model resolves 5 sedimentary layers of the Mesozoic, including the geothermally utilized carbonate Malm aquifer (e.g. Birner et al. 2011), as well as the combined Paleozoic basement. Assuming isostatic equilibrium of the system a lithosphere-asthenosphere-boundary (LAB) has been calculated and compared to other published LABs of the region. Subsequently the model has been further constrained by 3D gravity modeling. The outcomes show that Cretaceous sediments are restricted to a small region in the central to eastern model area and are mostly overlain by the Tertiary Molasse sediments. The Triassic sediments occur in the northern and western part of the model area and do not continue far under the Molasse basin proper, while the Jurassic can be tracked as far south as beneath the Alps. The evaluation of the gravity indicates that the crystalline crust consists of a lighter upper crust and a denser lower crust. Our final LAB is shallowest under the Triassic subbasin, descending below the Bohemian Massif and the Molasse Basin proper and rising again

  14. Monte Carlo generators for studies of the 3D structure of the nucleon

    SciTech Connect

    Avakian, Harut; D'Alesio, U.; Murgia, F.

    2015-01-23

    In this study, extraction of transverse momentum and space distributions of partons from measurements of spin and azimuthal asymmetries requires development of a self consistent analysis framework, accounting for evolution effects, and allowing control of systematic uncertainties due to variations of input parameters and models. Development of realistic Monte-Carlo generators, accounting for TMD evolution effects, spin-orbit and quark-gluon correlations will be crucial for future studies of quark-gluon dynamics in general and 3D structure of the nucleon in particular.

  15. Assessment of Damage Detection in Composite Structures Using 3D Vibrometry

    NASA Astrophysics Data System (ADS)

    Grigg, S.; Pearson, M.; Marks, R.; Featherston, C.; Pullin, R.

    2015-07-01

    Carbon fibre reinforced polymers (CFRP) have been used significantly more in recent years due to their increased specific strength over aluminium structures. One major area in which their use has grown is the aerospace industry where many now use CFRP in their construction. One major problem with CFRP's is their low resistance to impacts. Structural health monitoring (SHM) aims to continually monitor a structure throughout its entire life and can allow aircraft owners to identify impact damage as it occurs. This means that it can be repaired prior to growth, saving weight with the repair and the time that aircraft is grounded. Two areas of SHM being researched are Acoustic Emission (AE) monitoring and AcoustoUltrasonics (AU) both based on an understanding of the propagation of ultrasonic waves. 3D Scanning laser vibrometry was used to monitor the propagation of AU waves with the aim of gaining a better understanding their interaction with delamination in carbon fibre reinforced polymers. Three frequencies were exited with a PZT transducer and the received signal analysed by a cross correlation method. The results from this and the vibrometer scans revealed 100 kHz as the most effective propagating frequency of the three. A high resolution scan was then conducted at this frequency where it could be seen that only the out of plane component of the wave interacted with the damage, in particular the A0 mode. A 3D Fast Fourier Transform was then plotted, which identified the most effective frequency as 160 kHz.

  16. 3D X-rays application for precision measurement of the cell structure of extruded polystyrene

    NASA Astrophysics Data System (ADS)

    Lim, J. Y.; Kim, K. Y.; Shin, H. S.; Yeom, S.; Lee, S. E.

    2015-12-01

    While the thermal performance of existing insulation materials have been determined by blister gases, the thermal performance of future insulation materials will be dependent on the cell size and independent foam content as we use eco-friendly blister gases with a higher thermal conductivity. However, with the current technology we are only able to guess the whole cell size and independent foam content through SEM applied 2D fragmentary scanning but are still far from the level of accurate cell structure data extraction. Under this situation, we utilized X-ray CT scanned 3D images to identify and shape the cell structure and proposed a method of inferring the whole distribution and independent foam content as accurately as possible. According to X-ray CT scanning images and SEM images, the shape was similar but according to tracer applied CT scanning images, the cell size distribution was 380∼400 pm within the range of the general insulation diameter distribution which had the highest reliability. As for extrusion foaming polystyrene, we need additional image processing to identify the independent foam content as its density is too low. So, it is recommended to raise the 3D cell structure completeness of XPS by improving the scanning accuracy.

  17. Structural description and combined 3D display for superior analysis of cerebral vascularity from MRA

    NASA Astrophysics Data System (ADS)

    Szekely, Gabor; Koller, Thomas; Kikinis, Ron; Gerig, Guido

    1994-09-01

    Medical image analysis has to support the clinicians ability to identify, manipulate and quantify anatomical structures. On scalar 2D image data, a human observer is often superior to computer assisted analysis, but the interpretation of vector- valued data or data combined from different modalities, especially in 3D, can benefit from computer assistance. The problem of how to convey the complex information to the clinician is often tackled by providing colored multimodality renderings. We propose to go a step beyond by supplying a suitable modelling of anatomical and functional structures encoding important shape features and physical properties. The multiple attributes regarding geometry, topology and function are carried by the symbolic description and can be interactively queried and edited. Integrated 3D rendering of object surfaces and symbolic representation acts as a visual interface to allow interactive communication between the observer and the complex data, providing new possibilities for quantification and therapy planning. The discussion is guided by the prototypical example of investigating the cerebral vasculature in MRA volume data. Geometric, topological and flow-related information can be assessed by interactive analysis on a computer workstation, providing otherwise hidden qualitative and quantitative information. Several case studies demonstrate the potential usage for structure identification, definition of landmarks, assessment of topology for catheterization, and local simulation of blood flow.

  18. Comparison between measured turbine stage performance and the predicted performance using quasi-3D flow and boundary layer analyses

    NASA Technical Reports Server (NTRS)

    Boyle, R. J.; Haas, J. E.; Katsanis, T.

    1984-01-01

    A method for calculating turbine stage performance is described. The usefulness of the method is demonstrated by comparing measured and predicted efficiencies for nine different stages. Comparisons are made over a range of turbine pressure ratios and rotor speeds. A quasi-3D flow analysis is used to account for complex passage geometries. Boundary layer analyses are done to account for losses due to friction. Empirical loss models are used to account for incidence, secondary flow, disc windage, and clearance losses.

  19. Long term effects of CO2 on 3-D pore structure and 3-D phase distribution in reservoir sandstones from the Green River well (Utah, USA)

    NASA Astrophysics Data System (ADS)

    Barnhoorn, Auke; Kisoensingh, Shailesh

    2014-05-01

    Reservoir sandstones and cap rocks from the Green River area in Utah (USA) have been naturally exposed to CO2 fluids for hundreds of thousands of years, leading to compositional and microstructural alterations of the rocks. A 300m long section of this section of these Green river reservoir and cap rocks has been cored in 2012. Here, results of a high-resolution micro X-ray tomography study of a suite of samples from the well are reported detailing the 3D pore structure and phase distribution changes due to long term CO2 exposure. The reservoir sandstones from the Green River well (Utah) reveal the presence of various degrees of carbonate precipitation in the pores. Both reservoir sandstones (the shallower Entrada Formation and the deeper Navajo Formation) show variations in carbonate content and porosity structure. The Entrada sandstone exhibits widespread carbonate precipitation (up to 60% of infill of the original porosity), with the largest amount of carbonates at the boundary with the underlying Carmel cap rock. In an interval of a meter from the contact, carbonate precipitation decreases sharply till ~20%. The porosity is significantly reduced in the lowest 1 meter. The reduction in porosity lead to a reduction in pore connectivity and thereby permeability by the long-term CO2 exposure. On the other hand the Navajo sandstone shows predominantly only isolated spots of carbonate precipitation (up to 20% of the original porosity). Widespread carbonate precipitation is absent in the Navajo reservoir sandstone samples. Because carbonate precipitation is not present throughout, the large-scale permeability of the formation is likely not significantly affected by the CO2 exposure. The results show how the 3D distribution of the phases and the 3D shapes of the pores are affected by long term CO2 exposure and can be used as an example for potential changes to be expected in reservoir sandstones due to CO2 storage in future CO2 sequestration endeavours.

  20. Fast similarity search for protein 3D structures using topological pattern matching based on spatial relations.

    PubMed

    Park, Sung-Hee; Ryu, Keun Ho; Gilbert, David

    2005-08-01

    Similarity search for protein 3D structures become complex and computationally expensive due to the fact that the size of protein structure databases continues to grow tremendously. Recently, fast structural similarity search systems have been required to put them into practical use in protein structure classification whilst existing comparison systems do not provide comparison results on time. Our approach uses multi-step processing that composes of a preprocessing step to represent geometry of protein structures with spatial objects, a filter step to generate a small candidate set using approximate topological string matching, and a refinement step to compute a structural alignment. This paper describes the preprocessing and filtering for fast similarity search using the discovery of topological patterns of secondary structure elements based on spatial relations. Our system is fully implemented by using Oracle 8i spatial. We have previously shown that our approach has the advantage of speed of performance compared with other approach such as DALI. This work shows that the discovery of topological relations of secondary structure elements in protein structures by using spatial relations of spatial databases is practical for fast structural similarity search for proteins. PMID:16187404

  1. Fast 3D reconstruction of tool wear based on monocular vision and multi-color structured light illuminator

    NASA Astrophysics Data System (ADS)

    Wang, Zhongren; Li, Bo; Zhou, Yuebin

    2014-11-01

    Fast 3D reconstruction of tool wear from 2D images has great importance to 3D measuring and objective evaluating tool wear condition, determining accurate tool change and insuring machined part's quality. Extracting 3D information of tool wear zone based on monocular multi-color structured light can realize fast recovery of surface topography of tool wear, which overcomes the problems of traditional methods such as solution diversity and slow convergence when using SFS method and stereo match when using 3D reconstruction from multiple images. In this paper, a kind of new multi-color structured light illuminator was put forward. An information mapping model was established among illuminator's structure parameters, surface morphology and color images. The mathematical model to reconstruct 3D morphology based on monocular multi-color structured light was presented. Experimental results show that this method is effective and efficient to reconstruct the surface morphology of tool wear zone.

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

    PubMed Central

    Zhang, Quan; Zhang, Kai; Hu, Gengkai

    2016-01-01

    Complex fabrication process and expensive materials have restricted the development of smart three-dimensional (3D) lightweight structures, which are expected to possess self-shaping, self-folding and self-unfolding performances. Here we present a simple approach to fabricate smart lightweight structures by triggering shape transformation from thin printed composite sheets. The release of the internal strain in printed polymer materials enables the printed composite sheet to keep flat under heating and transform into a designed 3D configuration when cooled down to room temperature. The 3D lightweight structure can be switched between flat and 3D configuration under appropriate thermal stimuli. Our work exploits uniform internal strain in printed materials as a controllable tool to fabricate smart 3D lightweight structures, opening an avenue for possible applications in engineering fields. PMID:26926357

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

    PubMed

    Zhang, Quan; Zhang, Kai; Hu, Gengkai

    2016-01-01

    Complex fabrication process and expensive materials have restricted the development of smart three-dimensional (3D) lightweight structures, which are expected to possess self-shaping, self-folding and self-unfolding performances. Here we present a simple approach to fabricate smart lightweight structures by triggering shape transformation from thin printed composite sheets. The release of the internal strain in printed polymer materials enables the printed composite sheet to keep flat under heating and transform into a designed 3D configuration when cooled down to room temperature. The 3D lightweight structure can be switched between flat and 3D configuration under appropriate thermal stimuli. Our work exploits uniform internal strain in printed materials as a controllable tool to fabricate smart 3D lightweight structures, opening an avenue for possible applications in engineering fields. PMID:26926357

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

    NASA Astrophysics Data System (ADS)

    Zhang, Quan; Zhang, Kai; Hu, Gengkai

    2016-02-01

    Complex fabrication process and expensive materials have restricted the development of smart three-dimensional (3D) lightweight structures, which are expected to possess self-shaping, self-folding and self-unfolding performances. Here we present a simple approach to fabricate smart lightweight structures by triggering shape transformation from thin printed composite sheets. The release of the internal strain in printed polymer materials enables the printed composite sheet to keep flat under heating and transform into a designed 3D configuration when cooled down to room temperature. The 3D lightweight structure can be switched between flat and 3D configuration under appropriate thermal stimuli. Our work exploits uniform internal strain in printed materials as a controllable tool to fabricate smart 3D lightweight structures, opening an avenue for possible applications in engineering fields.

  5. Predictions of bubbly flows in vertical pipes using two-fluid models in CFDS-FLOW3D code

    SciTech Connect

    Banas, A.O.; Carver, M.B.; Unrau, D.

    1995-09-01

    This paper reports the results of a preliminary study exploring the performance of two sets of two-fluid closure relationships applied to the simulation of turbulent air-water bubbly upflows through vertical pipes. Predictions obtained with the default CFDS-FLOW3D model for dispersed flows were compared with the predictions of a new model (based on the work of Lee), and with the experimental data of Liu. The new model, implemented in the CFDS-FLOW3D code, included additional source terms in the {open_quotes}standard{close_quotes} {kappa}-{epsilon} transport equations for the liquid phase, as well as modified model coefficients and wall functions. All simulations were carried out in a 2-D axisymmetric format, collapsing the general multifluid framework of CFDS-FLOW3D to the two-fluid (air-water) case. The newly implemented model consistently improved predictions of radial-velocity profiles of both phases, but failed to accurately reproduce the experimental phase-distribution data. This shortcoming was traced to the neglect of anisotropic effects in the modelling of liquid-phase turbulence. In this sense, the present investigation should be considered as the first step toward the ultimate goal of developing a theoretically sound and universal CFD-type two-fluid model for bubbly flows in channels.

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

    PubMed

    Xu, Feng; Helfen, Lukas; Suhonen, Heikki; Elgrabli, Dan; Bayat, Sam; Reischig, Péter; Baumbach, Tilo; Cloetens, Peter

    2012-01-01

    Structure and composition at the nanoscale determine the behavior of biological systems and engineered materials. The drive to understand and control this behavior has placed strong demands on developing methods for high resolution imaging. In general, the improvement of three-dimensional (3D) resolution is accomplished by tightening constraints: reduced manageable specimen sizes, decreasing analyzable volumes, degrading contrasts, and increasing sample preparation efforts. Aiming to overcome these limitations, we present a non-destructive and multiple-contrast imaging technique, using principles of X-ray laminography, thus generalizing tomography towards laterally extended objects. We retain advantages that are usually restricted to 2D microscopic imaging, such as scanning of large areas and subsequent zooming-in towards a region of interest at the highest possible resolution. Our technique permits correlating the 3D structure and the elemental distribution yielding a high sensitivity to variations of the electron density via coherent imaging and to local trace element quantification through X-ray fluorescence. We demonstrate the method by imaging a lithographic nanostructure and an aluminum alloy. Analyzing a biological system, we visualize in lung tissue the subcellular response to toxic stress after exposure to nanotubes. We show that most of the nanotubes are trapped inside alveolar macrophages, while a small portion of the nanotubes has crossed the barrier to the cellular space of the alveolar wall. In general, our method is non-destructive and can be combined with different sample environmental or loading conditions. We therefore anticipate that correlative X-ray nano-laminography will enable a variety of in situ and in operando 3D studies. PMID:23185554

  7. 3D modeling method for computer animate based on modified weak structured light method

    NASA Astrophysics Data System (ADS)

    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.

  8. Correlative Nanoscale 3D Imaging of Structure and Composition in Extended Objects

    PubMed Central

    Xu, Feng; Helfen, Lukas; Suhonen, Heikki; Elgrabli, Dan; Bayat, Sam; Reischig, Péter; Baumbach, Tilo; Cloetens, Peter

    2012-01-01

    Structure and composition at the nanoscale determine the behavior of biological systems and engineered materials. The drive to understand and control this behavior has placed strong demands on developing methods for high resolution imaging. In general, the improvement of three-dimensional (3D) resolution is accomplished by tightening constraints: reduced manageable specimen sizes, decreasing analyzable volumes, degrading contrasts, and increasing sample preparation efforts. Aiming to overcome these limitations, we present a non-destructive and multiple-contrast imaging technique, using principles of X-ray laminography, thus generalizing tomography towards laterally extended objects. We retain advantages that are usually restricted to 2D microscopic imaging, such as scanning of large areas and subsequent zooming-in towards a region of interest at the highest possible resolution. Our technique permits correlating the 3D structure and the elemental distribution yielding a high sensitivity to variations of the electron density via coherent imaging and to local trace element quantification through X-ray fluorescence. We demonstrate the method by imaging a lithographic nanostructure and an aluminum alloy. Analyzing a biological system, we visualize in lung tissue the subcellular response to toxic stress after exposure to nanotubes. We show that most of the nanotubes are trapped inside alveolar macrophages, while a small portion of the nanotubes has crossed the barrier to the cellular space of the alveolar wall. In general, our method is non-destructive and can be combined with different sample environmental or loading conditions. We therefore anticipate that correlative X-ray nano-laminography will enable a variety of in situ and in operando 3D studies. PMID:23185554

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    Integration of complex photonic structures onto optical fiber facets enables powerful platforms with unprecedented optical functionalities. Conventional nanofabrication technologies, however, do not permit viable integration of complex photonic devices onto optical fibers owing to their low throughput and high cost. In this paper we report the fabrication of a three-dimensional structure achieved by direct nanoimprint lithography on the facet of an optical fiber. Nanoimprint processes and tools were specifically developed to enable a high lithographic accuracy and coaxial alignment of the optical device with respect to the fiber core. To demonstrate the capability of this new approach, a 3D beam splitter has been designed, imprinted and optically characterized. Scanning electron microscopy and optical measurements confirmed the good lithographic capabilities of the proposed approach as well as the desired optical performance of the imprinted structure. The inexpensive solution presented here should enable advancements in areas such as integrated optics and sensing, achieving enhanced portability and versatility of fiber optic components.

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

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  11. The 3D structure of QCD and the roots of the Standard Model

    NASA Astrophysics Data System (ADS)

    Mulders, P. J.

    2016-03-01

    For many phenomenological applications involving hadrons in high energy processes the hadronic structure can be taken care of by parton distribution functions (PDFs), in which only the collinear momenta of quarks and gluons are important. In principle the transverse structure, however, provides interesting new phenomenology. Taking into account transverse momenta of partons one works with transverse momentum dependent PDFs (TMDs), These allow all spin-spin correlations and also spin-orbit correlations that have a time reversal odd character and lead to new observables. In many theoretical developments the link to the collinear treatment is used. In this talk I will speculate on a novel view of the 3-dimensional (3D) structure of QCD, which fits in a broader study looking at the roots of the Standard Model of particle physics.

  12. Quantitative visualization of high-speed 3D turbulent flow structures using holographic interferometric tomography

    NASA Astrophysics Data System (ADS)

    Timmerman, B. H.; Watt, D. W.; Bryanston-Cross, P. J.

    1999-02-01

    Using holographic interferometry the three-dimensional structure of unsteady and large-scale motions within subsonic and transonic turbulent jet flows has been studied. The instantaneous 3D flow structure is obtained by tomographic reconstruction techniques from quantitative phase maps recorded using a rapid-switching, double reference beam, double pulse laser system. The reconstruction of the jets studied here reveal a three-dimensional nature of the flow. In particular an increasing complexity can be seen in the turbulence as the flow progresses from the jet nozzle. Furthermore, a coherent three-dimensional, possibly rotating, structure can be seen to exist within these jets. The type of flow features illustrated here are not just of fundamental importance for understanding the behavior of free jet flows, but are also common to a number of industrial applications, ranging from the combustion flow within an IC engine to the transonic flow through the stages of a gas turbine.

  13. The use of an in vitro 3D melanoma model to predict in vivo plasmid transfection using electroporation

    PubMed Central

    Marrero, Bernadette; Heller, Richard

    2012-01-01

    A large-scale in vitro 3D tumor model was generated to evaluate gene delivery procedures in vivo. This 3D tumor model consists of a “tissue-like” spheroid that provides a micro-environment supportive of melanoma proliferation, allowing cells to behave similarly to cells in vivo. This functional spheroid measures approximately 1 cm in diameter and can be used to effectively evaluate plasmid transfection when testing various electroporation (EP) electrode applicators. In this study, we identified EP conditions that efficiently transfect green fluorescent protein (GFP) and interleukin 15 (IL-15) plasmids into tumor cells residing in the 3D construct. We found that plasmids delivered using a 6-plate electrode applying 6 pulses with nominal electric field strength of 500 V/cm and pulse-length of 20 ms produced significant increase of GFP (7.3-fold) and IL-15 (3.0–fold) expression compared to controls. This in vitro 3D model demonstrates the predictability of cellular response toward delivery techniques, limits the numbers of animals employed for transfection studies, and may facilitate future developments of clinical trials for cancer therapies in vivo. PMID:22244695

  14. Advances in 3D cell culture technologies enabling tissue-like structures to be created in vitro.

    PubMed

    Knight, Eleanor; Przyborski, Stefan

    2015-12-01

    Research in mammalian cell biology often relies on developing in vitro models to enable the growth of cells in the laboratory to investigate a specific biological mechanism or process under different test conditions. The quality of such models and how they represent the behavior of cells in real tissues plays a critical role in the value of the data produced and how it is used. It is particularly important to recognize how the structure of a cell influences its function and how co-culture models can be used to more closely represent the structure of real tissue. In recent years, technologies have been developed to enhance the way in which researchers can grow cells and more readily create tissue-like structures. Here we identify the limitations of culturing mammalian cells by conventional methods on two-dimensional (2D) substrates and review the popular approaches currently available that enable the development of three-dimensional (3D) tissue models in vitro. There are now many ways in which the growth environment for cultured cells can be altered to encourage 3D cell growth. Approaches to 3D culture can be broadly categorized into scaffold-free or scaffold-based culture systems, with scaffolds made from either natural or synthetic materials. There is no one particular solution that currently satisfies all requirements and researchers must select the appropriate method in line with their needs. Using such technology in conjunction with other modern resources in cell biology (e.g. human stem cells) will provide new opportunities to create robust human tissue mimetics for use in basic research and drug discovery. Application of such models will contribute to advancing basic research, increasing the predictive accuracy of compounds, and reducing animal usage in biomedical science. PMID:25411113

  15. Unsteady diffusional screening in 3D pulmonary acinar structures: from infancy to adulthood.

    PubMed

    Hofemeier, Philipp; Shachar-Berman, Lihi; Tenenbaum-Katan, Janna; Filoche, Marcel; Sznitman, Josué

    2016-07-26

    Diffusional screening in the lungs is a physical phenomenon where the specific topological arrangement of alveolated airways of the respiratory region leads to a depletion, or 'screening', of oxygen molecules with increasing acinar generation. Here, we revisit diffusional screening phenomena in anatomically-inspired pulmonary acinar models under realistic breathing maneuvers. By modelling 3D bifurcating alveolated airways capturing both convection and diffusion, unsteady oxygen transport is investigated under cyclic breathing motion. To evaluate screening characteristics in the developing lungs during growth, four representative stages of lung development were chosen (i.e. 3 months, 1 year and 9 months, 3 years and adulthood) that capture distinct morphological acinar changes spanning alveolarization phases to isotropic alveolar growth. Numerical simulations unveil the dramatic changes in O2 transport occurring during lung development, where young infants exhibit highest acinar efficiencies that rapidly converge with age to predictions at adulthood. With increased ventilatory effort, transient dynamics of oxygen transport is fundamentally altered compared to tidal breathing and emphasizes the augmented role of convection. Resolving the complex convective acinar flow patterns in 3D acinar trees allows for the first time a spatially-localized and time-resolved characterization of oxygen transport in the pulmonary acinus, from infancy to adulthood. PMID:26699945

  16. RAG-3D: a search tool for RNA 3D substructures.

    PubMed

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-10-30

    To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D-a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool-designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

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

    NASA Astrophysics Data System (ADS)

    Zhang, Zhiwei; Tian, Jiwei; Qiu, Bo; Zhao, Wei; Chang, Ping; Wu, Dexing; Wan, Xiuquan

    2016-04-01

    Oceanic mesoscale eddies with horizontal scales of 50–300 km are the most energetic form of flows in the ocean. They are the oceanic analogues of atmospheric storms and are effective transporters of heat, nutrients, dissolved carbon, and other biochemical materials in the ocean. Although oceanic eddies have been ubiquitously observed in the world oceans since 1960s, our understanding of their three-dimensional (3D) structure, generation, and dissipation remains fragmentary due to lack of systematic full water-depth measurements. To bridge this knowledge gap, we designed and conducted a multi-months field campaign, called the South China Sea Mesoscale Eddy Experiment (S-MEE), in the northern South China Sea in 2013/2014. The S-MEE for the first time captured full-depth 3D structures of an anticyclonic and cyclonic eddy pair, which are characterized by a distinct vertical tilt of their axes. By observing the eddy evolution at an upstream versus downstream location and conducting an eddy energy budget analysis, the authors further proposed that generation of submesoscale motions most likely constitutes the dominant dissipation mechanism for the observed eddies.

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

    NASA Astrophysics Data System (ADS)

    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.

  19. Effect of sterilization on structural and material properties of 3-D silk fibroin scaffolds.

    PubMed

    Hofmann, Sandra; Stok, Kathryn S; Kohler, Thomas; Meinel, Anne J; Müller, Ralph

    2014-01-01

    The development of porous scaffolds for tissue engineering applications requires the careful choice of properties, as these influence cell adhesion, proliferation and differentiation. Sterilization of scaffolds is a prerequisite for in vitro culture as well as for subsequent in vivo implantation. The variety of methods used to provide sterility is as diverse as the possible effects they can have on the structural and material properties of the three-dimensional (3-D) porous structure, especially in polymeric or proteinous scaffold materials. Silk fibroin (SF) has previously been demonstrated to offer exceptional benefits over conventional synthetic and natural biomaterials in generating scaffolds for tissue replacements. This study sought to determine the effect of sterilization methods, such as autoclaving, heat-, ethylene oxide-, ethanol- or antibiotic-antimycotic treatment, on porous 3-D SF scaffolds. In terms of scaffold morphology, topography, crystallinity and short-term cell viability, the different sterilization methods showed only few effects. Nevertheless, mechanical properties were significantly decreased by a factor of two by all methods except for dry autoclaving, which seemed not to affect mechanical properties compared to the native control group. These data suggest that SF scaffolds are in general highly resistant to various sterilization treatments. Nevertheless, care should be taken if initial mechanical properties are of interest. PMID:24013025

  20. Poloidal structure of the plasma edge with 3D magnetic fields

    NASA Astrophysics Data System (ADS)

    Agostini, Matteo; Scarin, Paolo; Carraro, Lorella; Spizzo, Gianluca; Spolaore, Monica; Vianello, Nicola

    2015-11-01

    In the RFX-mod reversed-field pinch, when the magnetic field spontaneously develops a non axi-symmetric structure, also the plasma edge assumes a three dimensional shape. In previous RFX works, it has been shown that kinetic properties of the plasma (electron pressure, connection lengths, floating potential, influx, plasma flow) closely follow the symmetry of the 3D field, both in amplitude and phase, along the toroidal angle (i.e, the RFP perpendicular direction in the edge). Using a set of poloidally distributed diagnostics, it is shown that these same properties follow the poloidal periodicity (m =1) of the field. However, the behavior of the phase is more difficult to understand. In particular, the 3D modulation of the plasma potential can rotate in the poloidal direction with the typical velocity of 100m/s, similar in value with the phase velocity of the m =1 magnetic mode; or it can jump between inboard and outboard equatorial midplane. Moreover, when the floating potential structure rotates, there are preliminary indications that its direction depends on the plasma density: it follows the m =1 mode at higher density, and rotates in the opposite direction at lower density.

  1. 3D-Printed Broadband Dielectric Tube Terahertz Waveguide with Anti-Reflection Structure

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    Zhang, Zhiwei; Tian, Jiwei; Qiu, Bo; Zhao, Wei; Chang, Ping; Wu, Dexing; Wan, Xiuquan

    2016-01-01

    Oceanic mesoscale eddies with horizontal scales of 50-300 km are the most energetic form of flows in the ocean. They are the oceanic analogues of atmospheric storms and are effective transporters of heat, nutrients, dissolved carbon, and other biochemical materials in the ocean. Although oceanic eddies have been ubiquitously observed in the world oceans since 1960s, our understanding of their three-dimensional (3D) structure, generation, and dissipation remains fragmentary due to lack of systematic full water-depth measurements. To bridge this knowledge gap, we designed and conducted a multi-months field campaign, called the South China Sea Mesoscale Eddy Experiment (S-MEE), in the northern South China Sea in 2013/2014. The S-MEE for the first time captured full-depth 3D structures of an anticyclonic and cyclonic eddy pair, which are characterized by a distinct vertical tilt of their axes. By observing the eddy evolution at an upstream versus downstream location and conducting an eddy energy budget analysis, the authors further proposed that generation of submesoscale motions most likely constitutes the dominant dissipation mechanism for the observed eddies. PMID:27074710

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

    PubMed Central

    Zhang, Zhiwei; Tian, Jiwei; Qiu, Bo; Zhao, Wei; Chang, Ping; Wu, Dexing; Wan, Xiuquan

    2016-01-01

    Oceanic mesoscale eddies with horizontal scales of 50–300 km are the most energetic form of flows in the ocean. They are the oceanic analogues of atmospheric storms and are effective transporters of heat, nutrients, dissolved carbon, and other biochemical materials in the ocean. Although oceanic eddies have been ubiquitously observed in the world oceans since 1960s, our understanding of their three-dimensional (3D) structure, generation, and dissipation remains fragmentary due to lack of systematic full water-depth measurements. To bridge this knowledge gap, we designed and conducted a multi-months field campaign, called the South China Sea Mesoscale Eddy Experiment (S-MEE), in the northern South China Sea in 2013/2014. The S-MEE for the first time captured full-depth 3D structures of an anticyclonic and cyclonic eddy pair, which are characterized by a distinct vertical tilt of their axes. By observing the eddy evolution at an upstream versus downstream location and conducting an eddy energy budget analysis, the authors further proposed that generation of submesoscale motions most likely constitutes the dominant dissipation mechanism for the observed eddies. PMID:27074710

  4. A crust-scale 3D structural model of the Beaufort-Mackenzie Basin (Arctic Canada)

    NASA Astrophysics Data System (ADS)

    Sippel, Judith; Scheck-Wenderoth, Magdalena; Lewerenz, Björn; Kroeger, Karsten Friedrich

    2013-04-01

    The Beaufort-Mackenzie Basin was initiated in the Early Jurassic as part of an Arctic rifted passive continental margin which soon after became overprinted by Cordilleran foreland tectonics. Decades of industrial exploration and scientific research in this petroliferous region have produced a wide spectrum of geological and geophysical data as well as geoscientific knowledge. We have integrated available grids of sedimentary horizons, well data, seismic reflection and refraction data, and the observed regional gravity field into the first crust-scale 3D structural model of the Beaufort-Mackenzie Basin. Many characteristics of this model reflect the complex geodynamic and tectonostratigraphic history of the basin. The Mesozoic-Cenozoic sedimentary part of the model comprises seven clastic units (predominantly sandy shales) of which the modelled thickness distributions allow to retrace the well-established history of the basin comprising a gradual north(east)ward shift of the main depocentres as well as diverse phases of localised erosion. As a result of this development, the present-day configuration of the basin reveals that the sedimentary units tend to be younger, more porous, and thus less dense towards the north at a constant depth level. By integrating three refraction seismic profiles and performing combined isostatic and 3D gravity modelling, we have modelled the sub-sedimentary basement of the Beaufort-Mackenzie Basin. The continental basement spans from unstretched domains (as thick as about 42 km) in the south to extremely thinned domains (of less than 5 km thickness) in the north where it probably represents transitional crust attached to the oceanic crust of the Canada Basin. The uppermost parts of the continental crust are less dense (ρ = 2710 kg/m3) and most probably made up by pre-Mesozoic meta-sediments overlying a heavier igneous and metamorphic crust (ρ = 2850 kg/m3). The presented crust-scale 3D structural model shows that the greatest

  5. Predicting mechanical competence of trabecular bone using 3D tensor-scale-based parameters

    NASA Astrophysics Data System (ADS)

    Saha, Punam K.; Wald, Michael J.; Radin, Alex; Wehrli, Felix W.

    2005-04-01

    Trabecular bone (TB) consists of a network of interconnected struts and plates occurring near the joints of long bones and in the axial skeleton. In response to mechanical stresses it remodels such that trabeculae are aligned with the major stress lines, thus leading to a highly anisotropic network. Beside bone volume fraction, anisotropy and topological indices are known to be strong predictor of the TB mechanical competence. In osteoporosis, the most common bone disorder, the remodeling balance is perturbed due to increased resorption, resulting in net bone loss accompanied by architectural deterioration, leading to fragile bone and increased fracture risk. In vertebral osteoporosis, preferential loss of transverse trabeculae leads to increased anisotropy and change in topology, hence exact measurements of these parameters are of paramount interest. Current in vivo imaging yields voxel size comparable to TB thickness, thus resulting in inherently fuzzy representations. The commonly used methods for anisotropy require binarization which is difficult to achieve in the limited spatial resolution regime where the intensity histogram is mono-modal. Here, we present a new tensor scale (t-scale) based TB architectural measures that (1) obviates binarization, and (2) yields localized measures. We evaluate the performance of this method on micro-CT images of vertebral bone and test the hypothesis that the method, along with BMD and other structural parameters, allows prediction of TB"s mechanical competence. Toward this goal, we estimate Young"s modulus (YM) of (13mm)3 vertebral TB samples under uniaxial loading and examine linear correlation of different t-scale parameters computed via micro-CT imaging .

  6. Modeling the effects of 3-D slab geometry and oblique subduction on subduction zone thermal structure

    NASA Astrophysics Data System (ADS)

    Wada, I.; Wang, K.; He, J.

    2013-12-01

    In this study, we revisit the effects of along-strike variation in slab geometry and oblique subduction on subduction zone thermal structures. Along-strike variations in slab dip cause changes in the descending rate of the slab and generate trench-parallel pressure gradients that drive trench-parallel mantle flow (e.g., Kneller and van Keken, 2007). Oblique subduction also drives trench-parallel mantle flow. In this study, we use a finite element code PGCtherm3D and examine a range of generic subduction geometries and parameters to investigate the effects of the above two factors. This exercise is part of foundational work towards developing detailed 3-D thermal models for NE Japan, Nankai, and Cascadia to better constrain their 3-D thermal structures and to understand the role of temperature in controlling metamorphic, seismogenic, and volcanic processes. The 3-D geometry of the subducting slabs in the forearc and arc regions are well delineated at these three subduction zones. Further, relatively large compilations of surface heat flow data at these subduction zones make them excellent candidates for this study. At NE Japan, a megathrust earthquake occurred on March 11, 2011; at Nankai and Cascadia, there has been a great effort to constrain the scale of the next subduction thrust earthquake for the purpose of disaster prevention. Temperature influences the slip behavior of subduction faults by (1) affecting the rheology of the interface material and (2) controlling dehydration reactions, which can lead to elevated pore fluid pressure. Beyond the depths of subduction thrust earthquakes, the thermal structure is affected strongly by the pattern of mantle wedge flow. This flow is driven by viscous coupling between the subducting slab and the overriding mantle, and it brings in hot flowing mantle into the wedge. The trench-ward (up-dip) extent of the slab-mantle coupling is thus a key factor that controls the thermal structure. Slab-mantle decoupling at shallow

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

    PubMed

    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

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

    PubMed Central

    Borazjani, Iman; Ge, Liang; Sotiropoulos, Fotis

    2010-01-01

    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

  9. Global Structure of Idealized Stream Interaction Regions Using 3D MHD Simulations

    NASA Astrophysics Data System (ADS)

    Pahud, D. M.; Hughes, W. J.; Merkin, V. G.

    2014-12-01

    The global structure of the heliosphere during solar cycles (SC) 23 and 24 differed significantly in many ways, for example in terms of global magnetic field strength, velocity structure and the observed properties of Stream Interaction Region (SIR) and associated shocks. The differences considered in this study focus primarily on the effects of the three-dimensional (3D) structure of SIRs. During the minimum of SC 24, equatorial coronal holes were prevalent as sources of low-latitude high-speed solar wind. In contrast, the canonical depiction of SC 23's minimum wind configuration is of a band of slow wind undulating about the heliographic equator. Using the heliospheric adaptation of the Lyon-Fedder-Mobarry magnetohydrodynamic (MHD) model (LFM-helio), we have run simulations for two idealized global solar wind conditions. The first simulation approximates the classical tilted dipole, with fast solar wind at high latitudes and a band of slow wind tilted with respect to the heliographic equator, and the second consists of global slow solar wind with equatorial circular sources of high-speed streams. The evolution of the SIRs from 0.1 AU to 2.0 AU is characterized using the amplitude and location of the maximum compressions of the plasma and the magnetic field as well as the largest deflection of solar wind flow. The relation between plasma and magnetic field compressions differs between the two cases considered. The SIRs produced by the equatorial coronal holes have similar maximum densities to those of the tilted dipole case, but the magnetic field magnitude is larger and the plasma is hotter. This suggests that evolution depends on the 3D structure of the SIR and its effects on the competitive roles of the growth of the structure, driven by compression from dynamic pressure, and and relaxation from the plasma flow and magnetic field deflections occurring in the region. Magnetic field threading SIRs and tracing plasma parcels are examined.

  10. Representing geometric structures in 3D tomography soil images: Application to pore-space modeling

    NASA Astrophysics Data System (ADS)

    Monga, Olivier; Ndeye Ngom, Fatou; François Delerue, Jean

    2007-09-01

    Only in the last decade have geoscientists started to use 3D computed tomography (CT) images of soil for better understanding and modeling of soil properties. In this paper, we propose one of the first approaches to allow the definition and computation of stable (intrinsic) geometric representations of structures in 3D CT soil images. This addresses the open problem set by the description of volume shapes from discrete traces without any a priori information. The basic concept involves representing the volume shape by a piecewise approximation using simple volume primitives (bowls, cylinders, cones, etc.). This typical representation is assumed to optimize a criterion ensuring its stability. This criterion includes the representation scale, which characterizes the trade-off between the fitting error and the number of patches. We also take into account the preservation of topological properties of the initial shape: the number of connected components, adjacency relationships, etc. We propose an efficient computation method for this piecewise approximation using cylinders or bowls. For cylinders, we use optimal region growing in a valuated adjacency graph that represents the primitives and their adjacency relationships. For bowls, we compute a minimal set of Delaunay spheres recovering the skeleton. Our method is applied to modeling of a coarse pore space extracted from 3D CT soil images. The piecewise bowls approximation gives a geometric formalism corresponding to the intuitive notion of pores and also an efficient way to compute it. This geometric and topological representation of coarse pore space can be used, for instance, to simulate biological activity in soil.

  11. Gravimetric 3D Subsurface Modelling of the Cerro Do Jarau Structure, Rio Grande Do Sul, Brazil.

    NASA Astrophysics Data System (ADS)

    Giacomini, B. B.

    2014-12-01

    Although common in other bodies of the solar system, impact craters formed in basaltic terrains are rare on Earth and only a few examples are known. Two of these craters are located south of Brazil, the Vargeão and Vista Alegre impact craters. The Cerro do Jarau structure is not confirmed, but is a possible third Brazilian basaltic crater, formed above the Serra Geral basalt floods of the Paraná Basin like the other two. Cerro do Jarau is a 13 km circular landform that rises over 200 meters above the plains of the "pampas" in southern Brazil. The name, meaning "Jarau hills", is given after the crests of silicified and deformed Botucatu sandstones, which form a semiring of elevated hills in the northern part of the structure. This work focused on the construction of a 3D subsurface geological model that could explain a new set of ground gravimetric data. Bouguer anomalies were calculated from gravity acceleration measured at 313 stations irregularly distributed on the area of the impact structure. A regional component represented by a polynomial trend surface was extracted from the total Bouguer anomalies. The residual Bouguer map (fig. 1) shows a strong positive anomaly with a NE-SW trend, located in the northeastern part of the structure. This gravity feature is not common in other impact structures, being possibly related to a dike intrusion. However, the negative anomaly present in the center of the structure and the circular positive anomaly surrounding the central part of the structure could be related to an impact structure. The positive circular anomaly is not spatially coincident with the edges of the structure, a feature that is also observed at the Vargeão and Vista Alegre impact structures. Density values of basalts, sandstones and breccias were measured from rock samples and each average value were used as constraints for the 3D model developed with the Geosoft® VOXI Earth modelling.This model provided a better understanding of the subsurface design

  12. 2D and 3D reconstruction and geomechanical characterization of kilometre-scale complex folded structures

    NASA Astrophysics Data System (ADS)

    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.

  13. A simple configuration for fabrication of 2D and 3D photonic quasicrystals with complex structures

    NASA Astrophysics Data System (ADS)

    Sun, XiaoHong; Wang, Shuai; Liu, Wei; Jiang, LiuDi

    2016-06-01

    A simple method using a single-prism common-path interferometer is presented for the fabrication of complex quasicrystals in sub-micrometer scales. Multiple types of two-dimensional (2D) and three-dimensional (3D) quasicrystalline structures are designed and their diffraction patterns are obtained by using Fourier Transform method. Multi-fold rotational symmetries are demonstrated and compared. By using this method, a wide range of quasicrystals types can be produced with arbitrary complexities and rotational symmetries. The transmittance studies of 12-fold and 18-fold structures also reveal the existence of complete photonic bandgaps, which also demonstrates increased symmetry and significantly improved characteristics of photonic band-gaps.

  14. A 3D multi-block structured version of the KIVA 2 code

    NASA Astrophysics Data System (ADS)

    Habachi, C.; Torres, A.

    A numerical procedure is developed in the KIVA 2 code for calculating flows in complex geometries. Those geometries consist of an arbitrary number of 3D secondary domains which are connected with any angle to a main region. In this procedure, the governing equations are discretized on a system of partial overlapping structured grids. Calculations are performed in the different meshes of the computation domain which are linked by a fully conservative algorithm. By this numerical technique, calculations in those geometries are possible with a reasonable number of inactive cells involved by a structured code like KIVA 2. This algorithm was validated on an 1D analytical case and a 2D experimental case. It was then used for modeling an industrial problem, a two stroke engine with ports and moving boundaries.

  15. Structural, magnetic and conduction properties of 3d-metal monoatomic wires

    NASA Astrophysics Data System (ADS)

    García-Fuente, A.; Daul, C.

    2014-04-01

    From density functional theory calculations, we study the structure, magnetism and conduction properties of monoatomic wires made of all the 3d elements (Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu). Wires with equidistant and alternating bond lengths are considered. Both magnetism and structure are found to play an important role for the conduction properties of the wires. Ferromagnetic wires are found to present a spin filtering effect which is not directly related with the magnitude of their magnetic moment. On the other hand, the main effect of bond length alternation is to partially destroy the transmission around the Fermi level, especially from the d bands. Ni wires are found to present particularly interesting spin filtering properties, meanwhile Cr wires present promising magnetoresistive effects.