WorldWideScience

Sample records for 3d protein structure

  1. Links from Genome Proteins to Known 3-D Structures

    Wang, Yanli; Bryant, Stephen; Tatusov, Roman; Tatusova, Tatiana

    2000-01-01

    We describe a genome annotation service provided by the Entrez browser, http://www.ncbi.nlm.nih.gov/entrez. All protein products identified in fully sequenced microbial genomes have been compared with proteins with known 3-D structure by use of the BLAST sequence comparison algorithm. For the ∼20% of genome proteins in which unambiguous sequence similarity is detected, Entrez provides a link from the gene product to its predicted structure. The service uses the Cn3D molecular graphics viewer ...

  2. PGR: A Graph Repository of Protein 3D-Structures

    Dhifli, Wajdi; Diallo, Abdoulaye Baniré

    2016-01-01

    Graph theory and graph mining constitute rich fields of computational techniques to study the structures, topologies and properties of graphs. These techniques constitute a good asset in bioinformatics if there exist efficient methods for transforming biological data into graphs. In this paper, we present Protein Graph Repository (PGR), a novel database of protein 3D-structures transformed into graphs allowing the use of the large repertoire of graph theory techniques in protein mining. This ...

  3. Automating the determination of 3D protein structure

    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.

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

    Emmanuel D Levy

    2006-11-01

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

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

    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

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

    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

  7. Mining overrepresented 3D patterns of secondary structures in proteins.

    Comin, Matteo; Guerra, Concettina; Zanotti, Giuseppe

    2008-12-01

    We consider the problem of finding overrepresented arrangements of secondary structure elements (SSEs) in a given dataset of representative protein structures. While most papers in the literature study the distribution of geometrical properties, in particular angles and distances, between pairs of interacting SSEs, in this paper we focus on the distribution of angles of all quartets of SSEs and on the extraction of overrepresented angular patterns. We propose a variant of the Apriori method that obtains overrepresented arrangements of quartets of SSEs by combining arrangements of triplets of SSEs. This specific case will pose the basis for a natural extension of the problem to any given number of SSEs. We analyze the results of our method on a dataset of 300 nonredundant proteins. Supplementary material is available at (http://www.dei.unipd.it/nciompin/papers/CGZ-jbcb-suppl.pdf/). PMID:19090018

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

    Peng Zhihong; Chen Jie; Lin Xiwen; Sang Yanchao

    2007-01-01

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

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

    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…

  10. 3D structural analysis of proteins using electrostatic surfaces based on image segmentation

    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.

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

    Zemla, Adam T.

    2011-09-20

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

  12. Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure

    Vassura Marco

    2011-01-01

    Full Text Available Abstract Background The present knowledge of protein structures at atomic level derives from some 60,000 molecules. Yet the exponential ever growing set of hypothetical protein sequences comprises some 10 million chains and this makes the problem of protein structure prediction one of the challenging goals of bioinformatics. In this context, the protein representation with contact maps is an intermediate step of fold recognition and constitutes the input of contact map predictors. However contact map representations require fast and reliable methods to reconstruct the specific folding of the protein backbone. Methods In this paper, by adopting a GRID technology, our algorithm for 3D reconstruction FT-COMAR is benchmarked on a huge set of non redundant proteins (1716 taking random noise into consideration and this makes our computation the largest ever performed for the task at hand. Results We can observe the effects of introducing random noise on 3D reconstruction and derive some considerations useful for future implementations. The dimension of the protein set allows also statistical considerations after grouping per SCOP structural classes. Conclusions All together our data indicate that the quality of 3D reconstruction is unaffected by deleting up to an average 75% of the real contacts while only few percentage of randomly generated contacts in place of non-contacts are sufficient to hamper 3D reconstruction.

  13. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data.

    Lee, Woonghee; Petit, Chad M; Cornilescu, Gabriel; Stark, Jaime L; Markley, John L

    2016-06-01

    We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27-98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models. PMID:27169728

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

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

    2006-01-01

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

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

    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

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

    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

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

    Jansson Jesper

    2010-01-01

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

  18. MMDB: 3D structures and macromolecular interactions

    Madej, Thomas; Addess, Kenneth J.; Fong, Jessica H.; Geer, Lewis Y.; Geer, Renata C.; Lanczycki, Christopher J; Liu, Chunlei; Lu, Shennan; Marchler-Bauer, Aron; Panchenko, Anna R.; Chen, Jie; Thiessen, Paul A; Wang, Yanli; Zhang, Dachuan; Bryant, Stephen H.

    2011-01-01

    Close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3D) structure by standard sequence similarity searches. Potentially, a great deal can be learned about proteins or protein families of interest from considering 3D structure, and to this day 3D structure data may remain an underutilized resource. Here we present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically...

  19. Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures

    Gerstein Mark

    2004-01-01

    Full Text Available Abstract Background Hidden Markov Models (HMMs have proven very useful in computational biology for such applications as sequence pattern matching, gene-finding, and structure prediction. Thus far, however, they have been confined to representing 1D sequence (or the aspects of structure that could be represented by character strings. Results We develop an HMM formalism that explicitly uses 3D coordinates in its match states. The match states are modeled by 3D Gaussian distributions centered on the mean coordinate position of each alpha carbon in a large structural alignment. The transition probabilities depend on the spread of the neighboring match states and on the number of gaps found in the structural alignment. We also develop methods for aligning query structures against 3D HMMs and scoring the result probabilistically. For 1D HMMs these tasks are accomplished by the Viterbi and forward algorithms. However, these will not work in unmodified form for the 3D problem, due to non-local quality of structural alignment, so we develop extensions of these algorithms for the 3D case. Several applications of 3D HMMs for protein structure classification are reported. A good separation of scores for different fold families suggests that the described construct is quite useful for protein structure analysis. Conclusion We have created a rigorous 3D HMM representation for protein structures and implemented a complete set of routines for building 3D HMMs in C and Perl. The code is freely available from http://www.molmovdb.org/geometry/3dHMM, and at this site we also have a simple prototype server to demonstrate the features of the described approach.

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

    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

  1. 3-d structure-based amino acid sequence alignment of esterases, lipases and related proteins

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

    1993-05-13

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

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

    Rausch, Felix; Schicht, Martin; Paulsen, Friedrich; Ngueya, Ivan; Bräuer, Lars; Brandt, Wolfgang

    2012-01-01

    Surfactant proteins (SP) are well known from human lung. These proteins assist the formation of a monolayer of surface-active phospholipids at the liquid-air interface of the alveolar lining, play a major role in lowering the surface tension of interfaces, and have functions in innate and adaptive immune defense. During recent years it became obvious that SPs are also part of other tissues and fluids such as tear fluid, gingiva, saliva, the nasolacrimal system, and kidney. Recently, a putative new surfactant protein (SFTA2 or SP-G) was identified, which has no sequence or structural identity to the already know surfactant proteins. In this work, computational chemistry and molecular-biological methods were combined to localize and characterize SP-G. With the help of a protein structure model, specific antibodies were obtained which allowed the detection of SP-G not only on mRNA but also on protein level. The localization of this protein in different human tissues, sequence based prediction tools for posttranslational modifications and molecular dynamic simulations reveal that SP-G has physicochemical properties similar to the already known surfactant proteins B and C. This includes also the possibility of interactions with lipid systems and with that, a potential surface-regulatory feature of SP-G. In conclusion, the results indicate SP-G as a new surfactant protein which represents an until now unknown surfactant protein class. PMID:23094088

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

    Felix Rausch

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

  4. Computational Biomodelling and Analysis of 3D Structure of HUMAN Proto-oncogene c-Rel: A Tumorigenesis Activator Protein

    Atala Bihari Jena

    2013-09-01

    Full Text Available With the advent of biomedical research in the field of human science several protein are found in human body acts s a health hazard. The proto-oncogene c-Rel protein is mostly found in human is encoded by the REL gene and belongs to the Rel/NF- kB transcription factor family, which regulates a large variety of cellular functions. Proto-oncogene involved and plays a great role in differentiation and lymphopoiesis. Proto-oncogene may be harmful and cause cancer when they are mutated. To understand the operational mechanism of HUMAN Proto-oncogene c-Rel protein, it is imperative to understand the structural model of that particular protein but the three dimensional (3D structure has not yet been reported in Protein Data Bank (PDB. In the present study a complete structural analysis and 3-D modelling of HUMAN Proto-oncogene c-Rel of Homosapiens.Based on the PDB Blast report three dimensional structure of the Proto-oncogenec-Rel protein, was predicted by using the SWISS MODEL. Predicted model was further assessed by SAVES (PROCHEK, VERIFY 3D, ERRAT and Ramachandran Server, which show with acceptable scores and the reliability of final refined model. The overall result provides the evidence of good quality of model and furnishes an adequate foundation for functional analysis of experimentally derived crystal structures and also helps in cancer research with furnishes a novel starting point for structure based drug design of proto-oncogene c-Rel protein.

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

    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 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

  6. 3D protein structure prediction using Imperialist Competitive algorithm and half sphere exposure prediction.

    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

  7. Mining the protein data bank with CReF to predict approximate 3-D structures of polypeptides.

    Dorn, Márcio; de Souza, Osmar Norberto

    2010-01-01

    n this paper we describe CReF, a Central Residue Fragment-based method to predict approximate 3-D structures of polypeptides by mining the Protein Data Bank (PDB). The approximate predicted structures are good enough to be used as starting conformations in refinement procedures employing state-of-the-art molecular mechanics methods such as molecular dynamics simulations. CReF is very fast and we illustrate its efficacy in three case studies of polypeptides whose sizes vary from 34 to 70 amino acids. As indicated by the RMSD values, our initial results show that the predicted structures adopt the expected fold, similar to the experimental ones. PMID:20681480

  8. “SP-G”, a Putative New Surfactant Protein – Tissue Localization and 3D Structure

    Rausch, Felix; Schicht, Martin; Paulsen, Friedrich; Ngueya, Ivan; Bräuer, Lars; Brandt, Wolfgang

    2012-01-01

    Surfactant proteins (SP) are well known from human lung. These proteins assist the formation of a monolayer of surface-active phospholipids at the liquid-air interface of the alveolar lining, play a major role in lowering the surface tension of interfaces, and have functions in innate and adaptive immune defense. During recent years it became obvious that SPs are also part of other tissues and fluids such as tear fluid, gingiva, saliva, the nasolacrimal system, and kidney. Recently, a putativ...

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

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

    2016-05-01

    This study presents a new chemical cross-linking mass spectrometry (MS) method in combination with electrochemistry and isotope labeling strategy for probing both protein three-dimensional (3D) structures and conformational changes. For the former purpose, the target protein/protein complex is cross-linked with equal mole of premixed light and heavy isotope labeled cross-linkers carrying electrochemically reducible disulfide bonds (i.e., DSP-d0 and DSP-d8 in this study, DSP = dithiobis[succinimidyl propionate]), digested and then electrochemically reduced followed with online MS analysis. Cross-links can be quickly identified because of their reduced intensities upon electrolysis and the presence of doublet isotopic peak characteristics. In addition, electroreduction converts cross-links into linear peptides, facilitating MS/MS analysis to gain increased information about their sequences and modification sites. For the latter purpose of probing protein conformational changes, an altered procedure is adopted, in which the protein in two different conformations is cross-linked using DSP-d0 and DSP-d8 separately, and then the two protein samples are mixed in 1:1 molar ratio. The merged sample is subjected to digestion and electrochemical mass spectrometric analysis. In such a comparative cross-linking experiment, cross-links could still be rapidly recognized based on their responses to electrolysis. More importantly, the ion intensity ratios of light and heavy isotope labeled cross-links reveal the conformational changes of the protein, as exemplified by examining the effect of Ca(2+) on calmodulin conformation alternation. This new cross-linking MS method is fast and would have high value in structural biology. Graphical Abstract ᅟ. PMID:26902947

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

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

    2016-05-01

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

  11. 3D structure of muscle dihydropyridine receptor

    Montserrat Samsó

    2015-01-01

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

  12. Adding 3D-structural context to protein-protein interaction data from high-throughput experiments

    Jüttemann, Thomas

    2011-01-01

    In the past decade, automatisation has led to an immense increase of data in biology. Next generation sequencing techniques will produce a vast amount of sequences across all species in the coming years. In many cases, identifying the function and biological role of a protein from its sequence can be a complicated and time-intensive task. The identification of a protein's interaction partners is a tremendous help for understanding the biological context in which it is involved. In order to fu...

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

    2000-01-01

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

  14. Calibration for 3D Structured Light Measurement

    2007-01-01

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

  15. Determining the Architecture of a Protein-DNA Complex by Combining FeBABE Cleavage Analyses, 3-D Printed Structures, and the ICM Molsoft Program.

    James, Tamara; Hsieh, Meng-Lun; Knipling, Leslie; Hinton, Deborah

    2015-01-01

    Determining the structure of a protein-DNA complex can be difficult, particularly if the protein does not bind tightly to the DNA, if there are no homologous proteins from which the DNA binding can be inferred, and/or if only portions of the protein can be crystallized. If the protein comprises just a part of a large multi-subunit complex, other complications can arise such as the complex being too large for NMR studies, or it is not possible to obtain the amounts of protein and nucleic acids needed for crystallographic analyses. Here, we describe a technique we used to map the position of an activator protein relative to the DNA within a large transcription complex. We determined the position of the activator on the DNA from data generated using activator proteins that had been conjugated at specific residues with the chemical cleaving reagent, iron bromoacetamidobenzyl-EDTA (FeBABE). These analyses were combined with 3-D models of the available structures of portions of the activator protein and B-form DNA to obtain a 3-D picture of the protein relative to the DNA. Finally, the Molsoft program was used to refine the position, revealing the architecture of the protein-DNA within the transcription complex. PMID:26404142

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

    Krishnan Arun

    2008-03-01

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

  17. cyp51A-based mechanism of azole resistance in Aspergillus fumigatus: Illustration by a new 3D Structural Model of Aspergillus fumigatus CYP51A protein.

    Liu, Musang; Zheng, Nan; Li, Dongmei; Zheng, Hailin; Zhang, Lili; Ge, Hu; Liu, Weida

    2016-05-01

    Mutations of CYP51A protein (Cytochrome P450 14-α Sterol demethylase) play a central role in the azole resistance of Aspergillus fumigatus The available structural models of CYP51A protein ofA. fumigatus are built based on that of Homo sapiens and that of Mycobacterium tuberculosis, of which the amino acid homology is only 38% and 29% compared with CYP51A protein ofA. fumigatus, respectively. In the present study, we constructed a new 3D structural model ofA. fumigatus CYP51A protein based on a recently resolved crystal structure of the homologous protein in the fungus S. cerevisiae, which shares 50% amino acid homology with A. fumigatus CYP51A protein. Three azole molecules, itraconazole, voriconazole, and posaconazole, were docked to the wild-type and the mutant A. fumigatus CYP51A protein models, respectively, to illustrate the impact of cyp51A mutations to azole-resistance. We found the mutations that occurred at L98, M220, and Y431 positions would decrease the binding affinity of azoles to the CYP51A protein and therefore would reduce their inhibitory effects. Additionally, the mutations of L98 and G432 would reduce the stability of the protein, which might lead to conformational change of its binding pocket and eventually the resistance to azoles. PMID:26768370

  18. STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes

    Yamagishi Michel EB

    2004-08-01

    Full Text Available Abstract Background The integration of many aspects of protein/DNA structure analysis is an important requirement for software products in general area of structural bioinformatics. In fact, there are too few software packages on the internet which can be described as successful in this respect. We might say that what is still missing is publicly available, web based software for interactive analysis of the sequence/structure/function of proteins and their complexes with DNA and ligands. Some of existing software packages do have certain level of integration and do offer analysis of several structure related parameters, however not to the extent generally demanded by a user. Results We are reporting here about new Sting Millennium Suite (SMS version which is fully accessible (including for local files at client end, web based software for molecular structure and sequence/structure/function analysis. The new SMS client version is now operational also on Linux boxes and it works with non-public pdb formatted files (structures not deposited at the RCSB/PDB, eliminating earlier requirement for the registration if SMS components were to be used with user's local files. At the same time the new SMS offers some important additions and improvements such as link to ProTherm as well as significant re-engineering of SMS component ConSSeq. Also, we have added 3 new SMS mirror sites to existing network of global SMS servers: Argentina, Japan and Spain. Conclusion SMS is already established software package and many key data base and software servers worldwide, do offer either a link to, or host the SMS. SMS (Sting Millennium Suite is web-based publicly available software developed to aid researches in their quest for translating information about the structures of macromolecules into knowledge. SMS allows to a user to interactively analyze molecular structures, cross-referencing visualized information with a correlated one, available across the internet. SMS

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

    Khader Shameer

    2010-06-01

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

  20. Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies

    Stegmaier Philip

    2010-05-01

    Full Text Available Abstract Background Knowledge of transcription factor-DNA binding patterns is crucial for understanding gene transcription. Numerous DNA-binding proteins are annotated as transcription factors in the literature, however, for many of them the corresponding DNA-binding motifs remain uncharacterized. Results The position weight matrices (PWMs of transcription factors from different structural classes have been determined using a knowledge-based statistical potential. The scoring function calibrated against crystallographic data on protein-DNA contacts recovered PWMs of various members of widely studied transcription factor families such as p53 and NF-κB. Where it was possible, extensive comparison to experimental binding affinity data and other physical models was made. Although the p50p50, p50RelB, and p50p65 dimers belong to the same family, particular differences in their PWMs were detected, thereby suggesting possibly different in vivo binding modes. The PWMs of p63 and p73 were computed on the basis of homology modeling and their performance was studied using upstream sequences of 85 p53/p73-regulated human genes. Interestingly, about half of the p63 and p73 hits reported by the Match algorithm in the altogether 126 promoters lay more than 2 kb upstream of the corresponding transcription start sites, which deviates from the common assumption that most regulatory sites are located more proximal to the TSS. The fact that in most of the cases the binding sites of p63 and p73 did not overlap with the p53 sites suggests that p63 and p73 could influence the p53 transcriptional activity cooperatively. The newly computed p50p50 PWM recovered 5 more experimental binding sites than the corresponding TRANSFAC matrix, while both PWMs showed comparable receiver operator characteristics. Conclusions A novel algorithm was developed to calculate position weight matrices from protein-DNA complex structures. The proposed algorithm was extensively validated

  1. A structural basis for Staphylococcal complement subversion: X-ray structure of the complement-binding domain of Staphylococcus aureus protein Sbi in complex with ligand C3d

    Clark, E. A.; Crennell, S.; Upadhyay, A.; Zozulya, A. V.; Mackay, J. D.; Svergun, D.I.; Bagby, S; van den Elsen, J. M.

    2011-01-01

    The structure of the complement-binding domain of Staphylococcus aureus protein Sbi (Sbi-IV) in complex with ligand C3d is presented. The 1.7 Å resolution structure reveals the molecular details of the recognition of thioester-containing fragment C3d of the central complement component C3, involving interactions between residues of Sbi-IV helix α2 and the acidic concave surface of C3d. The complex provides a structural basis for the binding preference of Sbi for native C3 over C3b and explain...

  2. 3D structure prediction of histone acetyltransferase (HAC proteins of the p300/CBP family and their interactome in Arabidopsis thaliana

    Amar Cemanovic

    2014-09-01

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

  3. Understanding the Structure of 3D Shapes

    Livesu, Marco

    2014-01-01

    Compact representations of three dimensional objects are very often used in computer graphics to create effective ways to analyse, manipulate and transmit 3D models. Their ability to abstract from the concrete shapes and expose their structure is important in a number of applications, spanning from computer animation, to medicine, to physical simulations. This thesis will investigate new methods for the generation of compact shape representations. In the first part, the prob...

  4. InterMap3D: predicting and visualizing co-evolving protein residues

    Oliveira, Rodrigo Gouveia; Roque, francisco jose sousa simôes almeida; Wernersson, Rasmus; Sicheritz-Pontén, Thomas; Sackett, Peter Wad; Mølgaard, Anne; Pedersen, Anders Gorm

    2009-01-01

    InterMap3D predicts co-evolving protein residues and plots them on the 3D protein structure. Starting with a single protein sequence, InterMap3D automatically finds a set of homologous sequences, generates an alignment and fetches the most similar 3D structure from the Protein Data Bank (PDB). It...... can also accept a user-generated alignment. Based on the alignment, co-evolving residues are then predicted using three different methods: Row and Column Weighing of Mutual Information, Mutual Information/Entropy and Dependency. Finally, InterMap3D generates high-quality images of the protein with the...

  5. Symposium 20 - PABMB: Teaching biochemistry in a connected world: KEEPING 3D RESOURCES IN THE WEB TO LEARN ON PROTEIN STRUCTURE

    Raul Herrera

    2015-08-01

    Full Text Available Symposium 20 - PABMB: Teaching biochemistry in a connected world Chair: Miguel Castanho, Universidade de Lisboa, PortugalAbstract:The new paradigm of higher education requires new teaching strategies to meet the learning objectives of biochemistry courses. Teaching biochemistry in the current state of science and society requires a special motivation for learning, especially for students of degrees other than Biochemistry. The traditional way of teaching, based on the teacher-student relationship, mostly unidirectional, does not fulfil the needs imposed in this era. Considering the current situation universities students require new abilities in their training and the use of computers can constitute a place for discovery and research, enabling the experience of new and diverse situations. The design of teaching material for undergraduate students who take biochemistry courses as complementary subject on their careers should be seen as an opportunity to complement theoretical aspects on the current courses. Three different approaches could be used: (I a description of the basic concepts, like in a book but using dynamics figures. (II Modelling proteins highlighting key motifs at the three-dimensional structure and residues where inhibitors can be attached. And (III elaborating active quizzes where students can be driven on their learning. Building knowledge based on practical experience can improve student competences on basic science and the learning process can be complemented in the use of dynamics models. On the other hand, exploring protein structures from the web could give students a better comprehension of residues interaction and non-covalent forces involved in protein-protein or protein-ligand interaction. The use of dynamic models improves the comprehension of protein structure and their special link to amino acids residues or ligands. This work was supported by Anillo ACT1110 project. Key Words: protein structure, 3D source, learning

  6. 3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes

    Chen Yung-Chiang; Lo Yu-Shu; Yang Jinn-Moon

    2010-01-01

    Abstract Background Comprehensive exploration of protein-protein interactions is a challenging route to understand biological processes. For efficiently enlarging protein interactions annotated with residue-based binding models, we proposed a new concept "3D-domain interolog mapping" with a scoring system to explore all possible protein pairs between the two homolog families, derived from a known 3D-structure dimmer (template), across multiple species. Each family consists of homologous prote...

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

    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.

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

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

    2015-01-01

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

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

    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. 3-D structures of planetary nebulae

    Steffen, Wolfgang

    2016-01-01

    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.

  11. 3D printing of functional structures

    Krijnen, G.J.M.

    2016-01-01

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

  12. The 3-D Structure of Reconnection Jets

    Drake, J. F.; Swisdak, M. M.; Cassak, P.; Phan, T. D.

    2014-12-01

    We explore the propagation and structure of 3-D reconnection jets inthe Earth's magnetotail using a kinetic model. The finite cross-tailextent of the flow burst significantly changes the structure andevolution of the jet. Ambient ions reflected from the jet frontproduce a region of enhanced pressure that deflects the jet in thecross-tail direction and dissipates a significant fraction of the bulkflow energy. Thus, even subsonic jet fronts are dissipation sites forbulk flow energy. Jets that are narrow in the cross-tail direction aredeflected dominantly in the direction of the ambient ion drift (duskdirection) while wider jets are deflected in both directions. Massloading of the jet due to ions drifting into the jet from the dawnreduce the peak jet velocity below the Walen prediction. The body ofthe jet does not remain laminar but instead becomes strongly turbulentas a result of instabilities growing on the sharp boundaries thatdevelop on dawn and dusk sides of the jet. Both sheared flow andreconnection are drivers of this turbulence. These instabilities causethe reconnection component of the magnetic field Bz to be highlyvariable on spatial scales of around six ion inertial lengths, whichis consistent with that inferred from the typically bursty behavior ofBz in satellite observations of the jet body. Finally, we discussthe mechanisms that control the finite duration of flow bursts in themagnetotail.

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

    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

  14. 3D printing of functional structures

    Krijnen, G.J.M.

    2016-01-01

    The technology colloquial known as ‘3D printing’ has developed in such diversity in printing technologies and application fields that meanwhile it seems anything is possible. However, clearly the ideal 3D Printer, with high resolution, multi-material capability, fast printing, etc. is yet to be developed. Nevertheless, one can al- ready start to wonder what possibilities for electrical engineering applications will become available in the near future. Here I try to give a brief and balanced o...

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

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

    1998-01-01

    The baculovirus expression system was found to be efficient at expressing the 3D, the 3AB and the 3ABC non-structural proteins (NSP) of foot-and-mouth disease virus (FMDV) as antigens recognised by immune sera in ELISA. ELISA's using 3D, 3AB and 3ABC detected antibodies from day 8 and 10 after...... experimental infection of susceptible cattle and sheep and cattle remained seropositive for more than 395 days. The ELISA's detected antibodies against any of the seven serotypes of FMDV. The 3D ELISA was specific and precise and as sensitive as established ELISA's which measure antibody to structural proteins....... The assay may be used as a resource saving alternative to established ELISA's for the detection of antibodies against any of the seven serotypes. The 3AB and the 3ABC ELISA were also specific and precise. FMDV infected cattle could be differentiated from those that had been merely vaccinated as they gave...

  16. The ModFOLD4 server for the quality assessment of 3D protein models

    McGuffin, Liam J; Buenavista, Maria T.; Roche, Daniel B.

    2013-01-01

    Once you have generated a 3D model of a protein, how do you know whether it bears any resemblance to the actual structure? To determine the usefulness of 3D models of proteins, they must be assessed in terms of their quality by methods that predict their similarity to the native structure. The ModFOLD4 server is the latest version of our leading independent server for the estimation of both the global and local (per-residue) quality of 3D protein models. The server produces both machine reada...

  17. 3DSwap: Curated knowledgebase of proteins involved in 3D domain swapping

    Shameer, Khader

    2011-09-29

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

  18. Mechanical properties of structures 3D printed with cementitious powders

    Feng, Peng; Meng, Xinmiao; Chen, Jian Fei; Ye, Lieping

    2015-01-01

    The three dimensional (3D) printing technology has undergone rapid development in the last few years and it is now possible to print engineering structures. This paper presents a study of the mechanical behavior of 3D printed structures using cementitious powder. Microscopic observation reveals that the 3D printed products have a layered orthotropic microstructure, in which each layer consists of parallel strips. Compression and flexural tests were conducted to determine the mechanical proper...

  19. 3D monitoring of active tectonic structures

    Stemberk, Josef; Košťák, Blahoslav; Vilímek, V.

    2003-01-01

    Roč. 36, 1-2 (2003), s. 103-112. ISSN 0264-3707 R&D Projects: GA MŠk OC 625.10 Institutional research plan: CEZ:AV0Z3046908 Keywords : tectonics * monitoring * active structures Subject RIV: DB - Geology ; Mineralogy Impact factor: 0.754, year: 2003

  20. 3D visualization of middle ear structures

    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

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

    Meller Jaroslaw

    2007-08-01

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

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

    Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

    2010-01-01

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

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

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

    2016-03-15

    Herein we report a low cost, sensitive, supercapacitor-powered electrochemiluminescent (ECL) protein immunoarray fabricated by an inexpensive 3-dimensional (3D) printer. The immunosensor detects three cancer biomarker proteins in serum within 35 min. The 3D-printed device employs hand screen printed carbon sensors with gravity flow for sample/reagent delivery and washing. Prostate cancer biomarker proteins, prostate specific antigen (PSA), prostate specific membrane antigen (PSMA) and platelet factor-4 (PF-4) in serum were captured on the antibody-coated carbon sensors followed by delivery of detection-antibody-coated Ru(bpy)3(2+) (RuBPY)-doped silica nanoparticles in a sandwich immunoassay. ECL light was initiated from RuBPY in the silica nanoparticles by electrochemical oxidation with tripropylamine (TPrA) co-reactant using supercapacitor power and ECL was captured with a CCD camera. The supercapacitor was rapidly photo-recharged between assays using an inexpensive solar cell. Detection limits were 300-500f gmL(-1) for the 3 proteins in undiluted calf serum. Assays of 6 prostate cancer patient serum samples gave good correlation with conventional single protein ELISAs. This technology could provide sensitive onsite cancer diagnostic tests in resource-limited settings with the need for only moderate-level training. PMID:26406460

  4. Formal representation of 3D structural geological models

    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.

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

    Herzyk Pawel

    2007-08-01

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

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

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

    2009-04-30

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

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

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

  8. Capacitance extraction from complex 3D interconnect structures

    Cartwright, D.; Csanak, G.; George, D.; Walker, R.; Kuprat, A. [Los Alamos National Lab., NM (United States). Theoretical Div.; Dengi, A.; Grobman, W. [Motorola, Austin, TX (United States)

    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).

  9. 3-D structures viewed with the architect's approach

    Vanggaard, Ole

    2002-01-01

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

  10. 3D local structure around copper site of rabbit prion-related protein: Quantitative determination by XANES spectroscopy combined with multiple-scattering calculations

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

  11. 3D annotation and manipulation of medical anatomical structures

    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.

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

    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

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

    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.

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

    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

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

    Sael Lee

    2009-12-01

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

  16. Nested structures approach for bulk 3D negative index materials

    Andryieuski, Andrei; Malureanu, Radu; Lavrinenko, Andrei

    2009-01-01

    We propose a generic conceptual idea to obtain bulk 3D negative index metamaterials, which exhibit isotropic properties. The design is based on the nested structures approach, when one element providing magnetic response is inserted into another design with negative dielectric constant. Both...

  17. 3D Printing of Protein Models in an Undergraduate Laboratory: Leucine Zippers

    Meyer, Scott C.

    2015-01-01

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

  18. 3-D profile measurement for complex micro-structures

    HU Chun-guang; HU Xiao-dong; XU Lin-yan; GUO Tong; HU Xiao-tang

    2005-01-01

    Micro-structures 3-D profile measurement is an important measurement content for research on micro-machining and characterization of micro-dimension. In this paper,a new method involved 2-D structure template, which guides phase unwrapping,is proposed based on phase-shifting microscopic interferometry.It is fit not only for static measurement, but also for dynamic measurement,especially for motion of MEMS devices.3-D profile of active comb of micro-resonator is obtained by using the method.The theoretic precision in out-of-plane direction is better than 0.5 nm.The in-plane theoretic precision in micro-structures is better than 0.5 μm.But at the edge of micro-structures,it is on the level of micrometer mainly caused by imprecise edge analysis.Finally,its disadvantages and the following development are discussed.

  19. 3D printed components with ultrasonically arranged microscale structure

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

    2016-01-01

    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...

  20. 3D printed components with ultrasonically arranged microscale structure

    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.

  1. Skeleton-Sectional Structural Analysis for 3D Printing

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

    2016-01-01

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

  2. Method for 3D Rendering Based on Intersection Image Display Which Allows Representation of Internal Structure of 3D objects

    Kohei Arai

    2013-01-01

    Method for 3D rendering based on intersection image display which allows representation of internal structure is proposed. The proposed method is essentially different from the conventional volume rendering based on solid model which allows representation of just surface of the 3D objects. By using afterimage, internal structure can be displayed through exchanging the intersection images with internal structure for the proposed method. Through experiments with CT scan images, the proposed met...

  3. All dispenser printed flexible 3D structured thermoelectric generators

    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.

  4. 3D reconstruction methods of coronal structures by radio observations

    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.

  5. Combined shape and topology optimization of 3D structures

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

    2015-01-01

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

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

    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 a...

  7. The DynDom3D Webserver for the Analysis of Domain Movements in Multimeric Proteins.

    Girdlestone, Christopher; Hayward, Steven

    2016-01-01

    DynDom3D is a program for the analysis of domain movements in multimeric proteins. Its inputs are two structure files that indicate a possible domain movement, but the onus has been on the user to process the files so that there is the necessary one-to-one equivalence between atoms in the two atom lists. This is often a prohibitive task to carry out manually, which has limited the application of DynDom3D. Here we report on a webserver with a preprocessor that automatically creates an equivalence between atoms using sequence alignment methods. The processed structure files are passed to DynDom3D and the results are presented on a webpage that includes molecular graphics for easy visualization. PMID:26540459

  8. Automatic structural matching of 3D image data

    Ponomarev, Svjatoslav; Lutsiv, Vadim; Malyshev, Igor

    2015-10-01

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

  9. Polarization Control by Using Anisotropic 3D Chiral Structures

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

    2016-01-01

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

  10. Lifetimes and perturbations of the 3d94s(3D)4p structure in the spectrum of copper I

    Natural radiative lifetimes have been measured of the 2P, 2D, 2F and 4D5/2 terms in the 3d9 4s(3D) 4p structure of copper I. A pulsed hollow cathode was used to generate 3d9 4s22D metastable atoms. From these metastable levels the states investigated were populated by a pulsed dye laser pumped by a Nd:YAG laser. A comparison with theoretical and experimental literature values is given. (orig.)

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

    Carla Rubio-Villena

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

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

    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 ...

  13. Optimized designs for 2D and 3D thermoelastic structures

    Pedersen, Pauli; Pedersen, Niels Leergaard

    2011-01-01

    energy density (or uniform von Mises stress) is presented and applied, and it is shown by examples that the obtained designs are close to fulfilling also strength maximization. Explicit formulas for equivalent thermoelastic loads in 2D and 3D finite element analysis are derived and applied, including the...... proved for thermoelastic structures by compliance sensitivity analysis that return localized determination of sensitivities.The compliance is not identical to the total elastic energy (twice strain energy). An explicit formula for the difference is derived and numerically illustrated with examples. In...

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

    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

  15. Improving 3D structure prediction from chemical shift data

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

  16. Improving 3D structure prediction from chemical shift data

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

    2013-09-15

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

  17. Method for 3D Rendering Based on Intersection Image Display Which Allows Representation of Internal Structure of 3D objects

    Kohei Arai

    2013-06-01

    Full Text Available Method for 3D rendering based on intersection image display which allows representation of internal structure is proposed. The proposed method is essentially different from the conventional volume rendering based on solid model which allows representation of just surface of the 3D objects. By using afterimage, internal structure can be displayed through exchanging the intersection images with internal structure for the proposed method. Through experiments with CT scan images, the proposed method is validated. Also one of other applicable areas of the proposed for design of 3D pattern of Large Scale Integrated Circuit: LSI is introduced. Layered patterns of LSI can be displayed and switched by using human eyes only. It is confirmed that the time required for displaying layer pattern and switching the pattern to the other layer by using human eyes only is much faster than that using hands and fingers.

  18. 3D-structure of the Canes Venatici I Cloud

    Uklein, R I

    2009-01-01

    We present the improved distance moduli of 30 galaxies in the Canes Venatici I Cloud using advanced Tip of Red Giant Branch (TRGB) method (Makarov et.al. 2006). The method was determined for accurate estimation of the distances even if TRGB situated near photometric limit. The data were taken from the Archive of the Hubble Space Telescope (HST). Based on ACS and WFPC2 images of the HST we construct the color-magnitude diagrams of the resolved stellar population of the galaxies using Dolphot and HSTPhot packages. New refined method of the distance determination allows us to clarify the 3D structure of the Canes Venatici I Cloud. It consists of the central group of galaxies around M94 and the outskirt which is situated in gravitational field of the "core". The mass and mass-to-light ratio of the CVn have been estimated.

  19. Structural Indexing for 3D Solid Digital Library

    2001-01-01

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

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

    Kendra K. Schmid

    2012-01-01

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

  1. A new protein binding pocket similarity measure based on comparison of 3D atom clouds: application to ligand prediction

    Hoffmann, Brice; Zaslavskiy, Mikhail; Vert, Jean-Philippe; Stoven, Véronique

    2009-01-01

    Motivation: Prediction of ligands for proteins of known 3D structure is important to understand structure-function relationship, predict molecular function, or design new drugs.\\\\ Results: We explore a new approach for ligand prediction in which binding pockets are represented by atom clouds. Each target pocket is compared to an ensemble of pockets of known ligands. Pockets are aligned in 3D space with further use of convolution kernels between clouds of points. Performance of the new method ...

  2. PDB explorer -- a web based algorithm for protein annotation viewer and 3D visualization.

    Nayarisseri, Anuraj; Shardiwal, Rakesh Kumar; Yadav, Mukesh; Kanungo, Neha; Singh, Pooja; Shah, Pratik; Ahmed, Sheaza

    2014-12-01

    The PDB file format, is a text format characterizing the three dimensional structures of macro molecules available in the Protein Data Bank (PDB). Determined protein structure are found in coalition with other molecules or ions such as nucleic acids, water, ions, Drug molecules and so on, which therefore can be described in the PDB format and have been deposited in PDB database. PDB is a machine generated file, it's not human readable format, to read this file we need any computational tool to understand it. The objective of our present study is to develop a free online software for retrieval, visualization and reading of annotation of a protein 3D structure which is available in PDB database. Main aim is to create PDB file in human readable format, i.e., the information in PDB file is converted in readable sentences. It displays all possible information from a PDB file including 3D structure of that file. Programming languages and scripting languages like Perl, CSS, Javascript, Ajax, and HTML have been used for the development of PDB Explorer. The PDB Explorer directly parses the PDB file, calling methods for parsed element secondary structure element, atoms, coordinates etc. PDB Explorer is freely available at http://www.pdbexplorer.eminentbio.com/home with no requirement of log-in. PMID:25118648

  3. A 3D visualization system for molecular structures

    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.

  4. Basic properties of 3D cast skeleton structures

    M. Cholewa

    2011-12-01

    Full Text Available Purpose: of this paper is to present recent achievements in field of skeleton structures. The aim of this work is to show results of searching for mechanically and technologically advantageous micro- and macrostructures. Methods of microstructure controlling were described. Most important parameters of the manufacturing process were identified.Design/methodology/approach: The influence of internal topology to stress distribution was described with the use of computer simulations. Simulations of the mold filling processes were also carried out. Real experiments were performed to prove the simulation results. The Qualitative and quantitative metallographic analysis were also carried out.Findings: It was found that the octahedron shape of internal cell causes best stress distribution and that the skeleton castings are a good alternative for cellular materials such as metal foams, lattice structures and sandwich panels. Their structured arranged topology allows precise design of properties.Research limitations/implications: Casting methods used to manufacture materials such as described skeleton castings confirmed their usefulness. Not well known and used yet rheological properties of liquid metals allow obtaining shape complicated structures near to metallic foams but structured arranged.Practical implications: Technological parameters of the skeleton castings manufacturing process were developed. Without use of advanced techniques there is a possibility to manufacture cheap skeleton structures in a typical foundry. With use of advanced technology like 3D printing there are almost unlimited possibilities of the skeleton castings internal topologies.Originality/value: Three dimensional cast skeleton structures with internal topology of octahedron confirmed their usefulness as elements used for energy dissipation. Obtaining the homogenous microstructure in the whole volume of complicated shape castings can be achieved.

  5. 3D Imaging with Structured Illumination for Advanced Security Applications

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

    2015-09-01

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

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

    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

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

    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.

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

    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

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

    Earley, Clarke W

    2013-01-01

    Background While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also pr...

  10. 3D representations of amino acids—applications to protein sequence comparison and classification

    Jie Li

    2014-08-01

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

  11. Tangible 3D modeling of coherent and themed structures

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

    2016-01-01

    We present CubeBuilder, a system for interactive, tangible 3D shape modeling. CubeBuilder allows the user to create a digital 3D model by placing physical, non-interlocking cubic blocks. These blocks may be placed in a completely arbitrary fashion and combined with other objects. In effect, this...... turns the task of 3D modeling into a playful activity that hardly requires any learning on the part of the user. The blocks are registered using a depth camera and entered into the cube graph where each block is a node and adjacent blocks are connected by edges. From the cube graph, we transform the...

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

    Kasahara, Kota; Kinoshita, Kengo

    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....

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

    Scott, Mark Andrew

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

  14. Membrane transport mechanism 3D structure and beyond

    Ziegler, Christine

    2014-01-01

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

  15. Nano CT visualizing internal 3D structures with submicrometer resolution

    High-resolution Computed Tomography widely expands the spectrum of detectable internal microstructures. The new nanotom is the first 180 kV nanoCT system worldwide which is tailored completely to highest-resolution applications in material science, micro mechanics, electronics, geology etc. The CT results demonstrate the possibility to analyse the 3D-microstructure of material samples with minimal preparation and the exceptional resolution of less than 0.5 microns per voxel. (authors)

  16. Nano CT visualizing internal 3D structures with submicrometer resolution

    Neuser, E.; Suppes, A. [Phoenix X-Ray Systems, Services GmbH, Wunstorf (Germany)

    2007-07-01

    High-resolution Computed Tomography widely expands the spectrum of detectable internal microstructures. The new nanotom is the first 180 kV nanoCT system worldwide which is tailored completely to highest-resolution applications in material science, micro mechanics, electronics, geology etc. The CT results demonstrate the possibility to analyse the 3D-microstructure of material samples with minimal preparation and the exceptional resolution of less than 0.5 microns per voxel. (authors)

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

    Geronazzo, Michele

    2014-01-01

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

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

    2010-01-01

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

  19. 3D structure prediction of lignolytic enzymes lignin peroxidase and manganese peroxidase based on homology modelling

    SWAPNIL K. KALE

    2016-04-01

    Full Text Available Lignolytic enzymes have great biotechnological value in biopulping, biobleaching, and bioremediation. Manganese peroxidase (EC 1:11:1:13 and lignin peroxidase (EC 1:11:1:14 are extracellular and hem-containing peroxidases that catalyze H2O2-dependent oxidation of lignin. Because of their ability to catalyse oxidation of a wide range of organic compounds and even some inorganic compounds, they got tremendous industrial importance. In this study, 3D structure of lignin and manganese peroxidase has been predicted on the basis of homology modeling using Swiss PDB workspace. The physicochemical properties like molecular weight, isoelectric point, Grand average of hydropathy, instability and aliphatic index of the target enzymes were performed using Protparam. The predicted secondary structure of MnP has 18 helices and 6 strands, while LiP has 20 helices and 4 strands. Generated 3D structure was visualized in Pymol. The generated model for MnP and LiP has Z-score Qmean of 0.01 and -0.71, respectively. The predicted models were validated through Ramachandran Plot, which indicated that 96.1 and 95.5% of the residues are in most favored regions for MnP and LiP respectively. The quality of predicted models were assessed and confirmed by VERIFY 3D, PROCHECK and ERRAT. The modeled structure of MnP and LiP were submitted to the Protein Model Database.

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

    Z. Lou; T. Gevers; N. Hu

    2015-01-01

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

  1. 3D Reconstruction of virtual colon structures from colonoscopy images.

    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

  2. COSMOS: 3D weak lensing and the growth of structure

    Massey, R; Leauthaud, A; Capak, P; Ellis, R; Koekemoer, A; Réfrégier, A; Scoville, N; Taylor, J E; Albert, J; Berge, J; Heymans, C; Johnston, D; Kneib, J P; Mellier, Y; Mobasher, B; Semboloni, E; Shopbell, P; Van Waerbeke, L T L; Massey, Richard; Rhodes, Jason; Leauthaud, Alexie; Capak, Peter; Ellis, Richard; Koekemoer, Anton; Refregier, Alexandre; Scoville, Nick; Taylor, James E.; Albert, Justin; Berge, Joel; Heymans, Catherine; Johnston, David; Kneib, Jean-Paul; Mellier, Yannick; Mobasher, Bahram; Semboloni, Elisabetta; Shopbell, Patrick; Waerbeke, Lidia Tasca & Ludovic Van

    2007-01-01

    We present a three dimensional cosmic shear analysis of the Hubble Space Telescope COSMOS survey, the largest ever optical imaging program performed in space. We have measured the shapes of galaxies for the tell-tale distortions caused by weak gravitational lensing, and traced the growth of that signal as a function of redshift. Using both 2D and 3D analyses, we measure cosmological parameters Omega_m, the density of matter in the universe, and sigma_8, the normalization of the matter power spectrum. The introduction of redshift information tightens the constraints by a factor of three, and also reduces the relative sampling (or "cosmic") variance compared to recent surveys that may be larger but are only two dimensional. From the 3D analysis, we find sigma_8*(Omega_m/0.3)^-0.44=0.866+^0.085_-0.068 at 68% confidence limits, including both statistical and potential systematic sources of error in the total budget. Indeed, the absolute calibration of shear measurement methods is now the dominant source of uncert...

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

    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

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

    Shooji Yamada, Hiroshi Yamaguchi and Sunao Ishihara

    2009-01-01

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

  5. 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles.

    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

  6. Structured Prediction of 3D Human Pose with Deep Neural Networks

    Tekin, Bugra; Katircioglu, Isinsu; Salzmann, Mathieu; Lepetit, Vincent; Fua, Pascal

    2016-01-01

    Most recent approaches to monocular 3D pose estimation rely on Deep Learning. They either train a Convolutional Neural Network to directly regress from image to 3D pose, which ignores the dependencies between human joints, or model these dependencies via a max-margin structured learning framework, which involves a high computational cost at inference time. In this paper, we introduce a Deep Learning regression architecture for structured prediction of 3D human pose from monocular images that ...

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

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

    2016-01-01

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

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

    Lou, Zhongyu; Gevers, Theo; Hu, Ninghang

    2015-10-01

    Extracting the pixel-level 3D layout from a single image is important for different applications, such as object localization, image, and video categorization. Traditionally, the 3D layout is derived by solving a pixel-level classification problem. However, the image-level 3D structure can be very beneficial for extracting pixel-level 3D layout since it implies the way how pixels in the image are organized. In this paper, we propose an approach that first predicts the global image structure, and then we use the global structure for fine-grained pixel-level 3D layout extraction. In particular, image features are extracted based on multiple layout templates. We then learn a discriminative model for classifying the global layout at the image-level. Using latent variables, we implicitly model the sublevel semantics of the image, which enrich the expressiveness of our model. After the image-level structure is obtained, it is used as the prior knowledge to infer pixel-wise 3D layout. Experiments show that the results of our model outperform the state-of-the-art methods by 11.7% for 3D structure classification. Moreover, we show that employing the 3D structure prior information yields accurate 3D scene layout segmentation. PMID:25966478

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

    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

  10. 3D pressure field in lipid membranes and membrane-protein complexes

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

    2009-01-01

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

  11. Choice-related Activity in the Anterior Intraparietal Area during 3-D Structure Categorization.

    Verhoef, Bram-Ernst; Michelet, Pascal; Vogels, Rufin; Janssen, Peter

    2015-06-01

    The anterior intraparietal area (AIP) of macaques contains neurons that signal the depth structure of disparity-defined 3-D shapes. Previous studies have suggested that AIP's depth information is used for sensorimotor transformations related to the efficient grasping of 3-D objects. We trained monkeys to categorize disparity-defined 3-D shapes and examined whether neuronal activity in AIP may also underlie pure perceptual categorization behavior. We first show that neurons with a similar 3-D shape preference cluster in AIP. We then demonstrate that the monkeys' 3-D shape discrimination performance depends on the position in depth of the stimulus and that this performance difference is reflected in the activity of AIP neurons. We further reveal correlations between the neuronal activity in AIP and the subject's subsequent choices and RTs during 3-D shape categorization. Our findings propose AIP as an important processing stage for 3-D shape perception. PMID:25514653

  12. 3D-QSAR studies on Plasmodium falciparam proteins: a mini-review.

    Divakar, Selva; Hariharan, Sivaram

    2015-01-01

    3D-QSAR has become a very important tool in the field of Drug Discovery, especially in important areas like malarial research. The 3D-QSAR is principally a ligand-based drug design but the bioactive conformation of the ligand can also be taken into account in constructing a 3D-QSAR model. The induction of receptor-based 3D-QSAR has been proven to give more robust statistical models. In this review, we have discussed the various 3D-QSAR works done so far which were aimed at combating malaria caused by Plasmodium falciparam. We have also discussed the various enzymes/receptors (targets) in Plasmodium falciparam for which the 3D-QSAR had been generated. The enzymes - wild and mutated dihydrofolate reductase, enoyl acyl protein carrier protein reductase, farnesyltransferase, cytochrome bc1, and falcipains were the major targets for pharmacophore-based drug design. Apart from the above-mentioned targets there were many scaffolds for which the target macromolecule was undefined and could have single/multiple targets. The generated 3D-QSAR model can be used to identify hits by screening the pharmacophore against a chemical library. In this review, the hits identified against various targets of plasmodium falciparam that have been discussed along with their basic scaffold. The various software programs and chemical databases that have been used in the generation of 3D-QSAR and screening were given. From this review, we understand that there is a considerable need to develop novel scaffolds that are different from the existing ligands to overcome cross-resistance. PMID:25543683

  13. The 3D structure of the Galactic bulge

    Zoccali, M

    2016-01-01

    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 {\\it 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]$\\lesssim -0.5$ dex) trace a different structure, and also have different kinematics.

  14. Computation of Electrostatic Properties of 3D MEMS Structures

    Majumdar, N

    2006-01-01

    Micro-Electro-Mechanical Systems (MEMS) normally have fixed or moving structures with cross-sections of the order of microns ($\\mu m$) and lengths of the order of tens or hundreds of microns. These structures are often plates or array of thin beams which, owing to their smallness, can be moved or deflected easily through the application of low voltages. Since electrostatic forces play a very major role in maneuvering these devices, a thorough understanding of the electrostatic properties of these structures is of critical importance, especially in the design phase of MEMS. In many cases, the electrostatic analysis of MEMS is carried out using boundary element method (BEM), while the structural analysis is carried out using finite element method (FEM). In this paper, we focus on accurate electrostatic analysis of MEMS using BEM. In particular, we consider the problem of computing the charge distribution and capacitance of thin conducting plates relevant to the numerical simulation of MEMS. The reason behind th...

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

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

    2011-01-01

    Accurate descriptions of 3D grain structures in polycrystalline materials are of key interest as the grain structure is closely correlated to the macroscopic properties of the material. In the present study, we investigate the accuracy of using Laguerre tessellations to represent 3D grain...... structures from only the spatial center of mass location and the volume of the grains. The ability of Laguerre tessellations to describe accurate grain shapes and topologies of real 3D grain structures are revealed by direct comparison to 3D reconstructions of an un-deformed meta-stable β -titanium alloy...... obtained by phase-contrast micro-tomography. This study reveals that (volume weighted) Laguerre tessellations are superior to classical Voronoi tessellations when it comes to providing accurate representations of real 3D grain structures. Furthermore, although the Laguerre tessellations were only able to...

  16. String structures in driven 3D complex plasma clusters

    Wörner, L; Nosenko, V; Zhdanov, S K; Thomas, H M; Morfill, G E; Schablinski, J; Block, D

    2012-01-01

    The structure of driven three-dimensional complex plasma clusters was studied experimentally. The clusters consisted of around 60 hollow glass spheres with a diameter of 22 microns that were suspended in a plasma of rf discharge in argon. The particles were confined in a glass box with conductive yet transparent coating on its four side walls, this allowed to manipulate the particle cluster by biasing the confining walls in a certain sequence. In this work, a rotating electric field was used to drive the clusters. Depending on the excitation frequency, the clusters rotated (10^4 - 10^7 times slower than the rotating field) or remained stationary. The cluster structure was neither that of nested spherical shells nor simple chain structure. Strings of various lengths were found consisting of 2 to 5 particles, their spatial and temporal correlations were studied. The results are compared to recent simulations.

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

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

    2016-01-01

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

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

    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

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

    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.

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

    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.

  1. The 3D structure of human chromosomes in cell nuclei

    Lukášová, Emilie; Kozubek, Stanislav; Kozubek, Michal; Falk, Martin; Amrichová, J.

    2002-01-01

    Roč. 10, č. 7 (2002), s. 535-548. ISSN 0967-3849 R&D Projects: GA AV ČR IBS5004010; GA AV ČR IAA1065203; GA MZd NC5955; GA ČR GA202/01/0197; GA ČR GA301/01/0186 Institutional research plan: CEZ:AV0Z5004920 Keywords : confocal microscopy * mathematical models * chromosome structure Subject RIV: BO - Biophysics Impact factor: 1.828, year: 2002

  2. 3D Printing for Spacecraft Multi-Functional Structures

    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.

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

    Katharina F. Sonnen

    2012-08-01

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

  4. First images and orientation of fine structure from a 3-D seismic oceanography data set

    T. M. Blacic

    2010-04-01

    Full Text Available We present 3-D images of ocean fine structure from a unique industry-collected 3-D multichannel seismic dataset from the Gulf of Mexico that includes expendable bathythermograph casts for both swaths. 2-D processing reveals strong laterally continuous reflections throughout the upper ~800 m as well as a few weaker but still distinct reflections as deep as ~1100 m. We interpret the reflections to be caused by reversible fine structure from internal wave strains. Two bright reflections are traced across the 225-m-wide swath to produce reflection surface images that illustrate the 3-D nature of ocean fine structure. We show that the orientation of linear features in a reflection can be obtained by calculating the orientations of contours of reflection relief, or more robustly, by fitting a sinusoidal surface to the reflection. Preliminary 3-D processing further illustrates the potential of 3-D seismic data in interpreting images of oceanic features such as internal wave strains. This work demonstrates the viability of imaging oceanic fine structure in 3-D and shows that, beyond simply providing a way visualize oceanic fine structure, quantitative information such as the spatial orientation of features like fronts and solitons can be obtained from 3-D seismic images. We expect complete, optimized 3-D processing to improve both the signal to noise ratio and spatial resolution of our images resulting in increased options for analysis and interpretation.

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

    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.

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

    Schweitzer P.

    2014-03-01

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

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

    Mazhar Hussain Peerzada

    2013-01-01

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

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

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

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

    Yoshiki Yamaguchi

    2012-07-01

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

  10. The advanced simulation of fatigue crack growth in complex 3D structures

    Kolk, Karsten; Kuhn, Guenther [Institute of Applied Mechanics, Erlangen (Germany)

    2006-12-15

    An advanced incremental crack growth algorithm for the three-dimensional (3D) simulation of fatigue crack growth in complex 3D structures with linear elastic material behavior is presented. To perform the crack growth simulation as effectively as possible an accurate stress analysis is done by the boundary-element method (BEM) in terms of the 3D dual BEM. The question concerning a reliable 3D crack growth criterion is answered based on experimental observations. All criteria under consideration are numerically realized by a predictor-corrector procedure. The agreement between numerically determined and experimentally observed crack fronts will be shown on both fracture specimens and an industrial application. (orig.)

  11. 3D nano-structures for laser nano-manipulation

    Gediminas Seniutinas

    2013-09-01

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

  12. Atomic layer deposition in porous structures: 3D photonic crystals

    This paper reports recent results from studies of atomic layer deposition for the infiltration of three-dimensional photonic crystals. Infiltration of ZnS:Mn and TiO2 are reported for SiO2-based opal templates. It has been demonstrated that high filling fractions can be achieved and that the infiltrated material can be of high crystalline quality as assessed by photoluminescence measurements. The highly conformal and uniform coatings obtained in these studies are shown to contribute significantly to the photonic band gap properties. These investigations show the advantages of atomic layer deposition (ALD) as a flexible and practical pathway for attaining high performance photonic crystal structures and optical microcavities

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

    2002-01-01

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

  14. 3-D Structure of Sunspots Using Imaging Spectroscopy

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

    2006-12-01

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

  15. 3D Digital Design of Cranes' Structures Based on Hybrid Software Architecture

    WANG Chonghua; LI Hua

    2006-01-01

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

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

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

    2015-01-01

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

  17. Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle

    Reverter Antonio

    2008-10-01

    Full Text Available Abstract Background Myogenesis is an ordered process whereby mononucleated muscle precursor cells (myoblasts fuse into multinucleated myotubes that eventually differentiate into myofibres, involving substantial changes in gene expression and the organisation of structural components of the cells. To gain further insight into the orchestration of these structural changes we have overlaid the spatial organisation of the protein components of a muscle cell with their gene expression changes during differentiation using a new 3D visualisation tool: the Virtual Muscle 3D (VMus3D. Results Sets of generic striated muscle costamere, Z-disk and filament proteins were constructed from the literature and protein-interaction databases. Expression profiles of the genes encoding these proteins were obtained from mouse C2C12 cells undergoing myogenesis in vitro, as well as a mouse tissue survey dataset. Visualisation of the expression data in VMus3D yielded novel observations with significant relationships between the spatial location and the temporal expression profiles of the structural protein products of these genes. A muscle specificity index was calculated based on muscle expression relative to the median expression in all tissues and, as expected, genes with the highest muscle specificity were also expressed most dynamically during differentiation. Interestingly, most genes encoding costamere as well as some Z-disk proteins appeared to be broadly expressed across most tissues and showed little change in expression during muscle differentiation, in line with the broader cellular role described for some of these proteins. Conclusion By studying gene expression patterns from a structural perspective we have demonstrated that not all genes encoding proteins that are part of muscle specific structures are simply up-regulated during muscle cell differentiation. Indeed, a group of genes whose expression program appears to be minimally affected by the

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

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

    2003-01-01

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

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

    In this paper, we consider the general setting for constructing action principles for three-dimensional first-order autonomous equations. We present the results for some integrable and non-integrable cases of the Lotka-Volterra equation, and show Lagrangian descriptions which are valid for systems satisfying Shil'nikov criteria on the existence of strange attractors, though chaotic behaviour has not been verified up to now. The Euler-Lagrange equations we get for these systems usually present 'time reparametrization' invariance, though other kinds of invariance may be found according to the kernel of the associated symplectic 2-form. The formulation of a Hamiltonian structure (Poisson brackets and Hamiltonians) for these systems from the Lagrangian viewpoint leads to a method of finding new constants of the motion starting from known ones, which is applied to some systems found in the literature known to possess a constant of the motion, to find the other and thus showing their integrability. In particular, we show that the so-called ABC system is completely integrable if it possesses one constant of the motion

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

    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.

  1. Hydrothermal Synthesis, Crystal Structure and Characterization of a Microporous 3D Pillared-Layer 3d-4f Copper-Holmium Heterometallic Coordination Polymer

    A microporous 3D pillared-layer 3d-4f (Cu+-Ho3+) coordination polymer based on the linkages of 2D wavelike Ho-carboxylate layers and 1D Cu4Br4 inorganic chains in centipede-type structure by IN. pillars has been obtained. Furthermore, the magnetic properties of this complex have been investigated. Our results provide an intriguing example of 3D 3d-4f PCPs and further demonstrate that the pillared-layer approach can be used for constructing novel 3D 3d-4f PCPs. There has been more and more interest in recent years in the design and synthesis of porous coordination polymers (PCPs) not only for their fascinating structural diversity but also for their potential applications as functional materials in magnetism, molecular adsorption, gas storage, ion exchange, catalysis and separation. Up to now, almost all approaches to the construction of porous materials have focused on the 3D monometallic PCPs. However, the preparation of hetero-metallic PCPs especially containing lanthanide (Ln) and transition metal (TM) ions has been drawn less attention. A pillared-layer approach to the construction of 3D 3d-4f coordination polymers upon the connections of Ln-carboxylate layers and TM-inorganic motifs by organic pillars via coordination bonding has been reported. In most such 3D pillared-layer 3d-4f structures, TM-inorganic layers/chains generally obstruct the development of channels based on the pores formed by Ln-carboxylate layers

  2. Effect of sterilization on structural and material properties of 3-D silk fibroin scaffolds.

    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

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

    Mingchao Li; Yanqing Han; Gang Wang; Fugen Yan

    2014-01-01

    Based on abundant geological data of different regions and different scales in hydraulic engineering, a new approach of 3D engineering-scale and statistical-scale integrated modeling was put forward, considering the complex relationships among geological structures and discontinuities and hydraulic structures. For engineering-scale geological structures, the 3D rock mass model of the study region was built by the exact match modeling method and the reliability analysis technique. For statisti...

  4. 3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

    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.

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

    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.

  6. Protein Structure

    Asmus, Elaine Garbarino

    2007-01-01

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

  7. 3D Printers Can Provide an Added Dimension for Teaching Structure-Energy Relationships

    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.

  8. 3D structure of individual nanocrystals in solution by electron microscopy

    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.

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

    Theis, Corinna; Höner zu Siederdissen, Christian; Hofacker, Ivo L.;

    2013-01-01

    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 22495 3D modules in all PDB files results in 977 internal loop...

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

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

    2013-01-31

    The apoptotic ligand TNF-related apoptosis ligand (TRAIL) is expressed on the membrane of immune cells during HIV infection. The intracellular stockade of TRAIL in human primary CD4(+) T cells is not known. Here we investigated whether primary CD4(+) T cells expressed TRAIL in their intracellular compartment and whether TRAIL is relocalized on the plasma membrane under HIV activation. We found that TRAIL protein was stocked in intracellular compartment in non activated CD4(+) T cells and that the total level of TRAIL protein was not increased under HIV-1 stimulation. However, TRAIL was massively relocalized on plasma membrane when cells were cultured with HIV. Using three dimensional (3D) microscopy we localized TRAIL protein in human T cells and developed a new method to visualize plasma membrane without the need of a membrane marker. This method used the 3D interactive surface plot and bright light acquired images. PMID:23085529

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

    Buchan, D. W. A.; Rison, S. C. G.; Bray, J.E.; Lee, D; Pearl, F.; Thornton, J M; Orengo, C. 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 s...

  12. 3D image of protein visualization in a whole rice grain using an automatic precision microtome system

    Ogawa, Yukiharu; Ohtani, Toshio; Sugiyama, Junichi; Hagiwara, Shoji; Tanaka, Kunisuke; Kudoh, Ken-ichi; Higuchi, Toshiro

    2000-05-01

    The 3D image formation technique using confocal microscopy has allows visualization of the 3D chemical structure in small parts of the bio-body. However, the large-scale 3D structure such as the distribution of chemical components throughout the whole body has not been shown. To allow such large scale visualization of the 3D internal analysis technique for bio-body has been developed.

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

    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.

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

    Kotlarchyk, Maxwell Aaron

    2011-07-01

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

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

    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

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

    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.

  17. Resonant structure of the 3d electron's angular distribution in a free Mn+Ion

    The 3d-electron angular anisotropy parameter of the free Mn+ ion is calculated using the open-quotes spin-polarizedclose quotes random-phase approximation with exchange. Strong resonance structure is discovered, which is due to interference with the powerful 3p → 3d discrete excitation. The effect of the 3p → 4s transition is also noticeable. The ordering of these respective resonances with phonon energy increase proved to be opposite in angular anisotropy parameter to that in 3d-photoionization cross section. A paper describing these results was published

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

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

    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

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

    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

  1. BioShell-Threading: versatile Monte Carlo package for protein 3D threading

    Gniewek, Pawel; Kolinski, Andrzej; Kloczkowski, Andrzej; Gront, Dominik

    2014-01-01

    Background The comparative modeling approach to protein structure prediction inherently relies on a template structure. Before building a model such a template protein has to be found and aligned with the query sequence. Any error made on this stage may dramatically affects the quality of result. There is a need, therefore, to develop accurate and sensitive alignment protocols. Results BioShell threading software is a versatile tool for aligning protein structures, protein sequences or sequen...

  2. 3-D velocity structure in the central-eastern part of Qilianshan

    张元生; 周民都; 荣代潞; 张立光; 许中秋

    2004-01-01

    The 3-D velocity tomography image of the central-eastern part of Qilianshan is obtained by the joint inversion of3-D velocity structure and focal parameters based on the S-P data of micro-earthquakes recorded by the digitalseismic network set up for a Sino-French cooperation program since 1996. The inversed velocity structure doesprimarily reflect some important features of the deep structure in the region and provide the scientific backgroundfor the further study of active tectonic structure and the calculation of earthquake parameters.

  3. Phononic Band Gaps in 2D Quadratic and 3D Cubic Cellular Structures

    Franziska Warmuth

    2015-12-01

    Full Text Available The static and dynamic mechanical behaviour of cellular materials can be designed by the architecture of the underlying unit cell. In this paper, the phononic band structure of 2D and 3D cellular structures is investigated. It is shown how the geometry of the unit cell influences the band structure and eventually leads to full band gaps. The mechanism leading to full band gaps is elucidated. Based on this knowledge, a 3D cellular structure with a broad full band gap is identified. Furthermore, the dependence of the width of the gap on the geometry parameters of the unit cell is presented.

  4. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae's Inner Colliding Winds

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

    2015-01-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (>120 M_Sun), highly eccentric (e ~ 0.9) binary star system Eta Carinae. We demonstrate the methodology used to incorporate 3D interactive figures into a PDF journal publication and the benefits of using 3D visualization and 3D printing as tools to analyze data from multidimensional numerical simulations. Using a consumer-grade 3D printer (MakerBot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics (SPH) simulations of Eta Carinae's inner (r ~ 110 au) wind-wind collision interface at multiple orbital phases. The 3D prints and visualizations reveal important, previously unknown 'finger-like' structures at orbital phases shortly after periastron (phi ~ 1.045) that protrude radially outward from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. thin-shell, Rayleigh-Taylor) that arise a...

  5. Hyperfine structure of the 3d34s4p 6G multiplet of atomic vanadium

    The spectrum of atomic vanadium was recorded using high-resolution Fourier transform spectroscopy with optical bandpass filters in the wavelength range from 360 to 500 nm. Vanadium atoms are produced and excited in a hollow-cathode discharge. The main focus lies on the determination of the magnetic dipole hyperfine constants A of the lowest multiplet of odd parity, the 6G of the configuration 3d34s4p, the hyperfine structure (HFS) of which was unknown to date. The HFS of the lines, connecting this multiplet with the multiplets 3d34s5s 6F, 3d34s4d 6H and 3d34s4d 6G, was observed and analysed. New results are presented for all six levels belonging to 3d34s4p 6G as well as for seven high-lying levels belonging to 3d34s4d 6H and 3d34s4d 6G. The experimental results for the lowest multiplet of odd parity are compared with calculated magnetic dipole hyperfine constants which were estimated using the effective-operator formalism in the pure LS coupling case.

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

    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. (paper)

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

    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.

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

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

    Erika Fantino

    2016-07-01

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

  10. 3D plasma response to magnetic field structure in the Large Helical Device

    The three-dimensional (3D) plasma response to the magnetic eld structure is studied for high-β plasmas in the Large Helical Device (LHD). The radial electric field, Er, is measured in the peripheral region. The positive electric field appears in the region and that suggests the boundary between opened and closed field lines. The position of appearing positive Er is always the outside of the vacuum boundary. A 3D MHD modeling predicts the expanding of the effective plasma boundary by the 3D plasma response. The position of appearing strong Er is almost comparable to expanded plasma boundary of the modeling. That is, the 3D plasma response is identified in the LHD experiments. (author)

  11. 3D printing of weft knitted textile based structures by selective laser sintering of nylon powder

    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.

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

    Kumar, Dinesh

    2013-01-01

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

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

    S. Tavani

    2011-05-01

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

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

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

  14. 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.

    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

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

    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. MaxMod: a hidden Markov model based novel interface to MODELLER for improved prediction of protein 3D models.

    Parida, Bikram K; Panda, Prasanna K; Misra, Namrata; Mishra, Barada K

    2015-02-01

    Modeling the three-dimensional (3D) structures of proteins assumes great significance because of its manifold applications in biomolecular research. Toward this goal, we present MaxMod, a graphical user interface (GUI) of the MODELLER program that combines profile hidden Markov model (profile HMM) method with Clustal Omega program to significantly improve the selection of homologous templates and target-template alignment for construction of accurate 3D protein models. MaxMod distinguishes itself from other existing GUIs of MODELLER software by implementing effortless modeling of proteins using templates that bear modified residues. Additionally, it provides various features such as loop optimization, express modeling (a feature where protein model can be generated directly from its sequence, without any further user intervention) and automatic update of PDB database, thus enhancing the user-friendly control of computational tasks. We find that HMM-based MaxMod performs better than other modeling packages in terms of execution time and model quality. MaxMod is freely available as a downloadable standalone tool for academic and non-commercial purpose at http://www.immt.res.in/maxmod/. PMID:25636267

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

    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 sampl...

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

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

    2004-01-01

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

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

    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.

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

    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

  1. 3D Multiscale Integrated Modeling Approach of Complex Rock Mass Structures

    Mingchao Li

    2014-01-01

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

  2. 3D flexible NiTi-braided elastomer composites for smart structure applications

    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. (paper)

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

    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.

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

    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

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

    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.

  6. Evaluation and assessment of the seismic responses of 3-D base-isolated structures

    Hueffmann, G.K.; Sutton, W.T. [GERB Vibration Control Systems, Inc., Westmont, IL (United States)

    1995-12-01

    The 1994 Northridge earthquake offered the opportunity to evaluate and assess the seismic response of several base-isolated buildings. Assessment of 2-D base isolation is straightforward comparing separately the uncoupled horizontal and vertical building motions to the corresponding ground motions. With 3-D systems characterized by low vertical natural frequencies, the system assessment must include rocking of the structure. Neglecting this consideration leads to an erroneous conclusion that the system greatly amplifies vertical ground accelerations. The paper evaluates the seismic response of a 3-D base-isolated building as compared to the same structure on a 2-D system. The paper also shows that the vertical accelerations measured at extreme locations in the building on a 3-D base-isolation system develop mainly from rocking responses to the horizontal ground motion.

  7. 3D Coronal Density Reconstruction and Retrieving the Magnetic Field Structure during Solar Minimum

    Kramar, M; Mikić, Z; Davila, J

    2014-01-01

    Measurement of the coronal magnetic field is a crucial ingredient in understanding the nature of solar coronal phenomena at all scales. We employed STEREO/COR1 data obtained during a deep minimum of solar activity in February 2008 (Carrington rotation CR 2066) to retrieve and analyze the three-dimensional (3D) coronal electron density in the range of heights from 1.5 to 4 Rsun using a tomography method. With this, we qualitatively deduced structures of the coronal magnetic field. The 3D electron density analysis is complemented by the 3D STEREO/EUVI emissivity in the 195 A band obtained by tomography for the same CR. A global 3D MHD model of the solar corona was used to relate the reconstructed 3D density and emissivity to open/closed magnetic field structures. We show that the density maximum locations can serve as an indicator of current sheet position, while the locations of the density gradient maximum can be a reliable indicator of coronal hole boundaries. We find that the magnetic field configuration du...

  8. 3D Global Coronal Density Structure and Associated Magnetic Field near Solar Maximum

    Kramar, Maxim; Lin, Haosheng

    2016-01-01

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

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

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

    2015-01-01

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

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

    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.

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

    Claudia Hänel

    2014-05-01

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

  12. 3D Integral Model of Induction Heating of Thin Nonmagnetic Structures

    Barglik, J.; Doležel, Ivo; Škopek, M.; Šolín, Pavel; Ulrych, B.

    Perugia: University of Perugia, 2002. s. 276. [Biennial IEEE Conference on Electromagnetic Field Computation /10./. 16.06.2002-19.06.2002, Perugia] R&D Projects: GA MŠk ME 542 Keywords : 3D integral model * thin nonmagnetic structures Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering

  13. 3D micro-structures by piezoelectric inkjet printing of gold nanofluids

    Kullmann, Carmen

    2012-04-18

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

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

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

    2010-01-01

    This contribution presents our recent progress on developing an efficient fully-nonlinear potential flow model for simulating 3D wave-wave and wave-structure interaction over arbitrary depths (i.e. in coastal and offshore environment). The model is based on a high-order finite difference scheme...

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

    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

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

    Xiong Shishu; Huang Liting; Chen Jinfeng; Su Jingsu

    2005-01-01

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

  17. 3D micro-structures by piezoelectric inkjet printing of gold nanofluids

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

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

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

    2015-01-01

    Recent experimental and computational progress has revealed a large potential for RNA structure in the genome. This has been driven by computational strategies that exploit multiple genomes of related organisms to identify common sequences and secondary structures. However, these computational....... These modules can, for example, occur inside structural elements which in RNA 2D predictions appear as internal loops. Hence one question is if the use of such RNA 3D information can improve the prediction accuracy of RNA secondary structure at a genome-wide level. Here, we use RNAz in combination with...... below 25% when certain 3D module predictions are present in the window of the 2D prediction. We discuss the implications and prospects for further development of computational strategies for detection of RNA 2D structure in genomic sequence....

  19. Computational Approach in Formulating Mechanical Characteristics of 3D Star Honeycomb Auxetic Structure

    Mozafar Shokri Rad

    2015-01-01

    Full Text Available Auxetic materials exhibit a unique characteristic due to the altered microstructure. Different structures have been used to model these materials. This paper treats a development of finite element model and theoretical formulation of 3D star honeycomb structure of these materials. Various shape parameters of the structural cell were evaluated with respect to the basic mechanical properties of the cell. Finite element and analytical approach for various geometrical parameters were numerically used to formulate the characteristics of the material. The study aims at quantifying mechanical properties for any domain in which auxetic material is of interest for variations in geometrical parameters. It is evident that mechanical properties of the material could be controlled by changing the base wall angle of the configuration. The primary outcome of the study is a design guideline for the use of 3D star honeycomb auxetic cellular structure in structural applications.

  20. Better 3D Inspection with Structured Illumination Part I: Signal Formation and Precision

    Yang, Zheng; Häusler, Gerd

    2015-01-01

    For quality control in the factory, 3D-metrology faces increasing demands for high precision and for more space-bandwidth-speed-product SBSP (number of 3D-points/sec). As a potential solution, we will discuss Structured-Illumination Microscopy (SIM). We distinguish optically smooth and rough surfaces and develop a theoretical model of the signal formation for both surface species. This model is exploited to investigate the physical limits of the precision and to give rules to optimize the sensor parameters for best precision or high speed. This knowledge can profitably be combined with fast scanning strategies, to maximize the SBSP, which will be discussed in paper part II.

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

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

    2011-01-01

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

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

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

    2016-07-01

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

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

    Richter, T.S.

    2007-12-03

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

  4. Structural elements and collapse regimes in 3D flows on a slope

    The mechanisms and structural elements of an instability whose development results in the collapse of flow fragments have been studied in the scope of the Hamilton version of the “shallow water” 3D model on a slope. The study indicated that the 3D model differs from its 2D analog in a more varied set of collapsing solutions. In particular, the solutions describing anisotropic collapse, during which the area of a collapsing fragment in contact with the slope contracts into a segment rather than a point, exist together with the solutions describing radially symmetric (isotropic) collapse.

  5. Recursive 3D-reconstruction of structured scenes using a moving camera - application to robotics

    This thesis is devoted to the perception of a structured environment, and proposes a new method which allows a 3D-reconstruction of an interesting part of the world using a mobile camera. Our work is divided into three essential parts dedicated to 2D-information aspect, 3D-information aspect, and a validation of the method. In the first part, we present a method which produces a topologic and geometric image representation based on 'segment' and 'junction' features. Then, a 2D-matching method based on a hypothesis prediction and verification algorithm is proposed to match features issued from two successive images. The second part deals with 3D-reconstruction using a triangulation technique, and discuses our new method introducing an 'Estimation-Construction-Fusion' process. This ensures a complete and accurate 3D-representation, and a permanent position estimation of the camera with respect to the model. The merging process allows refinement of the 3D-representation using a powerful tool: a Kalman Filter. In the last part, experimental results issued from simulated and real data images are reported to show the efficiency of the method. (author)

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

    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

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

    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.

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

    Bai Shiye

    2016-05-01

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

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

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

    2015-01-15

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

  10. Multilayer based interferential-plasmonic structure: metal cluster 3D grating combined with dielectric mirror

    Janicki, V.; Sancho-Parramon, J.; Zorc, H. [Ruder Boskovic Institute, Zagreb (Croatia)

    2011-06-15

    A three-dimensional (3D) photonic microstructure consisting of metal clusters embedded in dielectric matrix is coated with a dielectric mirror. The produced photonic structure shows optical behaviour that combines the interferential effects of the multilayer stack and the surface plasmon resonance of metal clusters. Due to its feasibility and the possibility to widely modify the optical properties of the resulting interferential-plasmonic structure, this approach represents a promising method for the production of novel optical components. (orig.)

  11. Soil-structure interaction during tunnelling in urban area: observations and 3D numerical modelling

    Fargnoli, Valentina

    2015-01-01

    This work illustrates a soil-tunnel-structure interaction study performed by an integrated,geotechnical and structural,approach based on 3D finite element analyses and validated against experimental observations.The study aims at analysing the response of reinforced concrete framed buildings on discrete foundations in interaction with metro lines.It refers to the case of the twin tunnels of the Milan (Italy) metro line 5,recently built in coarse grained materials using EPB machines,for which ...

  12. A relational extension of the notion of motifs: application to the common 3D protein substructures searching problem.

    Pisanti, Nadia; Soldano, Henry; Carpentier, Mathilde; Pothier, Joel

    2009-12-01

    The geometrical configurations of atoms in protein structures can be viewed as approximate relations among them. Then, finding similar common substructures within a set of protein structures belongs to a new class of problems that generalizes that of finding repeated motifs. The novelty lies in the addition of constraints on the motifs in terms of relations that must hold between pairs of positions of the motifs. We will hence denote them as relational motifs. For this class of problems, we present an algorithm that is a suitable extension of the KMR paradigm and, in particular, of the KMRC as it uses a degenerate alphabet. Our algorithm contains several improvements that become especially useful when-as it is required for relational motifs-the inference is made by partially overlapping shorter motifs, rather than concatenating them. The efficiency, correctness and completeness of the algorithm is ensured by several non-trivial properties that are proven in this paper. The algorithm has been applied in the important field of protein common 3D substructure searching. The methods implemented have been tested on several examples of protein families such as serine proteases, globins and cytochromes P450 additionally. The detected motifs have been compared to those found by multiple structural alignments methods. PMID:20047489

  13. Optical scanning of dusty 3D-structures formed in a glow discharge

    Karasev, V. Yu.; Dzlieva, E. S.; Ivanov, A. Yu.; Éĭkhval'D, A. I.; Golubev, M. V.

    2009-06-01

    3D-quasi-crystals formed in strata of a glow discharge are scanned in the optical range with the help of a moving laser knife and high-speed videorecording. The spatial positions of dusty grains are determined. The ordering of structures and the type of arrangement of particles are determined from a comparison of pair correlation functions constructed for the structures under study with correlation functions corresponding to ideal crystalline structures. Several types of unit cells are found through the visual collation of separate parts of structures. As compared to data from the literature on experiments in a high-frequency discharge, the structures under study have a clearly pronounced anisotropy.

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

    2010-01-01

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

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

    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

  16. Grounded electrical source airborne transient EM (GREATEM) response for 3D structure

    Complete text of publication follows. Airborne electromagnetics (AEM) is a useful tool for investigating subsurface structures because it can survey large and inaccessible areas. Disadvantages include lower accuracy and limited depth of investigation. The Grounded Electrical Source Airborne Transient Electromagnetic (GREATEM) survey system was developed to increase the depth of investigation possible using AEM. The method was tested in some volcanoes at 2004-2005. Survey results were verified by comparing the GREATEM data with other geophysical surveys and LOTEM data for the same location based on the transient response and resistivity structure. The resistivity structures obtained from both systems were almost identical. GREATEM responses for 3D structures such as complicated subsurface and topographic effect are essential problem to apply it to survey in active tectonic area and volcano. Anomalous responses due to 3D structures are a potential cause of data distortion. Some researchers addressed this problem in the context of DIGHEM-type AEM, based on three-dimensional modeling. Their results showed that larger distortion appears at boundaries. In case of topographic effect, magnetic field responses decrease at the top of a trapezoidal hill and increase at its foot. The other hand, 3D effects in LOTEM data, obtained by three-dimensional modeling, such as effect of shallower complicated anomalous structure or topography are only significant at very early times, when it is manifest as a modification of the undistorted curve that nonetheless preserves its primary characteristics. We investigated the 3D structure effect on GREATEM data using a three dimensional modeling method. The effects are almost similar to that for LOTEM.

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

    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.

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

    TAO Jun

    2006-01-01

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

  19. The degree of π electron delocalization and the formation of 3D-extensible sandwich structures.

    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

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

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

    ). Furthermore, we show that any data structure for the d-dimensional orthogonal range reporting problem in the pointer machine model of computation that uses S(n) space must spend Ω((log n/ log(S(n)/n))⌊d/2⌋--1) time to answer queries. Thus, if S(n)/n is poly-logarithmic, then the query time is at least Ω......, this is not the case in higher dimensions. In this paper we provide a space optimal pointer machine data structure for 3-d orthogonal range reporting that answers queries in O(log n + k) time. Thus we settle the complexity of the problem in 3-d. We use this result to obtain improved structures in...

  1. Intra-chain 3D segment swapping spawns the evolution of new multidomain protein architectures.

    Szilágyi, András; Zhang, Yang; Závodszky, Péter

    2012-01-01

    Multidomain proteins form in evolution through the concatenation of domains, but structural domains may comprise multiple segments of the chain. In this work, we demonstrate that new multidomain architectures can evolve by an apparent three-dimensional swap of segments between structurally similar domains within a single-chain monomer. By a comprehensive structural search of the current Protein Data Bank (PDB), we identified 32 well-defined segment-swapped proteins (SSPs) belonging to 18 structural families. Nearly 13% of all multidomain proteins in the PDB may have a segment-swapped evolutionary precursor as estimated by more permissive searching criteria. The formation of SSPs can be explained by two principal evolutionary mechanisms: (i) domain swapping and fusion (DSF) and (ii) circular permutation (CP). By large-scale comparative analyses using structural alignment and hidden Markov model methods, it was found that the majority of SSPs have evolved via the DSF mechanism, and a much smaller fraction, via CP. Functional analyses further revealed that segment swapping, which results in two linkers connecting the domains, may impart directed flexibility to multidomain proteins and contributes to the development of new functions. Thus, inter-domain segment swapping represents a novel general mechanism by which new protein folds and multidomain architectures arise in evolution, and SSPs have structural and functional properties that make them worth defining as a separate group. PMID:22079367

  2. 3D structure and conductive thermal field of the Upper Rhine Graben

    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

  3. Continuous 3D particle focusing in a microchannel with curved and symmetric sharp corner structures

    A new microchannel that enables continuous three-dimensional (3D) particle focusing with a single sheath flow is reported. The 3D particle focusing is based on the combination of the microfluidic drifting effect induced by a curved microchannel and the momentum-change-induced inertial effect induced by a series of repeated symmetric sharp corner structures on both side walls of the microchannel. The microfluidic drifting effect induces particle focusing in the vertical direction (z direction) while the momentum-change-induced inertial effect induces particle focusing in the horizontal direction (on the x–y plane). Eventually, particles are three-dimensionally focused at the center of the microchannel. The 3D particle focusing behavior in the present microchannel was demonstrated by the experiment using 7.32 μm particles at a sample flow rate of 66.7 μL min−1 and a sheath flow rate of 400 μL min−1. Force analysis and computational fluid dynamics (CFD) simulation confirmed particles of different sizes (from 5 to 15 μm) could also be three-dimensionally focused in the present microchannel over a wide range of flow rates. In comparison with other 3D passive focusing techniques, this microchannel built in a single layer only requires a single sheath flow, and hence avoids complex flow control. With its simple structure and operation, this device can potentially be used in 3D particle focusing processes in many lab-on-a chip applications, such as micro flow cytometer. (paper)

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

    Carlos Morón

    2015-05-01

    Full Text Available This paper describes a new low-cost means to detect and locate mechanical impacts (collisions on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach.

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

    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.

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

    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

  7. 3D Temperature Mapping of Solar Photospheric Fine Structure Using Ca II H Filtergrams

    Henriques, V M J

    2012-01-01

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

  8. An active robot vision system for real-time 3-D structure recovery

    This paper presents an active approach for the task of computing the 3-D structure of a nuclear plant environment from an image sequence, more precisely the recovery of the 3-D structure of cylindrical objects. Active vision is considered by computing adequate camera motions using image-based control laws. This approach requires a real-time tracking of the limbs of the cylinders. Therefore, an original matching approach, which relies on an algorithm for determining moving edges, is proposed. This method is distinguished by its robustness and its easiness to implement. This method has been implemented on a parallel image processing board and real-time performance has been achieved. The whole scheme has been successfully validated in an experimental set-up

  9. 3D Structural Patterns in Scalable, Elastomeric Scaffolds Guide Engineered Tissue Architecture

    Kolewe, Martin E.; Park, Hyoungshin; Gray, Caprice; Ye, Xiaofeng; Langer, Robert; Freed, Lisa E.

    2013-01-01

    Microfabricated elastomeric scaffolds with 3D structural patterns are created by semi-automated layer-by-layer assembly of planar polymer sheets with through-pores. The meso-scale interconnected pore architectures governed by the relative alignment of layers are shown to direct cell and muscle-like fiber orientation in both skeletal and cardiac muscle, enabling scale up of tissue constructs towards clinically relevant dimensions.

  10. Continuous monitoring of bread dough fermentation using a 3D vision Structured Light technique

    Ivorra Martínez, Eugenio; Verdú Amat, Samuel; Sánchez Salmerón, Antonio José; Barat Baviera, José Manuel; Grau Meló, Raúl

    2014-01-01

    Fermentation of the dough is an important phase in the bread-making process which is affected by several important factors related to raw materials and processing. Changes in fermentation affect parameters in the final product, such as texture, palatability and general quality. For this reason, it is important to develop dynamic methods to study this phase. In this work, a 3D vision system based on Structured Light (SL) was used to monitor the fermentation phase. The evolution of the dough wa...

  11. Correlative Nanoscale 3D Imaging of Structure and Composition in Extended Objects

    Xu, Feng; Helfen, Lukas; Suhonen, Heikki; Elgrabli, Dan; Bayat, Sam; Reischig, Peter; Baumbach, Tilo; Cloetens, Peter

    2014-01-01

    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...

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

    Claudia Hänel; Peter Pieperhoff; Katrin Amunts

    2014-01-01

    The visualization of the progression of brain tissue loss in neurodegenerative diseases like corticobasal syndrome (CBS) can provide not only information about the localization and distribution of the volume loss, but also helps to understand the course and the causes of this neurodegenerative disorder. The visualization of such medical imaging data is often based on 2D sections, because they show both internal and external structures in one image. Spatial information, however, is lost. 3D vi...

  13. Bayesian Models for Multimodal Perception of 3D Structure and Motion

    Ferreira, J.F.; Bessière, Pierre; Mekhnacha, Kamel; Lobo, J.; J. Dias; Laugier, Christian

    2008-01-01

    In this text we will formalise a novel solution, the Bayesian Volumetric Map (BVM), as a framework for a metric, short-term, egocentric spatial memory for multimodal perception of 3D structure and motion. This solution will enable the implementation of top-down mechanisms of attention guidance of perception towards areas of high entropy/uncertainty, so as to promote active exploration of the environment by the robotic perceptual system. In the process, we will to try address the inherent chal...

  14. Correlative Nanoscale 3D Imaging of Structure and Composition in Extended Objects

    Feng Xu; Lukas Helfen; Heikki Suhonen; Dan Elgrabli; Sam Bayat; Péter Reischig; Tilo Baumbach; Peter Cloetens

    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...

  15. 3D Diagnostics of Coherent Structures in a Thermal Plasma Jet

    Hlína, Jan; Sekerešová, Zuzana; Šonský, Jiří

    Brno : Brno University of Technology, 2007, s. 93-96. ISBN 978-80-214-3359-5. [Symposium on Physics of Switching Arc - FSO 2007 /17./. Nové Město na Moravě (CZ), 10.09.2007-13.09.2007] R&D Projects: GA ČR GA202/05/0728 Institutional research plan: CEZ:AV0Z20570509 Keywords : coherent structure * thermal plasma jet * 3D reconstruction Subject RIV: BL - Plasma and Gas Discharge Physics

  16. Mechanical properties of 3D auxetic structures produced by additive manufacturing

    Jiroušek, O.; Koudelka_ml., Petr; Fíla, Tomáš

    Prague: Institute of theoretical and applied mechanics, Academy of Sciences of the Czech Republic, v. v. i., 2015 - (Náprstek, J.; Fischer, C.), s. 124-125 ISBN 978-80-86246-42-0. ISSN 1805-8248. [Engineering mechanics 2015 /21./. Svratka (CZ), 11.05.2015-14.05.2015] Institutional support: RVO:68378297 Keywords : auxetic structure * direct 3D printing * finite element method * digital image correlation Subject RIV: JJ - Other Materials

  17. Towards cost-efficient prospection and 3D visualization of underwater structures using compact ROVs

    Stal, Cornelis; Deruyter, Greet; Paelinck, Mieke; Vandenbulcke, Annelies; De Wulf, Alain

    2015-01-01

    The deployment of Remotely Operated Vehicles (ROV) for underwater prospection and 3D visualization has grown significantly in civil applications for a few decades. The demand for a wide range of optical and physical parameters of underwater environments is explained by an increasing complexity of the monitoring requirements of these environments. The prospection of engineering constructions (e.g. quay walls or enclosure doors) and underwater heritage (e.g. wrecks or sunken structures) heavily...

  18. Integration of nano-scale components and supports in micromachined 3D silicon structures

    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. (paper)

  19. 3-D Structure of the Slave and Rae Cratons Provides Clues to Their Construction

    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.

  20. 3D Axon structure extraction and analysis in confocal fluorescence microscopy images.

    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

  1. Syntheses, structures, luminescence, and magnetism of four 3D lanthanide 5-sulfosalicylates

    Four 3D lanthanide(III) complexes with 5-sulfosalicylic acid (H3SSA) as bridging ligands, Ln(SSA)(H2O)2 [Ln=Ce(III) (1), Pr(III) (2), Nd(III) (3) and Dy(III) (4)], have been synthesized and characterized by elemental analysis, IR, XRD and single-crystal X-ray diffraction. X-ray structural analysis reveals that isostructral complexes 1-4 possess 3D structures with 4664 topology. Complexes 1 and 2 exhibit broad intraligand fluorescent emission bands. Complexes 3 and 4 not only display intraligand fluorescent emission bands, but also present Nd(III) characteristic emission in the near-IR region and sensitized luminescence of Dy(III) ions in the visible region, respectively. Variable-temperature magnetic susceptibility measurements of 2-4 have been studied over the temperature range of 4-300 K. - Graphical abstract: Syntheses and crystal structures of four 3D lanthanide-5-sulfosalicylates, Ln(SSA)(H2O)2 [Ln=Ce(III) (1), Pr(III) (2), Nd(III) (3), and Dy(III) (4)], have been reported. In complexes 1-4, Ln(III) acting as 5-connected inorganic node and SSA3- ligand acing as 5-connected organic node interlink into rarely reported 4664 topology network. Luminescence and magnetism properties have also been studied

  2. Minimizing camera-eye optical aberrations during the 3D reconstruction of retinal structures

    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.

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

    An overview of the mathematical structure of the three-dimensional (3D) Ising model is given from the points of view of topology, algebra, and geometry. By analyzing the relationships among transfer matrices of the 3D Ising model, Reidemeister moves in the knot theory, Yang-Baxter and tetrahedron equations, the following facts are illustrated for the 3D Ising model. 1) The complex quaternion basis constructed for the 3D Ising model naturally represents the rotation in a (3+1)-dimensional space-time as a relativistic quantum statistical mechanics model, which is consistent with the 4-fold integrand of the partition function obtained by taking the time average. 2) A unitary transformation with a matrix that is a spin representation in 2n·l·o-space corresponds to a rotation in 2n·l·o-space, which serves to smooth all the crossings in the transfer matrices and contributes the non-trivial topological part of the partition function of the 3D Ising model. 3) A tetrahedron relationship would ensure the commutativity of the transfer matrices and the integrability of the 3D Ising model, and its existence is guaranteed by the Jordan algebra and the Jordan-von Neumann-Wigner procedures. 4) The unitary transformation for smoothing the crossings in the transfer matrices changes the wave functions by complex phases φx, φy, and φz. The relationship with quantum field and gauge theories and the physical significance of the weight factors are discussed in detail. The conjectured exact solution is compared with numerical results, and the singularities at/near infinite temperature are inspected. The analyticity in β = 1/(kBT) of both the hard-core and the Ising models has been proved only 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. (review)

  4. Protein structure database search and evolutionary classification

    Yang, Jinn-Moon; Tung, Chi-Hua

    2006-01-01

    As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the statistical significance (E-value) of an alignment to indicate the reliability of the prediction. Using...

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

    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

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

    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

  7. 3D measurement method based on combined temporal encoding structured light

    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.

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

    Ferro, Carlo Giovanni; Brischetto, Salvatore; Torre, Roberto; Maggiore, Paolo

    2016-07-01

    The Fused Deposition Modelling (FDM) technology is widely used in rapid prototyping. 3D printers for home desktop applications are usually employed to make non-structural objects. When the mechanical stresses are not excessive, this technology can also be successfully employed to produce structural objects, not only in prototyping stage but also in the realization of series pieces. The innovative idea of the present work is the application of this technology, implemented in a desktop 3D printer, to the realization of components for aeronautical use, especially for unmanned aerial systems. For this purpose, the paper is devoted to the statistical study of the performance of a desktop 3D printer to understand how the process performs and which are the boundary limits of acceptance. Mechanical and geometrical properties of ABS (Acrylonitrile Butadiene Styrene) specimens, such as tensile strength and stiffness, have been evaluated. ASTM638 type specimens have been used. A capability analysis has been applied for both mechanical and dimensional performances. Statistically stable limits have been determined using experimentally collected data.

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

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

    2000-01-01

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

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

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

    2010-01-01

    Patient motion during scanning deteriorates image quality, especially for high resolution PET scanners. A new proposal for a 3D head tracking system for motion correction in high resolution PET brain imaging is set up and demonstrated. A prototype tracking system based on structured light with a...... DLP projector and a CCD camera is set up on a model of the High Resolution Research Tomograph (HRRT). Methods to reconstruct 3D point clouds of simple surfaces based on phase-shifting interferometry (PSI) are demonstrated. The projector and camera are calibrated using a simple stereo vision procedure...... where the projector is treated as a camera. Additionally, the surface reconstructions are corrected for the non-linear projector output prior to image capture. The results are convincing and a first step toward a fully automated tracking system for measuring head motions in PET imaging...

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

    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.

  12. Shape optimization of 3D continuum structures via force approximation techniques

    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.

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

    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

  14. Isotropic 3D Nuclear Morphometry of Normal, Fibrocystic and Malignant Breast Epithelial Cells Reveals New Structural Alterations

    Nandakumar, Vivek; Kelbauskas, Laimonas; Hernandez, Kathryn F.; Lintecum, Kelly M.; Senechal, Patti; Bussey, Kimberly J.; Davies, Paul C.W.; Johnson, Roger H.; Meldrum, Deirdre R.

    2012-01-01

    Background Grading schemes for breast cancer diagnosis are predominantly based on pathologists' qualitative assessment of altered nuclear structure from 2D brightfield microscopy images. However, cells are three-dimensional (3D) objects with features that are inherently 3D and thus poorly characterized in 2D. Our goal is to quantitatively characterize nuclear structure in 3D, assess its variation with malignancy, and investigate whether such variation correlates with standard nuclear grading ...

  15. 3D visualization of deformation structures and potential fluid pathways at the Grimsel Test Site

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

    2015-04-01

    Knowledge on the ability of fluids to infiltrate subsurface rocks is of major importance for underground constructions, geothermal or radioactive waste disposal projects. In this study, we focus on the characterization of water infiltration pathways, their 3D geometries and origins. Based on surface and subsurface mapping in combination with drill core data, we developed by the use of MoveTM (Midland Valley Exploration Ltd.) a 3D structural model of the Grimsel Test Site (GTS). GTS is an underground laboratory operated by NAGRA, the Swiss organisation responsible for the management of nuclear waste. It is located within a suite of post-Variscan magmatic bodies comprising former granitic and granodioritic melts, which are dissected by mafic and aplitic dikes. During Alpine orogeny, the suite was tectonically overprinted within two stages of ductile deformation (Wehrens et al., in prep.) followed by brittle overprint of some of the shear zones during the retrograde exhumation history. It is this brittle deformation, which controls today's water infiltration network. However, the associated fractures, cataclasites and fault gouges are controlled themselves by aforementioned pre-existing mechanical discontinuities, whose origin ranges back as far as to the magmatic stage. For example, two sets of vertically oriented mafic dikes (E-W and NW-SE striking) and compositional heterogeneities induced by magmatic segregation processes in the plutonic host rocks served as nucleation sites for Alpine strain localization. Subsequently, NE-SW, E-W and NW-SE striking ductile shear zones were formed, in combination with high temperature fracturing while dissecting the host rocks in a complex 3D pattern (Wehrens et al, in prep.). Whether the ductile shear zones have been subjected to brittle reactivation and can serve as infiltration pathways or not, depends strongly on their orientations with respect to the principal stress field. Especially where deformation structures intersect

  16. Finite element analysis of the impact response of reinforced concrete structures using DYNA3D

    Reinforced concrete structures in nuclear installations are potentially subject to accidental impact from external or internally generated hazards. These include: soft impacts such as aircraft crash on containment structures; and hard impacts such as heavy dropped loads on pond floors, or plant-generated fragments on structural and protective walls. The explicit finite element code DYNA3D has been used extensively for analysis of the response of structures to dynamic loadings, and a constitutive material model for reinforced concrete has been developed within DYNA3D to represent local cracking and crushing due to impact loads, as well as treating the elastic and plastic global response modes of the structure. This model has been extensively validated against impact tests for simulated aircraft impact on containment structures, but more recent interest has concentrated on analysis of hard impacts on floors and walls. Whilst a simplified constitutive model is adequate for the response to soft impacts, in which the dominant response mode is flexural, the local damage and high rates experienced in hard impacts have required further development of the material model. This paper describes the main features of the constitutive model, and presents the results of a validation case of a heavy dropped load on a reinforced concrete floor. (author)

  17. PIV measurements in a microfluidic 3D-sheathing structure with three-dimensional flow behaviour

    Klank, Henning; Goranovic, Goran; Kutter, Jörg Peter; Gjelstrup, Henrik; Michelsen, J.; Westergaard, C.H.

    2002-01-01

    The design and production time for complex microfluidic systems is considerable, often up to several months. It is therefore important to be able to understand and predict the flow phenomena prior to design and fabrication of the microdevice in order to save costly fabrication resources. The...... structures are often of complex geometry and include strongly three-dimensional flow behaviour, which poses a challenge for the micro particle image velocimetry (micro-PIV) technique. The flow in a microfluidic 3D-sheathing structure has been measured throughout the volume using micro-PIV. In addition, a...

  18. DisPerSE: robust structure identification in 2D and 3D

    Sousbie, Thierry

    2013-01-01

    We present the DIScrete PERsistent Structures Extractor (DisPerSE), an open source software for the automatic and robust identification of structures in 2D and 3D noisy data sets. The software is designed to identify all sorts of topological structures, such as voids, peaks, sources, walls and filaments through segmentation, with a special emphasis put on the later ones. Based on discrete Morse theory, DisPerSE is able to deal directly with noisy datasets using the concept of persistence (a measure of the robustness of topological features) and can be applied indifferently to various sorts of data-sets defined over a possibly bounded manifold : 2D and 3D images, structured and unstructured grids, discrete point samples via the delaunay tesselation, Healpix tesselations of the sphere, ... Although it was initially developed with cosmology in mind, various I/O formats have been implemented and the current version is quite versatile. It should therefore be useful for any application where a robust structure iden...

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

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

    2003-01-01

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

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

    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

  1. Facile fabrication of super-hydrophobic surfaces with 3D pillar structures

    Zhai, Shengjie; Zhao, Hui; Jiang, Yingtao

    2012-11-01

    Super-hydrophobic surfaces have attracted growing interest due to their unique properties, including drag reduction, facilitation of heat transfer, self-cleaning, anti-corrosion, anti-sticking, and anti-contamination. However, the method of fabricating super-hydrophobic surfaces with regular 3D micro/nano pillars structures is still complicated. Here we present a simple, reliable, and low-cost fabrication method which can create complex 3D structures. Briefly, the commercial nanostamping products like CD, DVD,and bluray disc serve as the PDMS mold The pit size (LxWxH) of CD, DVD, and Blueray is 0.8 μm × 0.15 μm × 0.1 μm, 0.4 μm × 0.15 μm × 0.1 μm, and 0.15 μm × 0.15 μm × 0.1 μm. The PDMS surface with the relevant structures can be directly replicated from the molds by the soft lithography technology. The precise geometric structures including height, width, and density of pillar arrays can be readily controlled by using different optical discs. The contact angle is measured about 136-140 degree. We also study the relationship between the contact angle and different feature size. Finally, we measure the slip length for different structures.

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

    马艳平; 李嘉彬; 郝乐; 刘振兴; 冯国清; 周结珊; 柯浩

    2013-01-01

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

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

    M.-F. Robbe

    2006-01-01

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

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

    Platnick, Steven; Zinner, Tobias; Ackerman, S.

    2008-01-01

    Remote sensing of cloud particle size with passive sensors like MODIS is an important tool for cloud microphysical studies. As a measure of the radiatively relevant droplet size, effective radius can be retrieved with different combinations of visible through shortwave infrared channels. MODIS observations sometimes show significantly larger effective radii in marine boundary layer cloud fields derived from the 1.6 and 2.1 pm channel observations than for 3.7 pm retrievals. Possible explanations range from 3D radiative transport effects and sub-pixel cloud inhomogeneity to the impact of drizzle formation on the droplet distribution. To investigate the potential influence of these factors, we use LES boundary layer cloud simulations in combination with 3D Monte Carlo simulations of MODIS observations. LES simulations of warm cloud spectral microphysics for cases of marine stratus and broken stratocumulus, each for two different values of cloud condensation nuclei density, produce cloud structures comprising droplet size distributions with and without drizzle size drops. In this study, synthetic MODIS observations generated from 3D radiative transport simulations that consider the full droplet size distribution will be generated for each scene. The operational MODIS effective radius retrievals will then be applied to the simulated reflectances and the results compared with the LES microphysics.

  5. PACS-based interface for 3D anatomical structure visualization and surgical planning

    Koehl, Christophe; Soler, Luc; Marescaux, Jacques

    2002-05-01

    The interpretation of radiological image is routine but it remains a rather difficult task for physicians. It requires complex mental processes, that permit translation from 2D slices into 3D localization and volume determination of visible diseases. An easier and more extensive visualization and exploitation of medical images can be reached through the use of computer-based systems that provide real help from patient admission to post-operative followup. In this way, we have developed a 3D visualization interface linked to a PACS database that allows manipulation and interaction on virtual organs delineated from CT-scan or MRI. This software provides the 3D real-time surface rendering of anatomical structures, an accurate evaluation of volumes and distances and the improvement of radiological image analysis and exam annotation through a negatoscope tool. It also provides a tool for surgical planning allowing the positioning of an interactive laparoscopic instrument and the organ resection. The software system could revolutionize the field of computerized imaging technology. Indeed, it provides a handy and portable tool for pre-operative and intra-operative analysis of anatomy and pathology in various medical fields. This constitutes the first step of the future development of augmented reality and surgical simulation systems.

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

    Duelis Viana, Camila; Endlein, Arthur; Ademar da Cruz Campanha, Ginaldo; Henrique Grohmann, Carlos

    2016-05-01

    The acquisition of geological attitudes on rock cuts using traditional field compass survey can be a time consuming, dangerous, or even impossible task depending on the conditions and location of outcrops. The importance of this type of data in rock-mass classifications and structural geology has led to the development of new techniques, in which the application of photogrammetric 3D digital models has had an increasing use. In this paper we present two algorithms for extraction of attitudes of geological discontinuities from virtual outcrop models: ply2atti and scanline, implemented with the Python programming language. The ply2atti algorithm allows for the virtual sampling of planar discontinuities appearing on the 3D model as individual exposed surfaces, while the scanline algorithm allows the sampling of discontinuities (surfaces and traces) along a virtual scanline. Application to digital models of a simplified test setup and a rock cut demonstrated a good correlation between the surveys undertaken using traditional field compass reading and virtual sampling on 3D digital models.

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

    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

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

    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 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 areas. Our final 3D Earth model is tested using forward wave simulations of earthquakes (M ≥ 3.7) that were not used during the inversion process. The comparison of observed

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

    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.

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

    Ernie G. Kalnins

    2012-06-01

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

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

    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 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 nanotom® demonstrate that it is now possible to analyze the three-dimensional micro structure of materials and small objects with submicrometer resolution. Any internal difference in material, density or porosity within a sample can be visualized and data like distances can be measured

  12. Construction of conducting and photoconducting 3D structures with submicron resolution in electrooptical substrates

    It is shown that the implantation of protons in electrooptical substrates enables the construction of 3D structures with submicron features that are both conductive and photoconductive embedded in amorphized regions that possess reduced refractive index. The conductivity and photoconductivity are attributed to the transformation of the material into a degenerate semiconductor due to the formation of high concentration of OH- complexes that are created by the bonding of the implanted H+ ions to the O-2 ions of the lattice. It is argued that these results extend significantly the capabilities of integrated photonic circuits and devices fabricated by Refractive Index Engineering by ion implantations. (orig.)

  13. Phase Structure of a 3D Nonlocal U(1) Gauge Theory: Deconfinement by Gapless Matter Fields

    Arakawa, Gaku; Ichinose, Ikuo; Matsui, Tetsuo; Sakakibara, Kazuhiko; Takashima, Shunsuke

    2005-01-01

    In this paper, we study a 3D compact U(1) lattice gauge theory with a variety of nonlocal interactions that simulates the effects of gapless/gapful matter fields. This theory is quite important to investigate the phase structures of QED$_3$ and strongly-correlated electron systems like the 2D quantum spin models, the fractional quantum Hall effect, the t-J model of high-temperature superconductivity. We restrict the nonlocal interactions among gauge variables only to those along the temporal ...

  14. Quantification of spatial structure of human proximal tibial bone biopsies using 3D measures of complexity

    Saparin, Peter I.; Thomsen, Jesper Skovhus; Prohaska, Steffen; Zaikin, Alexei; Kurths, Jürgen; Hege, H.-C.; Gowin, Wolfgang

    3D data sets of human tibia bone biopsies acquired by a micro-CT scanner. In order to justify the newly proposed approach, the measures of complexity of the bone architecture were compared with the results of traditional 2D bone histomorphometry. The proposed technique is able to quantify the......Changes in trabecular bone composition during development of osteoporosis are used as a model for bone loss in microgravity conditions during a space flight. Symbolic dynamics and measures of complexity are proposed and applied to assess quantitatively the structural composition of bone tissue from...

  15. Preservation of protein fluorescence in embedded human dendritic cells for targeted 3D light and electron microscopy

    HÖHN, K.; Fuchs, J; FRÖBER, A.; KIRMSE, R.; Glass, B.; ANDERS‐ÖSSWEIN, M.; Walther, P.; KRÄUSSLICH, H.‐G.; Dietrich, C.

    2015-01-01

    Summary In this study, we present a correlative microscopy workflow to combine detailed 3D fluorescence light microscopy data with ultrastructural information gained by 3D focused ion beam assisted scanning electron microscopy. The workflow is based on an optimized high pressure freezing/freeze substitution protocol that preserves good ultrastructural detail along with retaining the fluorescence signal in the resin embedded specimens. Consequently, cellular structures of interest can readily ...

  16. 3-D analysis of semiconductor dopant distributions in a patterned structure using LEAP

    Moore, J.S. [Department of Materials Science and Engineering, University of Florida, P.O. Box 116130, 525 Engineering Builing, Gainesville, FL 32611 (United States)], E-mail: jsm200@ufl.edu; Jones, K.S. [Department of Materials Science and Engineering, University of Florida, P.O. Box 116130, 525 Engineering Builing, Gainesville, FL 32611 (United States); Kennel, H.; Corcoran, S. [Intel Corporation, Hillsboro, OR (United States)

    2008-05-15

    This work presents the first 3-D analysis of lateral dopant diffusion in a patterned structure using a pulsed laser-assisted local electrode atom probe (LEAP). A structure similar to a device channel was created for this work by performing a 3 keV, 1x10{sup 15} cm{sup -2} As{sup +} implant on a poly-Si line patterned wafer with 70 nm line width and 200 nm line pitch. The wafer was subsequently annealed at 950 deg. C for 1 s. LEAP samples were made using a site-selective in-situ focused ion beam (FIB) process. The results from LEAP analysis were then compared with high-resolution transmission electron microscopy (HRTEM) and Florida object-oriented process simulator (FLOOPS) results. Good structural agreement was found between the LEAP and HRTEM results. Several 1-D As concentration profiles extracted from the LEAP data were also found to be in good agreement with FLOOPS process simulation results. These profiles also represent for the first time that results from a 3-D process simulator have been able to be confirmed experimentally using a single sample.

  17. 3D X-rays application for precision measurement of the cell structure of extruded polystyrene

    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.

  18. Assessment of Damage Detection in Composite Structures Using 3D Vibrometry

    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.

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

    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.

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

    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

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

    Feng Xu

    Full Text Available Structure and composition at the nanoscale determine the behavior of biological systems and engineered materials. The drive to understand and control this behavior has placed strong demands on developing methods for high resolution imaging. In general, the improvement of three-dimensional (3D resolution is accomplished by tightening constraints: reduced manageable specimen sizes, decreasing analyzable volumes, degrading contrasts, and increasing sample preparation efforts. Aiming to overcome these limitations, we present a non-destructive and multiple-contrast imaging technique, using principles of X-ray laminography, thus generalizing tomography towards laterally extended objects. We retain advantages that are usually restricted to 2D microscopic imaging, such as scanning of large areas and subsequent zooming-in towards a region of interest at the highest possible resolution. Our technique permits correlating the 3D structure and the elemental distribution yielding a high sensitivity to variations of the electron density via coherent imaging and to local trace element quantification through X-ray fluorescence. We demonstrate the method by imaging a lithographic nanostructure and an aluminum alloy. Analyzing a biological system, we visualize in lung tissue the subcellular response to toxic stress after exposure to nanotubes. We show that most of the nanotubes are trapped inside alveolar macrophages, while a small portion of the nanotubes has crossed the barrier to the cellular space of the alveolar wall. In general, our method is non-destructive and can be combined with different sample environmental or loading conditions. We therefore anticipate that correlative X-ray nano-laminography will enable a variety of in situ and in operando 3D studies.

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

    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.

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

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

    2016-01-01

    Integration of complex photonic structures onto optical fiber facets enables powerful platforms with unprecedented optical functionalities. Conventional nanofabrication technologies, however, do not permit viable integration of complex photonic devices onto optical fibers owing to their low throughput and high cost. In this paper we report the fabrication of a three dimensional structure achieved by direct Nanoimprint Lithography on the facet of an optical fiber. Nanoimprint processes and tools were specifically developed to enable a high lithographic accuracy and coaxial alignment of the optical device with respect to the fiber core. To demonstrate the capability of this new approach, a 3D beam splitter has been designed, imprinted and optically characterized. Scanning electron microscopy and optical measurements confirmed the excellent lithographic capabilities of the proposed approach as well as the desired optical performance of the imprinted structure. The inexpensive solution presented here should enabl...

  4. Factors Affecting the Precision of Electrostatic Computation of 3D MEMS Structures

    Majumdar, N

    2006-01-01

    Micro-Electro-Mechanical Systems (MEMS) normally have fixed or moving structures (plates or array of thin beams) with cross-sections of the order of microns and lengths of the order of tens or hundreds of microns. Electrostatic forces play a very major role in maneuvering these devices, and hence, a thorough understanding of the electrostatic properties of these structures is of critical importance. Recently, a nearly exact boundary element method (neBEM) solver has been developed and used to solve difficult problems related to electrostatics of various devices. Because of the exact foundation expressions, this solver has been found to be very accurate while solving critical problems which normally necessitate special formulations involving elegant, but difficult mathematics. In this work, we investigate the effects of various possible approximations on the 3D electrostatic solutions obtained for MEMS structures. In particular, we investigate the effects of discretization, omission of surfaces with small amou...

  5. Novel ultra-high 3D resolution surface structuring and thin film stress investigation

    Messow, Ferdinand; Todorov, Daniel; Kusserow, Thomas; Wittzack, Stefan; Koehler, Florestan; Bartels, Martin; Hillmer, Hartmut [University of Kassel (Germany). Institute of Nanostructure Technologies and Analytics

    2009-07-01

    To improve the efficiency of photovoltaic systems, functional surfaces are attractive to guide light into photo sensitive regions - capable of mass production with easy and cheap structuring. Today, NanoImprint uses 2D templates in most cases. Our novel NanoImprint templates reveal residual surface roughness and accuracies down to 0.2 nm. High-resolution 3D imprinted structures are presented. Further efficiency increase can be achieved by anti-reflection coatings. Unfortunately most thin films provide stress and, therefore, define self-organized structures on viscoelastic organic materials due to stress release. Local stress of thin zirconium dioxide and silicon dioxide films deposited by ion beam sputter deposition was scrutinized, since these materials show no absorption in the UV-range, enlarging the range of usable light.

  6. An Acinetobacter trimeric autotransporter adhesin reaped from cells exhibits its nonspecific stickiness via a highly stable 3D structure.

    Yoshimoto, Shogo; Nakatani, Hajime; Iwasaki, Keita; Hori, Katsutoshi

    2016-01-01

    Trimeric autotransporter adhesins (TAAs), cell surface proteins of Gram-negative bacteria, mediate bacterial adhesion to host cells and extracellular matrix proteins. However, AtaA, a TAA in the nonpathogenic Acinetobacter sp. strain Tol 5, shows nonspecific, high adhesiveness to abiotic material surfaces as well as to biotic surfaces. AtaA is a homotrimer of polypeptides comprising 3,630 amino acids and forms long nanofibers; therefore, it is too large and structurally complex to be produced as a recombinant protein. In this study, we isolated AtaA's passenger domain (AtaA PSD), which is translocated to the cell surface through the C-terminal transmembrane domain and exhibits biological functions, using a new method. We introduced a protease recognition site and reaped AtaA nanofibers 225 nm in length from the cell surface through proteolytic cleavage with a specific protease. Biochemical and biophysical analyses of the purified native AtaA PSD revealed that it has a stable structure under alkaline and acidic conditions. Temperatures above 80 °C, which disrupted AtaA's higher-order structure but maintained the full-length AtaA polypeptide, inactivated AtaA's nonspecific adhesiveness, suggesting that the stickiness of AtaA requires its 3D structure. This finding refutes the widespread but vague speculation that large unfolded polypeptides readily stick to various surfaces. PMID:27305955

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

    2006-01-01

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

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

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

    2012-01-01

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

  9. 3D-Printed Broadband Dielectric Tube Terahertz Waveguide with Anti-Reflection Structure

    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.

  10. Poloidal structure of the plasma edge with 3D magnetic fields

    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.

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

    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.

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

    Ceylan, Duygu

    2014-01-01

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

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

    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. (paper)

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

    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

  15. Flow structure of the solids in a 3-D gas-liquid-solid fluidized bed

    Larachi, F.; Cassanello, M.; Chaouki, J.; Guy, C. [Ecole Polytechnique, Montreal, Quebec (Canada). Dept. of Chemical Engineering

    1996-09-01

    Gas-liquid-solid fluidized systems have made inroads into a variety of industrial applications from heavy oil, petroleum resid, and synthetic crude processing to fermentation and aerobic biological wastewater treatment. Local and macroscopic solids flow structure and kinematics in a 3-D gas-liquid-solid fluidized bed were studied using a noninvasive radioactive-particle tracking (RPT) technique. Based on the multisite detection of {gamma} radiations emitted from a single radiolabeled tracer particle freely moving in the fluidized bed, RPT permitted the authors to obtain fast sampling of 3-D trajectories of the tracer, whose physical properties were similar to those of the solids inventory. These trajectories showed the detailed motion sequences of the solid particles as entrained in the bubble wakes, fluctuating randomly or sinking deterministically in the liquid-solid emulsion. Based on measurements done in the vortical-spiral flow regime, the dynamic solids flow structure inside a three-phase fluidized bed can be viewed as a three-zone core-annulus-annulus structure: a central fast-bubble flow region with the particles swirling upward; a vortical flow region around the velocity inversion point with the particles momentarily captured in emulsion vortices; and a relatively bubble-free descending flow region where the particles spiral down between the velocity inversion point and vessel walls. The flow structure of dense fluidized beds are similar to the flow structure of liquid and/or solid in lean fluidized beds. Measured distributions of local ensemble-averaged particle velocities and turbulence intensities were consistent with the existence of a toroidal recirculatory solids flow pattern in the bed. Measured mean circumferential ensemble-averaged radial velocity was essentially zero throughout most of the bed. The solids flow turbulence field was nonisotropic, as radial turbulence intensities were generally lower than longitudinal turbulence intensities.

  16. 3D EBSD characterization of deformation structures in commercial purity aluminum

    A method to map the microstructure in deformed aluminum in three dimensions is presented. The method employs serial sectioning by mechanical polishing, and electropolishing to obtain a good surface quality, and orientation mapping of individual grains in each section by electron backscattered diffraction. Techniques to carefully align the sample and to accurately measure the thickness of the material removed in each serial section are described. A new method for stacking the two dimensional maps together to produce a three dimensional visualization of the microstructure is presented. The data are analyzed in terms of the deformation-induced orientation spread within each grain. In particular the advantage of using three dimensional data, as opposed to two dimensional data, is illustrated, by inclusion of information about the three dimensional morphology of a grain and its neighbors. - Research Highlights: The deformation structures in commercial purity aluminum were characterized in 3D. The method employs serial sectioning by mechanical polishing, and electropolishing to obtain a good surface quality, and orientation mapping of individual grains in each section by electron backscattered diffraction. Techniques to carefully align the sample and to accurately measure the thickness of the material removed in each serial section are described. A new method for stacking the two dimensional maps together to produce a three dimensional visualization of the microstructure is presented. The data are analyzed in terms of the deformation-induced orientation spread within each grain. In particular the advantage of using three dimensional data, as opposed to two dimensional data, is illustrated, by inclusion of information about the three dimensional morphology of a grain and its neighbors. The highlights of the paper include: → a method to obtain 3D EBSD data over a large volume → a modified method for section alignment based on characteristics of deformed grains

  17. 3D EBSD characterization of deformation structures in commercial purity aluminum

    Lin, F.X., E-mail: lnfe@risoe.dtu.dk [Laboratory of Advanced Materials, Department of Materials Science and Engineering, Tsinghua University, Beijing 100084 (China); Danish-Chinese Center for Nanometals, Materials Research Division, Riso National Laboratory for Sustainable Energy, Technical University of Denmark, DK-4000 Roskilde (Denmark); Godfrey, A. [Laboratory of Advanced Materials, Department of Materials Science and Engineering, Tsinghua University, Beijing 100084 (China); Jensen, D. Juul; Winther, G. [Danish-Chinese Center for Nanometals, Materials Research Division, Riso National Laboratory for Sustainable Energy, Technical University of Denmark, DK-4000 Roskilde (Denmark)

    2010-11-15

    A method to map the microstructure in deformed aluminum in three dimensions is presented. The method employs serial sectioning by mechanical polishing, and electropolishing to obtain a good surface quality, and orientation mapping of individual grains in each section by electron backscattered diffraction. Techniques to carefully align the sample and to accurately measure the thickness of the material removed in each serial section are described. A new method for stacking the two dimensional maps together to produce a three dimensional visualization of the microstructure is presented. The data are analyzed in terms of the deformation-induced orientation spread within each grain. In particular the advantage of using three dimensional data, as opposed to two dimensional data, is illustrated, by inclusion of information about the three dimensional morphology of a grain and its neighbors. - Research Highlights: The deformation structures in commercial purity aluminum were characterized in 3D. The method employs serial sectioning by mechanical polishing, and electropolishing to obtain a good surface quality, and orientation mapping of individual grains in each section by electron backscattered diffraction. Techniques to carefully align the sample and to accurately measure the thickness of the material removed in each serial section are described. A new method for stacking the two dimensional maps together to produce a three dimensional visualization of the microstructure is presented. The data are analyzed in terms of the deformation-induced orientation spread within each grain. In particular the advantage of using three dimensional data, as opposed to two dimensional data, is illustrated, by inclusion of information about the three dimensional morphology of a grain and its neighbors. The highlights of the paper include: {yields} a method to obtain 3D EBSD data over a large volume {yields} a modified method for section alignment based on characteristics of deformed

  18. Structural and thermodynamic properties of 3-d transition metals: Pseudopotential theory revisited

    Structural and thermodynamic properties of 3d-transition metals are calculated in terms of the pseudopotential theory. The s-p and d-electrons are treated in a pseudoadiabatic approximation in such a way so that the s-p and d-electron are treated separately under the same footing. The s-p electrons are treated in terms of the conventional second-order pseudopotential theory, while the tightly bound d-electrons are treated in terms of the Wills-Harrison prescription that makes use of the Fridel rectangular electron-density of states (DOS) model. The predictions of the structural phase stability and other relevant thermodynamic properties are found to be consistent with experiments for almost all of the metals. (author). 16 refs, 5 tabs

  19. Calculation of the electronic and magnetic structures of 3d impurities in the Hcp Fe matrix

    In this work we investigate the local magnetic properties and the electronic structure of HCP Fe, as well introducing transition metals atoms 3d (Cs, Ti, Cr, Mn, Co, Ni, Cu, Zn) in HCP iron matrix. We employed the discrete variational method (DVM), which is an orbital molecular method which incorporate the Hartree-Fock-Slater theory and the linear combination of atomic orbitals (LCAO), in the self-consistent charge approximation and the local density approximation of Von Barth and Hedin to the exchange-correlation potential. We used the embedded cluster model to investigate the electronic structure and the local magnetic properties for the central atom of a cluster of 27 atoms immersed in the microcrystal representing the HCP Fe. (author)

  20. Fabrication and optical properties of 3D composite photonic crystals of core-shell structures

    Liu Yanping [Department of Physics, Lanzhou University, Lanzhou 730000 (China); Yan Zhijun [Department of Physics, Lanzhou University, Lanzhou 730000 (China); Lan Wei [Department of Physics, Lanzhou University, Lanzhou 730000 (China); Huang Chunming [Department of Physics, Lanzhou University, Lanzhou 730000 (China); Wang Yinyue [Department of Physics, Lanzhou University, Lanzhou 730000 (China)]. E-mail: wangyy@lzu.edu.cn

    2007-08-31

    Three-dimensional (3D) composite colloidal photonic crystals with SiO{sub 2} core and ZnO shell were fabricated on borosilicate glass (BSG) substrate by a two-stage deposition method. Scanning electron microscopy (SEM) measurements show that both the pre-deposited SiO{sub 2} and SiO{sub 2}/ZnO core-shell structures are oriented with their (1 1 1) axes parallel to the substrates. Optical measurement reveals that the periodic arrays exhibit a photonic band gap in the (1 1 1) direction. The optical properties of SiO{sub 2}/ZnO core-shell structures strongly depend on the size dispersions of colloidal spheres and the intrinsic defects in the sample.

  1. Structural, magnetic and conduction properties of 3d-metal monoatomic wires

    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. (papers)

  2. 3D stochastic inversion of potential field data using structural geologic constraints

    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.

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

    Bo Huang

    2015-10-01

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

  4. 3D structural and atomic-scale analysis of lath martensite: Effect of the transformation sequence

    To improve the fundamental understanding of the multi-scale characteristics of martensitic microstructures and their micro-mechanical properties, a multi-probe methodology is developed and applied to low-carbon lath martensitic model alloys. The approach is based on the joint employment of electron channeling contrast imaging (ECCI), electron backscatter diffraction (EBSD), transmission electron microscopy (TEM), atom probe tomography (APT) and nanoindentation, in conjunction with high precision and large field-of-view 3D serial sectioning. This methodology enabled us to resolve (i) size variations of martensite sub-units, (ii) associated dislocation sub-structures, (iii) chemical heterogeneities, and (iv) the resulting local mechanical properties. The identified interrelated microstructure heterogeneity is discussed and related to the martensitic transformation sequence, which is proposed to intrinsically lead to formation of a nano-composite structure in low-carbon martensitic steels

  5. Millimeter radiation from a 3D model of the solar atmosphere I. Diagnosing chromospheric thermal structure

    Loukitcheva, Maria; Carlsson, Mats; White, Stephen

    2015-01-01

    Aims. We use advanced 3D NLTE radiative magnetohydrodynamic simulations of the solar atmosphere to carry out detailed tests of chromospheric diagnostics at millimeter and submillimeter wavelengths. Methods. We focused on the diagnostics of the thermal structure of the chromosphere in the wavelength bands from 0.4 mm up to 9.6 mm that can be accessed with the Atacama Large Millimeter/Submillimeter Array (ALMA) and investigated how these diagnostics are affected by the instrumental resolution. Results. We find that the formation height range of the millimeter radiation depends on the location in the simulation domain and is related to the underlying magnetic structure. Nonetheless, the brightness temperature is a reasonable measure of the gas temperature at the effective formation height at a given location on the solar surface. There is considerable scatter in this relationship, but this is significantly reduced when very weak magnetic fields are avoided. Our results indicate that although instrumental smearin...

  6. A 3D multi-block structured version of the KIVA 2 code

    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.

  7. Imaging 3D anisotropic upper mantle shear velocity structure of Southeast Asia using seismic waveform inversion

    Chong, J.; Yuan, H.; French, S. W.; Romanowicz, B. A.; Ni, S.

    2011-12-01

    Southeast Asia as a special region in the world which is seismically active and is surrounded by active tectonic belts, such as the Himalaya collision zone, western Pacific subduction zones and the Tianshan- Baikal tectonic belt. Seismic anisotropic tomography can shade light on the complex crust and upper mantle dynamics of this region, which is the subject of much debate. In this study, we applied full waveform time domain tomography to image 3D isotropic and anisotropic upper mantle shear velocity structure of Southeast Asia. Three component waveforms of teleseismic and far regional events (15 degree ≤ Δ≤ 165 degree) with magnitude ranges from Mw6.0 to Mw7.0 are collected from 91 permanent and 438 temporary broadband seismic stations in SE Asia. Wavepackets of both fundamental and overtone modes, filtered between 60 and 400 sec, are selected automatically according to the similarity between data and synthetic waveforms (Panning & Romanowicz, 2006). Wavepackets corresponding to event-station paths that sample the region considered are weighted according to path redundancy and signal to noise ratio. Higher modes and fundamental mode wavepackets are weighted separately in order to enhance the contribution of higher modes which are more sensitive to deeper structure compared to the fundamental mode. Synthetic waveforms and broadband sensitivity kernels are computed using normal mode asymptotic coupling theory (NACT, Li & Romanowicz, 1995). As a starting model, we consider a global anisotropic upper mantle shear velocity model based on waveform inversion using the Spectral Element Method (Lekic & Romanowicz, 2011), updated for more realistic crustal thickness (French et al., 2011) as our starting model, we correct waveforms for the effects of 3D structure outside of the region, and invert them for perturbations in the 3D structure of the target region only. We start with waveform inversion down to 60sec and after several iterations, we include shorter period

  8. Structural evolution of the VMS-hosting Kristineberg area, Sweden – constraints from structural analysis and 3-D-modelling

    Hübert, J.; García, M.; Juhlin, C.; M. Dehghannejad; Hermansson, T.; Bauer, T.; P. Skyttä; Weihed, P.

    2012-01-01

    Structural mapping and 3-D-modelling with constraints from magnetotelluric (MT) and reflection seismic investigations have been used to provide a geological synthesis of the geometrically complex Kristineberg area in the western part of the Palaeoproterozoic Skellefte district. The results indicate that, like the south-eastern parts of the Skellefte district, the area was subjected to SSE-NNW transpressional deformation at around 1.87 Ga. The contrasting structural geometries between the Kris...

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

    Dolžan, Erazem; Vrabec, Marko

    2015-04-01

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

  10. Structure, stability and evolution of 3D Rossby vortices in protoplanetary disks

    Richard, Samuel; Dizes, Stephane Le

    2013-01-01

    Large-scale persistent vortices are known to form easily in 2D disks via the Rossby wave or the baroclinic instability. In 3D, however, their formation and stability is a complex issue and still a matter of debate. We study the formation of vortices by the Rossby wave instability in a stratified inviscid disk and describe their three dimensional structure, stability and long term evolution. Numerical simulations are performed using a fully compressible hydrodynamical code based on a second order finite volume method. We assume a perfect gas law and a non-homentropic adiabatic flow.The Rossby wave instability is found to proceed in 3D in a similar way as in 2D. Vortices produced by the instability look like columns of vorticity in the whole disk thickness; the small vertical motions are related to a weak inclination of the vortex axis appearing during the development of the RWI. Vortices with aspect ratios larger than 6 are unaffected by the elliptical instability. They relax to a quasi-steady columnar structu...

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

    Cowley, Aidan

    2016-07-01

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

  12. Micro supercapacitors based on a 3D structure with symmetric graphene or activated carbon electrodes

    This paper presents three-dimensional (3D) micro supercapacitors with thick interdigital electrodes supported and separated by SU-8. Nanoporous carbon materials including graphene and activated carbon (AC) are used as active materials in self-supporting composites to build the electrodes. The SU-8 separators provide mechanical support for thick electrodes and allow a considerable amount of material to be loaded in a limited footprint area. The prototypes have been accomplished by a simple microelectromechanical systems (MEMS) fabrication process and sealed by polydimethylsiloxane (PDMS) caps with ionic liquid electrolytes injected into the electrode area. Electrochemical tests demonstrate that the graphene-based prototype with 100 µm thick electrodes shows good power performance and provides a considerable specific capacitance of about 60 mF cm−2. Two AC-based prototypes show larger capacitance of 160 mF cm−2 and 311 mF cm−2 with 100 µm and 200 µm thick electrodes respectively, because of higher volume density of the material. The results demonstrate that both thick 3D electrode structure and volume capacitance of the electrode material are key factors for high-performance micro supercapacitors, which can be potentially used in specific applications such as power suppliers and storage components for harvesters. (paper)

  13. Micro supercapacitors based on a 3D structure with symmetric graphene or activated carbon electrodes

    Li, Siwei; Wang, Xiaohong; Xing, Hexin; Shen, Caiwei

    2013-11-01

    This paper presents three-dimensional (3D) micro supercapacitors with thick interdigital electrodes supported and separated by SU-8. Nanoporous carbon materials including graphene and activated carbon (AC) are used as active materials in self-supporting composites to build the electrodes. The SU-8 separators provide mechanical support for thick electrodes and allow a considerable amount of material to be loaded in a limited footprint area. The prototypes have been accomplished by a simple microelectromechanical systems (MEMS) fabrication process and sealed by polydimethylsiloxane (PDMS) caps with ionic liquid electrolytes injected into the electrode area. Electrochemical tests demonstrate that the graphene-based prototype with 100 µm thick electrodes shows good power performance and provides a considerable specific capacitance of about 60 mF cm-2. Two AC-based prototypes show larger capacitance of 160 mF cm-2 and 311 mF cm-2 with 100 µm and 200 µm thick electrodes respectively, because of higher volume density of the material. The results demonstrate that both thick 3D electrode structure and volume capacitance of the electrode material are key factors for high-performance micro supercapacitors, which can be potentially used in specific applications such as power suppliers and storage components for harvesters.

  14. Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures.

    Maeda, Miki H; Kondo, Kazumi

    2013-03-25

    A database of 3D structures of natural metabolites has been developed called 3DMET. During the process of structure conversion from 2D to 3D, we found many structures were misconverted at chiral atoms and bonds. Several popular converters were tested in regard to their conversion accuracy. For verification, three canonical strings were also tested. No procedure could satisfactorily cover all the structures of the natural products. The misconverted structures had to be corrected manually. However, a nonnegligible number of mistakes were also observed even after manual curation, so a self-checking system was developed and introduced to our work flow. Thus, the 3D structures in our 3DMET database were evaluated in two steps: automatically and manually. The current version includes most of the natural products of the KEGG COMPOUND collection [ http://www.genome.jp/kegg/compound/ ] and is searchable by string, value range, and substructure. 3DMET can be accessed via http://www.3dmet.dna.affrc.go.jp/ , which also has detailed manuals. PMID:23293959

  15. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae's Inner Colliding Winds

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

    2015-01-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (>120 M_Sun), highly eccentric (e ~ 0.9) binary star system Eta Carinae. We demonstrate the methodology used to incorporate 3D interactive figures into a PDF journal publication and the benefits of using 3D visualization and 3D printing as tools to analyze data from multidimensional numerical simulations. Using a consumer-grade 3D printer (Make...

  16. Structural deformation upon protein-protein interaction: A structural alphabet approach

    Lecornet Hélène; Regad Leslie; Martin Juliette; Camproux Anne-Claude

    2008-01-01

    Abstract Background In a number of protein-protein complexes, the 3D structures of bound and unbound partners significantly differ, supporting the induced fit hypothesis for protein-protein binding. Results In this study, we explore the induced fit modifications on a set of 124 proteins available in both bound and unbound forms, in terms of local structure. The local structure is described thanks to a structural alphabet of 27 structural letters that allows a detailed description of the backb...

  17. Making and Remaking Dynamic 3D Structures by Shining Light on Flat Liquid Crystalline Vitrimer Films without a Mold.

    Yang, Yang; Pei, Zhiqiang; Li, Zhen; Wei, Yen; Ji, Yan

    2016-02-24

    Making dynamic three-dimensional (3D) structures capable of reversible shape changes or locomotion purely out of dry polymers is very difficult. Meanwhile, no previous dynamic 3D structures can be remade into new configurations while being resilient to mechanical damages and low temperature. Here, we show that light-activated transesterification in carbon nanotube dispersed liquid crystalline vitrimers enables flexible design and easy building of dynamic 3D structures out of flat films upon irradiation of light without screws, glues, or molds. Shining light also enables dynamic 3D structures to be quickly modified on demand, restored from distortion, repaired if broken, in situ healed when microcrack appears, assembled for more sophisticated structures, reconfigured, and recycled after use. Furthermore, the fabrication, reconfiguration, actuation, reparation, and assembly as well as healing can be performed even at extremely low temperatures (e.g., -130 °C). PMID:26840838

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

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

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

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

    2015-10-01

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

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

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

    2016-01-01

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

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

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

    2013-01-01

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

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

    Renata Ferrari

    2016-02-01

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

  3. Local electronic structure and magnetic properties of 3d transition metal doped GaAs

    LIN He; DUAN HaiMing

    2008-01-01

    The local electronic structure and magnetic properties of GaAs doped with 3d transition metal (Sc, Ti, V, Cr, Mn, Fe, Co, Ni) were studied by using discrete varia-tional method (DVM) based on density functional theory. The calculated result in-dicated that the magnetic moment of transition metal increases first and then de-creases, and reaches the maximum value when Mn is doped into GaAs. In the case of Mn concentration of 1.4%, the magnetic moment of Mn is in good agreement with the experimental result. The coupling between impure atoms in the system with two impure atoms was found to have obvious variation. For different transition metal, the coupling between the impure atom and the nearest neighbor As also has dif-ferent variation.

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

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

    2015-05-01

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

  5. Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming.

    Krijger, Peter Hugo Lodewijk; Di Stefano, Bruno; de Wit, Elzo; Limone, Francesco; van Oevelen, Chris; de Laat, Wouter; Graf, Thomas

    2016-05-01

    Forced expression of reprogramming factors can convert somatic cells into induced pluripotent stem cells (iPSCs). Here we studied genome topology dynamics during reprogramming of different somatic cell types with highly distinct genome conformations. We find large-scale topologically associated domain (TAD) repositioning and alterations of tissue-restricted genomic neighborhoods and chromatin loops, effectively erasing the somatic-cell-specific genome structures while establishing an embryonic stem-cell-like 3D genome. Yet, early passage iPSCs carry topological hallmarks that enable recognition of their cell of origin. These hallmarks are not remnants of somatic chromosome topologies. Instead, the distinguishing topological features are acquired during reprogramming, as we also find for cell-of-origin-dependent gene expression patterns. PMID:26971819

  6. Visualization of Segmented Structures in 3D Multimodal Medical Data Sets

    HERGHELEGIU, P.

    2011-08-01

    Full Text Available The simultaneous inspection of images obtained using different medical scanning methods represents a common practice for accurate medical diagnosis. The term multimodality refers to multiple medical data sets obtained by scanning a patient with the same method at different time moments or with different scanning techniques. Recent research efforts in computer graphics have attempted to solve the problem of visualizing multimodal data in the same scene, for a better understanding of human anatomy or for pathology tracking. This paper proposes a method of integrating segmented structures from a contrast enhanced MRI sequence into the volume reconstructed from the slices of another MRI sequence obtained with different scanning parameters. A direct volume rendering (DVR approach is used to represent focus and context information from the 3D data. The presented approach aims to help physicians in understanding pathologies and in the process of accurate diagnosis establishment.

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

    Coluccio, M. L.

    2015-05-01

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

  8. Intermolecular interactions and 3D structure in cellulose-NaOH-urea aqueous system.

    Jiang, Zhiwei; Fang, Yan; Xiang, Junfeng; Ma, Yanping; Lu, Ang; Kang, Hongliang; Huang, Yong; Guo, Hongxia; Liu, Ruigang; Zhang, Lina

    2014-08-28

    The dissolution of cellulose in NaOH/urea aqueous solution at low temperature is a key finding in cellulose science and technology. In this paper, (15)N and (23)Na NMR experiments were carried out to clarify the intermolecular interactions in cellulose/NaOH/urea aqueous solution. It was found that there are direct interactions between OH(-) anions and amino groups of urea through hydrogen bonds and no direct interaction between urea and cellulose. Moreover, Na(+) ions can interact with both cellulose and urea in an aqueous system. These interactions lead to the formation of cellulose-NaOH-urea-H2O inclusion complexes (ICs). (23)Na relaxation results confirmed that the formation of urea-OH(-) clusters can effectively enhance the stability of Na(+) ions that attracted to cellulose chains. Low temperature can enhance the hydrogen bonding interaction between OH(-) ions and urea and improve the binding ability of the NaOH/urea/H2O clusters that attached to cellulose chains. Cryo-TEM observation confirmed the formation of cellulose-NaOH-urea-H2O ICs, which is in extended conformation with mean diameter of about 3.6 nm and mean length of about 300 nm. Possible 3D structure of the ICs was proposed by the M06-2X/6-31+G(d) theoretical calculation, revealing the O3H···O5 intramolecular hydrogen bonds could remain in the ICs. This work clarified the interactions in cellulose/NaOH/urea aqueous solution and the 3D structure of the cellulose chain in dilute cellulose/NaOH/urea aqueous solution. PMID:25111839

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

    Coluccio, M. L.; Francardi, M.; Gentile, F.; Candeloro, P.; Ferrara, L.; Perozziello, G.; Di Fabrizio, E.

    2016-01-01

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

  10. Ion-beam enhanced etching for the 3D structuration of lithium niobate

    The present thesis deals with the usage of the ion-beam enhanced etching (IBEE) for the 3D structuration of lithium niobate (LiNbO3).Hereby the approach of the enhancement of the wet-chemical etching rate due to the irradiation with energetic ions is pursued. This method is very success promising for the realization of micro- and nanostructures with perpendicular structural walls as well as small roughnesses. The aim of this thesis consisted therein to form the foundations for the realization of three-dimensional micro- and nanostructures (for instance: Layer systems and photonic crystals) in LiNbO3 with high optical quality and to demonstrate on selected examples. Conditions for the success of the IBEE structuration technique is first of all the understanding of the defect formation under ion irradiation as well as the radiation-induced structure changes in the crystal and the change of the chemical resistance connected with this. For this the defect formation was studied in dependence on th ion mass, the ion energy, and the irradiation temperature. Thermally induced influences and effects on the radiation damage, as they can occur in intermediate steps in the complex processing, must be known and were studied by means of subsequent temperature treatment. The results from the defect studies were subsequently applied for the fabrication of micro- and nanostructures in LiNbO3. Shown is the realization of lateral structure with nearly perpendicular structure walls as well as the realization of thin membranes and slits. The subsequent combination of lateral structuration with the fabrication of thin membranes and slits allowed the three-dimensional structuration of LiNbO3. This is exemplarily shown for a microresonator and for a 2D photonic crystal with below lying air slit.

  11. Development of high vorticity structures in incompressible 3D Euler equations

    Agafontsev, D S; Mailybaev, A A

    2015-01-01

    We perform the systematic numerical study of high vorticity structures that develop in the 3D incompressible Euler equations from generic large-scale initial conditions. We observe that a multitude of high vorticity structures appear in the form of thin vorticity sheets (pancakes). Our analysis reveals the self-similarity of the pancakes evolution, which is governed by two different exponents $e^{-t/T_{\\ell}}$ and $e^{t/T_{\\omega}}$ describing compression in the transverse direction and the vorticity growth respectively, with the universal ratio $T_{\\ell}/T_{\\omega} \\approx 2/3$. We relate development of these structures to the gradual formation of the Kolmogorov energy spectrum $E_{k}\\propto\\, k^{-5/3}$, which we observe in a fully inviscid system. With the spectral analysis we demonstrate that the energy transfer to small scales is performed through the pancake structures, which accumulate in the Kolmogorov interval of scales and evolve according to the scaling law $\\omega_{\\max} \\propto \\ell^{-2/3}$ for th...

  12. Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models

    Jonikas, Magdalena A; RADMER, RANDALL J.; Altman, Russ B

    2009-01-01

    Motivation: The recent development of methods for modeling RNA 3D structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. Although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications. Results: We have developed a method for adding full atomic detail to coarse-grain models of RNA 3D structures. Our method [Coarse to Atomic (C2A)] uses geometries observed in known RNA ...

  13. Theoretical study of the Usutu virus helicase 3D structure, by means of computer-aided homology modelling

    Vlachakis Dimitrios

    2009-01-01

    Abstract Background Usutu virus belongs to the Flaviviridae viral family and constitutes an important pathogen. The viral helicase is an ideal target for inhibitor design, since this enzyme is essential for the survival, proliferation and transmission of the virus. Results Towards a drug-design approach, the 3D model of the Usutu virus helicase structure has been designed, using conventional homology modelling techniques and the known 3D-structure of the Murray Valley Encephalitis virus helic...

  14. Integration of 3D vision based structure estimation and visual robot control

    Prljaca, Naser

    1995-01-01

    Enabling robot manipulators to manipulate and/or recognise arbitrarily placed 3D objects under sensory control is one of the key issues in robotics. Such robot sensors should be capable of providing 3D information about objects in order to accomplish the above mentioned tasks. Such robot sensors should also provide the means for multisensor or multimeasurement integration. Finally, such 3D information should be efficiently used for performing desired tasks. This work develops a novel comp...

  15. Comparison and functional implications of the 3D architectures of viral tRNA-like structures.

    Hammond, John A; Rambo, Robert P; Filbin, Megan E; Kieft, Jeffrey S

    2009-02-01

    RNA viruses co-opt the host cell's biological machinery, and their infection strategies often depend on specific structures in the viral genomic RNA. Examples are tRNA-like structures (TLSs), found at the 3' end of certain plant viral RNAs, which can use the cell's aminoacyl tRNA-synthetases (AARSs) to drive addition of an amino acid to the 3' end of the viral RNA. TLSs are multifunctional RNAs involved in processes such as viral replication, translation, and viral RNA stability; these functions depend on their fold. Experimental result-based structural models of TLSs have been published. In this study, we further examine these structures using a combination of biophysical and biochemical approaches to explore the three-dimensional (3D) architectures of TLSs from the turnip yellow mosaic virus (TYMV), tobacco mosaic virus (TMV), and brome mosaic virus (BMV). We find that despite similar function, these RNAs are biophysically diverse: the TYMV TLS adopts a characteristic tRNA-like L shape, the BMV TLS has a large compact globular domain with several helical extensions, and the TMV TLS aggregates in solution. Both the TYMV and BMV TLS RNAs adopt structures with tight backbone packing and also with dynamic structural elements, suggesting complexities and subtleties that cannot be explained by simple tRNA mimicry. These results confirm some aspects of existing models and also indicate how these models can be improved. The biophysical characteristics of these TLSs show how these multifunctional RNAs might regulate various viral processes, including negative strand synthesis, and also allow comparison with other structured RNAs. PMID:19144910

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

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

    2013-01-01

    Understanding the topological configurations of chromatin may reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development. Here we generate high-resolution architecture maps across seven genomic loci in embryonic stem cells and neural progenitor cells. We observe a hierarchy of 3-D interactions that undergo marked reorganization at the sub-Mb scale during differentiation. Distinct combinations of CTCF, Mediator, and cohesin show widespread...

  17. 3D Modelling of Inaccessible Areas using UAV-based Aerial Photography and Structure from Motion

    Obanawa, Hiroyuki; Hayakawa, Yuichi; Gomez, Christopher

    2014-05-01

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

  18. Local backbone structure prediction of proteins.

    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

  19. 3D structural measurements of the proximal femur from 2D DXA images using a statistical atlas

    Ahmad, Omar M.; Ramamurthi, Krishna; Wilson, Kevin E.; Engelke, Klaus; Bouxsein, Mary; Taylor, Russell H.

    2009-02-01

    A method to obtain 3D structural measurements of the proximal femur from 2D DXA images and a statistical atlas is presented. A statistical atlas of a proximal femur was created consisting of both 3D shape and volumetric density information and then deformably registered to 2D fan-beam DXA images. After the registration process, a series of 3D structural measurements were taken on QCT-estimates generated by transforming the registered statistical atlas into a voxel volume. These measurements were compared to the equivalent measurements taken on the actual QCT (ground truth) associated with the DXA images for each of 20 human cadaveric femora. The methodology and results are presented to address the potential clinical feasibility of obtaining 3D structural measurements from limited angle DXA scans and a statistical atlas of the proximal femur in-vivo.

  20. 3D tomography analysis of the inner structure of pebbles and pebble beds

    An analytical tool to monitor the arrangement of pebbles in a pebble bed as well as the morphology of gas bubbles in as fabricated and neutron irradiated beryllium pebbles is presented. The context of this study is the Helium Cooled Pebble Bed (HPCB) blanket design for the forthcoming generation of fusion reactors. The thermal-mechanical behavior of pebble beds is a basic issue for the HPCB. It depends strongly on the configuration of the pebbles in the bed, and in particular on the number of contacts between pebbles, and between pebbles and the blanket walls. The related contact surfaces play also a major role. The knowledge on the inner structure of the pebbles is required since during the life cycle of a power reactor helium and tritium bubbles are produced inside the beryllium pebbles and the tritium build-up can be in excess of several kilograms, being thereby a key safety issue. All the non-destructive analyses are based on 3D computer aided microtomography using a very powerful synchrotron radiation x-ray source with high spatial resolution. The data analysis relies on a topological operator called filtered medial line applied to the entire data volumes and the related graph representation. By this technique the number of contacts between the pebbles in pebble packs and their angular distribution are obtained, as well as the corresponding contact surfaces. The evaluation of bubble sizes and densities in single pebbles, the assessment of the pore channel network topology, the 3D reconstruction of the fraction of interconnected bubble porosity, and the open-to-closed-porosity ratio are among the most interesting findings. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

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

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

    2016-04-01

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

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

    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

  3. Studies of Coupled Cavity Linac (CCL) Accelerating Structures with 3-D Codes

    Spalek, G; Smith, P D; Greninger, P T; Charman, C M

    2000-01-01

    The cw CCL being designed for the Accelerator Production of Tritium (APT) project accelerates protons from 96MeV to 211MeV. 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 result...

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

    Mihai V. Putz

    2016-07-01

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

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

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

    2016-01-01

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

  6. 3D-FE analysis of functionally graded structured dental posts.

    Abu Kasim, Noor H; Madfa, Ahmed A; Hamdi, Mohd; Rahbari, Ghahnavyeh R

    2011-01-01

    This study aimed to compare the biomechanical behaviour of functionally graded structured posts (FGSPs) and homogenous-type posts in simulated models of a maxillary central incisor. Two models of FGSPs consisting of a multilayer xTi-yHA composite design, where zirconia and alumina was added as the first layer for models A and B respectively were compared to homogenous zirconia post (model C) and a titanium post (model D). The amount of Ti and HA in the FGSP models was varied in gradations. 3D-FEA was performed on all models and stress distributions were investigated along the dental post. In addition, interface stresses between the posts and their surrounding structures were investigated under vertical, oblique, and horizontal loadings. Strain distribution along the post-dentine interface was also investigated. The results showed that FGSPs models, A and B demonstrated better stress distribution than models C and D, indicating that dental posts with multilayered structure dissipate localized and interfacial stress and strain more efficiently than homogenous-type posts. PMID:22123011

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

    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

  8. Fabrication of 3D fractal structures using nanoscale anisotropic etching of single crystalline silicon

    When it comes to high-performance filtration, separation, sunlight collection, surface charge storage or catalysis, the effective surface area is what counts. Highly regular fractal structures seem to be the perfect candidates, but manufacturing can be quite cumbersome. Here it is shown-–for the first time—that complex 3D fractals can be engineered using a recursive operation in conventional micromachining of single crystalline silicon. The procedure uses the built-in capability of the crystal lattice to form self-similar octahedral structures with minimal interference of the constructor. The silicon fractal can be used directly or as a mold to transfer the shape into another material. Moreover, they can be dense, porous, or like a wireframe. We demonstrate, after four levels of processing, that the initial number of octahedral structures is increased by a factor of 625. Meanwhile the size decreases 16 times down to 300 nm. At any level, pores of less than 100 nm can be fabricated at the octahedral vertices of the fractal. The presented technique supports the design of fractals with Hausdorff dimension D free of choice and up to D = 2.322. (paper)

  9. Modelling of 3D Attenuation Structure in the Mantle Using a Waveform Approach: Successes and Challenges

    Romanowicz, B. A.; Gung, Y.

    2003-12-01

    The study of lateral variations in Q in the upper mantle at the global scale is generally addressed using isolated phases in the seismogram (for example fundamental mode surface wave spectra), which limits the sampling and therefore the resolution of Q structure that can be achieved. The use of isolated phases has the advantage of working directly with amplitudes, thus making it easier to detect contamination of the anelastic attenuation signal by elastic focusing and scattering, a key problem in attenuation tomography. We here discuss recent progress on a waveform modeling approach, which allows us to work with entire seismograms and exploit the information contained both in fundamental mode surface waves, overtones and body waves. The method is based on a normal mode approach and proceeds iteratively. In the first step, we invert for 3D elastic structure using the NACT approach (Non-linear Asymptotic Coupling Theory; Li and Romanowicz, 1995), which aligns the phase part of the observed and synthetic seismograms. In the second step, we invert for Q. The crucial issue is how to account for elastic effects in the amplitudes (focusing)- we discuss asymptotic versus more exact methods to address this problem and illustrate the effects on the resulting models. We discuss prominent features in the lateral variations in Q in the upper mantle, their evolution with depth, and their relation with elastic structure, in particular from the point of view of resolving upwellings and the large scale signature of plumes.

  10. 3D numerical simulation on fluid-structure interaction of structure subjected to underwater explosion with cavitation

    A-man ZHANG; Shao-fei REN; Qing LI; Jia LI

    2012-01-01

    In the underwater-shock environment,cavitation occurs near the structural surface.The dynamic response of fluid-structure interactions is influenced seriously by the cavitation effects.It is also the difficulty in the field of underwater explosion.With the traditional boundary element method and the finite element method (FEM),it is difficult to solve the nonlinear problem with cavitation effects subjected to the underwater explosion.To solve this problem,under the consideration of the cavitation effects and fluid compressibility,with fluid viscidity being neglected,a 3D numerical model of transient nonlinear fluid-structure interaction subjected to the underwater explosion is built.The fluid spectral element method (SEM) and the FEM are adopted to solve this model.After comparison with the FEM,it is shown that the SEM is more precise than the FEM,and the SEM results are in good coincidence with benchmark results and experiment results.Based on this,combined with ABAQUS,the transient fluid-structure interaction mechanism of the 3D submerged spherical shell and ship stiffened plates subjected to the underwater explosion is discussed,and the cavitation region and its influence on the structural dynamic responses are presented.The paper aims at providing references for relevant research on transient fluid-structure interaction of ship structures subjected to the underwater explosion.

  11. 3D visualisation of the middle ear and adjacent structures using reconstructed multi-slice CT datasets, correlating 3D images and virtual endoscopy to the 2D cross-sectional images

    The 3D imaging of the middle ear facilitates better understanding of the patient's anatomy. Cross-sectional slices, however, often allow a more accurate evaluation of anatomical structures, as some detail may be lost through post-processing. In order to demonstrate the advantages of combining both approaches, we performed computed tomography (CT) imaging in two normal and 15 different pathological cases, and the 3D models were correlated to the cross-sectional CT slices. Reconstructed CT datasets were acquired by multi-slice CT. Post-processing was performed using the in-house software ''3D Slicer'', applying thresholding and manual segmentation. 3D models of the individual anatomical structures were generated and displayed in different colours. The display of relevant anatomical and pathological structures was evaluated in the greyscale 2D slices, 3D images, and the 2D slices showing the segmented 2D anatomy in different colours for each structure. Correlating 2D slices to the 3D models and virtual endoscopy helps to combine the advantages of each method. As generating 3D models can be extremely time-consuming, this approach can be a clinically applicable way of gaining a 3D understanding of the patient's anatomy by using models as a reference. Furthermore, it can help radiologists and otolaryngologists evaluating the 2D slices by adding the correct 3D information that would otherwise have to be mentally integrated. The method can be applied to radiological diagnosis, surgical planning, and especially, to teaching. (orig.)

  12. 3D Case Studies of Monitoring Dynamic Structural Tests using Long Exposure Imagery

    McCarthy, D. M. J.; Chandler, J. H.; Palmeri, A.

    2014-06-01

    Structural health monitoring uses non-destructive testing programmes to detect long-term degradation phenomena in civil engineering structures. Structural testing may also be carried out to assess a structure's integrity following a potentially damaging event. Such investigations are increasingly carried out with vibration techniques, in which the structural response to artificial or natural excitations is recorded and analysed from a number of monitoring locations. Photogrammetry is of particular interest here since a very high number of monitoring locations can be measured using just a few images. To achieve the necessary imaging frequency to capture the vibration, it has been necessary to reduce the image resolution at the cost of spatial measurement accuracy. Even specialist sensors are limited by a compromise between sensor resolution and imaging frequency. To alleviate this compromise, a different approach has been developed and is described in this paper. Instead of using high-speed imaging to capture the instantaneous position at each epoch, long-exposure images are instead used, in which the localised image of the object becomes blurred. The approach has been extended to create 3D displacement vectors for each target point via multiple camera locations, which allows the simultaneous detection of transverse and torsional mode shapes. The proposed approach is frequency invariant allowing monitoring of higher modal frequencies irrespective of a sampling frequency. Since there is no requirement for imaging frequency, a higher image resolution is possible for the most accurate spatial measurement. The results of a small scale laboratory test using off-the-shelf consumer cameras are demonstrated. A larger experiment also demonstrates the scalability of the approach.

  13. Cell Proliferation on Macro/Nano Surface Structure and Collagen Immobilization of 3D Polycaprolactone Scaffolds.

    Park, Young-Ouk; Myung, Sung-Woon; Kook, Min-Suk; Jung, Sang-Chul; Kim, Byung-Hoon

    2016-02-01

    In this study, 3D polycaprolactone (PCL) scaffolds were fabricated by 3D printing technique. The macro/nano morphology of, 3D PCL scaffolds surface was etched with oxygen plasma. Acrylic acid (AA) plasma-polymerization was performed to functionalize the macro/nano surface with carboxyl groups and then collagen was immobilized with plasma-polymerized 3D PCL scaffolds. After O2 plasma and AA plasma-polymerization, contact angles were decreased. The FE-SEM and AFM results showed that O2 plasma is increased the surface roughness. The MTT assay results showed that proliferation of the M3CT3-E1 cells increased on the oxygen plasma treated and collagen immobilized 3D PCL scaffolds. PMID:27433597

  14. Ion-beam enhanced etching for the 3D structuration of lithium niobate; Ionenstrahlverstaerktes Aetzen fuer die 3D-Strukturierung von Lithiumniobat

    Gischkat, Thomas

    2010-01-12

    The present thesis deals with the usage of the ion-beam enhanced etching (IBEE) for the 3D structuration of lithium niobate (LiNbO{sub 3}).Hereby the approach of the enhancement of the wet-chemical etching rate due to the irradiation with energetic ions is pursued. This method is very success promising for the realization of micro- and nanostructures with perpendicular structural walls as well as small roughnesses. The aim of this thesis consisted therein to form the foundations for the realization of three-dimensional micro- and nanostructures (for instance: Layer systems and photonic crystals) in LiNbO{sub 3} with high optical quality and to demonstrate on selected examples. Conditions for the success of the IBEE structuration technique is first of all the understanding of the defect formation under ion irradiation as well as the radiation-induced structure changes in the crystal and the change of the chemical resistance connected with this. For this the defect formation was studied in dependence on th ion mass, the ion energy, and the irradiation temperature. Thermally induced influences and effects on the radiation damage, as they can occur in intermediate steps in the complex processing, must be known and were studied by means of subsequent temperature treatment. The results from the defect studies were subsequently applied for the fabrication of micro- and nanostructures in LiNbO{sub 3}. Shown is the realization of lateral structure with nearly perpendicular structure walls as well as the realization of thin membranes and slits. The subsequent combination of lateral structuration with the fabrication of thin membranes and slits allowed the three-dimensional structuration of LiNbO{sub 3}. This is exemplarily shown for a microresonator and for a 2D photonic crystal with below lying air slit. [German] Die vorliegende Arbeit beschaeftigt sich mit der Ausnutzung des ionenstrahlverstaerkten Aetzens (IBEE: Ion Beam Enhanced Etching) fuer die 3D-Strukturierung von

  15. 3D Measurement Technology by Structured Light Using Stripe-Edge-Based Gray Code

    The key problem of 3D vision measurement using triangle method based on structured light is to acquiring projecting angle of projecting light accurately. In order to acquire projecting angle thereby determine the corresponding relationship between sampling point and image point, method for encoding and decoding structured light based on stripe edge of Gray code is presented. The method encoded with Gray code stripe and decoded with stripe edge acquired by sub-pixel technology instead of pixel centre, so latter one-bit decoding error was removed. Accuracy of image sampling point location and correspondence between image sampling point and object sampling point achieved sub-pixel degree. In addition, measurement error caused by dividing projecting angle irregularly by even-width encoding stripe was analysed and corrected. Encoding and decoding principle and decoding equations were described. Finally, 3dsmax and Matlab software were used to simulate measurement system and reconstruct measured surface. Indicated by experimental results, measurement error is about 0.05%

  16. Transfer-printing and host-guest properties of 3D supramolecular particle structures.

    Ling, Xing Yi; Phang, In Yee; Reinhoudt, David N; Vancso, G Julius; Huskens, Jurriaan

    2009-04-01

    Mechanically robust and crystalline supramolecular particle structures have been constructed by decoupling nanoparticle assembly and supramolecular glue infiltration into a sequential process. First, beta-cyclodextrin (CD)-functionalized polystyrene particles (d approximately 500 nm) were assembled on a CD-functionalized surface via convective assembly to form highly ordered, but mechanically unstable, particle crystals. Subsequently, the crystals were infiltrated by a solution of adamantyl-functionalized dendrimers, functioning as a supramolecular glue to bind neighboring particles together and to couple the entire particle crystal to the CD surface, both in a noncovalent manner. The supramolecular particle crystals are highly robust, as witnessed by their ability to withstand agitation by ultrasonication. When assembled on a poly(dimethylsiloxane) (PDMS) stamp, the dendrimer-infiltrated particle crystals could be transfer-printed onto a CD-functionalized target surface. By variation of the geometry and size of the PDMS stamps, single particle lines, interconnected particle rings, and V-shaped particle assemblies were obtained. The particle structures served as 3D receptors for the binding of (multiple) complementary guest molecules, indicating that the supramolecular host functionalities of the particle crystals were retained throughout the fabrication process. PMID:20356024

  17. Performance analysis of high quality parallel preconditioners applied to 3D finite element structural analysis

    Kolotilina, L.; Nikishin, A.; Yeremin, A. [and others

    1994-12-31

    The solution of large systems of linear equations is a crucial bottleneck when performing 3D finite element analysis of structures. Also, in many cases the reliability and robustness of iterative solution strategies, and their efficiency when exploiting hardware resources, fully determine the scope of industrial applications which can be solved on a particular computer platform. This is especially true for modern vector/parallel supercomputers with large vector length and for modern massively parallel supercomputers. Preconditioned iterative methods have been successfully applied to industrial class finite element analysis of structures. The construction and application of high quality preconditioners constitutes a high percentage of the total solution time. Parallel implementation of high quality preconditioners on such architectures is a formidable challenge. Two common types of existing preconditioners are the implicit preconditioners and the explicit preconditioners. The implicit preconditioners (e.g. incomplete factorizations of several types) are generally high quality but require solution of lower and upper triangular systems of equations per iteration which are difficult to parallelize without deteriorating the convergence rate. The explicit type of preconditionings (e.g. polynomial preconditioners or Jacobi-like preconditioners) require sparse matrix-vector multiplications and can be parallelized but their preconditioning qualities are less than desirable. The authors present results of numerical experiments with Factorized Sparse Approximate Inverses (FSAI) for symmetric positive definite linear systems. These are high quality preconditioners that possess a large resource of parallelism by construction without increasing the serial complexity.

  18. 2D and 3D multipactor modeling in dielectric-loaded accelerator structures

    Sinitsyn, Oleksandr; Nusinovich, Gregory; Antonsen, Thomas

    2010-11-01

    Multipactor (MP) is known as the avalanche growth of the number of secondary electrons emitted from a solid surface exposed to an RF electric field under vacuum conditions. MP is a severe problem in modern rf systems and, therefore, theoretical and experimental studies of MP are of great interest to the researchers working in various areas of physics and engineering. In this work we present results of MP studies in dielectric-loaded accelerator (DLA) structures. First, we show simulation results obtained with the use of the 2D self-consistent MP model (O. V. Sinitsyn, et. al., Phys. Plasmas, vol. 16, 073102 (2009)) and compare those to experimental ones obtained during recent extensive studies of DLA structures performed by Argonne National Laboratory, Naval Research Laboratory, SLAC National Accelerator Laboratory and Euclid TechLabs (C. Jing, et al., IEEE Trans. Plasma Sci., vol. 38, pp. 1354-1360 (2010)). Then we present some new results of 3D analysis of MP which include studies of particle trajectories and studies of MP development at the early stage.

  19. 3D modeling of soil structure in urban groundwater areas: case studies in Kolpene, Rovaniemi, Finland

    Kupila, Juho

    2015-04-01

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

  20. 3-D Isotropic and Anisotropic S-velocity Structure in the North American Upper Mantle

    Yuan, H.; Marone, F.; Romanowicz, B.; Abt, D.; Fischer, K.

    2008-12-01

    The tectonic diversity of the North American continent has led to a number of geological, tectonic and geodynamical models, many of which can be better tested with high resolution 3-d tomographic models of the isotropic and anisotropic mantle structure of the continent. In the framework of non-linear asymptotic coupling theory (NACT), we recently developed tools to invert long period seismic waveforms combined with SKS splitting data, for both isotropic and radial and azimuthal anisotropic S-wave velocity structure in the upper mantle at the continental scale (Marone et al., 2007; Marone and Romanowicz, 2007). Striking differences in both isotropic and anisotropic velocity structure were observed: beneath the high velocity stable cratonic region a distinct two-layer anisotropic domain is present, with the bottom layer fast axis direction aligned with the absolute plate motion, and a shallower lithospheric layer with north pointing fast axis most likely showing records of past tectonic history; under the active western US the direction of tomographically inferred anisotropy is stable with depth and compatible with the absolute plate motion direction. Here we present an updated model which includes nearly five more years of data, including data from newly operative USArray stations, and a somewhat more extended frequency band. Our new model confirms our previous results, and reveals greater yet complex details of the anisotropic velocity structure beneath the western U.S.. We also show initial results of incorporating constraints on the depth to the lithosphere-asthenosphere boundary (LAB) using teleseismic receiver functions. We discuss the different anisotropic domains resolved both laterally and in depth, in the context of tectonic history of the north American continent.

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

    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

  2. Can Alex Edit? Nanometre scale 3D nanomechanical imaging of semiconductor structures from few nm to sub-micrometre depths

    Kolosov, Oleg; Dinelli, Franco; Robson, Alexander; Krier, Anthony; Hayne, Manus; Falko, Vladimir; Henini, M

    2015-01-01

    Multilayer structures of active semiconductor devices (1), novel memories (2) and semiconductor interconnects are becoming increasingly three-dimensional (3D) with simultaneous decrease of dimensions down to the few nanometres length scale (3). Ability to test and explore these 3D nanostructures with nanoscale resolution is vital for the optimization of their operation and improving manufacturing processes of new semiconductor devices. While electron and scanning probe microscopes (SPMs) can ...

  3. Structural evolution of the VMS-hosting Kristineberg area, Sweden – constraints from structural analysis and 3-D-modelling

    J. Hübert

    2012-10-01

    Full Text Available Structural mapping and 3-D-modelling with constraints from magnetotelluric (MT and reflection seismic investigations have been used to provide a geological synthesis of the geometrically complex Kristineberg area in the western part of the Palaeoproterozoic Skellefte district. The results indicate that, like the south-eastern parts of the Skellefte district, the area was subjected to SSE-NNW transpressional deformation at around 1.87 Ga. The contrasting structural geometries between the Kristineberg and the central Skellefte district areas may be attributed to the termination and splaying of a major ESE-WNW-striking high-strain zone into several branches in the northern part of the Kristineberg area. The transpressional structural signature was preferentially developed within the southern of the two antiformal structures of the area, "the Southern antiform", which exposes the deepest cut through the crust and hosts all the economic volcanogenic massive sulphides (VMS deposits of the area. Partitioning of the SSE-NNW transpression into N–S and E–W components led to formation of a characteristic "flat-steep-flat" geometry defining a highly non-cylindrical hinge of for the Southern antiform. Recognition of the transpressional structural signatures including the "flat-steep-flat" geometry and the distinct pattern of sub-horizontal E–W trending to moderately SW-plunging mineral lineations in the deeper crustal parts of the Kristineberg area is of significance for VMS exploration in both near mine and regional scales. The 3-D-model illustrating the outcomes of this study is available as a 3-D-PDF document through the publication website.

  4. Laser Scanning Holographic Lithography for Flexible 3D Fabrication of Multi-Scale Integrated Nano-structures and Optical Biosensors

    Yuan, Liang (Leon); Herman, Peter R.

    2016-02-01

    Three-dimensional (3D) periodic nanostructures underpin a promising research direction on the frontiers of nanoscience and technology to generate advanced materials for exploiting novel photonic crystal (PC) and nanofluidic functionalities. However, formation of uniform and defect-free 3D periodic structures over large areas that can further integrate into multifunctional devices has remained a major challenge. Here, we introduce a laser scanning holographic method for 3D exposure in thick photoresist that combines the unique advantages of large area 3D holographic interference lithography (HIL) with the flexible patterning of laser direct writing to form both micro- and nano-structures in a single exposure step. Phase mask interference patterns accumulated over multiple overlapping scans are shown to stitch seamlessly and form uniform 3D nanostructure with beam size scaled to small 200 μm diameter. In this way, laser scanning is presented as a facile means to embed 3D PC structure within microfluidic channels for integration into an optofluidic lab-on-chip, demonstrating a new laser HIL writing approach for creating multi-scale integrated microsystems.

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

    Yamada, Shooji; Yamaguchi, Hiroshi; Ishihara, Sunao

    2009-06-01

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

  6. 3D plane-based egomotion for SLAM on semi-structured environment

    Viejo Hernando, Diego; Cazorla Quevedo, Miguel Ángel

    2007-01-01

    Several works deal with 3D data in SLAM problem. Data come from a 3D laser sweeping unit or a stereo camera, both providing a huge amount of data. In this paper, we detail an efficient method to extract planar patches from 3D raw data. Then, we use these patches in an ICP-like method in order to address the SLAM problem. Using ICP with planes is not a trivial task. It needs some adaptation from the original ICP. Some promising results are shown for outdoor environment. This work has been s...

  7. Protein structure search and local structure characterization

    Ku Shih-Yen

    2008-08-01

    Full Text Available Abstract Background Structural similarities among proteins can provide valuable insight into their functional mechanisms and relationships. As the number of available three-dimensional (3D protein structures increases, a greater variety of studies can be conducted with increasing efficiency, among which is the design of protein structural alphabets. Structural alphabets allow us to characterize local structures of proteins and describe the global folding structure of a protein using a one-dimensional (1D sequence. Thus, 1D sequences can be used to identify structural similarities among proteins using standard sequence alignment tools such as BLAST or FASTA. Results We used self-organizing maps in combination with a minimum spanning tree algorithm to determine the optimum size of a structural alphabet and applied the k-means algorithm to group protein fragnts into clusters. The centroids of these clusters defined the structural alphabet. We also developed a flexible matrix training system to build a substitution matrix (TRISUM-169 for our alphabet. Based on FASTA and using TRISUM-169 as the substitution matrix, we developed the SA-FAST alignment tool. We compared the performance of SA-FAST with that of various search tools in database-scale search tasks and found that SA-FAST was highly competitive in all tests conducted. Further, we evaluated the performance of our structural alphabet in recognizing specific structural domains of EGF and EGF-like proteins. Our method successfully recovered more EGF sub-domains using our structural alphabet than when using other structural alphabets. SA-FAST can be found at http://140.113.166.178/safast/. Conclusion The goal of this project was two-fold. First, we wanted to introduce a modular design pipeline to those who have been working with structural alphabets. Secondly, we wanted to open the door to researchers who have done substantial work in biological sequences but have yet to enter the field of protein

  8. A 3D bioprinting system to produce human-scale tissue constructs with structural integrity.

    Kang, Hyun-Wook; Lee, Sang Jin; Ko, In Kap; Kengla, Carlos; Yoo, James J; Atala, Anthony

    2016-03-01

    A challenge for tissue engineering is producing three-dimensional (3D), vascularized cellular constructs of clinically relevant size, shape and structural integrity. We present an integrated tissue-organ printer (ITOP) that can fabricate stable, human-scale tissue constructs of any shape. Mechanical stability is achieved by printing cell-laden hydrogels together with biodegradable polymers in integrated patterns and anchored on sacrificial hydrogels. The correct shape of the tissue construct is achieved by representing clinical imaging data as a computer model of the anatomical defect and translating the model into a program that controls the motions of the printer nozzles, which dispense cells to discrete locations. The incorporation of microchannels into the tissue constructs facilitates diffusion of nutrients to printed cells, thereby overcoming the diffusion limit of 100-200 μm for cell survival in engineered tissues. We demonstrate capabilities of the ITOP by fabricating mandible and calvarial bone, cartilage and skeletal muscle. Future development of the ITOP is being directed to the production of tissues for human applications and to the building of more complex tissues and solid organs. PMID:26878319

  9. Quasi 3-D measurements of turbulence structure in horizontal air-water bubbly flow

    Quasi 3-D measurements of the turbulence structure of air-water bubbly flow in a horizontal tube with 35 mm i.d. are undertaken with two TSI 'X''-type hot-film probes. The turbulent fluctuations, uf,vf,wf, in axial, radial and circumferential directions, respectively, and Reynolds tresses -UV-bar and -u w-bar are obtained. It is found that in the lower portion of the tube, the profiles of turbulent fluctuation and Reynolds tress resemble those of single phase flow; whereas in the upper portion of he tube, where the bubble population is high, the turbulence, especially the circumferential fluctuation wf, is substantially enhanced, and the radial turbulence assumes highest value in the radial position -0.7< r/R<0.5. The magnitudes of Reynolds stresses -u w-bar and -UV-bar in our measurements are in the same level except in the lower portion of the tube where -u w-bar assumes a value close to zero as is the case in single phase flow and vertical air-water bubbly flow

  10. On the 3D structure of the nebula around \\eta-Carinae

    Lorenzo, Zaninetti

    2010-01-01

    The asymmetric shape of the nebula around $\\eta$-Carinae (Homunculus) can be explained by a spherical expansion in a non-homogeneous medium. Two models are analyzed: an exponential and an inverse power law dependence for the density as a function of distance from the equatorial plane. The presence of a medium with variable density along the polar direction progressively converts the original spherical shell into a bipolar nebula. In the case of the nebula around $\\eta$-Carinae, we know the time elapsed since the great outburst in 1840. An exact match between observed radii and velocities can be obtained by fine tuning the parameters involved, such as initial radius, initial velocity and the typical scale that characterizes the gradient in density. The observed radius and velocity of the Homunculus as a function of the polar angle in spherical coordinates can be compared with the corresponding simulated data by introducing the efficiency in a single or multiple directions. Once the 3D spatial structure of the ...

  11. Determining the 3D Subsurface Density Structure of Taurus Littrow Valley Using Apollo 17 Gravity Data

    Urbancic, N.; Ghent, R.; Stanley, S,; Johnson, C. L.; Carroll, K. A.; Hatch, D.; Williamson, M. C.; Garry, W. B.; Talwani, M.

    2016-01-01

    Surface gravity surveys can detect subsurface density variations that can reveal subsurface geologic features. In 1972, the Apollo 17 (A17) mission conducted the Traverse Gravimeter Experiment (TGE) using a gravimeter that measured the local gravity field near Taurus Littrow Valley (TLV), located on the south-eastern rim of the Serenitatis basin. TLV is hypothesized to be a basaltfilled radial graben resulting from the impact that formed Mare Serenitatis. It is bounded by both the North and South Massifs (NM and SM) as well as other smaller mountains to the East that are thought to be mainly composed of brecciated highland material. The TGE is the first and only successful gravity survey on the surface of the Moon. Other more recent satellite surveys, such as NASA's Gravity Recovery and Interior Laboratory (GRAIL) mission (2011- 2012), have produced the best global gravity field to date (approx. 13km resolution). However, these satellite surveys are not sensitive enough to detect fine-scale (3D modelling techniques in combination with high-resolution topographical and image datasets can reveal additional fine-scale subsurface structure in TLV.

  12. Accuracy Investigation for Structured-light Based Consumer 3D Sensors

    J. Boehm

    2014-01-01

    This work focuses on the performance investigation of consumer 3D sensors with respect to their repeatability and accuracy. It explores currently available sensors based on the 3D sensing technology developed by PrimeSense and introduced to the market in the form of the Microsoft Kinect. Accuracy and repeatability can be crucial criteria for the use of these sensors outside their intended use for home entertainment. The test strategies for the study are motivated by the VDI/VDE 2634 guideline...

  13. 3D RECONSTRUCTION OF BUILDINGS WITH GABLED AND HIPPED STRUCTURES USING LIDAR DATA

    Amini, H; P. Pahlavani; R. Karimi

    2014-01-01

    Buildings are the most important objects in urban areas. Thus, building detection using photogrammetry and remote sensing data as well as 3D model of buildings are very useful for many applications such as mobile navigation, tourism, and disaster management. In this paper, an approach has been proposed for detecting buildings by LiDAR data and aerial images, as well as reconstructing 3D model of buildings. In this regard, firstly, building detection carried out by utilizing a Supper Vector Ma...

  14. Synthesis of 3D structured graphene as a high performance catalyst support for methanol electro-oxidation

    Li, Yecheng; Zhang, Lei; Hu, Zhuofeng; Yu, Jimmy C.

    2015-06-01

    A simple process for preparing 3D structured graphene (3D-G) by a solution combustion method is reported. The product was deposited with platinum and used for methanol electro-oxidation. The catalyst shows a considerable enhancement in both the activity and stability towards methanol electro-oxidation reaction. Characterization reveals that the Pt/3D-G catalyst has a more negative onset potential as well as a higher electrochemically active specific surface area than a commercial Pt/C catalyst. Moreover, the catalyst exhibits higher tolerance to corrosion than carbon black. This work provides an efficient way for preparing 3D-G as a promising support for the oxidation of small organic molecules in fuel cells.

  15. Structural analysis of San Leo (RN, Italy) east and north cliffs using 3D point clouds

    Spreafico, Margherita Cecilia; Bacenetti, Marco; Borgatti, Lisa; Cignetti, Martina; Giardino, Marco; Perotti, Luigi

    2013-04-01

    The town of San Leo, like many others in the historical region of Montefeltro (Northern Apennines, Italy), was built in medieval period on a calcarenite and sandstone slab, bordered by subvertical and overhanging cliffs up to 100 m high, for defense purposes. The slab and the underlying clayey substratum show widespread landslide phenomena: the first is tectonized and crossed by joints and faults, and it is affected by lateral spreading with associated rock falls, topples and tilting. Moreover, the underlying clayey substratum is involved in plastic movements, like earth flows and slides. The main cause of instability in the area, which brings about these movements, is the high deformability contrast between the plate and the underlying clays. The aim of our research is to set up a numerical model that can well describe the processes and take into account the different factors that influence the evolution of the movements. One of these factors is certainly the structural setting of the slab, characterized by several joints and faults; in order to better identify and detect the main joint sets affecting the study area a structural analysis was performed. Up to date, a series of scans of San Leo cliff taken in 2008 and 2011, with a Riegl Z420i were analyzed. Initially, we chose a test area, located in the east side of the cliff, in which analyses were performed using two different softwares: COLTOP 3D and Polyworks. We repeated the analysis using COLTOP for all the east wall and for a part of the north wall, including an area affected by a rock fall in 2006. In the test area we identified five sets with different dips and dip directions. The analysis of the east and north walls permitted to identify eight sets (seven plus the bedding) of discontinuities. We compared these results with previous ones from surveys taken by others authors in some areas and with some preliminary data from a traditional geological survey of the whole area. With traditional methods only a

  16. Isotropic 3D nuclear morphometry of normal, fibrocystic and malignant breast epithelial cells reveals new structural alterations.

    Vivek Nandakumar

    Full Text Available BACKGROUND: Grading schemes for breast cancer diagnosis are predominantly based on pathologists' qualitative assessment of altered nuclear structure from 2D brightfield microscopy images. However, cells are three-dimensional (3D objects with features that are inherently 3D and thus poorly characterized in 2D. Our goal is to quantitatively characterize nuclear structure in 3D, assess its variation with malignancy, and investigate whether such variation correlates with standard nuclear grading criteria. METHODOLOGY: We applied micro-optical computed tomographic imaging and automated 3D nuclear morphometry to quantify and compare morphological variations between human cell lines derived from normal, benign fibrocystic or malignant breast epithelium. To reproduce the appearance and contrast in clinical cytopathology images, we stained cells with hematoxylin and eosin and obtained 3D images of 150 individual stained cells of each cell type at sub-micron, isotropic resolution. Applying volumetric image analyses, we computed 42 3D morphological and textural descriptors of cellular and nuclear structure. PRINCIPAL FINDINGS: We observed four distinct nuclear shape categories, the predominant being a mushroom cap shape. Cell and nuclear volumes increased from normal to fibrocystic to metastatic type, but there was little difference in the volume ratio of nucleus to cytoplasm (N/C ratio between the lines. Abnormal cell nuclei had more nucleoli, markedly higher density and clumpier chromatin organization compared to normal. Nuclei of non-tumorigenic, fibrocystic cells exhibited larger textural variations than metastatic cell nuclei. At p<0.0025 by ANOVA and Kruskal-Wallis tests, 90% of our computed descriptors statistically differentiated control from abnormal cell populations, but only 69% of these features statistically differentiated the fibrocystic from the metastatic cell populations. CONCLUSIONS: Our results provide a new perspective on nuclear

  17. Imaging 3D geological structure of the Mygdonian basin (Northern Greece) with geological numerical modeling and geophysical methods.

    Cédric, Guyonnet-Benaize; Fabrice, Hollender; Maria, Manakou; Alexandros, Savvaidis; Elena, Zargli; Cécile, Cornou; Nikolaos, Veranis; Dimitrios, Raptakis; Artemios, Atzemoglou; Pierre-Yves, Bard; Nikolaos, Theodulidis; Kyriazis, Pitilakis; Emmanuelle, Chaljub

    2013-04-01

    The Mygdonian basin, located 30 km E-NE close to Thessaloniki, is a typical active tectonic basin, trending E-NW, filled by sediments 200 to 400 m thick. This basin has been chosen as a European experimental site since 1993 (European Commission research projects - EUROSEISTEST). It has been investigated for experimental and theoretical studies on site effects. The Mygdonian basin is currently covered by a permanent seismological network and has been mainly characterized in 2D and 3D with geophysical and geotechnical studies (Bastani et al, 2011; Cadet and Savvaidis, 2011; Gurk et al, 2007; Manakou et al, 2007; Manakou et al, 2010; Pitilakis et al, 1999; Raptakis et al, 2000; Raptakis et al, 2005). All these studies allowed understanding the influence of geological structures and local site conditions on seismic site response. For these reasons, this site has been chosen for a verification exercise for numerical simulations in the framework of an ongoing international collaborative research project (Euroseistest Verification and Validation Project - E2VP). The verification phase has been made using a first 3D geophysical and geotechnical model (Manakou, 2007) about 5 km wide and 15 km long, centered on the Euroseistest site. After this verification phase, it has been decided to update, optimize and extend this model in order to obtain a more detailed model of the 3D geometry of the entire basin, especially the bedrock 3D geometry which can affect drastically the results of numerical simulations for site effect studies. In our study, we build a 3D geological model of the present-day structure of the entire Mygdonian basin. This "precise" model is 12 km wide, 65 km long and is 400 m deep in average. It has been built using geophysical, geotechnical and geological data. The database is heterogeneous and composed of hydrogeological boreholes, seismic refraction surveys, array microtremor measurements, electrical and geotechnical surveys. We propose an integrated

  18. 2D and 3D GPR imaging of structural ceilings in historic and existing constructions

    Colla, Camilla

    2014-05-01

    GPR applications in civil engineering are to date quite diversified. With respect to civil constructions and monumental buildings, detection of voids, cavities, layering in structural elements, variation of geometry, of moisture content, of materials, areas of decay, defects, cracks have been reported in timber, concrete and masonry elements. Nonetheless, many more fields of investigation remain unexplored. This contribution gives an account of a variety of examples of structural ceilings investigation by GPR radar in reflection mode, either as 2D or 3D data acquisition and visualisation. Ceilings have a pre-eminent role in buildings as they contribute to a good structural behaviour of the construction. Primarily, the following functions can be listed for ceilings: a) they carry vertical dead and live loads on floors and distribute such loads to the vertical walls; b) they oppose to external horizontal forces such as wind loads and earthquakes helping to transfer such forces from the loaded element to the other walls; c) they contribute to create the box skeleton and behaviour of a building, connecting the different load bearing walls and reducing the slenderness and flexural instability of such walls. Therefore, knowing how ceilings are made in specific buildings is of paramount importance for architects and structural engineers. According to the type of building and age of construction, ceilings may present very different solutions and materials. Moreover, in existing constructions, ceilings may have been substituted, modified or strengthened due to material decay or to change of use of the building. These alterations may often go unrecorded in technical documentation or technical drawings may be unavailable. In many cases, the position, orientation and number of the load carrying elements in ceilings may be hidden or not be in sight, due for example to the presence of false ceilings or to technical plants. GPR radar can constitute a very useful tool for

  19. Preservation of protein fluorescence in embedded human dendritic cells for targeted 3D light and electron microscopy.

    Höhn, K; Fuchs, J; Fröber, A; Kirmse, R; Glass, B; Anders-Össwein, M; Walther, P; Kräusslich, H-G; Dietrich, C

    2015-08-01

    In this study, we present a correlative microscopy workflow to combine detailed 3D fluorescence light microscopy data with ultrastructural information gained by 3D focused ion beam assisted scanning electron microscopy. The workflow is based on an optimized high pressure freezing/freeze substitution protocol that preserves good ultrastructural detail along with retaining the fluorescence signal in the resin embedded specimens. Consequently, cellular structures of interest can readily be identified and imaged by state of the art 3D confocal fluorescence microscopy and are precisely referenced with respect to an imprinted coordinate system on the surface of the resin block. This allows precise guidance of the focused ion beam assisted scanning electron microscopy and limits the volume to be imaged to the structure of interest. This, in turn, minimizes the total acquisition time necessary to conduct the time consuming ultrastructural scanning electron microscope imaging while eliminating the risk to miss parts of the target structure. We illustrate the value of this workflow for targeting virus compartments, which are formed in HIV-pulsed mature human dendritic cells. PMID:25786567

  20. The Deep Structure of the South Atlantic Kwanza Basin - Insights from 3D Structural and Gravimetric modelling

    Nicolai, Christina V.; Scheck-Wenderoth, Magdalena; Warsitzka, Michael

    2010-05-01

    Three dimensional geological models constrained by potential field data have proven to be powerful tools for the investigation of areas where conventional seismic surveying fails to deliver satisfactory results. Especially in basins containing thick sedimentary and/or evaporite layers, the detection of crustal structures such as synrift halfgrabens or basement highs is considerably enhanced by potential field data. Knowledge on the distribution and configuration of crustal structures is inalienable for the reconstruction of the tectonic history of a continental margin. In this study, we present results from 3D gravimetric modelling of the Kwanza Basin offshore Angola accomplished to investigate the formation of the basin in response to the opening of the South Atlantic. Although the post-rift evolution of the Kwanza Basin is well studied, little is known about the basins early history. This is mainly due to the missing knowledge of its crustal structure owing to the masking effect of an up to 3 km thick salt layer, which seismically obscures the underlying basement. To get an insight into the deeper structure of the Angolan margin we combined 3D structural, isostatic and gravimetric modelling. 2D seismic reflection data was used to determine the structural setting and the configuration of the stratigraphic units in the sedimentary part of the basin, whereas its crustal structure was constrained by isostatic and gravity modelling. The resulting geological model confirms and extends previous observations, and adds new details to the hitherto dim picture of the Kwanza Basins crustal architecture. In addition, it raises new questions on the volcanic or non-volcanic origin of the margin, and the potential of transfer faults to dissect the latter into independently evolving tectonic segments.

  1. Recovering 3D structural properties of galaxies from SDSS-like photometry

    Tempel, Elmo; Tamm, Antti; Kipper, Rain; Tenjes, Teeter

    2015-10-01

    Because of the 3D nature of galaxies, an algorithm for constructing spatial density distribution models of galaxies on the basis of galaxy images has many advantages over approximations of the surface density distribution. We present a method for deriving the spatial structure and overall parameters of galaxies from images and estimate its accuracy and derived parameter degeneracies on a sample of idealised model galaxies. The test galaxies consist of a disc-like component and a spheroidal component with varying proportions and properties. Both components are assumed to be axially symmetric and coplanar. We simulate these test galaxies as if they had been observed in the SDSS project through ugriz filters, thus gaining a set of realistically imperfect images of galaxies with known intrinsic properties. These artificial SDSS galaxies were thereafter remodelled by approximating the surface brightness distribution with a 2D projection of a bulge+disc spatial distribution model and the restored parameters were compared to the initial ones. Down to the r-band limiting magnitude of 18, errors in the restored integral luminosities and colour indices remain within 0.05 mag and errors in the luminosities of individual components within 0.2 mag. Accuracy of the restored bulge-to-disc luminosity ratio (B/D) is within 40% in most cases, and becomes worse for galaxies with low B/D, but the general balance between bulges and discs is not shifted systematically. Assuming that the intrinsic disc axial ratio is ≤ 0.3, then the inclination angles can be estimated with errors reasons.

  2. Imaging of 3-D seismic velocity structure of Southern Sumatra region using double difference tomographic method

    Southern Sumatra region has a high level of seismicity due to the influence of the subduction system, Sumatra fault, Mentawai fault and stretching zone activities. The seismic activities of Southern Sumatra region are recorded by Meteorological Climatological and Geophysical Agency (MCGA’s) Seismograph network. In this study, we used earthquake data catalog compiled by MCGA for 3013 events from 10 seismic stations around Southern Sumatra region for time periods of April 2009 – April 2014 in order to invert for the 3-D seismic velocities structure (Vp, Vs, and Vp/Vs ratio). We applied double-difference seismic tomography method (tomoDD) to determine Vp, Vs and Vp/Vs ratio with hypocenter adjustment. For the inversion procedure, we started from the initial 1-D seismic velocity model of AK135 and constant Vp/Vs of 1.73. The synthetic travel time from source to receiver was calculated using ray pseudo-bending technique, while the main tomographic inversion was applied using LSQR method. The resolution model was evaluated using checkerboard test and Derivative Weigh Sum (DWS). Our preliminary results show low Vp and Vs anomalies region along Bukit Barisan which is may be associated with weak zone of Sumatran fault and migration of partial melted material. Low velocity anomalies at 30-50 km depth in the fore arc region may indicated the hydrous material circulation because the slab dehydration. We detected low seismic seismicity in the fore arc region that may be indicated as seismic gap. It is coincides contact zone of high and low velocity anomalies. And two large earthquakes (Jambi and Mentawai) also occurred at the contact of contrast velocity

  3. A 3D gravity model of crustal structure in the Central-Eastern Alpine sector

    S. Scarascia

    1997-06-01

    Full Text Available Assuming as a starting model the pattern of the Moho boundary as interpreted in a recent study on the basis of the available DSS profiles, a preliminary 3D gravity model of the crustal structures in the Central-Eastern Alpine sector is proposed. The aim of the present work is to confirm the seismic results concerning the Moho and to better shape the main discontinuities in the intermediate and upper crust, where the seismic data are too scattered to allow a reliable interpretation. The gravity field is calculated along twelve cross-sections oriented S-N and crossing the Alpine range from the Padan-Venetian plain to the Bavarian molasse and to the Austrian calcareous Alps. The westernmost section coincides with the European Geotraverse while the easternmost one is positioned at the longitude of about 14ºeast. The assumed density model is very simple (only 6 layers; for each unit the density is maintained constant. The model describes a European mantle dipping southwards underneath an overlapping, uplifted Adriatic mantle. As far as the lower crust is concerned, its top is found at depths between 18 and 28 km, the deepest values being reached in the south-eastern sector; the density appears higher in the Adriatic domain than in the European one and the Adriatic lower crust seems to be deeply indented northwards. The low density surface layers appear very thin in a large area of the northwestern sector, while in the south and southeast their thickness reaches about 10 km. This study must be considered as a complement to the seismic interpretation both as a validation of the model of the deep crust and Moho boundary and as an additional source of information on the upper crust.

  4. Imaging of 3-D seismic velocity structure of Southern Sumatra region using double difference tomographic method

    Lestari, Titik, E-mail: t2klestari@gmail.com [Meteorological Climatological and Geophysical Agency (MCGA), Jalan Angkasa I No.2 Kemayoran, Jakarta Pusat, 10720 (Indonesia); Faculty of Earth Science and Technology, Bandung Institute of Technology, Jalan Ganesa No.10, Bandung 40132 (Indonesia); Nugraha, Andri Dian, E-mail: nugraha@gf.itb.ac.id [Global Geophysical Research Group, Faculty of Mining and Petroleum Engineering, Bandung Institute of Technology, Jalan Ganesa 10 Bandung 40132 (Indonesia)

    2015-04-24

    Southern Sumatra region has a high level of seismicity due to the influence of the subduction system, Sumatra fault, Mentawai fault and stretching zone activities. The seismic activities of Southern Sumatra region are recorded by Meteorological Climatological and Geophysical Agency (MCGA’s) Seismograph network. In this study, we used earthquake data catalog compiled by MCGA for 3013 events from 10 seismic stations around Southern Sumatra region for time periods of April 2009 – April 2014 in order to invert for the 3-D seismic velocities structure (Vp, Vs, and Vp/Vs ratio). We applied double-difference seismic tomography method (tomoDD) to determine Vp, Vs and Vp/Vs ratio with hypocenter adjustment. For the inversion procedure, we started from the initial 1-D seismic velocity model of AK135 and constant Vp/Vs of 1.73. The synthetic travel time from source to receiver was calculated using ray pseudo-bending technique, while the main tomographic inversion was applied using LSQR method. The resolution model was evaluated using checkerboard test and Derivative Weigh Sum (DWS). Our preliminary results show low Vp and Vs anomalies region along Bukit Barisan which is may be associated with weak zone of Sumatran fault and migration of partial melted material. Low velocity anomalies at 30-50 km depth in the fore arc region may indicated the hydrous material circulation because the slab dehydration. We detected low seismic seismicity in the fore arc region that may be indicated as seismic gap. It is coincides contact zone of high and low velocity anomalies. And two large earthquakes (Jambi and Mentawai) also occurred at the contact of contrast velocity.

  5. Characterizing Vegetation 3D structure Globally using Spaceborne Lidar and Radar.

    Simard, M.; Pinto, N.; Riddick, S.

    2008-12-01

    We characterized global vegetation 3D structure using ICEsat-I/Geoscience Laser Altimeter (GLAS) and improved spatial resolution using ALOS/Phased Array L-band Synthetic Aperture radar (PALSAR) data over 3 sites in the United States. GLAS is a 70m footprint lidar altimeter sampling the ground along-track every 170m with a track separation near the equator around 30km. Forest type classes were initially defined according to the Global Land Cover 2000 map (GLC2000), and 5-degree latitude intervals. This strategy enabled analysis of canopy structure as a function of land cover type and latitude. This produced an irregular grid geographically consistant with GLC2000. To estimate canopy height we removed the ground component from the lidar waveform and computed the centroid of the component due to the forest canopy. Canopy height within a grid cell was produced by computing the weighted mean of the GLAS estimates contained within that cell. The weights were used to reduce the impact of slope on Lidar height estimation errors. Slope is the single most significant source of error when estimating height with a large footprint lidar. It stretches the waveform and causes false estimates of canopy height. The Shuttle Radar Topography Mission (SRTM) elevation data was used to derive slope and weights. Thus, data points located in flat areas were assigned a higher weight than points located in slopes. For each forest type, we modeled the relationship between Lidar-estimated canopy height and five environmental variables: temperature, precipitation, slope, elevation, and anthropogenic disturbance. This ecological model was constructed using the machine learning method Random Forest, due to its flexibility and non-parametric nature. Model accuracy was calculated by subsampling the Lidar data set: using 75% of the data set to produce the map previously described and the remaining 25% for validation. This approach was chosen to characterize individual forest canopy types and their

  6. 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

    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 (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 Computers and parallelized code. Results are compared with field data. Preliminary results show an excellent match with field data using the 3-d fdtd technique.

  7. Recent Advances in Unconventional Lithography for Challenging 3D Hierarchical Structures and Their Applications

    Jong Uk Kim

    2016-01-01

    Full Text Available In nanoscience and nanotechnology, nanofabrication is critical. Among the required processes for nanofabrication, lithography is one of core issues. Although conventional photolithography with recent remarkable improvement has contributed to the industry during the past few decades, fabrication of 3-dimensional (3D nanostructure is still challenging. In this review, we summarize recent advances for the construction of 3D nanostructures by unconventional lithography and the combination of two top-down approaches or top-down and bottom-up approaches. We believe that the 3D hierarchical nanostructures described here will have a broad range of applications having adaptable levels of functional integration of precisely controlled nanoarchitectures that are required by not only academia, but also industry.

  8. Fabrication, Characterization, And Deformation of 3D Structural Meta-Materials

    Montemayor, Lauren C.

    Current technological advances in fabrication methods have provided pathways to creating architected structural meta-materials similar to those found in natural organisms that are structurally robust and lightweight, such as diatoms. Structural meta-materials are materials with mechanical properties that are determined by material properties at various length scales, which range from the material microstructure (nm) to the macro-scale architecture (mum -- mm). It is now possible to exploit material size effect, which emerge at the nanometer length scale, as well as structural effects to tune the material properties and failure mechanisms of small-scale cellular solids, such as nanolattices. This work demonstrates the fabrication and mechanical properties of 3-dimensional hollow nanolattices in both tension and compression. Hollow gold nanolattices loaded in uniaxial compression demonstrate that strength and stiffness vary as a function of geometry and tube wall thickness. Structural effects were explored by increasing the unit cell angle from 30° to 60° while keeping all other parameters constant; material size effects were probed by varying the tube wall thickness, t, from 200nm to 635nm, at a constant relative density and grain size. In-situ uniaxial compression experiments reveal an order-of-magnitude increase in yield stress and modulus in nanolattices with greater lattice angles, and a 150% increase in the yield strength without a concomitant change in modulus in thicker-walled nanolattices for fixed lattice angles. These results imply that independent control of structural and material size effects enables tunability of mechanical properties of 3-dimensional architected meta-materials and highlight the importance of material, geometric, and microstructural effects in small-scale mechanics. This work also explores the flaw tolerance of 3D hollow-tube alumina kagome nanolattices with and without pre-fabricated notches, both in experiment and simulation

  9. Protein structure database search and evolutionary classification.

    Yang, Jinn-Moon; Tung, Chi-Hua

    2006-01-01

    As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the statistical significance (E-value) of an alignment to indicate the reliability of the prediction. Using this method, we first identified 23 states of the structural alphabet that represent pattern profiles of the backbone fragments and then used them to represent protein structure databases as structural alphabet sequence databases (SADB). Our method enhanced BLAST as a search method, using a new structural alphabet substitution matrix (SASM) to find the longest common substructures with high-scoring structured segment pairs from an SADB database. Using personal computers with Intel Pentium4 (2.8 GHz) processors, our method searched more than 10 000 protein structures in 1.3 s and achieved a good agreement with search results from detailed structure alignment methods. [3D-BLAST is available at http://3d-blast.life.nctu.edu.tw]. PMID:16885238

  10. Synthesis on structure and properties of zinc nanocrystal in high ordered 3D nanostructures

    The wet impregnation method was employed to prepare ZnO encapsulated in mesoporous silica (ZnO/KIT-6). The prepared ZnO/KIT-6 samples have been studied by X-ray diffraction, transmission electron microscope, and nitrogen adsorption–desorption isotherm. The low angle powder XRD patterns of Calcined ZnO/KIT-6 materials showed a phase that can be indexed to cubic Ia3d. Tem images revealed well ordered cubic 3D nanoporous chennels. The ZnO encapsulated in KIT-6 can be used as light-emitting diodes and ultraviolet nanolasers

  11. Introduction of DC line structures into a superconducting microwave 3D cavity

    We report a technique that can noninvasively add multiple DC wires into a 3D superconducting microwave cavity for electronic devices that require DC electrical terminals. We studied the influence of our DC lines on the cavity performance systematically. We found that the quality factor of the cavity is reduced if any of the components of the electrical wires cross the cavity equipotential planes. Using this technique, we were able to incorporate a quantum dot (QD) device into a 3D cavity. We then controlled and measured the QD transport signal using the DC lines. We have also studied the heating effects of the QD by the microwave photons in the cavity

  12. Novel techniques for protein structure characterization using graph representation of proteins

    Küçükural, Alper; Kucukural, Alper

    2009-01-01

    Proteins exhibit an infinite variety of structures. Around 50K 3D structures of proteins exist in PDB database among unlimited possibilities. The three dimensional structure of a protein is crucial to its function. Even within a common structure family, proteins vary in length, size, and sequence. This variation is the reflection of evolution on protein sequences. The intrinsic information in protein structures can be captured by their graph representations. The structural similarities betwee...

  13. A study of the effects of degraded imagery on tactical 3D model generation using structure-from-motion

    Bolick, Leslie; Harguess, Josh

    2016-05-01

    An emerging technology in the realm of airborne intelligence, surveillance, and reconnaissance (ISR) systems is structure-from-motion (SfM), which enables the creation of three-dimensional (3D) point clouds and 3D models from two-dimensional (2D) imagery. There are several existing tools, such as VisualSFM and open source project OpenSfM, to assist in this process, however, it is well-known that pristine imagery is usually required to create meaningful 3D data from the imagery. In military applications, such as the use of unmanned aerial vehicles (UAV) for surveillance operations, imagery is rarely pristine. Therefore, we present an analysis of structure-from-motion packages on imagery that has been degraded in a controlled manner.

  14. 3D polycarprolactone (PCL) scaffold with hierarchical structure fabricated by a piezoelectric transducer (PZT)-assisted bioplotter

    Kim, Geun Hyung; Son, Joon Gon

    2009-03-01

    The 3D bioplotter, which is one of the rapid-prototyping systems, enables us to produce the design-based scaffolds which could control good mechanical properties and pore structures for mimicking human organs. Although the plotting system has several advantages to fabricate a variety of designed scaffolds, the main disadvantage of scaffolds fabricated by the system is that the strand surfaces are too smooth and tend to discourage initial cell attachment within the scaffolds. To overcome the problem, we suggest a new 3D plotting method supplemented by piezoelectric vibration system for fabricating scaffolds that have hierarchical surface structures, which increase the surface roughness of the scaffold without any additional chemical process. The surface-modified 3D scaffold exhibited various positive qualities including enhanced compressive modulus and improved initial cell attachment and proliferation. Cell culturing results demonstrated that the interactions between chondrocytes and the scaffold were much more favorable than those between the cells and conventionally plotted 3D scaffolds. This process provides a feasible new technique for fabricating high-quality 3D scaffolds for tissue engineering applications.

  15. 3D structure prediction of human β1-adrenergic receptor via threading-based homology modeling for implications in structure-based drug designing.

    Zaheer Ul-Haq

    Full Text Available 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.

  16. Fluoride Bridges as Structure-Directing Motifs in 3d-4f Cluster Chemistry

    Birk, Torben; Pedersen, Kasper; Thuesen, Christian Aa.;

    2012-01-01

    The use of kinetically robust chromium(III) fluorido complexes as synthons for mixed 3d-4f clusters is reported. The tendency toward linear {CrIII–F–LnIII} units dictates the cluster topology. Specifically, we show that reaction of cis-[CrIIIF2(NN)2]NO3 (NN = 1,10-phenanthroline (“phen”) or 2,2′-...

  17. Structuring Narrative in 3D Digital Game-Based Learning Environments to Support Second Language Acquisition

    Neville, David O.

    2010-01-01

    The essay is a conceptual analysis from an instructional design perspective exploring the feasibility of using three-dimensional digital game-based learning (3D-DGBL) environments to assist in second language acquisition (SLA). It examines the shared characteristics of narrative within theories of situated cognition, context-based approaches to…

  18. Theoretical study of relative width of photonic band gap for the 3-D dielectric structure

    G K Johri; Akhilesh Tiwari; Saumya Saxena; Rajesh Sharma; Kuldeep Srivastava; Manoj Johri

    2002-03-01

    Calculations for the relative width (/0) as a function of refractive index and relative radius of the photonic band gap for the fcc closed packed 3-D dielectric microstructure are reported and comparison of experimental observations and theoretical predictions are given. This work is useful for the understanding of photonic crystals and occurrence of the photonic band gap.

  19. The structural feasibility of 3D-printing houses using printable polymers

    Van der Veen, A.C.; Coenders, J.L.; Veer, F.A.; Nijsse, R.; Houtman, R.; Schonwalder, J.

    2015-01-01

    At this point in time, 3D-printing techniques in general, but especially applied for the building industry, still are in a phase of early experiments. One of the experimental attempts is to print a full-scale, three-story high, house in Amsterdam, using an up scaled version of a FDM-printer that is

  20. PRONTO3D users` instructions: A transient dynamic code for nonlinear structural analysis

    Attaway, S.W.; Mello, F.J.; Heinstein, M.W.; Swegle, J.W.; Ratner, J.A. [Sandia National Labs., Albuquerque, NM (United States); Zadoks, R.I. [Univ. of Texas, El Paso, TX (United States)

    1998-06-01

    This report provides an updated set of users` instructions for PRONTO3D. PRONTO3D is a three-dimensional, transient, solid dynamics code for analyzing large deformations of highly nonlinear materials subjected to extremely high strain rates. This Lagrangian finite element program uses an explicit time integration operator to integrate the equations of motion. Eight-node, uniform strain, hexahedral elements and four-node, quadrilateral, uniform strain shells are used in the finite element formulation. An adaptive time step control algorithm is used to improve stability and performance in plasticity problems. Hourglass distortions can be eliminated without disturbing the finite element solution using either the Flanagan-Belytschko hourglass control scheme or an assumed strain hourglass control scheme. All constitutive models in PRONTO3D are cast in an unrotated configuration defined using the rotation determined from the polar decomposition of the deformation gradient. A robust contact algorithm allows for the impact and interaction of deforming contact surfaces of quite general geometry. The Smooth Particle Hydrodynamics method has been embedded into PRONTO3D using the contact algorithm to couple it with the finite element method.

  1. Virtual 3D reconstruction of embryonic head structures from physical sections

    Janáček, Jiří; Kundrát, M.

    2004-01-01

    Roč. 260, č. 3 (2004), s. 302. ISSN 0362-2525 R&D Projects: GA AV ČR(CZ) KJB6111301 Institutional research plan: CEZ:AV0Z5011922 Keywords : embryonic heads * 3D reconstruction Subject RIV: EA - Cell Biology Impact factor: 1.528, year: 2004

  2. Fabrication of scalable and structured tissue engineering scaffolds using water dissolvable sacrificial 3D printed moulds

    Mohanty, Soumyaranjan; Larsen, Layla Bashir; Trifol Guzman, Jon;

    2015-01-01

    One of the major challenges in producing large scale engineered tissue is the lack of ability to create large highly perfused scaffolds in which cells can grow at a high cell density and viability. Here, we explore 3D printed polyvinyl alcohol (PVA) as a sacrificial mould in a polymer casting...

  3. An Innovative Cell Microincubator for Drug Discovery Based on 3D Silicon Structures

    Francesca Aredia

    2016-01-01

    Full Text Available We recently employed three-dimensional (3D silicon microstructures (SMSs consisting in arrays of 3 μm-thick silicon walls separated by 50 μm-deep, 5 μm-wide gaps, as microincubators for monitoring the biomechanical properties of tumor cells. They were here applied to investigate the in vitro behavior of HT1080 human fibrosarcoma cells driven to apoptosis by the chemotherapeutic drug Bleomycin. Our results, obtained by fluorescence microscopy, demonstrated that HT1080 cells exhibited a great ability to colonize the narrow gaps. Remarkably, HT1080 cells grown on 3D-SMS, when treated with the DNA damaging agent Bleomycin under conditions leading to apoptosis, tended to shrink, reducing their volume and mimicking the normal behavior of apoptotic cells, and were prone to leave the gaps. Finally, we performed label-free detection of cells adherent to the vertical silicon wall, inside the gap of 3D-SMS, by exploiting optical low coherence reflectometry using infrared, low power radiation. This kind of approach may become a new tool for increasing automation in the drug discovery area. Our results open new perspectives in view of future applications of the 3D-SMS as the core element of a lab-on-a-chip suitable for screening the effect of new molecules potentially able to kill tumor cells.

  4. How Children Determine the Size of 3D Structures: Investigating Factors Influencing Strategy Choice

    Vasilyeva, Marina; Ganley, Colleen M.; Casey, Beth M.; Dulaney, Alana; Tillinger, Miriam; Anderson, Karen

    2013-01-01

    This study explores changes in students' strategies as they solve different types of volume problems. Fifth graders were presented with pictures showing 3D objects and a unit cube; they determined how many cubes made up the object and explained their responses. We examined whether children transferred strategies across problem types, varying in…

  5. Impact of 3-D printed PLA- and chitosan-based scaffolds on human monocyte/macrophage responses: unraveling the effect of 3-D structures on inflammation.

    Almeida, Catarina R; Serra, Tiziano; Oliveira, Marta I; Planell, Josep A; Barbosa, Mário A; Navarro, Melba

    2014-02-01

    Recent studies have pointed towards a decisive role of inflammation in triggering tissue repair and regeneration, while at the same time it is accepted that an exacerbated inflammatory response may lead to rejection of an implant. Within this context, understanding and having the capacity to regulate the inflammatory response elicited by 3-D scaffolds aimed for tissue regeneration is crucial. This work reports on the analysis of the cytokine profile of human monocytes/macrophages in contact with biodegradable 3-D scaffolds with different surface properties, architecture and controlled pore geometry, fabricated by 3-D printing technology. Fabrication processes were optimized to create four different 3-D platforms based on polylactic acid (PLA), PLA/calcium phosphate glass or chitosan. Cytokine secretion and cell morphology of human peripheral blood monocytes allowed to differentiate on the different matrices were analyzed. While all scaffolds supported monocyte/macrophage adhesion and stimulated cytokine production, striking differences between PLA-based and chitosan scaffolds were found, with chitosan eliciting increased secretion of tumor necrosis factor (TNF)-α, while PLA-based scaffolds induced higher production of interleukin (IL)-6, IL-12/23 and IL-10. Even though the material itself induced the biggest differences, the scaffold geometry also impacted on TNF-α and IL-12/23 production, with chitosan scaffolds having larger pores and wider angles leading to a higher secretion of these pro-inflammatory cytokines. These findings strengthen the appropriateness of these 3-D platforms to study modulation of macrophage responses by specific parameters (chemistry, topography, scaffold architecture). PMID:24211731

  6. Construction of a 3D meso-structure and analysis of mechanical properties for deposit body medium

    石崇; 陈凯华; 徐卫亚; 张海龙; 王海礼; 王盛年

    2015-01-01

    For deposit body medium, the internal structural properties may be the controlling factors for the strength of the material and the mechanical response. Based on the results of soil-rock meso-statistics using digital imaging, a simulated annealing algorithm is adopted to expand the meso-structural features of deposit bodies in 3D. The construction of the 3D meso-structure of a deposit body is achieved, and then the particle flow analysis program PFC3D is used to simulate the mechanical properties of the deposit body. It is shown that with a combination of the simulated annealing algorithm and the statistical feature functions, the randomness and heterogeneity of the rock distribution in the 3D inner structure of deposit body medium can be realized, and the reconstructed structural features of the deposit medium can match the features of the digital images well. The spatial utilizations and the compacting effects of the body-centered cubic, hexagonal close and face-centered packing models are high, so these structures can be applied in the simulations of the deposit structures. However, the shear features of the deposit medium vary depending on the different model constructive modes. Rocks, which are the backbone of the deposit, are the factors that determine the shear strength and deformation modulus of the deposit body. The modeling method proposed is useful for the construction of 3D meso-scope models from 2D meso-scope statistics and can be used for studying the mechanical properties of mixed media, such as deposit bodies.

  7. 3D gravity imaging of deep geological structure of Huangling Anticline in Three Gorges area, China

    Zhang, Y.; Chen, C.

    2010-12-01

    Three Gorges Dam is the largest hydraulic project in the world. Previous studies showed that Huangling Anticline is one of the main geological units in this area and has great influence on the safety of the dam, so it is important to investigate deep geological structure and evaluate stability of Huangling Anticline. Huangling Anticline locates in northern margin of Yangtze Block. It is surrounded by a few faults, and two of them are Xiannushan Fault and Yuan’an Fault, with NNW direction. There are also two main faults named Xinhua Fault and Yuyangguan-Tumen Fault with NNE and NE direction. These faults are regional faults with different sizes and cutting depth, and take charge of the development of geological structures in Three Gorges area with a long time. Two main arguments about the ability of inducing earthquakes of these faults were presented. One of the arguments suggested that these faults has weak or no enough activity to induce strong earthquakes, their key evidence is the thermoluminescence (TL) dating with some geological characteristics; the other was just opposite, in their opinion, Xiannushan Fault and Yuan’an Fault has deep cutting depth with great activity to induce strong earthquakes. However, they can not provide the evidences of deep geological structures and cutting depth of these faults. In our paper, 3D density structure of upper and middle crust beneath Three Gorges Dam and its adjacent regions is reconstructed by gravity imaging, using the Bouguer gravity anomaly and surface density constraints. Results of gravity imaging indicate that Huangling Anticline is a relatively high density zone. (1) Horizontally, Huangling Anticline is a huge U-shaped crystal rock controlled by Xiannushan Fault and Yuan’an Fault along NNW direction. In the southeast, Yuyangguan-Tumen Fault becomes the boundary of the anticline, and in the west, Xinhua Fault and Xiannushan Fault separate Huangling Anticline from Zigui basin; (2) From vertical profiles of

  8. PRISM: a web server and repository for prediction of protein–protein interactions and modeling their 3D complexes

    Baspinar, Alper; Cukuroglu, Engin; Nussinov, Ruth; Keskin, Ozlem; Gursoy, Attila

    2014-01-01

    The PRISM web server enables fast and accurate prediction of protein–protein interactions (PPIs). The prediction algorithm is knowledge-based. It combines structural similarity and accounts for evolutionary conservation in the template interfaces. The predicted models are stored in its repository. Given two protein structures, PRISM will provide a structural model of their complex if a matching template interface is available. Users can download the complex structure, retrieve the interface r...

  9. 3D printing of high-resolution PLA-based structures by hybrid electrohydrodynamic and fused deposition modeling techniques

    Recently, the three-dimensional (3D) printing technique has received much attention for shape forming and manufacturing. The fused deposition modeling (FDM) printer is one of the various 3D printers available and has become widely used due to its simplicity, low-cost, and easy operation. However, the FDM technique has a limitation whereby its patterning resolution is too low at around 200 μm. In this paper, we first present a hybrid mechanism of electrohydrodynamic jet printing with the FDM technique, which we name E-FDM. We then develop a novel high-resolution 3D printer based on the E-FDM process. To determine the optimal condition for structuring, we also investigated the effect of several printing parameters, such as temperature, applied voltage, working height, printing speed, flow-rate, and acceleration on the patterning results. This method was capable of fabricating both high resolution 2D and 3D structures with the use of polylactic acid (PLA). PLA has been used to fabricate scaffold structures for tissue engineering, which has different hierarchical structure sizes. The fabrication speed was up to 40 mm/s and the pattern resolution could be improved to 10 μm. (paper)

  10. Single-shot 3D structure determination of nanocrystals with femtosecond X-ray free electron laser pulses

    Xu, Rui; Song, Changyong; Rodriguez, Jose A; Huang, Zhifeng; Chen, Chien-Chun; Nam, Daewoong; Park, Jaehyun; Gallagher-Jones, Marcus; Kim, Sangsoo; Kim, Sunam; Suzuki, Akihiro; Takayama, Yuki; Oroguchi, Tomotaka; Takahashi, Yukio; Fan, Jiadong; Zou, Yunfei; Hatsui, Takaki; Inubushi, Yuichi; Kameshima, Takashi; Yonekura, Koji; Tono, Kensuke; Togashi, Tadashi; Sato, Takahiro; Yamamoto, Masaki; Nakasako, Masayoshi; Yabashi, Makina; Ishikawa, Tetsuya; Miao, Jianwei

    2013-01-01

    Coherent diffraction imaging (CDI) using synchrotron radiation, X-ray free electron lasers (X-FELs), high harmonic generation, soft X-ray lasers, and optical lasers has found broad applications across several disciplines. An active research direction in CDI is to determine the structure of single particles with intense, femtosecond X-FEL pulses based on diffraction-before-destruction scheme. However, single-shot 3D structure determination has not been experimentally realized yet. Here we report the first experimental demonstration of single-shot 3D structure determination of individual nanocrystals using ~10 femtosecond X-FEL pulses. Coherent diffraction patterns are collected from high-index-faceted nanocrystals, each struck by a single X-FEL pulse. Taking advantage of the symmetry of the nanocrystal, we reconstruct the 3D structure of each nanocrystal from a single-shot diffraction pattern at ~5.5 nm resolution. As symmetry exists in many nanocrystals and virus particles, this method can be applied to 3D st...

  11. How Students and Field Geologists Reason in Integrating Spatial Observations from Outcrops to Visualize a 3-D Geological Structure

    Kastens, Kim A.; Agrawal, Shruti; Liben, Lynn S.

    2009-01-01

    Geologists and undergraduate students observed eight artificial "rock outcrops" in a realistically scaled field area, and then tried to envision a geological structure that might plausibly be formed by the layered rocks in the set of outcrops. Students were videotaped as they selected which of fourteen 3-D models they thought best represented the…

  12. 3D printing of high-resolution PLA-based structures by hybrid electrohydrodynamic and fused deposition modeling techniques

    Zhang, Bin; Seong, Baekhoon; Nguyen, VuDat; Byun, Doyoung

    2016-02-01

    Recently, the three-dimensional (3D) printing technique has received much attention for shape forming and manufacturing. The fused deposition modeling (FDM) printer is one of the various 3D printers available and has become widely used due to its simplicity, low-cost, and easy operation. However, the FDM technique has a limitation whereby its patterning resolution is too low at around 200 μm. In this paper, we first present a hybrid mechanism of electrohydrodynamic jet printing with the FDM technique, which we name E-FDM. We then develop a novel high-resolution 3D printer based on the E-FDM process. To determine the optimal condition for structuring, we also investigated the effect of several printing parameters, such as temperature, applied voltage, working height, printing speed, flow-rate, and acceleration on the patterning results. This method was capable of fabricating both high resolution 2D and 3D structures with the use of polylactic acid (PLA). PLA has been used to fabricate scaffold structures for tissue engineering, which has different hierarchical structure sizes. The fabrication speed was up to 40 mm/s and the pattern resolution could be improved to 10 μm.

  13. Simultaneous spatiotemporal mapping of in situ pH and bacterial activity within an intact 3D microcolony structure.

    Hwang, Geelsu; Liu, Yuan; Kim, Dongyeop; Sun, Victor; Aviles-Reyes, Alejandro; Kajfasz, Jessica K; Lemos, Jose A; Koo, Hyun

    2016-01-01

    Biofilms are comprised of bacterial-clusters (microcolonies) enmeshed in an extracellular matrix. Streptococcus mutans can produce exopolysaccharides (EPS)-matrix and assemble microcolonies with acidic microenvironments that can cause tooth-decay despite the surrounding neutral-pH found in oral cavity. How the matrix influences the pH and bacterial activity locally remains unclear. Here, we simultaneously analyzed in situ pH and gene expression within intact biofilms and measured the impact of damage to the surrounding EPS-matrix. The spatiotemporal changes of these properties were characterized at a single-microcolony level following incubation in neutral-pH buffer. The middle and bottom-regions as well as inner-section within the microcolony 3D structure were resistant to neutralization (vs. upper and peripheral-region), forming an acidic core. Concomitantly, we used a green fluorescent protein (GFP) reporter to monitor expression of the pH-responsive atpB (PatpB::gfp) by S. mutans within microcolonies. The atpB expression was induced in the acidic core, but sharply decreased at peripheral/upper microcolony regions, congruent with local pH microenvironment. Enzymatic digestion of the surrounding matrix resulted in nearly complete neutralization of microcolony interior and down-regulation of atpB. Altogether, our data reveal that biofilm matrix facilitates formation of an acidic core within microcolonies which in turn activates S. mutans acid-stress response, mediating both the local environment and bacterial activity in situ. PMID:27604325

  14. Sand transverse dune aerodynamics: 3D Coherent Flow Structures from a computational study

    Bruno, Luca

    2015-01-01

    The engineering interest about dune fields is dictated by the their interaction with a number of human infrastructures in arid environments. The aerodynamic behaviour of sand dunes in atmospheric boundary layer belongs to the class of bluff bodies. Because of their simple geometry and their frequent occurrence in desert area, transverse sand dunes are usually adopted in literature as a benchmark to investigate dune aerodynamics by means of both computational or experimental approach, usually in nominally 2D setups. The writers suspect the flow in the wake is characterised by 3D features and affected by wind tunnel setup - e.g. blockage effect, duct side wall boundary layer, incoming velocity profile - when experimental studies are carried out. The present study aims at evaluating the 3D flow features of an idealised transverse dune under different setup conditions by means of computational simulations and to compare the obtained results with experimental measurements.

  15. 3D RECONSTRUCTION OF BUILDINGS WITH GABLED AND HIPPED STRUCTURES USING LIDAR DATA

    H. Amini

    2014-10-01

    Full Text Available Buildings are the most important objects in urban areas. Thus, building detection using photogrammetry and remote sensing data as well as 3D model of buildings are very useful for many applications such as mobile navigation, tourism, and disaster management. In this paper, an approach has been proposed for detecting buildings by LiDAR data and aerial images, as well as reconstructing 3D model of buildings. In this regard, firstly, building detection carried out by utilizing a Supper Vector Machine (SVM as a supervise method. The supervise methods need training data that could be collected from some features. Hence, LiDAR data and aerial images were utilized to produce some features. The features were selected by considering their abilities for separating buildings from other objects. The evaluation results of building detection showed high accuracy and precision of the utilized approach. The detected buildings were labeled in order to reconstruct buildings, individually. Then the planes of each building were separated and adjacent planes were recognized to reduce the calculation volume and to increase the accuracy. Subsequently, the bottom planes of each building were detected in order to compute the corners of hipped roofs using intersection of three adjacent planes. Also, the corners of gabled roofs were computed by both calculating the intersection line of the adjacent planes and finding the intersection between the planes intersection line and their detected parcel. Finally, the coordinates of some nodes in building floor were computed and 3D model reconstruction was carried out. In order to evaluate the proposed method, 3D model of some buildings with different complexity level were generated. The evaluation results showed that the proposed method has reached credible performance.

  16. Computational technology for analysis of 3D meso-structure effects on damage and failure of concrete

    Wang, X.; Zhang, M.; Jivkov, A. P.

    2016-01-01

    Methodology for analysis of meso-structure effects on longer-scale mechanical response of concrete is developed. Efficient algorithms for particle generation and packing are proposed to represent 3D meso-structures as collections of discrete features distributed randomly in a continuous phase. Specialised to concrete, the continuous phase represents mortar, while the features are aggregates and voids. Intra- and inter-phase cohesive zones are used for failure initiation and crack propagation....

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

    Quan Zhang; Kai Zhang; Gengkai Hu

    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 h...

  18. Sampling-Based Sweep Planning to Exploit Local Planarity in the Inspection of Complex 3d Structures

    Englot, Brendan J.; Hover, Franz S.

    2012-01-01

    We present a hybrid algorithm that plans feasible paths for 100% sensor coverage of complex 3D structures. The structures to be inspected are segmented to isolate planar areas, and back-and-forth sweep paths are generated to view as much of these planar areas as possible while avoiding collision. A randomized planning procedure fills in the remaining gaps in coverage. The problem of selecting an order to traverse the elements of the inspection is solved by reduction to the traveling salesman ...

  19. Wakefield Simulation of CLIC PETS Structure Using Parallel 3D Finite Element Time-Domain Solver T3P

    Candel, A.; Kabel, A.; Lee, L.; Li, Z.; Ng, C.; Schussman, G.; Ko, K.; /SLAC; Syratchev, I.; /CERN

    2009-06-19

    In recent years, SLAC's Advanced Computations Department (ACD) has developed the parallel 3D Finite Element electromagnetic time-domain code T3P. Higher-order Finite Element methods on conformal unstructured meshes and massively parallel processing allow unprecedented simulation accuracy for wakefield computations and simulations of transient effects in realistic accelerator structures. Applications include simulation of wakefield damping in the Compact Linear Collider (CLIC) power extraction and transfer structure (PETS).

  20. A NOVEL APPROACH TO SMOOTHING ON 3D STRUCTURED ADAPTIVE MESH OF THE KINECT-BASED MODELS

    Erdal Özbay

    2013-11-01

    Full Text Available 3-dimensional object modelling of real world objects in steady state by means of multiple point cloud (pcl depth scans taken by using sensing camera and application of smoothing algorithm are suggested in this study. Polygon structure, which is constituted by coordinates of point cloud (x,y,z corresponding to the position of 3D model in space and obtained by nodal points and connection of these points by means of triangulation, is utilized for the demonstration of 3D models. Gaussian smoothing and developed methods are applied to the mesh consisting of merge of these polygons, and a new mesh simplification and augmentation algorithm are suggested for the over the 3D modelling. Mesh consisting of merge of polygons can be demonstrated in a more packed, smooth and fluent way. In this study is shown that applied the triangulation and smoothing method for 3D modelling, perform to a fast and robust mesh structures compared to existing methods therewithal no remeshing is necessary for refinement and reduction.

  1. Constructing Templates for Protein Structure Prediction by Simulation of Protein Folding Pathways

    Kifer, Ilona; Nussinov, Ruth; Wolfson, Haim J.

    2008-01-01

    How a one-dimensional protein sequence folds into a specific 3D structure remains a difficult challenge in structural biology. Many computational methods have been developed in an attempt to predict the tertiary structure of the protein; most of these employ approaches that are based on the accumulated knowledge of solved protein structures.

  2. Structural characterization of supramolecular assemblies by {sup 13}C spin dilution and 3D solid-state NMR

    Habenstein, Birgit; Loquet, Antoine; Giller, Karin; Becker, Stefan; Lange, Adam, E-mail: adla@nmr.mpibpc.mpg.de [Max Planck Institute for Biophysical Chemistry, Department of NMR-based Structural Biology (Germany)

    2013-01-15

    {sup 13}C spin diluted protein samples can be produced using [1-{sup 13}C] and [2-{sup 13}C]-glucose (Glc) carbon sources in the bacterial growth medium. The {sup 13}C spin dilution results in favorable {sup 13}C spectral resolution and polarization transfer behavior. We recently reported the combined use of [1-{sup 13}C]- and [2-{sup 13}C]-Glc labeling to facilitate the structural analysis of insoluble and non-crystalline biological systems by solid-state NMR (ssNMR), including sequential assignment, detection of long-range contacts and structure determination of macromolecular assemblies. In solution NMR the beneficial properties of sparsely labeled samples using [2-{sup 13}C]-glycerol ({sup 13}C labeled C{alpha} sites on a {sup 12}C diluted background) have recently been exploited to provide a bi-directional assignment method (Takeuchi et al. in J Biomol NMR 49(1):17-26, 2011 ). Inspired by this approach and our own recent results using [2-{sup 13}C]-Glc as carbon sources for the simplification of ssNMR spectra, we present a strategy for a bi-directional sequential assignment of solid-state NMR resonances and additionally the detection of long-range contacts using the combination of {sup 13}C spin dilution and 3D NMR spectroscopy. We illustrate our results with the sequential assignment and the collection of distance restraints on an insoluble and non-crystalline supramolecular assembly, the Salmonella typhimurium type III secretion system needle.

  3. Structured Light Based 3d Scanning for Specular Surface by the Combination of Gray Code and Phase Shifting

    Zhang, Yujia; Yilmaz, Alper

    2016-06-01

    Surface reconstruction using coded structured light is considered one of the most reliable techniques for high-quality 3D scanning. With a calibrated projector-camera stereo system, a light pattern is projected onto the scene and imaged by the camera. Correspondences between projected and recovered patterns are computed in the decoding process, which is used to generate 3D point cloud of the surface. However, the indirect illumination effects on the surface, such as subsurface scattering and interreflections, will raise the difficulties in reconstruction. In this paper, we apply maximum min-SW gray code to reduce the indirect illumination effects of the specular surface. We also analysis the errors when comparing the maximum min-SW gray code and the conventional gray code, which justifies that the maximum min-SW gray code has significant superiority to reduce the indirect illumination effects. To achieve sub-pixel accuracy, we project high frequency sinusoidal patterns onto the scene simultaneously. But for specular surface, the high frequency patterns are susceptible to decoding errors. Incorrect decoding of high frequency patterns will result in a loss of depth resolution. Our method to resolve this problem is combining the low frequency maximum min-SW gray code and the high frequency phase shifting code, which achieves dense 3D reconstruction for specular surface. Our contributions include: (i) A complete setup of the structured light based 3D scanning system; (ii) A novel combination technique of the maximum min-SW gray code and phase shifting code. First, phase shifting decoding with sub-pixel accuracy. Then, the maximum min-SW gray code is used to resolve the ambiguity resolution. According to the experimental results and data analysis, our structured light based 3D scanning system enables high quality dense reconstruction of scenes with a small number of images. Qualitative and quantitative comparisons are performed to extract the advantages of our new

  4. Study of the structure of 3D-ordered macroporous GaN-ZnS:Mn nanocomposite films

    Kurdyukov, D. A., E-mail: kurd@gvg.ioffe.ru; Shishkin, I. I.; Grudinkin, S. A.; Sitnikova, A. A.; Zamoryanskaya, M. V.; Golubev, V. G. [Russian Academy of Sciences, Ioffe Physical-Technical Institute (Russian Federation)

    2015-05-15

    A film-type 3D-ordered macroporous GaN-ZnS:Mn nanocomposite with the structure of an inverted opal is fabricated. Structural studies of the nanocomposite are performed, and it is shown that GaN and ZnS:Mn introduced into the pores of the silica opal are nanocrystallites misoriented with respect to each other. It is shown that the nanocomposite is a structurally perfect 3D photonic crystal. The efficiency of using a buffer of GaN crystallites to preclude interaction between the surface of the spherical a-SiO{sub 2} particles forming the opal matrix and chemically active substances introduced into the pores is demonstrated.

  5. Design and Fabrication of 3D-Structured Contactless Capacitive-Type Detector for Capillary Electrophoresis Microchip

    Using simple and reliable microfabrication techniques, this study develops a capillary electrophoresis (CE) microchip with 3-dimensional-structured (3D-structured) contactless capacitive detector electrodes mounted parallel to the separation channel. The offchannel electrodes are deposited by Au sputtering and patterned using a standard 'lift-off' process. A vacuum fusion bonding process is employed to seal the lower substrate containing the microchannels and electrodes to an upper glass cover plate. The variation in the capacitance between the electrodes in the side channels is measured as different samples and ions pass through the detection region of the CE separation channel. Samples of Rhodamine B and a commercial sports drink are mixed in different buffer solutions and successfully separated and detected using the developed device. The 3D-structured contactless capacitive-type detection device has microscale dimensions and provides a valuable contribution to the realization of the lab-on-a-chip concept

  6. Study of the structure of 3D-ordered macroporous GaN-ZnS:Mn nanocomposite films

    A film-type 3D-ordered macroporous GaN-ZnS:Mn nanocomposite with the structure of an inverted opal is fabricated. Structural studies of the nanocomposite are performed, and it is shown that GaN and ZnS:Mn introduced into the pores of the silica opal are nanocrystallites misoriented with respect to each other. It is shown that the nanocomposite is a structurally perfect 3D photonic crystal. The efficiency of using a buffer of GaN crystallites to preclude interaction between the surface of the spherical a-SiO2 particles forming the opal matrix and chemically active substances introduced into the pores is demonstrated

  7. 3D Reconstruction of the Glycocalyx Structure in Mammalian Capillaries using Electron Tomography

    Arkill, Kp; Neal, Cr; Mantell, Jm;

    2012-01-01

    Visualising the molecular strands making up the glycocalyx in the lumen of small blood vessels has proved to be difficult using conventional transmission electron microscopy techniques. Images obtained from tissue stained in a variety of ways have revealed a regularity in the organisation of the...... success (e.g. freeze fracture). A new approach is therefore needed. Here we demonstrate the effectiveness of using the relatively novel electron microscopy technique of 3D electron tomography ontwo differently stained preparations to reveal details of the architecture of the glycocalyx just above the...

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

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

    2014-01-01

    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 (less than or equal to 45 nt) including pseudoknots into their native-like structures from their sequences, with an overall mean RMSD of 3.5 {\\AA} and an overall minimum RMSD of 1.9 {\\AA} 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 degrees Celsius of melting temperatures, as compared wi...

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

    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.

  10. Statistical tracking of tree-like tubular structures with efficient branching detection in 3D medical image data

    Wang, X; Heimann, T; Lo, P;

    2012-01-01

    The segmentation of tree-like tubular structures such as coronary arteries and airways is an essential step for many 3D medical imaging applications. Statistical tracking techniques for the extraction of elongated structures have received considerable attention in recent years due to their...... robustness against image noise and pathological changes. However, most tracking methods are limited to a specific application and do not support branching structures efficiently. In this work, we present a novel statistical tracking approach for the extraction of different types of tubular structures with...

  11. Multimodal visualization of 3D enhanced MRI and CT of acoustic schwannoma and related structures

    Kucharski, Tomasz; Kujawinska, Malgorzata; Niemczyk, Kazimierz; Marchel, Andrzej

    2005-09-01

    According to the necessity of supporting vestibular schwannoma surgery, there is a demand to develop a convenient method of medical data visualization. The process of making choice of optimal operating access way has been uncomfortable for a surgeon so far, because there has been a necessity of analyzing two independent 3D images series (CT -bone tissues visible, MRI - soft tissues visible) in the region of ponto-cerebellar angle tumors. The authors propose a solution that will improve this process. The system used is equipped with stereoscopic helmet mounted display. It allows merged CT and MRI data representing tissues in the region of of ponto-cerebellar angle to be visualized in stereoscopic way. The process of data preparation for visualization includes: -automated segmentation algorithms, -different types of 3D images (CT, MRI) fusion. The authors focused on the development of novel algorithms for segmentation of vestibular schwannoma. It is important and difficult task due to different types of tumors and their inhomogeneous character dependent on growth models. The authors propose algorithms based on histogram spectrum and multimodal character of MRI imaging (T1 and T2 modes). However due to a variety of objects the library of algorithms with specific modifications matching to selected types of images is proposed. The applicability and functionality of the algorithms and library was proved on the series of data delivered by Warsaw Central Medical University Hospital.

  12. Rapid and Inexpensive Reconstruction of 3D Structures for Micro-Objects Using Common Optical Microscopy

    Berejnov, V V

    2009-01-01

    A simple method of constructing the 3D surface of non-transparent micro-objects by extending the depth-of-field on the whole attainable surface is presented. The series of images of a sample are recorded by the sequential movement of the sample with respect to the microscope focus. The portions of the surface of the sample appear in focus in the different images in the series. The indexed series of the in-focus portions of the sample surface is combined in one sharp 2D image and interpolated into the 3D surface representing the surface of an original micro-object. For an image acquisition and processing we use a conventional upright stage microscope that is operated manually, the inexpensive Helicon Focus software, and the open source MeshLab software. Three objects were tested: an inclined flat glass slide with an imprinted 10 um calibration grid, a regular metal 100x100 per inch mesh, and a highly irregular surface of a material known as a porous electrode used in polyelectrolyte fuel cells. The accuracy of...

  13. A simple method for fabricating multi-layer PDMS structures for 3D microfluidic chips

    Zhang, Mengying

    2010-01-01

    We report a simple methodology to fabricate PDMS multi-layer microfluidic chips. A PDMS slab was surface-treated by trichloro (1H,1H,2H,2H-perfluorooctyl) silane, and acts as a reusable transferring layer. Uniformity of the thickness of the patterned PDMS layer and the well-alignment could be achieved due to the transparency and proper flexibility of this transferring layer. Surface treatment results are confirmed by XPS and contact angle testing, while bonding forces between different layers were measured for better understanding of the transferring process. We have also designed and fabricated a few simple types of 3D PDMS chip, especially one consisting of 6 thin layers (each with thickness of 50 μm), to demonstrate the potential utilization of this technique. 3D fluorescence images were taken by a confocal microscope to illustrate the spatial characters of essential parts. This fabrication method is confirmed to be fast, simple, repeatable, low cost and possible to be mechanized for mass production. © The Royal Society of Chemistry 2010.

  14. Autoblocking dose-limiting normal structures within a radiation treatment field: 3-D computer optimization of 'unconventional' field arrangements

    Purpose/Objective: To demonstrate that one can obtain a homogeneous dose distribution within a specified gross tumor volume (GTV) while severely limiting the dose to a structure surrounded by that tumor volume. We present three clinical examples below. Materials and Methods: Using planning CT scans from previously treated patients, we designed variety of radiation treatment plans in which the dose-critical normal structure was blocked, even if it meant blocking some of the tumor. To deal with the resulting dose inhomogeneities within the tumor, we introduced 3D compensation. Examples presented here include (1) blocking the spinal cord segment while treating an entire vertebral body, (2) blocking both kidneys while treating the entire peritoneal cavity, and (3) blocking one parotid gland while treating the oropharynx in its entirety along with regional nodes. A series of multiple planar and non-coplanar beam templates with automatic anatomic blocking and field shaping were designed for each scenario. Three-dimensional compensators were designed that gave the most homogeneous dose-distribution for the GTV. For each beam, rays were cast from the beam source through a 2D compensator grid and out through the tumor. The average tumor dose along each ray was then used to adjust the compensator thickness over successive iterations to achieve a uniform average dose. DVH calculations for the GTV, normal structures, and the 'auto-blocked' structure were made and used for inter-plan comparisons. Results: These optimized treatment plans successfully decreased dose to the dose-limiting structure while at the same time preserving or even improving the dose distribution to the tumor volume as compared to traditional treatment plans. Conclusion: The use of 3D compensation allows one to obtain dose distributions that are, theoretically, at least, far superior to those in common clinical use. Sensible beam templates, auto-blocking, auto-field shaping, and 3D compensators form a

  15. Structural, electronic, and magnetic properties of 3D metal trioxide and tetraoxide superhalogen cluster-doped monolayer BN

    Meng, Jingjing; Li, Dan; Niu, Yuan; Zhao, Hongmin; Liang, Chunjun; He, Zhiqun

    2016-07-01

    The structural, electronic, and magnetic properties of monolayer BN doped with 3D metal trioxide and tetraoxide superhalogen clusters are investigated using first-principle calculations. TMO3(4)-doped monolayer BN exhibits a low negative formation energy, whereas TM atoms embedded in monolayer BN show a high positive formation energy. TMO3(4) clusters are embedded more easily in monolayer BN than TM atoms. Compared with TMO3-doped structures, TMO4-doped structures have a higher structural stability because of their higher binding energies. Given their low negative formation energies, TMO4-doped structures are more favored for specific applications than TMO3-doped structures and TM atom-doped structures. Large magnetic moments per supercell and significant ferromagnetic couplings between a TM atom and neighboring B and N atoms on the BN layer were observed in all TMO4-doped structures, except for TiO4-doped structures.

  16. Mechanical Simulation of the Localized Deformation in the Aluminum Foams: A Three-dimensional (3D) Structure Based Study

    Kai, Zhu; Enyu, Guo; Wenqian, Zhou; Sansan, Shuai; Tao, Jing; Hongliang, Hou; Yanjin, Xu

    2015-06-01

    Metal-foam materials have been used increasingly in industry for their low-density, high-toughness and high impact resistance properties. Understanding the macro-scale mechanical properties of these materials is essential to evaluate their actual performance and thus to optimize the structures and properties accordingly. Synchrotron radiation X-ray microtomographytechnique is a promising method to study 3D structures at small length scales, which provides high spatial resolution and allows the researchers to observe the change of structures/features in situ without destroying the original objects. In this work, the real 3D structure of closed-cell aluminum foam was obtained by using synchrotron radiation X-ray microtomography. The reconstructed 3D model of the foam was further utilized as input for the subsequent mechanical study to investigate the localized deformation behaviors and evolution process of the foam under longitudinal quasi-static uniaxial compressive loading. By analyzing the simulated results, it is demonstrated that the deformation bands always initiate and propagate along the cell walls which are finally folded upon loading. And the large spherical cells are more susceptible to yielding, as well as to the stress concentration than the cells with other shapes. This finding is consistent with the experimental results.

  17. Construction of 3D Arrays of Cylindrically Hierarchical Structures with ZnO Nanorods Hydrothermally Synthesized on Optical Fiber Cores

    Weixuan Jing

    2014-01-01

    Full Text Available With ZnO nanorods hydrothermally synthesized on manually assembled arrays of optical fiber cores, 3D arrays of ZnO nanorod-based cylindrically hierarchical structures with nominal pitch 250 μm or 375 μm were constructed. Based on micrographs of scanning electron microscopy and image processing operators of MATLAB software, the 3D arrays of cylindrically hierarchical structures were quantitatively characterized. The values of the actual diameters, the actual pitches, and the parallelism errors suggest that the process capability of the manual assembling is sufficient and the quality of the 3D arrays of cylindrically hierarchical structures is acceptable. The values of the characteristic parameters such as roughness, skewness, kurtosis, correlation length, and power spectrum density show that the surface morphologies of the cylindrically hierarchical structures not only were affected significantly by Zn2+ concentration of the growth solution but also were anisotropic due to different curvature radii of the optical fiber core at side and front view.

  18. Isotope shifts and hyperfine structure in the 3d 2DJ→4p 2PJ transitions in calcium II

    The isotope shift and hyperfine structure in the three 3d 2D3/2,5/2→4p2P1/2,3/2 - transitions in Ca II have been studied by fast ion beam collinear laser spectroscopy for all stable Ca isotopes. The metastable 3d states were populated within the surface ionization source of a mass separator with a probability of about 0.1%. After resonant excitation to the 4p levels with diode laser light around 850 nm the UV photons from the 4p →4s transitions to the ground state were used for detection. Hyperfine structure parameters A and B for the odd isotope 43Ca, as evaluated from the splittings observed, agree well with theoretical predictions from relativistic many-body perturbation theory. Field shift constants KFS and specific mass shift constants KSMS were extracted from the measured isotope shifts and are discussed in comparison with expectation values from theory. (orig.)

  19. Spectrally resolved white-light interferometry for 3D inspection of a thin-film layer structure

    We describe an improved scheme of spectrally resolved white-light interferometry, which provides 3D visual inspection of a thin-film layer structure with nanometer level resolutions. Compared to the authors' previous method [Appl. Phys. Lett.91, 091903 (2007)APPLAB0003-695110.1063/1.2776015], 3D tomographic information of thin films can be obtained by decoupling the film thickness and top surface profile, which is embodied by inducing spectral carrier frequency to the reference arm and applying a low-pass filter to the interferogram instead of two troublesome measurement steps of activating and deactivating a mechanical shutter. We test and verify our proposed method by measuring a patterned thin-film layer structure as well as standard specimens of thin films with various thicknesses

  20. Development of input structure software for MARS 1D-3D graphic user interface

    A user-friendly Input Software for MARS 1D-3D GUI called MARA (MARS Adjunct Reactor Assembler) has been developed. Extension of the current MARA to the overall input system for MARS will result in an integrated commercial GUI comparable to those for computational analysis codes ANSYS, ABAQUS, FLUENT and CFX. MARA will help accelerate marketing of MARS and other potential system analysis codes to developing countries in Southeast Asia planning to put nuclear power in their electrical grids. MARS code and associated developmental technology are in the process of being disseminated to twenty-two organizations spanning the industry, academia and laboratories across the country. MARA will find its way to practical applications in a variety of engineering problems

  1. 3D hydrodynamical simulations of the large scale structure of W50-SS433

    Zavala, Jesús; Cerqueira, Adriano H; Dubner, Gloria M

    2008-01-01

    We present 3D hydrodynamical simulations of a precessing jet propagating inside a supernova remnant (SNR) shell, particularly applied to the W50-SS433 system in a search for the origin of its peculiar elongated morphology. Several runs were carried out with different values for the mass loss rate of the jet, the initial radius of the SNR, and the opening angle of the precession cone. We found that our models successfully reproduce the scale and morphology of W50 when the opening angle of the jets is set to 10$\\degr$ or if this angle linearly varies with time. For these models, more realistic runs were made considering that the remnant is expanding into an interstellar medium (ISM) with an exponential density profile (as HI observations suggest). Taking into account all these ingredients, the large scale morphology of the W50-SS 433 system, including the asymmetry between the lobes (formed by the jet-SNR interaction), is well reproduced.

  2. 3D mapping of nanoscale electric potentials in semiconductor structures using electron-holographic tomography

    Wolf, Daniel; Lubk, Axel; Prete, Paola; Lovergine, Nico; Lichte, Hannes

    2016-09-01

    Off-axis electron holography (EH) is a powerful method for mapping projected electric potentials, such as built-in potentials in semiconductor devices, in two dimensions (2D) at nanometer resolution. However, not well-defined thickness profiles, surface effects, and composition changes of the sample under investigation complicate the interpretation of the projected potentials. Here, we demonstrate how these problems can be overcome by combining EH with tomographic techniques, that is, electron holographic tomography (EHT), reconstructing electric potentials in 3D. We present EHT reconstructions of an n-type MOSFET including its dopant-related built-in potentials inside the device, as well as of a GaAs/AlGaAs core-multishell nanowire containing a 5 nm thick quantum well tube.

  3. Influence of Young's moduli in 3D fluid-structure coupled models of the human cochlea

    Böhnke, Frank; Semmelbauer, Sebastian; Marquardt, Torsten

    2015-12-01

    The acoustic wave propagation in the human cochlea was studied using a tapered box-model with linear assumptions respective to all mechanical parameters. The discretisation and evaluation is conducted by a commercial finite element package (ANSYS). The main difference to former models of the cochlea was the representation of the basilar membrane by a 3D elastic solid. The Young's moduli of this solid were modified to study their influence on the travelling wave. The lymph in the scala vestibuli and scala tympani was represented by a viscous and nearly incompressible fluid finite element approach. Our results show the maximum displacement for f = 2kHz at half of the length of the cochlea in accordance with former experiments. For low frequencies f <200 Hz nearly zero phase shifts were found, whereas for f =1 kHz it reaches values up to -12 cycles depending on the degree of orthotropy.

  4. 3-D structure below Aevroe Island from high-resolution reflection seismic studies, southeastern Sweden

    Reflection seismology has served as a useful tool for imaging and mapping of fracture zones in crystalline rock along 2-D lines in nuclear waste disposal studies. Two 1-km-long perpendicular seismic reflection lines were acquired on Aevroe Island, southeast Sweden, in October 1996 in order to (1) test the seismic reflection method for future site investigations, (2) map known fracture zones, and (3) add to the Swedish database of reflection seismic studies of the shallow crystalline crust. An east-west line was shot with 5-m geophone and shot-point spacing, and a north-south line was shot with 10-m geophone and shotpoint spacing. An explosive source with a charge size of 100 g was used along both lines. The data clearly image three major dipping reflectors and one subhorizontal one in the upper 200 ms (600 m). The dipping reflectors (to the south, east, and northwest) intersect or project to the surface at or close to where surface-mapped fracture zones exist. The south-dipping reflector correlates with the top of a heavily fractured interval observed in a borehole (KAV01) at about 400 m. The subhorizontal zone at about 100--200 m correlates with a known fracture zone in the same borehole (KAV01). 3-D effects are apparent in the data, and only where the profiles cross can the true orientation of the reflecting events be determined. To properly orient and locate all events observed on the lines requires acquisition of 3-D data

  5. Effect of 3-D viscoelastic structure on post-seismic relaxation from the 2004 M = 9.2 Sumatra earthquake

    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.

  6. Fabrication of 3D copper oxide structure by holographic lithography for photoelectrochemical electrodes.

    Jin, Woo-Min; Kang, Ji-Hwan; Moon, Jun Hyuk

    2010-11-01

    We fabricated three-dimensional copper oxide structure by holographic lithography and electroless deposition. A five-beam interference pattern defined a woodpile structure of SU-8. The surface modification of SU-8 structure was achieved by multilayer coating of polyelectrolyte, which is critical for activating the surface for the reduction of copper. Copper was deposited onto the surface of the structure by electroless deposition, and subsequent calcinations removed the SU-8 structure and simultaneously oxidized the copper into copper oxide. The porous copper oxide structure was used as a photoelectrochemical electrode. Because of the highly porous structure, our structure showed higher photocurrent efficiency. PMID:21062017

  7. Study of materials and machines for 3D printed large-scale, flexible electronic structures using fused deposition modeling

    Hwang, Seyeon

    The 3 dimensional printing (3DP), called to additive manufacturing (AM) or rapid prototyping (RP), is emerged to revolutionize manufacturing and completely transform how products are designed and fabricated. A great deal of research activities have been carried out to apply this new technology to a variety of fields. In spite of many endeavors, much more research is still required to perfect the processes of the 3D printing techniques especially in the area of the large-scale additive manufacturing and flexible printed electronics. The principles of various 3D printing processes are briefly outlined in the Introduction Section. New types of thermoplastic polymer composites aiming to specified functional applications are also introduced in this section. Chapter 2 shows studies about the metal/polymer composite filaments for fused deposition modeling (FDM) process. Various metal particles, copper and iron particles, are added into thermoplastics polymer matrices as the reinforcement filler. The thermo-mechanical properties, such as thermal conductivity, hardness, tensile strength, and fracture mechanism, of composites are tested to figure out the effects of metal fillers on 3D printed composite structures for the large-scale printing process. In Chapter 3, carbon/polymer composite filaments are developed by a simple mechanical blending process with an aim of fabricating the flexible 3D printed electronics as a single structure. Various types of carbon particles consisting of multi-wall carbon nanotube (MWCNT), conductive carbon black (CCB), and graphite are used as the conductive fillers to provide the thermoplastic polyurethane (TPU) with improved electrical conductivity. The mechanical behavior and conduction mechanisms of the developed composite materials are observed in terms of the loading amount of carbon fillers in this section. Finally, the prototype flexible electronics are modeled and manufactured by the FDM process using Carbon/TPU composite filaments and

  8. 3DProIN: Protein-Protein Interaction Networks and Structure Visualization

    Hui LI; Liu, Chunmei

    2014-01-01

    3DProIN is a computational tool to visualize protein–protein interaction networks in both two dimensional (2D) and three dimensional (3D) view. It models protein-protein interactions in a graph and explores the biologically relevant features of the tertiary structures of each protein in the network. Properties such as color, shape and name of each node (protein) of the network can be edited in either 2D or 3D views. 3DProIN is implemented using 3D Java and C programming languages. The interne...

  9. 3D Effect of Ferromagnetic Materials on Alpha Particle Power Loads on First Wall Structures and Equilibrium on ITER

    Full text: The finite number and limited toroidal extent of the TF coils cause a periodic variation of the toroidal field called the magnetic ripple. This ripple can provide a significant channel for fast particle leakage, leading to very localized fast particle loads on the walls. Ferromagnetic inserts will be embedded in the double wall structure of the vacuum vessel in order to reduce the ripple. In ITER the toroidal field deviations are locally further enhanced by the presence of discrete ferromagnetic structures, e.g. TBM. Thus, there are complex symmetry-breaking effects. It is not yet fully understood how superimposing the periodic ripple and a local perturbation affect the fast ion confinement and concerns have been voiced that the combined effect might lead to significant channelling of the alpha power. In this work, the wall power loads due to fusion-born alpha particles were restudied for a variety of cases addressing issues such as different wall configurations, proper inclusion of the TBM effect on the magnetic background, and the possible corrections to 3D equilibrium introduced by the ferromagnetic materials using the 3D equilibrium code, VMEC, since 3D corrections to the equilibrium might enhance the alpha particle loss. To properly include the TBM effect on the magnetic background, the FEMAG code was used, and the effect was calculated on the total field including the poloidal field by the plasma current as well as the vacuum field. In the VMEC analysis, it was found that the difference between a full 3D equilibrium reconstruction and 'an axisymmetric equilibrium + vacuum fields' was small. Thus, it was concluded that no 3D equilibrium reconstruction was needed and that it was sufficient to add the vacuum field perturbations onto an axisymmetric equilibrium. Under the new boundary condition, the wall load calculation was carried out by using ASCOT, DELTA5D, and F3D OFMC code. Including the plasma current contribution in the magnetic field

  10. Constructing 3D CAD models of complex structured environments using a scanning laser camera

    The nature of the plant operated by British Nuclear Fuels Plc. (BNFL) dictates that most of the maintenance and decommissioning has to be performed robotically. In order to perform tasks robotically in an efficient and safe manner an accurate three dimensional volumetric model of the operating environment is required. There are several measurement systems available, employing different techniques, discussed later, that could be employed to map an environment. Following a review of these options, BNFL Engineers concluded that these would be unsuitable for the envisaged operations. Consequently, British Nuclear Fuels initiated a joint project with UK Robotics, formerly Advanced Robotic Research Ltd (ARRL), to investigate the technology and techniques that would be required to construct 3D CAD models of plant environments. The project delivered a prototype modelling system known as AEMS, Advanced Engineering Modelling System. This is being further refined by UK Robotics into a product called Architect to be launched in 1996. This paper describes the techniques and technologies developed during the project and experience gained using the system on plant at Sellafield. (UK)

  11. Constructing 3D CAD models of complex structured environments using a scanning laser camera

    The nature of the plant operated by British Nuclear Fuel Plc. (BNFL) dictates that most of the maintenance and decommissioning has to be performed robotically. In order to perform tasks robotically in an efficient and safe manner an accurate three dimensional volumetric model of the operating environment is required. There are several measurement systems available, employing different techniques, discussed later, that could be employed to map an environment. Following a review of these options, BNFL Engineers concluded that these would be unsuitable for the envisaged operations. Consequently, British Nuclear Fuels initiated a joint project with UK Robotics, formerly Advanced Robotic Research Ltd (ARRL), to investigate the technology and techniques that would be required to construct 3D CAD models of plant environments. The project delivered a prototype modelling system known as AEMS, Advanced Engineering Modelling System. This is being further refined by UK Robotics into a product called Architect to be launched in 1996. This paper describes the techniques and technologies developed during the project and experience gained using the system on plant at Sellafield. (UK)

  12. The 3-D structural geology of the PRZ [Potential Repository Zone]. Supplementary proof of evidence

    Supplementary Proof of Evidence by an expert witness is presented in support of the case by Friends of the Earth (FOE) against the proposed construction by UK Nirex Ltd of an underground Rock Characterisation Facility (RCF) at a site in the Sellafield area. The RCF is part of an investigation by Nirex into a suitable site for an underground repository for the disposal of radioactive waste. The objections were raised at a Planning Inquiry in 1995. Various points raised by a Nirex witness in connection with earlier evidence to the Inquiry by FOE are addressed. This evidence dealt with the need for an accurate hydrogeological model of the Potential Repository Zone (PRZ) and the perceived inadequacies of the Nirex approach. The issues addressed in this supplementary evidence are: disagreements over 3D seismic surveys; inconsistencies in the Nirex geological interpretation; the evolution of interpretation of the PRZ; the oil exploration analogy; site potential; the need for deterministic models; and the selective use of information. (2 figures; 1 table). (UK)

  13. Residual resistance of 2D and 3D structures and Joule heat release.

    Gurevich, V L; Kozub, V I

    2011-06-22

    We consider a residual resistance and Joule heat release in 2D nanostructures as well as in ordinary 3D conductors. We assume that elastic scattering of conduction electrons by lattice defects is predominant. Within a rather intricate situation in such systems we discuss in detail two cases. (1) The elastic scattering alone (i.e. without regard of inelastic mechanisms of scattering) leads to a transition of the mechanical energy (stored by the electrons under the action of an electric field) into heat in a traditional way. This process can be described by the Boltzmann equation where it is possible to do the configuration averaging over defect positions in the electron-impurity collision term. The corresponding conditions are usually met in metals. (2) The elastic scattering can be considered with the help of the standard electron-impurity collision integral only in combination with some additional averaging procedure (possibly including inelastic scattering or some mechanisms of electron wavefunction phase destruction). This situation is typical for degenerate semiconductors with a high concentration of dopants and conduction electrons. Quite often, heat release can be observed via transfer of heat to the lattice, i.e. via inelastic processes of electron-phonon collisions and can take place at distances much larger than the size of the device. However, a direct heating of the electron system can be registered too by, for instance, local measurements of the current noise or direct measurement of an electron distribution function. PMID:21628783

  14. Residual resistance of 2D and 3D structures and Joule heat release

    We consider a residual resistance and Joule heat release in 2D nanostructures as well as in ordinary 3D conductors. We assume that elastic scattering of conduction electrons by lattice defects is predominant. Within a rather intricate situation in such systems we discuss in detail two cases. (1) The elastic scattering alone (i.e. without regard of inelastic mechanisms of scattering) leads to a transition of the mechanical energy (stored by the electrons under the action of an electric field) into heat in a traditional way. This process can be described by the Boltzmann equation where it is possible to do the configuration averaging over defect positions in the electron-impurity collision term. The corresponding conditions are usually met in metals. (2) The elastic scattering can be considered with the help of the standard electron-impurity collision integral only in combination with some additional averaging procedure (possibly including inelastic scattering or some mechanisms of electron wavefunction phase destruction). This situation is typical for degenerate semiconductors with a high concentration of dopants and conduction electrons. Quite often, heat release can be observed via transfer of heat to the lattice, i.e. via inelastic processes of electron-phonon collisions and can take place at distances much larger than the size of the device. However, a direct heating of the electron system can be registered too by, for instance, local measurements of the current noise or direct measurement of an electron distribution function.

  15. Identification of a 145,000 Mr membrane protein as the C3d receptor (CR2) of human B lymphocytes.

    Weis, J J; Tedder, T F; D.T. Fearon

    1984-01-01

    The C3d receptor (CR2) of human B lymphocytes mediates the binding to these cells of immune complexes that have activated the complement system and bear the fragments of C3, iC3b, C3d,g, and C3d. A 145,000 Mr membrane protein previously described as being recognized by the monoclonal antibody HB-5 and shown to be expressed only by B lymphocytes and B lymphoblastoid cell lines, such as Raji, was assessed for its possible identity as CR2. Treatment of Raji cells with HB-5 and goat F(ab')2 anti-...

  16. Comparative velocity structure of active Hawaiian volcanoes from 3-D onshore-offshore seismic tomography

    Park, J.; Morgan, J.K.; Zelt, C.A.; Okubo, P.G.; Peters, L.; Benesh, N.

    2007-01-01

    We present a 3-D P-wave velocity model of the combined subaerial and submarine portions of the southeastern part of the Island of Hawaii, based on first-arrival seismic tomography of marine airgun shots recorded by the onland seismic network. Our model shows that high-velocity materials (6.5-7.0??km/s) lie beneath Kilauea's summit, Koae fault zone, and the upper Southwest Rift Zone (SWRZ) and upper and middle East Rift Zone (ERZ), indicative of magma cumulates within the volcanic edifice. A separate high-velocity body of 6.5-6.9??km/s within Kilauea's lower ERZ and upper Puna Ridge suggests a distinct body of magma cumulates, possibly connected to the summit magma cumulates at depth. The two cumulate bodies within Kilauea's ERZ may have undergone separate ductile flow seaward, influencing the submarine morphology of Kilauea's south flank. Low velocities (5.0-6.3??km/s) seaward of Kilauea's Hilina fault zone, and along Mauna Loa's seaward facing Kao'iki fault zone, are attributed to thick piles of volcaniclastic sediments deposited on the submarine flanks. Loihi seamount shows high-velocity anomalies beneath the summit and along the rift zones, similar to the interpreted magma cumulates below Mauna Loa and Kilauea volcanoes, and a low-velocity anomaly beneath the oceanic crust, probably indicative of melt within the upper mantle. Around Kilauea's submarine flank, a high-velocity anomaly beneath the outer bench suggests the presence of an ancient seamount that may obstruct outward spreading of the flank. Mauna Loa's southeast flank is also marked by a large, anomalously high-velocity feature (7.0-7.4??km/s), interpreted to define an inactive, buried volcanic rift zone, which might provide a new explanation for the westward migration of Mauna Loa's current SWRZ and the growth of Kilauea's SWRZ. ?? 2007 Elsevier B.V. All rights reserved.

  17. Exploring single-molecule interactions through 3D optical trapping and tracking: From thermal noise to protein refolding

    Wong, Wesley Philip

    The focus of this thesis is the development and application of a novel technique for investigating the structure and dynamics of weak interactions between and within single-molecules. This approach is designed to explore unusual features in bi-directional transitions near equilibrium. The basic idea is to infer molecular events by observing changes in the three-dimensional Brownian fluctuations of a functionalized microsphere held weakly near a reactive substrate. Experimentally, I have developed a unique optical tweezers system that combines an interference technique for accurate 3D tracking (˜1 nm vertically, and ˜2-3 nm laterally) with a continuous autofocus system which stabilizes the trap height to within 1-2 mn over hours. A number of different physical and biological systems were investigated with this instrument. Data interpretation was assisted by a multi-scale Brownian Dynamics simulation that I have developed. I have explored the 3D signatures of different molecular tethers, distinguishing between single and multiple attachments, as well as between stiff and soft linkages. As well, I have developed a technique for measuring the force-dependent compliance of molecular tethers from thermal noise fluctuations and demonstrated this with a short ssDNA oligomer. Another practical approach that I have developed for extracting information from fluctuation measurements is Inverse Brownian Dynamics, which yields the underlying potential of mean force and position dependent diffusion coefficient from the Brownian motion of a particle. I have also developed a new force calibration method that takes into account video motion blur, and that uses this information to measure bead dynamics. Perhaps most significantly, I have trade the first direct observations of the refolding of spectrin repeats under mechanical force, and investigated the force-dependent kinetics of this transition.

  18. Imaging the 3D structure of secondary osteons in human cortical bone using phase-retrieval tomography

    Arhatari, B D; Peele, A G [Department of Physics, La Trobe University, Victoria 3086 (Australia); Cooper, D M L [Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon (Canada); Thomas, C D L; Clement, J G [Melbourne Dental School, University of Melbourne, Victoria 3010 (Australia)

    2011-08-21

    By applying a phase-retrieval step before carrying out standard filtered back-projection reconstructions in tomographic imaging, we were able to resolve structures with small differences in density within a densely absorbing sample. This phase-retrieval tomography is particularly suited for the three-dimensional segmentation of secondary osteons (roughly cylindrical structures) which are superimposed upon an existing cortical bone structure through the process of turnover known as remodelling. The resulting images make possible the analysis of the secondary osteon structure and the relationship between an osteon and the surrounding tissue. Our observations have revealed many different and complex 3D structures of osteons that could not be studied using previous methods. This work was carried out using a laboratory-based x-ray source, which makes obtaining these sorts of images readily accessible.

  19. 3D radiative transfer simulations of Eta Carinae's inner colliding winds - II: Ionization structure of helium at periastron

    Clementel, Nicola; Kruip, Chael J H; Paardekooper, Jan-Pieter

    2015-01-01

    Spectral observations of the massive colliding wind binary Eta Carinae show phase-dependent variations, in intensity and velocity, of numerous helium emission and absorption lines throughout the entire 5.54-year orbit. Approaching periastron, the 3D structure of the wind-wind interaction region (WWIR) gets highly distorted due to the eccentric ($e \\sim 0.9$) binary orbit. The secondary star ($\\eta_{\\mathrm{B}}$) at these phases is located deep within the primary's dense wind photosphere. The combination of these effects is thought to be the cause of the particularly interesting features observed in the helium lines at periastron. We perform 3D radiative transfer simulations of $\\eta$ Car's interacting winds at periastron. Using the SimpleX radiative transfer algorithm, we post-process output from 3D smoothed particle hydrodynamic simulations of the inner 150 au of the $\\eta$ Car system for two different primary star mass-loss rates ($\\dot{M}_{\\eta_{\\mathrm{A}}}$). Using previous results from simulations at ap...

  20. Virtual teeth: a 3D method for editing and visualizing small structures in CT scans

    Bro-Nielsen, Morten; Larsen, Per; Kreiborg, Sven;

    1996-01-01

    The paper presents an interactive method for segmentation and visualization of small structures in CT scans. A combination of isosurface generation, spatial region growing and interactive graphics tools are used to extract small structures interactively. A practical example of segmentation of the...... dentition in a CT scan is shown...

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

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

    2015-01-01

    limited to flat or simple shaped geometries. In this paper, 3 approaches for fabricating micro and nano- structured surfaces on a mold cavity for injection moulding are investigated and compared. The first approach is to use pre-fabricated plate with micro-structured surface as an insert for the mold, in...

  2. 3D structure of the Earth's crust beneath the northern part of the Bohemian Massif

    Majdański, M.; Kozlovskaya, E.; Grad, M.; Behm, M.; Bodoky, T.; Brinkmann, R.; Brož, Milan; Brueckl, E.; Czuba, W.; Fancsik, T.; Forkmann, B.; Fort, M.; Gaczyński, E.; Geissler, W.H.; Greschke, R.; Guterch, A.; Harder, S.; Hegedus, E.; Hemmann, A.; Hrubcová, Pavla; Janik, T.; Jentzsch, G.; Kaip, G.; Keller, G. R.; Komminaho, K.; Korn, M.; Karousová, Olga; Málek, Jiří; Malinowski, M.; Miller, K.C.; Rumpfhuber, E.M.; Špičák, Aleš; Środa, P.; Takacs, E.; Tiira, T.; Vozár, J.; Wilde-Piorko, M.; Yliniemi, J.; Zelazniewicz, A.

    Roč. 437, 1-4 ( 2007 ), s. 17-36. ISSN 0040-1951 Institutional research plan: CEZ:AV0Z30460519; CEZ:AV0Z30120515 Keywords : crustal structure * travel time tomography * Sudetes 2003 Subject RIV: DC - Siesmology, Volcanology, Earth Structure Impact factor: 1.729, year: 2007

  3. 3D Digital Modelling

    Hundebøl, Jesper

    wave of new building information modelling tools demands further investigation, not least because of industry representatives' somewhat coarse parlance: Now the word is spreading -3D digital modelling is nothing less than a revolution, a shift of paradigm, a new alphabet... Research qeustions. Based...... on empirical probes (interviews, observations, written inscriptions) within the Danish construction industry this paper explores the organizational and managerial dynamics of 3D Digital Modelling. The paper intends to - Illustrate how the network of (non-)human actors engaged in the promotion (and arrest) of 3......D Modelling (in Denmark) stabilizes - Examine how 3D Modelling manifests itself in the early design phases of a construction project with a view to discuss the effects hereof for i.a. the management of the building process. Structure. The paper introduces a few, basic methodological concepts...

  4. 3D segmentation of rodent brain structures using hierarchical shape priors and deformable models.

    Zhang, Shaoting; Huang, Junzhou; Uzunbas, Mustafa; Shen, Tian; Delis, Foteini; Huang, Xiaolei; Volkow, Nora; Thanos, Panayotis; Metaxas, Dimitris N

    2011-01-01

    In this paper, we propose a method to segment multiple rodent brain structures simultaneously. This method combines deformable models and hierarchical shape priors within one framework. The deformation module employs both gradient and appearance information to generate image forces to deform the shape. The shape prior module uses Principal Component Analysis to hierarchically model the multiple structures at both global and local levels. At the global level, the statistics of relative positions among different structures are modeled. At the local level, the shape statistics within each structure is learned from training samples. Our segmentation method adaptively employs both priors to constrain the intermediate deformation result. This prior constraint improves the robustness of the model and benefits the segmentation accuracy. Another merit of our prior module is that the size of the training data can be small, because the shape prior module models each structure individually and combines them using global statistics. This scheme can preserve shape details better than directly applying PCA on all structures. We use this method to segment rodent brain structures, such as the cerebellum, the left and right striatum, and the left and right hippocampus. The experiments show that our method works effectively and this hierarchical prior improves the segmentation performance. PMID:22003750

  5. Materials ``alchemy'': Shape-preserving chemical transformation of micro-to-macroscopic 3-D structures

    Sandhage, Kenneth H.

    2010-06-01

    The scalable fabrication of nano-structured materials with complex morphologies and tailorable chemistries remains a significant challenge. One strategy for such synthesis consists of the generation of a solid structure with a desired morphology (a “preform”), followed by reactive conversion of the preform into a new chemistry. Several gas/solid and liquid/solid reaction processes that are capable of such chemical conversion into new micro-to-nano-structured materials, while preserving the macroscopic-to-microscopic preform morphologies, are described in this overview. Such shape-preserving chemical transformation of one material into another could be considered a modern type of materials “alchemy.”

  6. Statistical tracking of tree-like tubular structures with efficient branching detection in 3D medical image data

    The segmentation of tree-like tubular structures such as coronary arteries and airways is an essential step for many 3D medical imaging applications. Statistical tracking techniques for the extraction of elongated structures have received considerable attention in recent years due to their robustness against image noise and pathological changes. However, most tracking methods are limited to a specific application and do not support branching structures efficiently. In this work, we present a novel statistical tracking approach for the extraction of different types of tubular structures with ringlike cross-sections. Domain-specific knowledge is learned from training data sets and integrated into the tracking process by simple adaption of parameters. In addition, an efficient branching detection algorithm is presented. This approach was evaluated by extracting coronary arteries from 32 CTA data sets and distal airways from 20 CT scans. These data sets were provided by the organizers of the workshop ‘3D Segmentation in the Clinic: A Grand Challenge II-Coronary Artery Tracking (CAT08)’ and ‘Extraction of Airways from CT 2009 (EXACT’09)’. On average, 81.5% overlap and 0.51 mm accuracy for the tracking of coronary arteries were achieved. For the extraction of airway trees, 51.3% of the total tree length, 53.6% of the total number of branches and a 4.98% false positive rate were attained. In both experiments, our approach is comparable to state-of-the-art methods. (paper)

  7. An asymptotic homogenization model for smart 3D grid-reinforced composite structures with generally orthotropic constituents

    A comprehensive micromechanical model for smart 3D composite structures reinforced with a periodic grid of generally orthotropic cylindrical reinforcements that also exhibit piezoelectric behavior is developed. The original boundary value problem characterizing the piezothermoelastic behavior of these structures is decoupled into a set of three simpler unit cell problems dealing, separately, with the elastic, piezoelectric and thermal expansion characteristics of the smart composite. The technique used is that of asymptotic homogenization and the solution of the unit cell problems permits determination of the effective elastic, piezoelectric and thermal expansion coefficients. The general orthotropy of the constituent materials is very important from the practical viewpoint and makes the analysis much more complicated. Several examples of practical interest are used to illustrate the work including smart 3D composites with cubic and conical embedded grids as well as diagonally reinforced smart structures. It is also shown in this work that in the limiting particular case of 2D grid-reinforced structures with isotropic reinforcements our results converge to earlier published results

  8. The 3D structure of the hadrons: recents results and experimental program at Jefferson Lab

    Muñoz Camacho C.

    2014-04-01

    Full Text Available The understanding of Quantum Chromodynamics (QCD at large distances still remains one of the main outstanding problems of nuclear physics. Studying the internal structure of hadrons provides a way to probe QCD in the non-perturbative domain and can help us unravel the internal structure of the most elementary blocks of matter. Jefferson Lab (JLab has already delivered results on how elementary quarks and gluons create nucleon structure and properties. The upgrade of JLab to 12 GeV will allow the full exploration of the valence-quark structure of nucleons and the extraction of real threedimensional pictures. I will present recent results and review the future experimental program at JLab.

  9. Structure in the 3D Galaxy Distribution: II. Voids and Watersheds of Local Maxima and Minima

    Way, M J; Scargle, Jeffrey D

    2014-01-01

    The major uncertainties in studies of the multi-scale structure of the Universe arise not from observational errors but from the variety of legitimate definitions and detection methods for individual structures. To facilitate the study of these methodological dependencies we have carried out 12 different analyses defining structures in various ways. This has been done in a purely geometrical way by utilizing the HOP algorithm as a unique parameter-free method of assigning groups of galaxies to local density maxima or minima. From three density estimation techniques (smoothing kernels, Bayesian Blocks and self organizing maps) applied to three data sets (the Sloan Digital Sky Survey Data Release 7, the Millennium Simulation and randomly distributed points) we tabulate information that can be used to construct catalogs of structures connected to local density maxima and minima. The resulting sizes follow continuous multi-scale distributions with no indication of the presence of a discrete hierarchy. We also int...

  10. Inorganic chiral 3-D photonic crystals with bicontinuous gyroid structure replicated from butterfly wing scales

    Mille, Christian; Tyrode, Eric; Corkery, Robert W.

    2011-01-01

    Three dimensional silica photonic crystals with the gyroid minimal surface structure have been synthesized. The butterfly Callophrys rubi was used as a biotemplate. This material represents a significant addition to the small family of synthetic bicontinuous photonic crystals. QC 20110913

  11. On a new structural form of C with 3D distribution of covalent sp2-bonds

    The structure of a new carbon phase with density intermediate between those of graphite and diamond has been studied. This phase is formed together with diamond at high-temperature shock compression of carbon black and charcoal. It is shown that the intermediate phase has amorphous structure with short-range order in the atomic arrangement with three-dimensional distribution of covalent sp2 bonds

  12. Accurate 3D rigid-body target motion and structure estimation by using GMTI/HRR with template information

    Wu, Shunguang; Hong, Lang

    2008-04-01

    A framework of simultaneously estimating the motion and structure parameters of a 3D object by using high range resolution (HRR) and ground moving target indicator (GMTI) measurements with template information is given. By decoupling the motion and structure information and employing rigid-body constraints, we have developed the kinematic and measurement equations of the problem. Since the kinematic system is unobservable by using only one scan HRR and GMTI measurements, we designed an architecture to run the motion and structure filters in parallel by using multi-scan measurements. Moreover, to improve the estimation accuracy in large noise and/or false alarm environments, an interacting multi-template joint tracking (IMTJT) algorithm is proposed. Simulation results have shown that the averaged root mean square errors for both motion and structure state vectors have been significantly reduced by using the template information.

  13. An Optimized Data Structure for High Throughput 3D Proteomics Data: mzRTree

    Nasso, Sara; Tisiot, Francesco; Di Camillo, Barbara; Pietracaprina, Andrea; Toffolo, Gianna Maria

    2010-01-01

    As an emerging field, MS-based proteomics still requires software tools for efficiently storing and accessing experimental data. In this work, we focus on the management of LC-MS data, which are typically made available in standard XML-based portable formats. The structures that are currently employed to manage these data can be highly inefficient, especially when dealing with high-throughput profile data. LC-MS datasets are usually accessed through 2D range queries. Optimizing this type of operation could dramatically reduce the complexity of data analysis. We propose a novel data structure for LC-MS datasets, called mzRTree, which embodies a scalable index based on the R-tree data structure. mzRTree can be efficiently created from the XML-based data formats and it is suitable for handling very large datasets. We experimentally show that, on all range queries, mzRTree outperforms other known structures used for LC-MS data, even on those queries these structures are optimized for. Besides, mzRTree is also mor...

  14. STRUCTURE IN THE 3D GALAXY DISTRIBUTION. II. VOIDS AND WATERSHEDS OF LOCAL MAXIMA AND MINIMA

    The major uncertainties in studies of the multi-scale structure of the universe arise not from observational errors but from the variety of legitimate definitions and detection methods for individual structures. To facilitate the study of these methodological dependencies, we have carried out 12 different analyses defining structures in various ways. This has been done in a purely geometrical way by utilizing the HOP algorithm as a unique parameter-free method of assigning groups of galaxies to local density maxima or minima. From three density estimation techniques (smoothing kernels, Bayesian blocks, and self-organizing maps) applied to three data sets (the Sloan Digital Sky Survey Data Release 7, the Millennium simulation, and randomly distributed points) we tabulate information that can be used to construct catalogs of structures connected to local density maxima and minima. We also introduce a void finder that utilizes a method to assemble Delaunay tetrahedra into connected structures and characterizes regions empty of galaxies in the source catalog

  15. The internal geometry of salt structures - A first look using 3D seismic data from the Zechstein of the Netherlands

    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.

  16. Structural study of the low-temperature phase transition in Cs3D(SeO4)2

    The X-ray structure of tricaesium deuteriumbiselenate, Cs3D(SeO4)2, Mr = 686.7, has been studied at 25, 190 and 297 K with particular attention being paid to the low-temperature phase transition at Tc3 = 180 K. The structure of Cs3H(SeO4)2 has also been studied at 297 K. The data were refined in the monoclinic space group C2/m, Z = 2, at 297 and 190 K, and in P21/m, Z = 2, at 25 K (Mo Kα radiation, λ = 0.71073 A). Temperature effects on the structure are mainly noticeable in the Cs--O bond distances of the oxygen coordination polyhedra of Cs (0.016 A per 100 K on average). Accompanying the Tc3 transition, the space group changes from C2/m to P21/m, and the two SeO4 groups in the dimer become non-equivalent with one adopting HSeO-4 character and the other SeO2-4 character. As a result, the dimers have a net dipole moment and are arranged in an antipolar way, similar to K3D(SO4)2. An examination of the room-temperature structure of Cs3D(SeO4)2 and other M3H(XO4)2-type crystals reveals that the non-H atoms lie in approximately the same position in both cases and that the only major difference is that half of the hydrogens in other M3H(XO4)2-type crystals are involved in hydrogen-bonded dimers which are formed with two different adjacent selenate groups. The successive transitions in Cs3D(SeO4)2 are characterized as an order-disorder transition of the donor-oxygen atom at Tc1, reorganization of the hydrogen bonds at Tc2 and an order-disorder transition of the proton at Tc3. (orig./GSCH)

  17. 3D quantification of soil structure and functioning based on PET and CT scanning techniques

    Garbout, Amin

    This thesis explores the potential of PET and CT scanning techniques to quantify and visualize soil structure, root development, and soil/plant interactions. At the investigated scale, these non-invasive and nondestructive techniques have some obvious advantages compared with most other techniques....... The processed measurements show some expected and a few unexpected effects (or lack of effects) on different characteristics of soil structure. The combination of CT and PET scanning in an air plant soil controller system revealed some very interesting research possibilities. Interactions between soil...

  18. Non-biased enrichment does not improve quantitative proteomic delineation of reovirus T3D-infected HeLa cell protein alterations

    Jieyuan eJiang

    2012-09-01

    Full Text Available Mass spectrometry-based methods have allowed elucidation of alterations in complex proteomes, such as eukaryotic cells. Such studies have identified and measured relative abundances of thousands of host proteins after cells are infected with a virus. One of the potential limitations in such studies is that generally only the most abundant proteins are identified, leaving the deep richness of the cellular proteome largely unexplored. We differentially labeled HeLa cells with light and heavy stable isotopic forms of lysine and arginine (SILAC and infected cells with reovirus strain T3D. Cells were harvested at 24 hours post-infection. Heavy-labeled infected and light-labeled mock-infected cells were mixed together 1:1. Cells were then divided into cytosol and nuclear fractions and each fraction analyzed, both by standard 2D-HPLC/MS, and also after each fraction had been reacted with a random hexapeptide library (Proteominer® beads to attempt to enrich for low-abundance cellular proteins. A total of 2736 proteins were identified by 2 or more peptides at >99% confidence, of which 66 were significantly up-regulated and 67 were significantly down-regulated. Up-regulated proteins included those involved in antimicrobial and antiviral responses, GTPase activity, nucleotide binding, interferon signaling, and enzymes associated with energy generation. Down-regulated proteins included those involved in cell and biological adhesion, regulation of cell proliferation, structural molecule activity, and numerous molecular binding activities. Comparisons of the r2 correlations, degree of dataset overlap, and numbers of peptides detected suggest that non-biased enrichment approaches may not provide additional data to allow deeper quantitative and comparative mining of complex proteomes.

  19. 3D modeling of genome macroorganization on the basis of its structural changes after action of radiation

    At present, after 120 years of the theoretical and experimental works, the issue of the genome macroarchitecture as the highest level of interphase chromosome organization in somatic cell nuclei remains still unresolved. The problem of the spatial arrangement of interphase chromosomes in haploid germ cells has never even been studied. A 3D simulation of packaging of the entire second chromosome in Drosophila mature sperms has been performed by using mathematical approaches and visualization methods to present macromolecular structure data. As genetic markers for simulation, frequency and location of the second inversion breakpoints for 72 structural υg mutants induced by ionizing radiation were used supposing that both ends of each inversion are topologically brought together forming loop of appropriate size. For the account of a degree of spatial affinity and visualization of chromosomal loops modern 3D-modeling methods with application of splines, libraries OpenGL, language Delphi, program Gmax were used. According to the model proposed, the entire second chromosome within mature sperm nuclei seems to be packaged in the form of a megarosette-loop structure which may be a basic principle of organization of the genome macro-architecture in animal haploid germ cells

  20. Efficient 3D Kinetic Monte Carlo Method for Modeling of Molecular Structure and Dynamics

    Panshenskov, Mikhail; Solov'yov, Ilia; Solov'yov, Andrey V.

    2014-01-01

    Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures...