WorldWideScience

Sample records for protein 3d structures

  1. 3D bioprinting of structural proteins.

    Science.gov (United States)

    Włodarczyk-Biegun, Małgorzata K; Del Campo, Aránzazu

    2017-07-01

    3D bioprinting is a booming method to obtain scaffolds of different materials with predesigned and customized morphologies and geometries. In this review we focus on the experimental strategies and recent achievements in the bioprinting of major structural proteins (collagen, silk, fibrin), as a particularly interesting technology to reconstruct the biochemical and biophysical composition and hierarchical morphology of natural scaffolds. The flexibility in molecular design offered by structural proteins, combined with the flexibility in mixing, deposition, and mechanical processing inherent to bioprinting technologies, enables the fabrication of highly functional scaffolds and tissue mimics with a degree of complexity and organization which has only just started to be explored. Here we describe the printing parameters and physical (mechanical) properties of bioinks based on structural proteins, including the biological function of the printed scaffolds. We describe applied printing techniques and cross-linking methods, highlighting the modifications implemented to improve scaffold properties. The used cell types, cell viability, and possible construct applications are also reported. We envision that the application of printing technologies to structural proteins will enable unprecedented control over their supramolecular organization, conferring printed scaffolds biological properties and functions close to natural systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. 3dRPC: a web server for 3D RNA-protein structure prediction.

    Science.gov (United States)

    Huang, Yangyu; Li, Haotian; Xiao, Yi

    2018-04-01

    RNA-protein interactions occur in many biological processes. To understand the mechanism of these interactions one needs to know three-dimensional (3D) structures of RNA-protein complexes. 3dRPC is an algorithm for prediction of 3D RNA-protein complex structures and consists of a docking algorithm RPDOCK and a scoring function 3dRPC-Score. RPDOCK is used to sample possible complex conformations of an RNA and a protein by calculating the geometric and electrostatic complementarities and stacking interactions at the RNA-protein interface according to the features of atom packing of the interface. 3dRPC-Score is a knowledge-based potential that uses the conformations of nucleotide-amino-acid pairs as statistical variables and that is used to choose the near-native complex-conformations obtained from the docking method above. Recently, we built a web server for 3dRPC. The users can easily use 3dRPC without installing it locally. RNA and protein structures in PDB (Protein Data Bank) format are the only needed input files. It can also incorporate the information of interface residues or residue-pairs obtained from experiments or theoretical predictions to improve the prediction. The address of 3dRPC web server is http://biophy.hust.edu.cn/3dRPC. yxiao@hust.edu.cn.

  3. Cancer3D: understanding cancer mutations through protein structures.

    Science.gov (United States)

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

    2015-01-01

    The new era of cancer genomics is providing us with extensive knowledge of mutations and other alterations in cancer. The Cancer3D database at http://www.cancer3d.org gives an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins in which they are found. The database also helps users analyze the distribution patterns of the mutations as well as their relationship to changes in drug activity through two algorithms: e-Driver and e-Drug. These algorithms use knowledge of modular structure of genes and proteins to separately study each region. This approach allows users to find novel candidate driver regions or drug biomarkers that cannot be found when similar analyses are done on the whole-gene level. The Cancer3D database provides access to the results of such analyses based on data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE). In addition, it displays mutations from over 14,700 proteins mapped to more than 24,300 structures from PDB. This helps users visualize the distribution of mutations and identify novel three-dimensional patterns in their distribution. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    Directory of Open Access Journals (Sweden)

    Debora S Marks

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

  5. 3D complex: a structural classification of protein complexes.

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    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.

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

    Science.gov (United States)

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

    2014-07-01

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

  7. I-TASSER server for protein 3D structure prediction

    Directory of Open Access Journals (Sweden)

    Zhang Yang

    2008-01-01

    Full Text Available Abstract Background Prediction of 3-dimensional protein structures from amino acid sequences represents one of the most important problems in computational structural biology. The community-wide Critical Assessment of Structure Prediction (CASP experiments have been designed to obtain an objective assessment of the state-of-the-art of the field, where I-TASSER was ranked as the best method in the server section of the recent 7th CASP experiment. Our laboratory has since then received numerous requests about the public availability of the I-TASSER algorithm and the usage of the I-TASSER predictions. Results An on-line version of I-TASSER is developed at the KU Center for Bioinformatics which has generated protein structure predictions for thousands of modeling requests from more than 35 countries. A scoring function (C-score based on the relative clustering structural density and the consensus significance score of multiple threading templates is introduced to estimate the accuracy of the I-TASSER predictions. A large-scale benchmark test demonstrates a strong correlation between the C-score and the TM-score (a structural similarity measurement with values in [0, 1] of the first models with a correlation coefficient of 0.91. Using a C-score cutoff > -1.5 for the models of correct topology, both false positive and false negative rates are below 0.1. Combining C-score and protein length, the accuracy of the I-TASSER models can be predicted with an average error of 0.08 for TM-score and 2 Å for RMSD. Conclusion The I-TASSER server has been developed to generate automated full-length 3D protein structural predictions where the benchmarked scoring system helps users to obtain quantitative assessments of the I-TASSER models. The output of the I-TASSER server for each query includes up to five full-length models, the confidence score, the estimated TM-score and RMSD, and the standard deviation of the estimations. The I-TASSER server is freely available

  8. Progression of 3D Protein Structure and Dynamics Measurements

    Science.gov (United States)

    Sato-Tomita, Ayana; Sekiguchi, Hiroshi; Sasaki, Yuji C.

    2018-06-01

    New measurement methodologies have begun to be proposed with the recent progress in the life sciences. Here, we introduce two new methodologies, X-ray fluorescence holography for protein structural analysis and diffracted X-ray tracking (DXT), to observe the dynamic behaviors of individual single molecules.

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

    Science.gov (United States)

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

    2010-01-01

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

  10. Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures.

    Science.gov (United States)

    Matsuoka, Masanari; Sugita, Masatake; Kikuchi, Takeshi

    2014-09-18

    Proteins that share a high sequence homology while exhibiting drastically different 3D structures are investigated in this study. Recently, artificial proteins related to the sequences of the GA and IgG binding GB domains of human serum albumin have been designed. These artificial proteins, referred to as GA and GB, share 98% amino acid sequence identity but exhibit different 3D structures, namely, a 3α bundle versus a 4β + α structure. Discriminating between their 3D structures based on their amino acid sequences is a very difficult problem. In the present work, in addition to using bioinformatics techniques, an analysis based on inter-residue average distance statistics is used to address this problem. It was hard to distinguish which structure a given sequence would take only with the results of ordinary analyses like BLAST and conservation analyses. However, in addition to these analyses, with the analysis based on the inter-residue average distance statistics and our sequence tendency analysis, we could infer which part would play an important role in its structural formation. The results suggest possible determinants of the different 3D structures for sequences with high sequence identity. The possibility of discriminating between the 3D structures based on the given sequences is also discussed.

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

    Science.gov (United States)

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-10-01

    Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided. Copyright © 2013 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Zemla, Adam T [Brentwood, CA

    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.

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

    International Nuclear Information System (INIS)

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

    2016-01-01

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States); Petit, Chad M. [University of Alabama at Birmingham, Department of Biochemistry and Molecular Genetics (United States); Cornilescu, Gabriel; Stark, Jaime L.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States)

    2016-06-15

    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.

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

    Science.gov (United States)

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

    2017-01-04

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.' Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Deposit3D: a tool for automating structure depositions to the Protein Data Bank

    International Nuclear Information System (INIS)

    Badger, J.; Hendle, J.; Burley, S. K.; Kissinger, C. R.

    2005-01-01

    This paper describes a Python script that may be used to gather all required structure-annotation information into an mmCIF file for upload through the RCSB PDB ADIT structure-deposition interface. Almost all successful protein structure-determination projects in the public sector culminate in a structure deposition to the Protein Data Bank (PDB). In order to expedite the deposition proces, Deposit3D has been developed. This command-line script calculates or gathers all the required structure-deposition information and outputs this data into a mmCIF file for subsequent upload through the RCSB PDB ADIT interface. Deposit3D might be particularly useful for structural genomics pipeline projects because it allows workers involved with various stages of a structure-determination project to pool their different categories of annotation information before starting a deposition session

  17. Deposit3D: a tool for automating structure depositions to the Protein Data Bank

    Energy Technology Data Exchange (ETDEWEB)

    Badger, J., E-mail: jbadger@active-sight.com; Hendle, J.; Burley, S. K.; Kissinger, C. R. [SGX Inc., 10505 Roselle Street, San Diego, CA 92121 (United States)

    2005-09-01

    This paper describes a Python script that may be used to gather all required structure-annotation information into an mmCIF file for upload through the RCSB PDB ADIT structure-deposition interface. Almost all successful protein structure-determination projects in the public sector culminate in a structure deposition to the Protein Data Bank (PDB). In order to expedite the deposition proces, Deposit3D has been developed. This command-line script calculates or gathers all the required structure-deposition information and outputs this data into a mmCIF file for subsequent upload through the RCSB PDB ADIT interface. Deposit3D might be particularly useful for structural genomics pipeline projects because it allows workers involved with various stages of a structure-determination project to pool their different categories of annotation information before starting a deposition session.

  18. G2S: A web-service for annotating genomic variants on 3D protein structures.

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    Wang, Juexin; Sheridan, Robert; Sumer, S Onur; Schultz, Nikolaus; Xu, Dong; Gao, Jianjiong

    2018-01-27

    Accurately mapping and annotating genomic locations on 3D protein structures is a key step in structure-based analysis of genomic variants detected by recent large-scale sequencing efforts. There are several mapping resources currently available, but none of them provides a web API (Application Programming Interface) that support programmatic access. We present G2S, a real-time web API that provides automated mapping of genomic variants on 3D protein structures. G2S can align genomic locations of variants, protein locations, or protein sequences to protein structures and retrieve the mapped residues from structures. G2S API uses REST-inspired design conception and it can be used by various clients such as web browsers, command terminals, programming languages and other bioinformatics tools for bringing 3D structures into genomic variant analysis. The webserver and source codes are freely available at https://g2s.genomenexus.org. g2s@genomenexus.org. Supplementary data are available at Bioinformatics online. © The Author (2018). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

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

    DEFF Research Database (Denmark)

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

    2006-01-01

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

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

    Science.gov (United States)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

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

  1. Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER.

    Science.gov (United States)

    Han, Xusi; Wei, Qing; Kihara, Daisuke

    2017-12-08

    With the rapid growth in the number of solved protein structures stored in the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB), it is essential to develop tools to perform real-time structure similarity searches against the entire structure database. Since conventional structure alignment methods need to sample different orientations of proteins in the three-dimensional space, they are time consuming and unsuitable for rapid, real-time database searches. To this end, we have developed 3D-SURFER and EM-SURFER, which utilize 3D Zernike descriptors (3DZD) to conduct high-throughput protein structure comparison, visualization, and analysis. Taking an atomic structure or an electron microscopy map of a protein or a protein complex as input, the 3DZD of a query protein is computed and compared with the 3DZD of all other proteins in PDB or EMDB. In addition, local geometrical characteristics of a query protein can be analyzed using VisGrid and LIGSITE CSC in 3D-SURFER. This article describes how to use 3D-SURFER and EM-SURFER to carry out protein surface shape similarity searches, local geometric feature analysis, and interpretation of the search results. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  2. PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.

    Science.gov (United States)

    Lee, Woonghee; Kim, Jin Hae; Westler, William M; Markley, John L

    2011-06-15

    PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY ((13)C-edited and/or (15)N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means. The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/.

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

    Science.gov (United States)

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

    2016-12-15

    The Protein Data Bank (PDB) now contains more than 120,000 three-dimensional (3D) structures of biological macromolecules. To allow an interpretation of how PDB data relates to other publicly available annotations, we developed a novel data integration platform that maps 3D structural information across various datasets. This integration bridges from the human genome across protein sequence to 3D structure space. We developed novel software solutions for data management and visualization, while incorporating new libraries for web-based visualization using SVG graphics. The new views are available from http://www.rcsb.org and software is available from https://github.com/rcsb/. andreas.prlic@rcsb.orgSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  4. i3Drefine software for protein 3D structure refinement and its assessment in CASP10.

    Science.gov (United States)

    Bhattacharya, Debswapna; Cheng, Jianlin

    2013-01-01

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

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

    Science.gov (United States)

    Bhattacharya, Debswapna; Cheng, Jianlin

    2013-01-01

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

  6. BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank.

    Science.gov (United States)

    Gao, Jianjiong; Prlic, Andreas; Bi, Chunxiao; Bluhm, Wolfgang F; Dimitropoulos, Dimitris; Xu, Dong; Bourne, Philip E; Rose, Peter W

    2017-07-01

    We developed a new software tool, BioJava-ModFinder, for identifying protein modifications observed in 3D structures archived in the Protein Data Bank (PDB). Information on more than 400 types of protein modifications were collected and curated from annotations in PDB, RESID, and PSI-MOD. We divided these modifications into three categories: modified residues, attachment modifications, and cross-links. We have developed a systematic method to identify these modifications in 3D protein structures. We have integrated this package with the RCSB PDB web application and added protein modification annotations to the sequence diagram and structure display. By scanning all 3D structures in the PDB using BioJava-ModFinder, we identified more than 30 000 structures with protein modifications, which can be searched, browsed, and visualized on the RCSB PDB website. BioJava-ModFinder is available as open source (LGPL license) at ( https://github.com/biojava/biojava/tree/master/biojava-modfinder ). The RCSB PDB can be accessed at http://www.rcsb.org . pwrose@ucsd.edu. © The Author 2017. Published by Oxford University Press.

  7. Prediction of protein-protein interaction sites in sequences and 3D structures by random forests.

    Directory of Open Access Journals (Sweden)

    Mile Sikić

    2009-01-01

    Full Text Available Identifying interaction sites in proteins provides important clues to the function of a protein and is becoming increasingly relevant in topics such as systems biology and drug discovery. Although there are numerous papers on the prediction of interaction sites using information derived from structure, there are only a few case reports on the prediction of interaction residues based solely on protein sequence. Here, a sliding window approach is combined with the Random Forests method to predict protein interaction sites using (i a combination of sequence- and structure-derived parameters and (ii sequence information alone. For sequence-based prediction we achieved a precision of 84% with a 26% recall and an F-measure of 40%. When combined with structural information, the prediction performance increases to a precision of 76% and a recall of 38% with an F-measure of 51%. We also present an attempt to rationalize the sliding window size and demonstrate that a nine-residue window is the most suitable for predictor construction. Finally, we demonstrate the applicability of our prediction methods by modeling the Ras-Raf complex using predicted interaction sites as target binding interfaces. Our results suggest that it is possible to predict protein interaction sites with quite a high accuracy using only sequence information.

  8. Cloud4Psi: cloud computing for 3D protein structure similarity searching.

    Science.gov (United States)

    Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Kłapciński, Artur

    2014-10-01

    Popular methods for 3D protein structure similarity searching, especially those that generate high-quality alignments such as Combinatorial Extension (CE) and Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists (FATCAT) are still time consuming. As a consequence, performing similarity searching against large repositories of structural data requires increased computational resources that are not always available. Cloud computing provides huge amounts of computational power that can be provisioned on a pay-as-you-go basis. We have developed the cloud-based system that allows scaling of the similarity searching process vertically and horizontally. Cloud4Psi (Cloud for Protein Similarity) was tested in the Microsoft Azure cloud environment and provided good, almost linearly proportional acceleration when scaled out onto many computational units. Cloud4Psi is available as Software as a Service for testing purposes at: http://cloud4psi.cloudapp.net/. For source code and software availability, please visit the Cloud4Psi project home page at http://zti.polsl.pl/dmrozek/science/cloud4psi.htm. © The Author 2014. Published by Oxford University Press.

  9. A constraint logic programming approach to associate 1D and 3D structural components for large protein complexes.

    Science.gov (United States)

    Dal Palù, Alessandro; Pontelli, Enrico; He, Jing; Lu, Yonggang

    2007-01-01

    The paper describes a novel framework, constructed using Constraint Logic Programming (CLP) and parallelism, to determine the association between parts of the primary sequence of a protein and alpha-helices extracted from 3D low-resolution descriptions of large protein complexes. The association is determined by extracting constraints from the 3D information, regarding length, relative position and connectivity of helices, and solving these constraints with the guidance of a secondary structure prediction algorithm. Parallelism is employed to enhance performance on large proteins. The framework provides a fast, inexpensive alternative to determine the exact tertiary structure of unknown proteins.

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

    Directory of Open Access Journals (Sweden)

    Yun-Shiang Chang

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

  11. 3D protein-structure-oriented discovery of clinical relation across chronic lymphocytic leukemia patients

    DEFF Research Database (Denmark)

    Mochament, Konstantinos; Agathangelidis, Andreas; Polychronidou, Eleftheria

    2017-01-01

    Chronic lymphocytic leukemia (CLL) is the most common adult leukemia with still unclear etiology. Indications of antigenic pressure have been hinted, using sequence and structure-based reasoning. The accuracy of such approaches, and in particular of the ones derived from 3D models obtained from t...

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

    Directory of Open Access Journals (Sweden)

    Felix Rausch

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

  13. An Augmented Pocketome: Detection and Analysis of Small-Molecule Binding Pockets in Proteins of Known 3D Structure.

    Science.gov (United States)

    Bhagavat, Raghu; Sankar, Santhosh; Srinivasan, Narayanaswamy; Chandra, Nagasuma

    2018-03-06

    Protein-ligand interactions form the basis of most cellular events. Identifying ligand binding pockets in proteins will greatly facilitate rationalizing and predicting protein function. Ligand binding sites are unknown for many proteins of known three-dimensional (3D) structure, creating a gap in our understanding of protein structure-function relationships. To bridge this gap, we detect pockets in proteins of known 3D structures, using computational techniques. This augmented pocketome (PocketDB) consists of 249,096 pockets, which is about seven times larger than what is currently known. We deduce possible ligand associations for about 46% of the newly identified pockets. The augmented pocketome, when subjected to clustering based on similarities among pockets, yielded 2,161 site types, which are associated with 1,037 ligand types, together providing fold-site-type-ligand-type associations. The PocketDB resource facilitates a structure-based function annotation, delineation of the structural basis of ligand recognition, and provides functional clues for domains of unknown functions, allosteric proteins, and druggable pockets. Copyright © 2018 Elsevier Ltd. All rights reserved.

  14. Sequence and 3D structure based analysis of TNT degrading proteins in Arabidopsis thaliana.

    Science.gov (United States)

    Bhattacherjee, Amrita; Mandal, Rahul Shubhra; Das, Santasabuj; Kundu, Sudip

    2014-03-01

    TNT, accidentally released at several manufacturing sites, contaminates ground water and soil. It has a toxic effect to algae and invertebrate, and chronic exposure to TNT also causes harmful effects to human. On the other hand, many plants including Arabidopsis thaliana have the ability to metabolize TNT either completely or at least to a reduced less toxic form. In A. thaliana, the enzyme UDP glucosyltransferase (UDPGT) can further conjugate the reduced forms 2-HADNT and 4-HADNT (2-hydroxylamino-4, 6- dinitrotoluene and 4-hydroxylamino-2, 6- dinitrotoluene) of TNT. Based on the experimental analysis, existing literature and phylogenetic analysis, it is evident that among 107 UDPGT proteins only six are involved in the TNT degrading process. A total of 13 UDPGT proteins including five of these TNT degrading proteins fall within the same group of phylogeny. Thus, these 13 UDPGT proteins have been classified into two groups, TNT-degrading and TNT-non-degrading proteins. To understand the differences in TNT-degrading capacities; using homology modeling we first predicted two structures, taking one representative sequence from both the groups. Next, we performed molecular docking of the modeled structure and TNT reduced form 2-hydroxylamino-4, 6- dinitrotoluene (2-HADNT). We observed that while the Trp residue located within the active site region of the TNT- degrading protein showed π-Cation interaction; such type of interaction was absent in TNT-non-degrading protein, as the respective Trp residue lay outside of the pocket in this case. We observed the conservation of this π-Cation interaction during MD simulation of TNT-degrading protein. Thus, the position and the orientation of the active site residue Trp could explain the presence and absence of TNT-degrading capacity of the UDPGT proteins.

  15. FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures.

    Science.gov (United States)

    Huang, Yi-Fei; Golding, G Brian

    2015-02-15

    A number of statistical phylogenetic methods have been developed to infer conserved functional sites or regions in proteins. Many methods, e.g. Rate4Site, apply the standard phylogenetic models to infer site-specific substitution rates and totally ignore the spatial correlation of substitution rates in protein tertiary structures, which may reduce their power to identify conserved functional patches in protein tertiary structures when the sequences used in the analysis are highly similar. The 3D sliding window method has been proposed to infer conserved functional patches in protein tertiary structures, but the window size, which reflects the strength of the spatial correlation, must be predefined and is not inferred from data. We recently developed GP4Rate to solve these problems under the Bayesian framework. Unfortunately, GP4Rate is computationally slow. Here, we present an intuitive web server, FuncPatch, to perform a fast approximate Bayesian inference of conserved functional patches in protein tertiary structures. Both simulations and four case studies based on empirical data suggest that FuncPatch is a good approximation to GP4Rate. However, FuncPatch is orders of magnitudes faster than GP4Rate. In addition, simulations suggest that FuncPatch is potentially a useful tool complementary to Rate4Site, but the 3D sliding window method is less powerful than FuncPatch and Rate4Site. The functional patches predicted by FuncPatch in the four case studies are supported by experimental evidence, which corroborates the usefulness of FuncPatch. The software FuncPatch is freely available at the web site, http://info.mcmaster.ca/yifei/FuncPatch golding@mcmaster.ca Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  16. Strategies for the structural analysis of multi-protein complexes: lessons from the 3D-Repertoire project.

    Science.gov (United States)

    Collinet, B; Friberg, A; Brooks, M A; van den Elzen, T; Henriot, V; Dziembowski, A; Graille, M; Durand, D; Leulliot, N; Saint André, C; Lazar, N; Sattler, M; Séraphin, B; van Tilbeurgh, H

    2011-08-01

    Structural studies of multi-protein complexes, whether by X-ray diffraction, scattering, NMR spectroscopy or electron microscopy, require stringent quality control of the component samples. The inability to produce 'keystone' subunits in a soluble and correctly folded form is a serious impediment to the reconstitution of the complexes. Co-expression of the components offers a valuable alternative to the expression of single proteins as a route to obtain sufficient amounts of the sample of interest. Even in cases where milligram-scale quantities of purified complex of interest become available, there is still no guarantee that good quality crystals can be obtained. At this step, protein engineering of one or more components of the complex is frequently required to improve solubility, yield or the ability to crystallize the sample. Subsequent characterization of these constructs may be performed by solution techniques such as Small Angle X-ray Scattering and Nuclear Magnetic Resonance to identify 'well behaved' complexes. Herein, we recount our experiences gained at protein production and complex assembly during the European 3D Repertoire project (3DR). The goal of this consortium was to obtain structural information on multi-protein complexes from yeast by combining crystallography, electron microscopy, NMR and in silico modeling methods. We present here representative set case studies of complexes that were produced and analyzed within the 3DR project. Our experience provides useful insight into strategies that are more generally applicable for structural analysis of protein complexes. Copyright © 2011 Elsevier Inc. All rights reserved.

  17. Prediction of residues in discontinuous B-cell epitopes using protein 3D structures

    DEFF Research Database (Denmark)

    Andersen, P.H.; Nielsen, Morten; Lund, Ole

    2006-01-01

    . We show that the new structure-based method has a better performance for predicting residues of discontinuous epitopes than methods based solely on sequence information, and that it can successfully predict epitope residues that have been identified by different techniques. DiscoTope detects 15...... experimental epitope mapping in both rational vaccine design and development of diagnostic tools, and may lead to more efficient epitope identification....

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

    Science.gov (United States)

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

    2014-11-01

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

  19. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

    Science.gov (United States)

    Westbrook, John D; Feng, Zukang; Persikova, Irina; Sala, Raul; Sen, Sanchayita; Berrisford, John M; Swaminathan, G Jawahar; Oldfield, Thomas J; Gutmanas, Aleksandras; Igarashi, Reiko; Armstrong, David R; Baskaran, Kumaran; Chen, Li; Chen, Minyu; Clark, Alice R; Di Costanzo, Luigi; Dimitropoulos, Dimitris; Gao, Guanghua; Ghosh, Sutapa; Gore, Swanand; Guranovic, Vladimir; Hendrickx, Pieter M S; Hudson, Brian P; Ikegawa, Yasuyo; Kengaku, Yumiko; Lawson, Catherine L; Liang, Yuhe; Mak, Lora; Mukhopadhyay, Abhik; Narayanan, Buvaneswari; Nishiyama, Kayoko; Patwardhan, Ardan; Sahni, Gaurav; Sanz-García, Eduardo; Sato, Junko; Sekharan, Monica R; Shao, Chenghua; Smart, Oliver S; Tan, Lihua; van Ginkel, Glen; Yang, Huanwang; Zhuravleva, Marina A; Markley, John L; Nakamura, Haruki; Kurisu, Genji; Kleywegt, Gerard J; Velankar, Sameer; Berman, Helen M; Burley, Stephen K

    2018-01-01

    Abstract The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. The worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability, Accessibility, Interoperability and Reusability. The wwPDB recently developed OneDep, a unified tool for deposition, validation and biocuration of structures of biological macromolecules. All data deposited to the PDB undergo critical review by wwPDB Biocurators. This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a high-quality archive. Structural data submitted to the PDB are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources and validated for scientific/technical accuracy. We illustrate how biocuration is integral to PDB data archiving, as it facilitates accurate, consistent and comprehensive representation of biological structure data, allowing efficient and effective usage by research scientists, educators, students and the curious public worldwide. Database URL: https://www.wwpdb.org/ PMID:29688351

  20. Towards a molecular interpretation of astringency: synthesis, 3D structure, colloidal state, and human saliva protein recognition of procyanidins.

    Science.gov (United States)

    Cala, Olivier; Fabre, Sandy; Pinaud, Noël; Dufourc, Erick J; Fouquet, Eric; Laguerre, Michel; Pianet, Isabelle

    2011-07-01

    Astringency is a sensation in the mouth used in judging the quality of red wine. The rough, dry, and puckering sensation called astringency is the result of an interaction between tannins and saliva proteins, mainly proline-rich proteins (PRP), which leads to the formation and precipitation of a complex. A dry and rough sensation is then perceived in the mouth. To get an insight into astringency at the molecular level we investigated: (i) An efficient and iterative method for 4-8 procyanidin synthesis, which gives rise to all possible 4-8 procyanidins up to the tetramer with total control of degree of oligomerization and stereochemistry. (ii) The 3D-structural preferences, which take into account their internal movements, using 2D NMR and molecular modeling. (iii) The self-association process in water or hydroalcoholic solutions using diffusion NMR spectroscopy that gives the active proportion of tannins able to fix proteins. (iv) A comprehensive description of the PRP-procyanidin complex formation to get information about stoichiometry, binding site localization, and affinity constants for different procyanidins. The data collected suggest that the interactions are controlled by both procyanidin conformational and colloidal state preferences. All these results provide new insights into the molecular interpretation of tannin astringency. © Georg Thieme Verlag KG Stuttgart · New York.

  1. Correlation between spatial (3D) structure of pea and bean thylakoid membranes and arrangement of chlorophyll-protein complexes.

    Science.gov (United States)

    Rumak, Izabela; Mazur, Radosław; Gieczewska, Katarzyna; Kozioł-Lipińska, Joanna; Kierdaszuk, Borys; Michalski, Wojtek P; Shiell, Brian J; Venema, Jan Henk; Vredenberg, Wim J; Mostowska, Agnieszka; Garstka, Maciej

    2012-05-25

    The thylakoid system in plant chloroplasts is organized into two distinct domains: grana arranged in stacks of appressed membranes and non-appressed membranes consisting of stroma thylakoids and margins of granal stacks. It is argued that the reason for the development of appressed membranes in plants is that their photosynthetic apparatus need to cope with and survive ever-changing environmental conditions. It is not known however, why different plant species have different arrangements of grana within their chloroplasts. It is important to elucidate whether a different arrangement and distribution of appressed and non-appressed thylakoids in chloroplasts are linked with different qualitative and/or quantitative organization of chlorophyll-protein (CP) complexes in the thylakoid membranes and whether this arrangement influences the photosynthetic efficiency. Our results from TEM and in situ CLSM strongly indicate the existence of different arrangements of pea and bean thylakoid membranes. In pea, larger appressed thylakoids are regularly arranged within chloroplasts as uniformly distributed red fluorescent bodies, while irregular appressed thylakoid membranes within bean chloroplasts correspond to smaller and less distinguished fluorescent areas in CLSM images. 3D models of pea chloroplasts show a distinct spatial separation of stacked thylakoids from stromal spaces whereas spatial division of stroma and thylakoid areas in bean chloroplasts are more complex. Structural differences influenced the PSII photochemistry, however without significant changes in photosynthetic efficiency. Qualitative and quantitative analysis of chlorophyll-protein complexes as well as spectroscopic investigations indicated a similar proportion between PSI and PSII core complexes in pea and bean thylakoids, but higher abundance of LHCII antenna in pea ones. Furthermore, distinct differences in size and arrangements of LHCII-PSII and LHCI-PSI supercomplexes between species are suggested

  2. 3D structure of muscle dihydropyridine receptor

    Directory of Open Access Journals (Sweden)

    Montserrat Samsó

    2015-01-01

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

  3. MSX-3D: a tool to validate 3D protein models using mass spectrometry.

    Science.gov (United States)

    Heymann, Michaël; Paramelle, David; Subra, Gilles; Forest, Eric; Martinez, Jean; Geourjon, Christophe; Deléage, Gilbert

    2008-12-01

    The technique of chemical cross-linking followed by mass spectrometry has proven to bring valuable information about the protein structure and interactions between proteic subunits. It is an effective and efficient way to experimentally investigate some aspects of a protein structure when NMR and X-ray crystallography data are lacking. We introduce MSX-3D, a tool specifically geared to validate protein models using mass spectrometry. In addition to classical peptides identifications, it allows an interactive 3D visualization of the distance constraints derived from a cross-linking experiment. Freely available at http://proteomics-pbil.ibcp.fr

  4. 3D Printing of Fluid Flow Structures

    OpenAIRE

    Taira, Kunihiko; Sun, Yiyang; Canuto, Daniel

    2017-01-01

    We discuss the use of 3D printing to physically visualize (materialize) fluid flow structures. Such 3D models can serve as a refreshing hands-on means to gain deeper physical insights into the formation of complex coherent structures in fluid flows. In this short paper, we present a general procedure for taking 3D flow field data and producing a file format that can be supplied to a 3D printer, with two examples of 3D printed flow structures. A sample code to perform this process is also prov...

  5. Microfabricating 3D Structures by Laser Origami

    Science.gov (United States)

    2011-11-09

    10.1117/2.1201111.003952 Microfabricating 3D structures by laser origami Alberto Piqué, Scott Mathews, Andrew Birnbaum, and Nicholas Charipar A new...folding known as origami allows the transformation of flat patterns into 3D shapes. A similar approach can be used to generate 3D structures com... geometries . The overarching challenge is to move away from traditional planar semiconductor photolitho- graphic techniques, which severely limit the type of

  6. ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins.

    Science.gov (United States)

    Ruiz-Blanco, Yasser B; Paz, Waldo; Green, James; Marrero-Ponce, Yovani

    2015-05-16

    The exponential growth of protein structural and sequence databases is enabling multifaceted approaches to understanding the long sought sequence-structure-function relationship. Advances in computation now make it possible to apply well-established data mining and pattern recognition techniques to these data to learn models that effectively relate structure and function. However, extracting meaningful numerical descriptors of protein sequence and structure is a key issue that requires an efficient and widely available solution. We here introduce ProtDCal, a new computational software suite capable of generating tens of thousands of features considering both sequence-based and 3D-structural descriptors. We demonstrate, by means of principle component analysis and Shannon entropy tests, how ProtDCal's sequence-based descriptors provide new and more relevant information not encoded by currently available servers for sequence-based protein feature generation. The wide diversity of the 3D-structure-based features generated by ProtDCal is shown to provide additional complementary information and effectively completes its general protein encoding capability. As demonstration of the utility of ProtDCal's features, prediction models of N-linked glycosylation sites are trained and evaluated. Classification performance compares favourably with that of contemporary predictors of N-linked glycosylation sites, in spite of not using domain-specific features as input information. ProtDCal provides a friendly and cross-platform graphical user interface, developed in the Java programming language and is freely available at: http://bioinf.sce.carleton.ca/ProtDCal/ . ProtDCal introduces local and group-based encoding which enhances the diversity of the information captured by the computed features. Furthermore, we have shown that adding structure-based descriptors contributes non-redundant additional information to the features-based characterization of polypeptide systems. This

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

    OpenAIRE

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Khader Shameer

    2010-06-01

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

  9. Mosaic amino acid conservation in 3D-structures of surface protein and polymerase of hepatitis B virus

    NARCIS (Netherlands)

    van Hemert, Formijn J.; Zaaijer, Hans L.; Berkhout, Ben; Lukashov, Vladimir V.

    2008-01-01

    Surface protein and polymerase of hepatitis B virus provide a striking example of gene overlap. Inclusion of more coding constraints in the phylogenetic analysis forces the tree toward accepted topology. Three-dimensional protein modeling demonstrates that participation in local protein function

  10. 3D structure prediction of histone acetyltransferase (HAC proteins of the p300/CBP family and their interactome in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Amar Cemanovic

    2014-09-01

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

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

    Directory of Open Access Journals (Sweden)

    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

  12. Generation of 3D templates of active sites of proteins with rigid prosthetic groups

    OpenAIRE

    Nebel, Jean-Christophe

    2006-01-01

    MOTIVATION: With the increasing availability of protein structures, the generation of biologically meaningful 3D patterns from the simultaneous alignment of several protein structures is an exciting prospect: active sites could be better understood, protein functions and protein 3D structures could be predicted more accurately. Although patterns can already be generated at the fold and topological levels, no system produces high-resolution 3D patterns including atom and cavity positions. To a...

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

    DEFF Research Database (Denmark)

    Oliveira, Rodrigo Gouveia; Roque, francisco jose sousa simôes almeida; Wernersson, Rasmus

    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...

  14. 3D Printed Shock Mitigating Structures

    Science.gov (United States)

    Schrand, Amanda; Elston, Edwin; Dennis, Mitzi; Metroke, Tammy; Chen, Chenggang; Patton, Steven; Ganguli, Sabyasachi; Roy, Ajit

    Here we explore the durability, and shock mitigating potential, of solid and cellular 3D printed polymers and conductive inks under high strain rate, compressive shock wave and high g acceleration conditions. Our initial designs include a simple circuit with 4 resistors embedded into circular discs and a complex cylindrical gyroid shape. A novel ink consisting of silver-coated carbon black nanoparticles in a thermoplastic polyurethane was used as the trace material. One version of the disc structural design has the advantage of allowing disassembly after testing for direct failure analysis. After increasing impacts, printed and traditionally potted circuits were examined for functionality. Additionally, in the open disc design, trace cracking and delamination of resistors were able to be observed. In a parallel study, we examined the shock mitigating behavior of 3D printed cellular gyroid structures on a Split Hopkinson Pressure Bar (SHPB). We explored alterations to the classic SHPB setup for testing the low impedance, cellular samples to most accurately reflect the stress state inside the sample (strain rates from 700 to 1750 s-1). We discovered that the gyroid can effectively absorb the impact of the test resulting in crushing the structure. Future studies aim to tailor the unit cell dimensions for certain frequencies, increase print accuracy and optimize material compositions for conductivity and adhesion to manufacture more durable devices.

  15. Three barium diphosphonates with 3-D structures

    Science.gov (United States)

    Tuikka, Matti; Haukka, Matti; Ahlgrén, Markku

    2007-06-01

    The gel crystallization method was exploited in this work in order to study the 3-D solid state structures of barium diphosphonates. This technique proved to be an effective tool for the growth of single crystals of diphosphonates for structure analysis. By using this approach, three barium diphosphonates, Ba[HO 3P(CH 2) 2PO 3H] ( 1), Ba 2[O 3P(CH 2) 3PO 3]·3H 2O ( 2) and Ba[HO 3P(CH 2) 4PO 3H] ( 3), with different three dimensional structures, were synthesized and characterized. The structures of compounds 1 and 2 were determined by single crystal X-ray diffraction and the structure of 3 by the powder diffraction method. In the structure of 1, the diphosphonate ligand is completely surrounded by the Ba atoms, which is an unusual arrangement in a diphosphonate system. The structures of 2 and 3 are more conventional. They are organized in typical pillared layers in which the separation of the layers can be adjusted by varying the length of the hydrocarbon chain.

  16. 3D-Printed Millimeter Wave Structures

    Science.gov (United States)

    2016-03-14

    demonstrates the resolution of the printer with a 10 micron nozzle. Figure 2: Measured loss tangent of SEBS and SBS samples. 3D - Printed Millimeter... 3D printing of styrene-butadiene-styrene (SBS) and styrene ethylene/butylene-styrene (SEBS) is used to demonstrate the feasibility of 3D - printed ...Additionally, a dielectric lens is printed which improves the antenna gain of an open-ended WR-28 waveguide from 7 to 8.5 dBi. Keywords: 3D printing

  17. Generation of 3D templates of active sites of proteins with rigid prosthetic groups.

    Science.gov (United States)

    Nebel, Jean-Christophe

    2006-05-15

    With the increasing availability of protein structures, the generation of biologically meaningful 3D patterns from the simultaneous alignment of several protein structures is an exciting prospect: active sites could be better understood, protein functions and protein 3D structures could be predicted more accurately. Although patterns can already be generated at the fold and topological levels, no system produces high-resolution 3D patterns including atom and cavity positions. To address this challenge, our research focuses on generating patterns from proteins with rigid prosthetic groups. Since these groups are key elements of protein active sites, the generated 3D patterns are expected to be biologically meaningful. In this paper, we present a new approach which allows the generation of 3D patterns from proteins with rigid prosthetic groups. Using 237 protein chains representing proteins containing porphyrin rings, our method was validated by comparing 3D templates generated from homologues with the 3D structure of the proteins they model. Atom positions were predicted reliably: 93% of them had an accuracy of 1.00 A or less. Moreover, similar results were obtained regarding chemical group and cavity positions. Results also suggested our system could contribute to the validation of 3D protein models. Finally, a 3D template was generated for the active site of human cytochrome P450 CYP17, the 3D structure of which is unknown. Its analysis showed that it is biologically meaningful: our method detected the main patterns of the cytochrome P450 superfamily and the motifs linked to catalytic reactions. The 3D template also suggested the position of a residue, which could be involved in a hydrogen bond with CYP17 substrates and the shape and location of a cavity. Comparisons with independently generated 3D models comforted these hypotheses. Alignment software (Nestor3D) is available at http://www.kingston.ac.uk/~ku33185/Nestor3D.html

  18. 3D Structure of Tillage Soils

    Science.gov (United States)

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

    2015-04-01

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

  19. 3D printing of functional structures

    NARCIS (Netherlands)

    Krijnen, Gijsbertus J.M.

    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

  20. Analyzing the 3D Structure of Human Carbonic Anhydrase II and Its Mutants Using Deep View and the Protein Data Bank

    Science.gov (United States)

    Ship, Noam J.; Zamble, Deborah B.

    2005-01-01

    The self directed study of a 3D image of a biomolecule stresses the complex nature of the intra- and intermolecular interactions that come together to define its structure. This is made up of a series of in vitro experiments with a wild-type and mutants forms of human carbonic anhydrase II (hCAII) that examine the structure function relationship…

  1. p3d--Python module for structural bioinformatics.

    Science.gov (United States)

    Fufezan, Christian; Specht, Michael

    2009-08-21

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

  2. p3d – Python module for structural bioinformatics

    Directory of Open Access Journals (Sweden)

    Fufezan Christian

    2009-08-01

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

  3. 3D Protein Dynamics in the Cell Nucleus.

    Science.gov (United States)

    Singh, Anand P; Galland, Rémi; Finch-Edmondson, Megan L; Grenci, Gianluca; Sibarita, Jean-Baptiste; Studer, Vincent; Viasnoff, Virgile; Saunders, Timothy E

    2017-01-10

    The three-dimensional (3D) architecture of the cell nucleus plays an important role in protein dynamics and in regulating gene expression. However, protein dynamics within the 3D nucleus are poorly understood. Here, we present, to our knowledge, a novel combination of 1) single-objective based light-sheet microscopy, 2) photoconvertible proteins, and 3) fluorescence correlation microscopy, to quantitatively measure 3D protein dynamics in the nucleus. We are able to acquire >3400 autocorrelation functions at multiple spatial positions within a nucleus, without significant photobleaching, allowing us to make reliable estimates of diffusion dynamics. Using this tool, we demonstrate spatial heterogeneity in Polymerase II dynamics in live U2OS cells. Further, we provide detailed measurements of human-Yes-associated protein diffusion dynamics in a human gastric cancer epithelial cell line. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. Automated assignment and 3D structure calculations using combinations of 2D homonuclear and 3D heteronuclear NOESY spectra

    International Nuclear Information System (INIS)

    Oezguen, Numan; Adamian, Larisa; Xu Yuan; Rajarathnam, Krishna; Braun, Werner

    2002-01-01

    The NOAH/DIAMOD suite uses feedback filtering and self-correcting distance geometry to generate 3D structures from unassigned NOESY spectra. In this study we determined the minimum set of experiments needed to generate a high quality structure bundle. Different combinations of 3D 15 N-edited, 13 C-edited HSQC-NOESY and 2D homonuclear 1 H- 1 H NOESY spectra of the 77 amino acid protein, myeloid progenitor inhibitory factor-1 (MPIF-1) were used as input for NOAH/DIAMOD calculations. The quality of the assignments of NOESY cross peaks and the accuracy of the automatically generated 3D structures were compared to those obtained with a conventional manual procedure. Combining data from two types of experiments synergistically increased the number of peaks assigned unambiguously in both individual spectra. As a general trend for the accuracy of the structures we observed structural variations in the backbone fold of the final structures of about 2 A for single spectral data, of 1 A to 1.5 A for double spectral data, and of 0.6 A for triple spectral data sets. The quality of the assignments and 3D structures from the optimal data using all three spectra were similar to those obtained from traditional assignment methods with structural variations within the bundle of 0.6 A and 1.3 A for backbone and heavy atoms, respectively. Almost all constraints (97%) of the automatic NOESY cross peak assignments were cross compatible with the structures from the conventional manual assignment procedure, and an even larger proportion (99%) of the manually derived constraints were compatible with the automatically determined 3D structures. The two mean structures determined by both methods differed only by 1.3 A rmsd for the backbone atoms in the well-defined regions of the protein. Thus NOAD/DIAMOD analysis of spectra from labeled proteins provides a reliable method for high throughput analysis of genomic targets

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

    DEFF Research Database (Denmark)

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

    1998-01-01

    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...

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

    OpenAIRE

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

    2013-01-01

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

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

    OpenAIRE

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

    2015-01-01

    Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants. This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud regi...

  8. 3DSwap: Curated knowledgebase of proteins involved in 3D domain swapping

    KAUST Repository

    Shameer, Khader

    2011-09-29

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

  9. Solving a 3D structural puzzle

    DEFF Research Database (Denmark)

    Hoeck, Casper

    Nuclear magnetic resonance (NMR) spectroscopy is a versatile tool in analytical chemistry, highly suitable for structural elucidation of organic molecules – as well as multiple other areas of research. The subjects covered within this thesis all concern methods which allow a shift from covalent t...

  10. 3D monitoring of active tectonic structures

    Czech Academy of Sciences Publication Activity Database

    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

  11. Unit cell geometry of 3-D braided structures

    Science.gov (United States)

    Du, Guang-Wu; Ko, Frank K.

    1993-01-01

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

  12. 3D Animations for Exploring Nucleon Structure

    Science.gov (United States)

    Gorman, Waverly; Burkardt, Matthias

    2016-09-01

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

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

    Science.gov (United States)

    Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

    2010-01-01

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

  14. 3D-SURFER: software for high-throughput protein surface comparison and analysis.

    Science.gov (United States)

    La, David; Esquivel-Rodríguez, Juan; Venkatraman, Vishwesh; Li, Bin; Sael, Lee; Ueng, Stephen; Ahrendt, Steven; Kihara, Daisuke

    2009-11-01

    We present 3D-SURFER, a web-based tool designed to facilitate high-throughput comparison and characterization of proteins based on their surface shape. As each protein is effectively represented by a vector of 3D Zernike descriptors, comparison times for a query protein against the entire PDB take, on an average, only a couple of seconds. The web interface has been designed to be as interactive as possible with displays showing animated protein rotations, CATH codes and structural alignments using the CE program. In addition, geometrically interesting local features of the protein surface, such as pockets that often correspond to ligand binding sites as well as protrusions and flat regions can also be identified and visualized. 3D-SURFER is a web application that can be freely accessed from: http://dragon.bio.purdue.edu/3d-surfer dkihara@purdue.edu Supplementary data are available at Bioinformatics online.

  15. Femtosecond Laser Direct Write Integration of Multi-Protein Patterns and 3D Microstructures into 3D Glass Microfluidic Devices

    Directory of Open Access Journals (Sweden)

    Daniela Serien

    2018-01-01

    Full Text Available Microfluidic devices and biochips offer miniaturized laboratories for the separation, reaction, and analysis of biochemical materials with high sensitivity and low reagent consumption. The integration of functional or biomimetic elements further functionalizes microfluidic devices for more complex biological studies. The recently proposed ship-in-a-bottle integration based on laser direct writing allows the construction of microcomponents made of photosensitive polymer inside closed microfluidic structures. Here, we expand this technology to integrate proteinaceous two-dimensional (2D and three-dimensional (3D microstructures with the aid of photo-induced cross-linking into glass microchannels. The concept is demonstrated with bovine serum albumin and enhanced green fluorescent protein, each mixed with photoinitiator (Sodium 4-[2-(4-Morpholino benzoyl-2-dimethylamino] butylbenzenesulfonate. Unlike the polymer integration, fabrication over the entire channel cross-section is challenging. Two proteins are integrated into the same channel to demonstrate multi-protein patterning. Using 50% w/w glycerol solvent instead of 100% water achieves almost the same fabrication resolution for in-channel fabrication as on-surface fabrication due to the improved refractive index matching, enabling the fabrication of 3D microstructures. A glycerol-water solvent also reduces the risk of drying samples. We believe this technology can integrate diverse proteins to contribute to the versatility of microfluidics.

  16. Combining 3D structure of real video and synthetic objects

    Science.gov (United States)

    Kim, Man-Bae; Song, Mun-Sup; Kim, Do-Kyoon

    1998-04-01

    This paper presents a new approach of combining real video and synthetic objects. The purpose of this work is to use the proposed technology in the fields of advanced animation, virtual reality, games, and so forth. Computer graphics has been used in the fields previously mentioned. Recently, some applications have added real video to graphic scenes for the purpose of augmenting the realism that the computer graphics lacks in. This approach called augmented or mixed reality can produce more realistic environment that the entire use of computer graphics. Our approach differs from the virtual reality and augmented reality in the manner that computer- generated graphic objects are combined to 3D structure extracted from monocular image sequences. The extraction of the 3D structure requires the estimation of 3D depth followed by the construction of a height map. Graphic objects are then combined to the height map. The realization of our proposed approach is carried out in the following steps: (1) We derive 3D structure from test image sequences. The extraction of the 3D structure requires the estimation of depth and the construction of a height map. Due to the contents of the test sequence, the height map represents the 3D structure. (2) The height map is modeled by Delaunay triangulation or Bezier surface and each planar surface is texture-mapped. (3) Finally, graphic objects are combined to the height map. Because 3D structure of the height map is already known, Step (3) is easily manipulated. Following this procedure, we produced an animation video demonstrating the combination of the 3D structure and graphic models. Users can navigate the realistic 3D world whose associated image is rendered on the display monitor.

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

    Science.gov (United States)

    Venkatraman, Vishwesh; Yang, Yifeng D; Sael, Lee; Kihara, Daisuke

    2009-12-09

    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. 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-alphaRMSD 3D Zernike descriptors are adept in capturing shape complementarity at the protein-protein interface and useful for protein docking prediction. Rigorous benchmark studies show that our docking approach has a superior performance compared to existing methods.

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Science.gov (United States)

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

    2014-02-01

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

  20. Three-dimensional (3D) structure prediction and function analysis of the chitin-binding domain 3 protein HD73_3189 from Bacillus thuringiensis HD73.

    Science.gov (United States)

    Zhan, Yiling; Guo, Shuyuan

    2015-01-01

    Bacillus thuringiensis (Bt) is capable of producing a chitin-binding protein believed to be functionally important to bacteria during the stationary phase of its growth cycle. In this paper, the chitin-binding domain 3 protein HD73_3189 from B. thuringiensis has been analyzed by computer technology. Primary and secondary structural analyses demonstrated that HD73_3189 is negatively charged and contains several α-helices, aperiodical coils and β-strands. Domain and motif analyses revealed that HD73_3189 contains a signal peptide, an N-terminal chitin binding 3 domains, two copies of a fibronectin-like domain 3 and a C-terminal carbohydrate binding domain classified as CBM_5_12. Moreover, analysis predicted the protein's associated localization site to be the cell wall. Ligand site prediction determined that amino acid residues GLU-312, TRP-334, ILE-341 and VAL-382 exposed on the surface of the target protein exhibit polar interactions with the substrate.

  1. 3D-DART: a DNA structure modelling server

    NARCIS (Netherlands)

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

    2009-01-01

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

  2. 3D local structure around copper site of rabbit prion-related protein: Quantitative determination by XANES spectroscopy combined with multiple-scattering calculations

    International Nuclear Information System (INIS)

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

    2014-01-01

    Prion-related protein (PrP), a cell-surface copper-binding glycoprotein, is considered to be responsible for a number of transmissible spongiform encephalopathies (TSEs). The structural conversion of PrP from the normal cellular isoform (PrP C ) to the post-translationally modified form (PrP Sc ) is thought to be relevant to Cu 2+ 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 (RaPrP C ) 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

  3. Superpose3D: a local structural comparison program that allows for user-defined structure representations.

    Directory of Open Access Journals (Sweden)

    Pier Federico Gherardini

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

  4. Modelling reinforced concrete structures in DYNA3D

    International Nuclear Information System (INIS)

    Broadhouse, B.J.; Neilson, A.J.

    1987-10-01

    A material model for reinforced concrete has been implemented in the transient structural dynamics code DYNA3D. This paper outlines the constitutive material model, and presents comparisons of DYNA3D calculations and experiments on impulsively loaded panels, covering the full range of panel damage states from light cracking through to panel collapse or perforation. The results are presented using the post-processor code TAURUS, which has also been modified to provide mesh diagrams with superimposed crack patterns from the DYNA3D predictions. (author)

  5. Topology optimization of 3D shell structures with porous infill

    DEFF Research Database (Denmark)

    Clausen, Anders; Andreassen, Erik; Sigmund, Ole

    2017-01-01

    This paper presents a 3D topology optimization approach for designing shell structures with a porous or void interior. It is shown that the resulting structures are significantly more robust towards load perturbations than completely solid structures optimized under the same conditions. The study...... indicates that the potential benefit of using porous structures is higher for lower total volume fractions. Compared to earlier work dealing with 2D topology optimization, we found several new effects in 3D problems. Most notably, the opportunity for designing closed shells significantly improves...

  6. Comparative Study on Cushion Performance Between 3D Printed Kelvin Structure and 3D Printed Lattice Structure

    Science.gov (United States)

    Priyadarshini, Lakshmi

    Frequently transported packaging goods are more prone to damage due to impact, jolting or vibration in transit. Fragile goods, for example, glass, ceramics, porcelain are susceptible to mechanical stresses. Hence ancillary materials like cushions play an important role when utilized within package. In this work, an analytical model of a 3D cellular structure is established based on Kelvin model and lattice structure. The research will provide a comparative study between the 3D printed Kelvin unit structure and 3D printed lattice structure. The comparative investigation is based on parameters defining cushion performance such as cushion creep, indentation, and cushion curve analysis. The applications of 3D printing is in rapid prototyping where the study will provide information of which model delivers better form of energy absorption. 3D printed foam will be shown as a cost-effective approach as prototype. The research also investigates about the selection of material for 3D printing process. As cushion development demands flexible material, three-dimensional printing with material having elastomeric properties is required. Further, the concept of cushion design is based on Kelvin model structure and lattice structure. The analytical solution provides the cushion curve analysis with respect to the results observed when load is applied over the cushion. The results are reported on basis of attenuation and amplification curves.

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

    International Nuclear Information System (INIS)

    Laranjeira, M.S.; Dias, A.G.; Santos, J.D.; Fernandes, M.H.

    2009-01-01

    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. SAFE-3D, Stress Analysis of 3-D Composite Structure by Finite Elements Method

    International Nuclear Information System (INIS)

    Cornell, D.C.; Jadhav, K.; Crowell, J.S.

    1969-01-01

    1 - Description of problem or function: SAFE-3D is a finite-element program for the three-dimensional elastic analysis of heterogeneous composite structures. The program uses the following types of finite elements - (1) tetrahedral elements to represent the continuum, (2) triangular plane stress membrane elements to represent inner liner or outer case, and (3) uniaxial tension-compression elements to represent internal reinforcement. The structure can be of arbitrary geometry and have any distribution of material properties, temperatures, surface loadings, and boundary conditions. 2 - Method of solution: The finite-element variational method is used. Equilibrium equations are solved by the alternating component iterative method. 3 - Restrictions on the complexity of the problem - Maxima of: 5000 nodes; 16000 elements. The program cannot be applied to incompressible solids and is not recommended for Poisson's ratio in the range of nu between 0.495 and 0.5

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

    Science.gov (United States)

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

    2014-01-01

    The rich indigenous and endemic plants in Taiwan serve as a resourceful bank for biologically active phytochemicals. Based on our TIPdb database curating bioactive phytochemicals from Taiwan indigenous plants, this study presents a three-dimensional (3D) chemical structure database named TIPdb-3D to support the discovery of novel pharmacologically active compounds. The Merck Molecular Force Field (MMFF94) was used to generate 3D structures of phytochemicals in TIPdb. The 3D structures could facilitate the analysis of 3D quantitative structure-activity relationship, the exploration of chemical space and the identification of potential pharmacologically active compounds using protein-ligand docking. Database URL: http://cwtung.kmu.edu.tw/tipdb. © The Author(s) 2014. Published by Oxford University Press.

  10. 3D printing of nano- and micro-structures

    Science.gov (United States)

    Ramasamy, Mouli; Varadan, Vijay K.

    2016-04-01

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

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

    Science.gov (United States)

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

    2013-07-01

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

  12. 3D-printing soft sEMG sensing structures

    NARCIS (Netherlands)

    Wolterink, Gerjan; Sanders, Remco; Muijzer, Frodo; van Beijnum, Bert-Jan; Krijnen, Gijs

    2017-01-01

    This paper describes the development and characterization of soft and flexible 3D-printed sEMG electrodes. The electrodes are printed in one go on a low cost consumer multi-material FDM printer. The printed structures do not need any further production steps to give them conductive properties.

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

    Directory of Open Access Journals (Sweden)

    Sael Lee

    2009-12-01

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

  14. Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction.

    Science.gov (United States)

    Daberdaku, Sebastian; Ferrari, Carlo

    2018-02-06

    The correct determination of protein-protein interaction interfaces is important for understanding disease mechanisms and for rational drug design. To date, several computational methods for the prediction of protein interfaces have been developed, but the interface prediction problem is still not fully understood. Experimental evidence suggests that the location of binding sites is imprinted in the protein structure, but there are major differences among the interfaces of the various protein types: the characterising properties can vary a lot depending on the interaction type and function. The selection of an optimal set of features characterising the protein interface and the development of an effective method to represent and capture the complex protein recognition patterns are of paramount importance for this task. In this work we investigate the potential of a novel local surface descriptor based on 3D Zernike moments for the interface prediction task. Descriptors invariant to roto-translations are extracted from circular patches of the protein surface enriched with physico-chemical properties from the HQI8 amino acid index set, and are used as samples for a binary classification problem. Support Vector Machines are used as a classifier to distinguish interface local surface patches from non-interface ones. The proposed method was validated on 16 classes of proteins extracted from the Protein-Protein Docking Benchmark 5.0 and compared to other state-of-the-art protein interface predictors (SPPIDER, PrISE and NPS-HomPPI). The 3D Zernike descriptors are able to capture the similarity among patterns of physico-chemical and biochemical properties mapped on the protein surface arising from the various spatial arrangements of the underlying residues, and their usage can be easily extended to other sets of amino acid properties. The results suggest that the choice of a proper set of features characterising the protein interface is crucial for the interface prediction

  15. Tangible 3D modeling of coherent and themed structures

    DEFF Research Database (Denmark)

    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......, allows the user to tangibly build structures of greater details than the blocks provide in and of themselves. We show a number of shapes that have been modeled by users and are indicative of the expressive power of the system. Furthermore, we demonstrate the scalability of the tangible interface which...

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

    Science.gov (United States)

    Lietzke, Susan E; Barnes, Cindy L.

    1998-01-01

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

  17. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine.

    Science.gov (United States)

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

    2017-02-27

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

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

    Science.gov (United States)

    Meyer, Scott C.

    2015-01-01

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

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

    Science.gov (United States)

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

    2015-07-29

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

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

    Directory of Open Access Journals (Sweden)

    Thuy Tuong Nguyen

    2015-07-01

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

  1. An analysis of 3D solvation structure in biomolecules: application to coiled coil serine and bacteriorhodopsin.

    Science.gov (United States)

    Hirano, Kenji; Yokogawa, Daisuke; Sato, Hirofumi; Sakaki, Shigeyoshi

    2010-06-17

    Three-dimensional (3D) solvation structure around coiled coil serine (Coil-Ser) and inner 3D hydration structure in bacteriorhodopsin (bR) were studied using a recently developed method named multicenter molecular Ornstein-Zernike equation (MC-MOZ) theory. In addition, a procedure for analyzing the 3D solvent distribution was proposed. The method enables us to calculate the coordination number of solvent water as well as the strength of hydrogen bonding between the water molecule and the protein. The results for Coil-Ser and bR showed very good agreement with the experimental observations.

  2. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    Science.gov (United States)

    Ishikawa, Takashi

    2013-01-01

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

  3. 3D printed components with ultrasonically arranged microscale structure

    Science.gov (United States)

    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.

  4. e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design.

    Science.gov (United States)

    Pihan, Emilie; Colliandre, Lionel; Guichou, Jean-François; Douguet, Dominique

    2012-06-01

    In the drug discovery field, new uses for old drugs, selective optimization of side activities and fragment-based drug design (FBDD) have proved to be successful alternatives to high-throughput screening. e-Drug3D is a database of 3D chemical structures of drugs that provides several collections of ready-to-screen SD files of drugs and commercial drug fragments. They are natural inputs in studies dedicated to drug repurposing and FBDD. e-Drug3D collections are freely available at http://chemoinfo.ipmc.cnrs.fr/e-drug3d.html either for download or for direct in silico web-based screenings.

  5. Embedded sensing: integrating sensors in 3-D printed structures

    Directory of Open Access Journals (Sweden)

    A. Dijkshoorn

    2018-03-01

    Full Text Available Current additive manufacturing allows for the implementation of electrically interrogated 3-D printed sensors. In this contribution various technologies, sensing principles and applications are discussed. We will give both an overview of some of the sensors presented in literature as well as some of our own recent work on 3-D printed sensors. The 3-D printing methods discussed include fused deposition modelling (FDM, using multi-material printing and poly-jetting. Materials discussed are mainly thermoplastics and include thermoplastic polyurethane (TPU, both un-doped as well as doped with carbon black, polylactic acid (PLA and conductive inks. The sensors discussed are based on biopotential sensing, capacitive sensing and resistive sensing with applications in surface electromyography (sEMG and mechanical and tactile sensing. As these sensors are based on plastics they are in general flexible and therefore open new possibilities for sensing in soft structures, e.g. as used in soft robotics. At the same time they show many of the characteristics of plastics like hysteresis, drift and non-linearity. We will argue that 3-D printing of embedded sensors opens up exciting new possibilities but also that these sensors require us to rethink how to exploit non-ideal sensors.

  6. Real-Time 3D Profile Measurement Using Structured Light

    International Nuclear Information System (INIS)

    Xu, L; Zhang, Z J; Ma, H; Yu, Y J

    2006-01-01

    The paper builds a real-time system of 3D profile measurement using structured-light imaging. It allows a hand-held object to rotate free in the space-time coded light field, which is projected by the projector. The surface of measured objects with projected coded light is imaged; the system shows surface reconstruction results of objects online. This feedback helps user to adjust object's pose in the light field according to the dismissed or error data, which would achieve the integrality of data used in reconstruction. This method can acquire denser data cloud and have higher reconstruction accuracy and efficiency. According to the real-time requirements, the paper presents the non-restricted light plane modelling which suits stripe structured light system, designs the three-frame stripes space-time coded pattern, and uses the advance ICP algorithms to acquire 3D data alignment from multiple view

  7. All dispenser printed flexible 3D structured thermoelectric generators

    Science.gov (United States)

    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.

  8. Combined shape and topology optimization of 3D structures

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  9. The role of 3D structure and protein conformation on the innate and adaptive immune responses to silk-based biomaterials.

    Science.gov (United States)

    Bhattacharjee, Maumita; Schultz-Thater, Elke; Trella, Emanuele; Miot, Sylvie; Das, Sanskrita; Loparic, Marko; Ray, Alok R; Martin, Ivan; Spagnoli, Giulio C; Ghosh, Sourabh

    2013-11-01

    We have investigated monocyte and T cell responsiveness to silk based biomaterials of different physico-chemical characteristics. Here we report that untransformed CD14+ human monocytes respond to overnight exposure to silk fibroin-based biomaterials in tridimensional form by IL-1β and IL-6, but not IL-10 gene expression and protein production. In contrast, fibroin based materials in bidimensional form are unable to stimulate monocyte responsiveness. The elicitation of these effects critically requires contact between biomaterials and responding cells, is not sustained and becomes undetectable in longer term cultures. We also observed that NF-κβ and p38 MAP kinase play key roles in monocyte activation by silk-based biomaterials. On the other hand, fibroin based materials, irrespective of their physico-chemical characteristics appeared to be unable to induce the activation of peripheral blood T cells from healthy donors, as evaluated by the expression of activation markers and IFN-γ gene. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

    Singh, Suryabhan; Bhim, Anupam

    2016-12-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

  12. Inductance calculation of 3D superconducting structures with ground plane

    International Nuclear Information System (INIS)

    Teh, C.H.; Kitagawa, M.; Okabe, Y.

    1999-01-01

    An inductance calculation method, which is based on calculating the current distribution of a fluxoid-trapped superconducting loop by using the expression of momentum and the Maxwell equations, is reconstructed to enable calculation of arbitrary 3D structures which have a ground plane (GP). Calculation of the mutual inductances of the superconductor system is also incorporated into the algorithm. The method of images is used to save computational resources, and the mirror plane is demonstrated to be just at the effective penetration depth below the upper boundary of the GP. The algorithm offers accurate results with reasonable calculation time. (author)

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

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Suryabhan, E-mail: sbs.bhu@gmail.com; Bhim, Anupam

    2016-12-15

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

  14. 3D-finite element impact simulation on concrete structures

    Energy Technology Data Exchange (ETDEWEB)

    Heider, N.

    1989-12-15

    The analysis of impact processes is an interesting application of full 3D Finite Element calculations. This work presents a simulation of the penetration process of a Kinetic Energy projectile into a concrete target. Such a calculation requires an adequate FE model, especially a proper description of the crack opening process in front of the projectile. The aim is the prediction of the structural survival of the penetrator case with the help of an appropriate failure criterion. Also, the computer simulation allows a detailed analysis of the physical phenomena during impact. (orig.) With 4 refs., 14 figs.

  15. Improving 3D structure prediction from chemical shift data

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-09-15

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

  16. A 3D Image Filter for Parameter-Free Segmentation of Macromolecular Structures from Electron Tomograms

    Science.gov (United States)

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

    2012-01-01

    3D image reconstruction of large cellular volumes by electron tomography (ET) at high (≤5 nm) resolution can now routinely resolve organellar and compartmental membrane structures, protein coats, cytoskeletal filaments, and macromolecules. However, current image analysis methods for identifying in situ macromolecular structures within the crowded 3D ultrastructural landscape of a cell remain labor-intensive, time-consuming, and prone to user-bias and/or error. This paper demonstrates the development and application of a parameter-free, 3D implementation of the bilateral edge-detection (BLE) algorithm for the rapid and accurate segmentation of cellular tomograms. The performance of the 3D BLE filter has been tested on a range of synthetic and real biological data sets and validated against current leading filters—the pseudo 3D recursive and Canny filters. The performance of the 3D BLE filter was found to be comparable to or better than that of both the 3D recursive and Canny filters while offering the significant advantage that it requires no parameter input or optimisation. Edge widths as little as 2 pixels are reproducibly detected with signal intensity and grey scale values as low as 0.72% above the mean of the background noise. The 3D BLE thus provides an efficient method for the automated segmentation of complex cellular structures across multiple scales for further downstream processing, such as cellular annotation and sub-tomogram averaging, and provides a valuable tool for the accurate and high-throughput identification and annotation of 3D structural complexity at the subcellular level, as well as for mapping the spatial and temporal rearrangement of macromolecular assemblies in situ within cellular tomograms. PMID:22479430

  17. Spontaneous Self-Formation of 3D Plasmonic Optical Structures.

    Science.gov (United States)

    Choi, Inhee; Shin, Yonghee; Song, Jihwan; Hong, SoonGweon; Park, Younggeun; Kim, Dongchoul; Kang, Taewook; Lee, Luke P

    2016-08-23

    Self-formation of colloidal oil droplets in water or water droplets in oil not only has been regarded as fascinating fundamental science but also has been utilized in an enormous number of applications in everyday life. However, the creation of three-dimensional (3D) architectures by a liquid droplet and an immiscible liquid interface has been less investigated than other applications. Here, we report interfacial energy-driven spontaneous self-formation of a 3D plasmonic optical structure at room temperature without an external force. Based on the densities and interfacial energies of two liquids, we simulated the spontaneous formation of a plasmonic optical structure when a water droplet containing metal ions meets an immiscible liquid polydimethylsiloxane (PDMS) interface. At the interface, the metal ions in the droplet are automatically reduced to form an interfacial plasmonic layer as the liquid PDMS cures. The self-formation of both an optical cavity and integrated plasmonic nanostructure significantly enhances the fluorescence by a magnitude of 1000. Our findings will have a huge impact on the development of various photonic and plasmonic materials as well as metamaterials and devices.

  18. Dual multispectral and 3D structured light laparoscope

    Science.gov (United States)

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

    2015-03-01

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

  19. How membrane lipids control the 3D structure and function of receptors

    Directory of Open Access Journals (Sweden)

    Jacques Fantini

    2018-02-01

    Full Text Available The cohabitation of lipids and proteins in the plasma membrane of mammalian cells is controlled by specific biochemical and biophysical rules. Lipids may be either constitutively tightly bound to cell-surface receptors (non-annular lipids or less tightly attached to the external surface of the protein (annular lipids. The latter are exchangeable with surrounding bulk membrane lipids on a faster time scale than that of non-annular lipids. Not only do non-annular lipids bind to membrane proteins through stereoselective mechanisms, they can also help membrane receptors acquire (or maintain a functional 3D structure. Cholesterol is the prototype of membrane lipids that finely controls the 3D structure and function of receptors. However, several other lipids such as sphingolipids may also modulate the function of membrane proteins though conformational adjustments. All these concepts are discussed in this review in the light of representative examples taken from the literature.

  20. Simulating the 3-D Structure of Titan's Upper Atmosphere

    Science.gov (United States)

    Bell, J. M.; Waite, H.; Westlake, J.; Magee, B.

    2009-05-01

    We present results from the 3-D Titan Global Ionosphere-Thermosphere Model (Bell et al [2009], PSS, in review). We show comparisons between simulated N2, CH4, and H2 density fields and the in-situ data from the Cassini Ion Neutral Mass Spectrometer (INMS). We describe the temperature and wind fields consistent with these density calculations. Variations with local time, longitude, and latitude will be addressed. Potential plasma heating sources can be estimated using the 1-D model of De La Haye et al [2007, 2008] and the impacts on the thermosphere of Titan can be assessed in a global sense in Titan-GITM. Lastly, we will place these findings within the context of recent work in modeling the 2-D structure of Titan's upper atmosphere (Mueller-Wodarg et al [2008]).

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

    Directory of Open Access Journals (Sweden)

    Kendra K. Schmid

    2012-01-01

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

  2. 3D Imaging with Structured Illumination for Advanced Security Applications

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-09-01

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

  3. Photonic bandgap structure of 3-D fcc silica nanospheres

    Energy Technology Data Exchange (ETDEWEB)

    Woo, Y. K.; Ha, N. Y.; Hwang, Ji Soo; Chang, H. J.; Wu, J. W. [Dept. of Physics, Ewha Womans University, Seoul (Korea, Republic of)

    2002-07-01

    Photonic crystal is an artificial optical material with a periodic dielectric potential, hence exhibiting a bandgap for a propagating electromagnetic wave. We fabricated crystal possessing 3-D fcc opal structure from silica nanospheres. The crystals are self-assembled on a flat glass by evaporating the solvent in the nanosphere suspension at the room temperature. The suspension consists of silica nanospheres with a diameter of 200 nm. The microscopic arrangement of nanospheres is identified by a scanning electron microscope, the resulting structure being fcc.Transmission spectrum of the fabricated photonic crystal in the visible and near-infrared regions is measured at different incident angles to find the distinct Bragg peaks, analysis of which further confirmed the fcc structure of the photonic crystal. From the optical microscopic image, we find that the opal domain varies from 30 μm to 125 μm in size. In order to relate the observed Bragg peaks with the microscopic arrangement of silica nanospheres, we introduced the scalar wave approximation, where the electric field in the medium is treated as a scalar rather than a vector quantity. It is found that the theoretical prediction of the position of bandgap is in a good agreement with the experimental measurement.

  4. Photonic bandgap structure of 3-D fcc silica nanospheres

    International Nuclear Information System (INIS)

    Woo, Y. K.; Ha, N. Y.; Hwang, Ji Soo; Chang, H. J.; Wu, J. W.

    2002-01-01

    Photonic crystal is an artificial optical material with a periodic dielectric potential, hence exhibiting a bandgap for a propagating electromagnetic wave. We fabricated crystal possessing 3-D fcc opal structure from silica nanospheres. The crystals are self-assembled on a flat glass by evaporating the solvent in the nanosphere suspension at the room temperature. The suspension consists of silica nanospheres with a diameter of 200 nm. The microscopic arrangement of nanospheres is identified by a scanning electron microscope, the resulting structure being fcc.Transmission spectrum of the fabricated photonic crystal in the visible and near-infrared regions is measured at different incident angles to find the distinct Bragg peaks, analysis of which further confirmed the fcc structure of the photonic crystal. From the optical microscopic image, we find that the opal domain varies from 30 μm to 125 μm in size. In order to relate the observed Bragg peaks with the microscopic arrangement of silica nanospheres, we introduced the scalar wave approximation, where the electric field in the medium is treated as a scalar rather than a vector quantity. It is found that the theoretical prediction of the position of bandgap is in a good agreement with the experimental measurement.

  5. Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking.

    Science.gov (United States)

    Kihara, Daisuke; Sael, Lee; Chikhi, Rayan; Esquivel-Rodriguez, Juan

    2011-09-01

    The tertiary structures of proteins have been solved in an increasing pace in recent years. To capitalize the enormous efforts paid for accumulating the structure data, efficient and effective computational methods need to be developed for comparing, searching, and investigating interactions of protein structures. We introduce the 3D Zernike descriptor (3DZD), an emerging technique to describe molecular surfaces. The 3DZD is a series expansion of mathematical three-dimensional function, and thus a tertiary structure is represented compactly by a vector of coefficients of terms in the series. A strong advantage of the 3DZD is that it is invariant to rotation of target object to be represented. These two characteristics of the 3DZD allow rapid comparison of surface shapes, which is sufficient for real-time structure database screening. In this article, we review various applications of the 3DZD, which have been recently proposed.

  6. 3D Seismic Imaging over a Potential Collapse Structure

    Science.gov (United States)

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

    2016-04-01

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

  7. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

    NARCIS (Netherlands)

    McGuire, R.; Verhoeven, S.; Vass, M.; Vriend, G.; Esch, I.J. de; Lusher, S.J.; Leurs, R.; Ridder, L.; Kooistra, A.J.; Ritschel, T.; Graaf, C. de

    2017-01-01

    3D-e-Chem-VM is an open source, freely available Virtual Machine ( http://3d-e-chem.github.io/3D-e-Chem-VM/ ) that integrates cheminformatics and bioinformatics tools for the analysis of protein-ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools

  8. 3D-e-Chem-VM : Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

    NARCIS (Netherlands)

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

    2017-01-01

    3D-e-Chem-VM is an open source, freely available Virtual Machine ( http://3d-e-chem.github.io/3D-e-Chem-VM/ ) that integrates cheminformatics and bioinformatics tools for the analysis of protein-ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools

  9. 3D-SURFER 2.0: web platform for real-time search and characterization of protein surfaces.

    Science.gov (United States)

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

    2014-01-01

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

  10. 3D silicon breast surface mapping via structured light profilometry

    Science.gov (United States)

    Vairavan, R.; Ong, N. R.; Sauli, Z.; Kirtsaeng, S.; Sakuntasathien, S.; Shahimin, M. M.; Alcain, J. B.; Lai, S. L.; Paitong, P.; Retnasamy, V.

    2017-09-01

    Digital fringe projection technique is one of the promising optical methods for 3D surface imaging as it demonstrates non contact and non invasive characteristics. The potential of this technique matches the requirement for human body evaluation, as it is vital for disease diagnosis and for treatment option selection. Thus, the digital fringe projection has addressed this requirement with its wide clinical related application and studies. However, the application of this technique for 3D surface mapping of the breast is very minimal. Hence, in this work, the application of digital fringe projection for 3D breast surface mapping is reported. Phase shift fringe projection technique was utilized to perform the 3D breast surface mapping. Maiden results have confirmed the feasibility of using the digital fringe projection method for 3D surface mapping of the breast and it can be extended for breast cancer detection.

  11. 3D representations of amino acids—applications to protein sequence comparison and classification

    Directory of Open Access Journals (Sweden)

    Jie Li

    2014-08-01

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

  12. 3D modelling of the pathogenic Leptospira protein LipL32: A bioinformatics approach.

    Science.gov (United States)

    Kumaran, Sharmilah Kumari; Bakar, Mohd Faizal Abu; Mohd-Padil, Hirzahida; Mat-Sharani, Shuhaila; Sakinah, S; Poorani, K; Alsaeedy, Hiba; Peli, Amira; Wei, Teh Seoh; Ling, Mok Pooi; Hamat, Rukman Awang; Neela, Vasantha Kumari; Higuchi, Akon; Alarfaj, Abdullah A; Rajan, Mariappan; Benelli, Giovanni; Arulselvan, Palanisamy; Kumar, S Suresh

    2017-12-01

    Leptospirosis is a widespread zoonotic disease caused by pathogenic Leptospira species (Leptospiraceae). LipL32 is an abundant lipoprotein from the outer membrane proteins (OMPs) group, highly conserved among pathogenic and intermediate Leptospira species. Several studies used LipL32 as a specific gene to identify the presence of leptospires. This research was aimed to study the characteristics of LipL32 protein gene code, to fill the knowledge gap concerning the most appropriate gene that can be used as antigen to detect the Leptospira. Here, we investigated the features of LipL32 in fourteen Leptospira pathogenic strains based on comparative analyses of their primary, secondary structures and 3D modeling using a bioinformatics approach. Furthermore, the physicochemical properties of LipL32 in different strains were studied, shedding light on the identity of signal peptides, as well as on the secondary and tertiary structure of the LipL32 protein, supported by 3D modelling assays. The results showed that the LipL32 gene was present in all the fourteen pathogenic Leptospira strains used in this study, with limited diversity in terms of sequence conservation, hydrophobic group, hydrophilic group and number of turns (random coil). Overall, these results add basic knowledge to the characteristics of LipL32 protein, contributing to the identification of potential antigen candidates in future research, in order to ensure prompt and reliable detection of pathogenic Leptospira species. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Characteristics and structure of turbulent 3D offset jets

    International Nuclear Information System (INIS)

    Agelin-Chaab, M.; Tachie, M.F.

    2011-01-01

    Highlights: → We investigated three-dimensional turbulent offset jets using particle image velocimetry. → We examined the effects of offset height and Reynolds number on the structure of 3D offset jets. → Effects of Reynolds number and offset height on the decay and growth rates exist close to the exit. → This study provides additional insight and comprehensive data for validating numerical models. - Abstract: Three-dimensional turbulent offset jets were investigated using a particle image velocimetry technique. The measurements were performed at three different exit Reynolds numbers and for four offset heights. The results in the early region of flow development clearly show significant effects of Reynolds number and offset height on the decay of maximum mean velocity and growth of the shear layer. On the contrary, the decay and spread rates were found to be nearly independent of offset height at larger downstream distances. The decay rates of 1.18 ± 0.03 as well as the spread rates of 0.055 ± 0.001 and 0.250 ± 0.005 obtained, respectively, in the wall-normal and lateral directions fall in the range of values reported in previous studies. The locations of the maximum mean velocities increased nearly linearly with streamwise distance in the self-similar region. Analysis from two-point velocity correlations revealed substantially larger structures in the outer layer and self-similar region than in the inner layer and developing region. It was also observed that the hairpin vortices in the inner regions of the wall jets are inclined at angles of 11.2 o ± 0.6 o , which are in good agreement with reported values in boundary layer studies.

  14. Membrane transport mechanism 3D structure and beyond

    CERN Document Server

    Ziegler, Christine

    2014-01-01

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

  15. Embedded sensing : Integrating sensors in 3-D printed structures

    NARCIS (Netherlands)

    Dijkshoorn, Alexander; Werkman, Patrick; Welleweerd, Marcel; Wolterink, Gerhard Jan Willem; Eijking, Bram; Delamare, John; Sanders, Remco; Krijnen, Gijs J.M.

    2018-01-01

    Current additive manufacturing allows for the implementation of electrically interrogated 3-D printed sensors. In this contribution various technologies, sensing principles and applications are discussed. We will give both an overview of some of the sensors presented in literature as well as some of

  16. 3D, parallel fluid-structure interaction code

    CSIR Research Space (South Africa)

    Oxtoby, Oliver F

    2011-01-01

    Full Text Available The authors describe the development of a 3D parallel Fluid–Structure–Interaction (FSI) solver and its application to benchmark problems. Fluid and solid domains are discretised using and edge-based finite-volume scheme for efficient parallel...

  17. 3D concrete printing – a structural engineering perspective

    NARCIS (Netherlands)

    Salet, T.A.M.; Bos, F.P.; Wolfs, R.J.M.; Ahmed, Z.Y.; Hordijk, D.A.; Luković, M.

    2017-01-01

    3D Concrete Printing (3DCP) is being developed in an increasing number of places around the globe. The focus is mainly on a trial-and-error based exploration of the possibilities. However, to obtain a viable manufacturing technology and realize the 3DCP potential, a higher level of process control

  18. Optimising 3D printed concrete structures using topology optimisation

    NARCIS (Netherlands)

    Martens, P.; Mathot, M.; Bos, F.P.; Coenders, J.; Hordijk, D.A.; Luković, M.

    2017-01-01

    Additive manufacturing and 3D printing are rapidly developing digital fabrication techniques (Lu et al. 2015). After the first steps in small scale printing of metals (Frazier 2014) and plastics (Gibson et al. 2014) have been made, research from various groups around the world is now also focusing

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

    OpenAIRE

    Kensuke Takagishi; Shinjiro Umezu

    2017-01-01

    The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able...

  20. Rclick: a web server for comparison of RNA 3D structures.

    Science.gov (United States)

    Nguyen, Minh N; Verma, Chandra

    2015-03-15

    RNA molecules play important roles in key biological processes in the cell and are becoming attractive for developing therapeutic applications. Since the function of RNA depends on its structure and dynamics, comparing and classifying the RNA 3D structures is of crucial importance to molecular biology. In this study, we have developed Rclick, a web server that is capable of superimposing RNA 3D structures by using clique matching and 3D least-squares fitting. Our server Rclick has been benchmarked and compared with other popular servers and methods for RNA structural alignments. In most cases, Rclick alignments were better in terms of structure overlap. Our server also recognizes conformational changes between structures. For this purpose, the server produces complementary alignments to maximize the extent of detectable similarity. Various examples showcase the utility of our web server for comparison of RNA, RNA-protein complexes and RNA-ligand structures. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  1. Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors.

    Science.gov (United States)

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2012-06-14

    A novel computational method for fitting high-resolution structures of multiple proteins into a cryoelectron microscopy map is presented. The method named EMLZerD generates a pool of candidate multiple protein docking conformations of component proteins, which are later compared with a provided electron microscopy (EM) density map to select the ones that fit well into the EM map. The comparison of docking conformations and the EM map is performed using the 3D Zernike descriptor (3DZD), a mathematical series expansion of three-dimensional functions. The 3DZD provides a unified representation of the surface shape of multimeric protein complex models and EM maps, which allows a convenient, fast quantitative comparison of the three-dimensional structural data. Out of 19 multimeric complexes tested, near native complex structures with a root-mean-square deviation of less than 2.5 Å were obtained for 14 cases while medium range resolution structures with correct topology were computed for the additional 5 cases.

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

    Science.gov (United States)

    Ghanizadeh Tabriz, Atabak; Mills, Christopher G; Mullins, John J; Davies, Jamie A; Shu, Wenmiao

    2017-01-01

    Development of a simple, straightforward 3D fabrication method to culture cells in 3D, without relying on any complex fabrication methods, remains a challenge. In this paper, we describe a new technique that allows fabrication of scalable 3D cell-laden hydrogel structures easily, without complex machinery: the technique can be done using only apparatus already available in a typical cell biology laboratory. The fabrication method involves micro dip-coating of cell-laden hydrogels covering the surface of a metal bar, into the cross-linking reagents calcium chloride or barium chloride to form hollow tubular structures. This method can be used to form single layers with thickness ranging from 126 to 220 µm or multilayered tubular structures. This fabrication method uses alginate hydrogel as the primary biomaterial and a secondary biomaterial can be added depending on the desired application. We demonstrate the feasibility of this method, with survival rate over 75% immediately after fabrication and normal responsiveness of cells within these tubular structures using mouse dermal embryonic fibroblast cells and human embryonic kidney 293 cells containing a tetracycline-responsive, red fluorescent protein (tHEK cells).

  3. Visualization of Hyperconjugation and Subsequent Structural Distortions through 3D Printing of Crystal Structures.

    Science.gov (United States)

    Mithila, Farha J; Oyola-Reynoso, Stephanie; Thuo, Martin M; Atkinson, Manza Bj

    2016-01-01

    Structural distortions due to hyperconjugation in organic molecules, like norbornenes, are well captured through X-ray crystallographic data, but are sometimes difficult to visualize especially for those applying chemical knowledge and are not chemists. Crystal structure from the Cambridge database were downloaded and converted to .stl format. The structures were then printed at the desired scale using a 3D printer. Replicas of the crystal structures were accurately reproduced in scale and any resulting distortions were clearly visible from the macroscale models. Through space interactions or effect of through space hyperconjugation was illustrated through loss of symmetry or distortions thereof. The norbornene structures exhibits distortion that cannot be observed through conventional ball and stick modelling kits. We show that 3D printed models derived from crystallographic data capture even subtle distortions in molecules. We translate such crystallographic data into scaled-up models through 3D printing.

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

    NARCIS (Netherlands)

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

    2010-01-01

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

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

    Science.gov (United States)

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-05

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

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

    Science.gov (United States)

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-01

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

  7. Programmatic conversion of crystal structures into 3D printable files using Jmol

    OpenAIRE

    Scalfani, Vincent F.; Williams, Antony J.; Tkachenko, Valery; Karapetyan, Karen; Pshenichnov, Alexey; Hanson, Robert M.; Liddie, Jahred M.; Bara, Jason E.

    2016-01-01

    Background Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable files. Results A collection of over 30,000 crystal structures in crystallographic information file (CIF) format from...

  8. Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?

    Directory of Open Access Journals (Sweden)

    Gibrat Jean-François

    2008-01-01

    Full Text Available Abstract Background Recent approaches for predicting the three-dimensional (3D structure of proteins such as de novo or fold recognition methods mostly rely on simplified energy potential functions and a reduced representation of the polypeptide chain. These simplifications facilitate the exploration of the protein conformational space but do not permit to capture entirely the subtle relationship that exists between the amino acid sequence and its native structure. It has been proposed that physics-based energy functions together with techniques for sampling the conformational space, e.g., Monte Carlo or molecular dynamics (MD simulations, are better suited to the task of modelling proteins at higher resolutions than those of models obtained with the former type of methods. In this study we monitor different protein structural properties along MD trajectories to discriminate correct from erroneous models. These models are based on the sequence-structure alignments provided by our fold recognition method, FROST. We define correct models as being built from alignments of sequences with structures similar to their native structures and erroneous models from alignments of sequences with structures unrelated to their native structures. Results For three test sequences whose native structures belong to the all-α, all-β and αβ classes we built a set of models intended to cover the whole spectrum: from a perfect model, i.e., the native structure, to a very poor model, i.e., a random alignment of the test sequence with a structure belonging to another structural class, including several intermediate models based on fold recognition alignments. We submitted these models to 11 ns of MD simulations at three different temperatures. We monitored along the corresponding trajectories the mean of the Root-Mean-Square deviations (RMSd with respect to the initial conformation, the RMSd fluctuations, the number of conformation clusters, the evolution of

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

    Directory of Open Access Journals (Sweden)

    Shooji Yamada, Hiroshi Yamaguchi and Sunao Ishihara

    2009-01-01

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

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

    Science.gov (United States)

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

    2015-10-01

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

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

    Science.gov (United States)

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

    2016-11-04

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

  12. Lower bound plane stress element for modelling 3D structures

    DEFF Research Database (Denmark)

    Herfelt, Morten Andersen; Poulsen, Peter Noe; Hoang, Linh Cao

    2017-01-01

    In-plane action is often the primary load-carrying mechanism of reinforced concrete structures. The plate bending action will be secondary, and the behaviour of the structure can be modelled with a reasonable accuracy using a generalised three-dimensional plane stress element. In this paper...

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

    OpenAIRE

    Cook, Kevin; Canning, John; 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.

  14. Gallium nitride heterostructures on 3D structured silicon

    Energy Technology Data Exchange (ETDEWEB)

    Fuendling, Soenke; Soekmen, Uensal; Peiner, Erwin; Bakin, Andrey; Wehmann, Hergo-Heinrich; Waag, Andreas [Institut fuer Halbleitertechnik, Hans-Sommer-Strasse 66, 38106 Braunschweig (Germany); Weimann, Thomas; Hinze, Peter [Physikalisch Technische Bundesanstalt, Bundesallee 100, 38116 Braunschweig (Germany); Jahn, Uwe; Trampert, Achim; Riechert, Henning [Paul-Drude-Institut fuer Festkoerperelektronik, Hausvogteiplatz 5-7, 10117 Berlin (Germany)], E-mail: s.fuendling@tu-bs.de

    2008-10-08

    We investigated GaN-based heterostructures grown on three-dimensionally patterned Si(111) substrates by metal organic vapour phase epitaxy, with the goal of fabricating well controlled high quality, defect reduced GaN-based nanoLEDs. The high aspect ratios of such pillars minimize the influence of the lattice mismatched substrate and improve the material quality. In contrast to other approaches, we employed deep etched silicon substrates to achieve a controlled pillar growth. For that a special low temperature inductively coupled plasma etching process has been developed. InGaN/GaN multi-quantum-well structures have been incorporated into the pillars. We found a pronounced dependence of the morphology of the GaN structures on the size and pitch of the pillars. Spatially resolved optical properties of the structures are analysed by cathodoluminescence.

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

    Science.gov (United States)

    Lou, Zhongyu; Gevers, Theo; Hu, Ninghang

    2015-10-01

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

  16. 3D pressure field in lipid membranes and membrane-protein complexes

    DEFF Research Database (Denmark)

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

    2009-01-01

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

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

    DEFF Research Database (Denmark)

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

    2016-01-01

    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...

  18. 3D engineered fiberboard : a new structural building product

    Science.gov (United States)

    John F. Hunt; Jerrold E. Winandy

    2002-01-01

    To help meet the need for sustainable forest management tools, the USDA Forest Products Laboratory is developing an economically viable process to produce three-dimensional structural fibreboard products that can utilize a wide range of lignocellulosic fibres contained in the forest undergrowth and in underutilized timber. This will encourage the public and private...

  19. Determination and validation of mTOR kinase-domain 3D structure by homology modeling

    Directory of Open Access Journals (Sweden)

    Lakhlili W

    2015-07-01

    Full Text Available Wiame Lakhlili,1 Gwénaël Chevé,2 Abdelaziz Yasri,2 Azeddine Ibrahimi1 1Laboratoire de Biotechnologie (MedBiotech, Faculté de Médecine et de Pharmacie de Rabat, Université Mohammed V de Rabat, Rabat, Morroco; 2OriBase Pharma, Cap Gamma, Parc Euromédecine, Montpellier, France Abstract: The AKT/mammalian target of rapamycin (mTOR pathway is considered as one of the commonly activated and deregulated signaling pathways in human cancer. mTOR is associated with other proteins in two molecular complexes: mTOR complex 1/Raptor and the mTOR complex 2/Rictor. Using the crystal structure of the related lipid kinase PI3Kγ, we built a model of the catalytic region of mTOR. The modeling of the three-dimensional (3D structure of the mTOR was performed by homology modeling program SWISS-MODEL. The quality and validation of the obtained model were performed using PROCHECK and PROVE softwares. The overall stereochemical property of the protein was assessed by the Ramachandran plot. The model validation was also done by docking of known inhibitors. In this paper, we describe and validate a 3D model for the mTOR catalytic site.Keywords: mTOR, homology modeling, mTOR kinase-domain, docking

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

    Science.gov (United States)

    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. Electronic structure of some 3D transition-metal pyrites

    NARCIS (Netherlands)

    Folkerts, W.; Sawatzky, G.A.; Haas, C.; Groot, R.A. de; Hillebrecht, F.U.

    1987-01-01

    Bremsstrahlung Isochromat spectra of FeS2, NiS2, NiS1.2Se0.8 and NiSe2 are reported. These are the first direct experimental evidence for a sharp antibonding p-like state above the Fermi level. A comparison is made with experimental results in the literature. For FeS2, band-structure calculations

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

    DEFF Research Database (Denmark)

    Pedersen, Pauli; Pedersen, Niels Leergaard

    2011-01-01

    . This is 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 compliance minimization it may be advantageous to decrease the total volume, but for strength maximization it is argued to keep the total permissible volume. For direct strength maximization the sensitivity analysis of local von Mises stresses is demanding. A simple recursive procedure to obtain uniform...

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

    International Nuclear Information System (INIS)

    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 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

  4. 3D bioprinting matrices with controlled pore structure and release function guide in vitro self-organization of sweat gland.

    Science.gov (United States)

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

    2016-10-03

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

  5. 3D-structured illumination microscopy provides novel insight into architecture of human centrosomes

    Directory of Open Access Journals (Sweden)

    Katharina F. Sonnen

    2012-08-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

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

    International Nuclear Information System (INIS)

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

    2008-01-01

    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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-06-15

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

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

    Directory of Open Access Journals (Sweden)

    Mazhar Hussain Peerzada

    2013-01-01

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

  10. Investigations of Structural Requirements for BRD4 Inhibitors through Ligand- and Structure-Based 3D QSAR Approaches

    Directory of Open Access Journals (Sweden)

    Adeena Tahir

    2018-06-01

    Full Text Available The bromodomain containing protein 4 (BRD4 recognizes acetylated histone proteins and plays numerous roles in the progression of a wide range of cancers, due to which it is under intense investigation as a novel anti-cancer drug target. In the present study, we performed three-dimensional quantitative structure activity relationship (3D-QSAR molecular modeling on a series of 60 inhibitors of BRD4 protein using ligand- and structure-based alignment and different partial charges assignment methods by employing comparative molecular field analysis (CoMFA and comparative molecular similarity indices analysis (CoMSIA approaches. The developed models were validated using various statistical methods, including non-cross validated correlation coefficient (r2, leave-one-out (LOO cross validated correlation coefficient (q2, bootstrapping, and Fisher’s randomization test. The highly reliable and predictive CoMFA (q2 = 0.569, r2 = 0.979 and CoMSIA (q2 = 0.500, r2 = 0.982 models were obtained from a structure-based 3D-QSAR approach using Merck molecular force field (MMFF94. The best models demonstrate that electrostatic and steric fields play an important role in the biological activities of these compounds. Hence, based on the contour maps information, new compounds were designed, and their binding modes were elucidated in BRD4 protein’s active site. Further, the activities and physicochemical properties of the designed molecules were also predicted using the best 3D-QSAR models. We believe that predicted models will help us to understand the structural requirements of BRD4 protein inhibitors that belong to quinolinone and quinazolinone classes for the designing of better active compounds.

  11. Immunological compatibility status of placenta-derived stem cells is mediated by scaffold 3D structure.

    Science.gov (United States)

    Azizian, Sara; Khatami, Fatemeh; Modaresifar, Khashayar; Mosaffa, Nariman; Peirovi, Habibollah; Tayebi, Lobat; Bahrami, Soheyl; Redl, Heinz; Niknejad, Hassan

    2018-02-23

    Placenta-derived amniotic epithelial cells (AECs), a great cell source for tissue engineering and stem cell therapy, are immunologically inert in their native state; however, immunological changes in these cells after culture and differentiation have challenged their applications. The aim of this study was to investigate the effect of 2D and 3D scaffolds on human lymphocyte antigens (HLA) expression by AECs. The effect of different preparation parameters including pre-freezing time and temperature was evaluated on 3D chitosan-gelatine scaffolds properties. Evaluation of MHC class I, HLA-DR and HLA-G expression in AECs after 7 d culture on 2D bed and 3D scaffold of chitosan-gelatine showed that culture of AECs on the 2D substrate up-regulated MHC class I and HLA-DR protein markers on AECs surface and down-regulated HLA-G protein. In contrast, 3D scaffold did not increase protein expression of MHC class I and HLA-DR. Moreover, HLA-G protein expression remained unchanged in 3D culture. These results confirm that 3D scaffold can remain AECs in their native immunological state and modification of physical properties of the scaffold is a key regulator of immunological markers at the gene and protein expression levels; a strategy which circumvents rejection challenge of amniotic stem cells to be translated into the clinic.

  12. Design and Structure-Function Characterization of 3D Printed Synthetic Porous Biomaterials for Tissue Engineering.

    Science.gov (United States)

    Kelly, Cambre N; Miller, Andrew T; Hollister, Scott J; Guldberg, Robert E; Gall, Ken

    2018-04-01

    3D printing is now adopted for use in a variety of industries and functions. In biomedical engineering, 3D printing has prevailed over more traditional manufacturing methods in tissue engineering due to its high degree of control over both macro- and microarchitecture of porous tissue scaffolds. However, with the improved flexibility in design come new challenges in characterizing the structure-function relationships between various architectures and both mechanical and biological properties in an assortment of clinical applications. Presently, the field of tissue engineering lacks a comprehensive body of literature that is capable of drawing meaningful relationships between the designed structure and resulting function of 3D printed porous biomaterial scaffolds. This work first discusses the role of design on 3D printed porous scaffold function and then reviews characterization of these structure-function relationships for 3D printed synthetic metallic, polymeric, and ceramic biomaterials. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. High-Resolution Printing of 3D Structures Using an Electrohydrodynamic Inkjet with Multiple Functional Inks.

    Science.gov (United States)

    An, Byeong Wan; Kim, Kukjoo; Lee, Heejoo; Kim, So-Yun; Shim, Yulhui; Lee, Dae-Young; Song, Jun Yeob; Park, Jang-Ung

    2015-08-05

    Electrohydrodynamic-inkjet-printed high-resolution complex 3D structures with multiple functional inks are demonstrated. Printed 3D structures can have a variety of fine patterns, such as vertical or helix-shaped pillars and straight or rounded walls, with high aspect ratios (greater than ≈50) and narrow diameters (≈0.7 μm). Furthermore, the formation of freestanding, bridge-like Ag wire structures on plastic substrates suggests substantial potentials as high-precision, flexible 3D interconnects. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. 3D high-resolution two-photon crosslinked hydrogel structures for biological studies.

    Science.gov (United States)

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

    2017-06-01

    Hydrogels are widely used as matrices for cell growth due to the their tuneable chemical and physical properties, which mimic the extracellular matrix of natural tissue. The microfabrication of hydrogels into arbitrarily complex 3D structures is becoming essential for numerous biological applications, and in particular for investigating the correlation between cell shape and cell function in a 3D environment. Micrometric and sub-micrometric resolution hydrogel scaffolds are required to deeply investigate molecular mechanisms behind cell-matrix interaction and downstream cellular processes. We report the design and development of high resolution 3D gelatin hydrogel woodpile structures by two-photon crosslinking. Hydrated structures of lateral linewidth down to 0.5µm, lateral and axial resolution down to a few µm are demonstrated. According to the processing parameters, different degrees of polymerization are obtained, resulting in hydrated scaffolds of variable swelling and deformation. The 3D hydrogels are biocompatible and promote cell adhesion and migration. Interestingly, according to the polymerization degree, 3D hydrogel woodpile structures show variable extent of cell adhesion and invasion. Human BJ cell lines show capability of deforming 3D micrometric resolved hydrogel structures. The design and development of high resolution 3D gelatin hydrogel woodpile structures by two-photon crosslinking is reported. Significantly, topological and mechanical conditions of polymerized gelatin structures were suitable for cell accommodation in the volume of the woodpiles, leading to a cell density per unit area comparable to the bare substrate. The fabricated structures, presenting micrometric features of high resolution, are actively deformed by cells, both in terms of cell invasion within rods and of cell attachment in-between contiguous woodpiles. Possible biological targets for this 3D approach are customized 3D tissue models, or studies of cell adhesion

  15. Ray calibration and phase mapping for structured-light-field 3D reconstruction.

    Science.gov (United States)

    Cai, Zewei; Liu, Xiaoli; Peng, Xiang; Gao, Bruce Z

    2018-03-19

    In previous work, we presented a structured light field (SLF) method combining light field imaging with structured illumination to perform multi-view depth measurement. However, the previous work just accomplishes depth rather than 3D reconstruction. In this paper, we propose a novel active method involving ray calibration and phase mapping, to achieve SLF 3D reconstruction. We performed the ray calibration for the first time to determine each light field ray with metric spatio-angular parameters, making the SLF realize multi-view 3D reconstruction. Based on the ray parametric equation, we further derived the phase mapping in the SLF that spatial coordinates can be directly mapped from phase. A flexible calibration strategy was correspondently designed to determine mapping coefficients for each light field ray, achieving high-efficiency SLF 3D reconstruction. Experimental results demonstrated that the proposed method was suitable for high-efficiency multi-view 3D reconstruction in the SLF.

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

    DEFF Research Database (Denmark)

    Marcatili, Paolo; Mochament, Konstantinos; Agathangelidis, Andreas

    2016-01-01

    study, we used the structure prediction tools PIGS and I-TASSER for creating the 3D models and the TM-align algorithm to superpose them. The innovation of the current methodology resides in the usage of methods adapted from 3D content-based search methodologies to determine the local structural...... determine it are extremely laborious and demanding. Hence, the ability to gain insight into the structure of Igs at large relies on the availability of tools and algorithms for producing accurate Ig structural models based on their primary sequence alone. These models can then be used to determine...... to achieve an optimal solution to this task yet their results were hindered mainly due to the lack of efficient clustering methods based on the similarity of 3D structure descriptors. Here, we present a novel workflow for robust Ig 3D modeling and automated clustering. We validated our protocol in chronic...

  17. Computerized modeling techniques predict the 3D structure of H₄R: facts and fiction.

    Science.gov (United States)

    Zaid, Hilal; Ismael-Shanak, Siba; Michaeli, Amit; Rayan, Anwar

    2012-01-01

    The functional characterization of proteins presents a daily challenge r biochemical, medical and computational sciences, especially when the structures are undetermined empirically, as in the case of the Histamine H4 Receptor (H₄R). H₄R is a member of the GPCR superfamily that plays a vital role in immune and inflammatory responses. To date, the concept of GPCRs modeling is highlighted in textbooks and pharmaceutical pamphlets, and this group of proteins has been the subject of almost 3500 publications in the scientific literature. The dynamic nature of determining the GPCRs structure was elucidated through elegant and creative modeling methodologies, implemented by many groups around the world. H₄R which belongs to the GPCR family was cloned in 2000; understandably, its biological activity was reported only 65 times in pubmed. Here we attempt to cover the fundamental concepts of H₄R structure modeling and its implementation in drug discovery, especially those that have been experimentally tested and to highlight some ideas that are currently being discussed on the dynamic nature of H₄R and GPCRs computerized techniques for 3D structure modeling.

  18. 3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

    Science.gov (United States)

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

    2015-06-01

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

  19. Functionalization of 3D scaffolds with protein-releasing biomaterials for intracellular delivery.

    Science.gov (United States)

    Seras-Franzoso, Joaquin; Steurer, Christoph; Roldán, Mònica; Vendrell, Meritxell; Vidaurre-Agut, Carla; Tarruella, Anna; Saldaña, Laura; Vilaboa, Nuria; Parera, Marc; Elizondo, Elisa; Ratera, Imma; Ventosa, Nora; Veciana, Jaume; Campillo-Fernández, Alberto J; García-Fruitós, Elena; Vázquez, Esther; Villaverde, Antonio

    2013-10-10

    Appropriate combinations of mechanical and biological stimuli are required to promote proper colonization of substrate materials in regenerative medicine. In this context, 3D scaffolds formed by compatible and biodegradable materials are under continuous development in an attempt to mimic the extracellular environment of mammalian cells. We have here explored how novel 3D porous scaffolds constructed by polylactic acid, polycaprolactone or chitosan can be decorated with bacterial inclusion bodies, submicron protein particles formed by releasable functional proteins. A simple dipping-based decoration method tested here specifically favors the penetration of the functional particles deeper than 300μm from the materials' surface. The functionalized surfaces support the intracellular delivery of biologically active proteins to up to more than 80% of the colonizing cells, a process that is slightly influenced by the chemical nature of the scaffold. The combination of 3D soft scaffolds and protein-based sustained release systems (Bioscaffolds) offers promise in the fabrication of bio-inspired hybrid matrices for multifactorial control of cell proliferation in tissue engineering under complex architectonic setting-ups. © 2013.

  20. Large-scale Comparative Study of Hi-C-based Chromatin 3D Structure Modeling Methods

    KAUST Repository

    Wang, Cheng

    2018-01-01

    Chromatin is a complex polymer molecule in eukaryotic cells, primarily consisting of DNA and histones. Many works have shown that the 3D folding of chromatin structure plays an important role in DNA expression. The recently proposed Chro- mosome

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

    KAUST Repository

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

    2015-01-01

    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

  2. 3D structure of individual nanocrystals in solution by electron microscopy

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

    2015-07-17

    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. Copyright © 2015, American Association for the Advancement of Science.

  4. 3D Printers Can Provide an Added Dimension for Teaching Structure-Energy Relationships

    Science.gov (United States)

    Blauch, David N.; Carroll, Felix A.

    2014-01-01

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

  5. Comparison of Enzymes / Non-Enzymes Proteins Classification Models Based on 3D, Composition, Sequences and Topological Indices

    OpenAIRE

    Munteanu, Cristian Robert

    2014-01-01

    Comparison of Enzymes / Non-Enzymes Proteins Classification Models Based on 3D, Composition, Sequences and Topological Indices, German Conference on Bioinformatics (GCB), Potsdam, Germany (September, 2007)

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

    International Nuclear Information System (INIS)

    Hoshi, Toru; Matsuno, Ryosuke; Sawaguchi, Takashi; Konno, Tomohiro; Takai, Madoka; Ishihara, Kazuhiko

    2008-01-01

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

  7. Ultrathin nickel hydroxide on carbon coated 3D-porous copper structures for high performance supercapacitors.

    Science.gov (United States)

    Kang, Kyeong-Nam; Kim, Ik-Hee; Ramadoss, Ananthakumar; Kim, Sun-I; Yoon, Jong-Chul; Jang, Ji-Hyun

    2018-01-03

    An ultrathin nickel hydroxide layer electrodeposited on a carbon-coated three-dimensional porous copper structure (3D-C/Cu) is suggested as an additive and binder-free conductive electrode with short electron path distances, large electrochemical active sites, and improved structural stability, for high performance supercapacitors. The 3D-porous copper structure (3D-Cu) provides high electrical conductivity and facilitates electron transport between the Ni(OH) 2 active materials and the current collector of the Ni-plate. A carbon coating was applied to the 3D-Cu to prevent the oxidation of Cu, without degrading the electron transport behavior of the 3D-Cu. The 3D-Ni(OH) 2 /C/Cu exhibited a high specific capacitance of 1860 F g -1 at 1 A g -1 , and good cycling performance, with an 86.5% capacitance retention after 10 000 cycles. When tested in a two-electrode system, an asymmetric supercapacitor exhibited an energy density of 147.9 W h kg -1 and a power density of 37.0 kW kg -1 . These results open a new area of ultrahigh-performance supercapacitors, supported by 3D-Cu electrodes.

  8. Toxin structures as evolutionary tools: Using conserved 3D folds to study the evolution of rapidly evolving peptides.

    Science.gov (United States)

    Undheim, Eivind A B; Mobli, Mehdi; King, Glenn F

    2016-06-01

    Three-dimensional (3D) structures have been used to explore the evolution of proteins for decades, yet they have rarely been utilized to study the molecular evolution of peptides. Here, we highlight areas in which 3D structures can be particularly useful for studying the molecular evolution of peptide toxins. Although we focus our discussion on animal toxins, including one of the most widespread disulfide-rich peptide folds known, the inhibitor cystine knot, our conclusions should be widely applicable to studies of the evolution of disulfide-constrained peptides. We show that conserved 3D folds can be used to identify evolutionary links and test hypotheses regarding the evolutionary origin of peptides with extremely low sequence identity; construct accurate multiple sequence alignments; and better understand the evolutionary forces that drive the molecular evolution of peptides. Also watch the video abstract. © 2016 WILEY Periodicals, Inc.

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

    Science.gov (United States)

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

    1998-07-01

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

  10. Hyperfine structure in 5s4d 3D-5snf transitions of 87Sr

    International Nuclear Information System (INIS)

    Bushaw, B.A.; Kluge, H.J.; Lantzsch, J.; Schwalbach, R.; Stenner, J.; Stevens, H.; Wendt, K.; Zimmer, K.

    1993-01-01

    The hyperfine spectra of the 5s4d 3 D 1 -5s20f, 5s4d 3 D 2 -5s23f, and 5s4d 3 D 3 -5s32f transitions of 87 Sr (I=9/2) have been measured by collinear fast beam laser spectroscopy. The structure in the upper configurations is highly perturbed by fine structure splitting that is of comparable size to the hyperfine interaction energy. These perturbations can be adequately treated with conventional matrix diagonalization methods, using the 5s-electron magnetic dipole interaction term a 5s and the unperturbed fine structure splittings as input parameters. Additionally, hyperfine constants for the lower 5s4d 3 D configurations, including the A- and B-factors and a separation of the individual s- and d-electron contributions to these factors, are derived. (orig.)

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

    Directory of Open Access Journals (Sweden)

    Kristin Verena Kaltdorf

    2017-01-01

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

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

    International Nuclear Information System (INIS)

    Zhang Fengxiang; Low, Hong Yee

    2008-01-01

    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

  13. A novel knowledge-based potential for RNA 3D structure evaluation

    Science.gov (United States)

    Yang, Yi; Gu, Qi; Zhang, Ben-Gong; Shi, Ya-Zhou; Shao, Zhi-Gang

    2018-03-01

    Ribonucleic acids (RNAs) play a vital role in biology, and knowledge of their three-dimensional (3D) structure is required to understand their biological functions. Recently structural prediction methods have been developed to address this issue, but a series of RNA 3D structures are generally predicted by most existing methods. Therefore, the evaluation of the predicted structures is generally indispensable. Although several methods have been proposed to assess RNA 3D structures, the existing methods are not precise enough. In this work, a new all-atom knowledge-based potential is developed for more accurately evaluating RNA 3D structures. The potential not only includes local and nonlocal interactions but also fully considers the specificity of each RNA by introducing a retraining mechanism. Based on extensive test sets generated from independent methods, the proposed potential correctly distinguished the native state and ranked near-native conformations to effectively select the best. Furthermore, the proposed potential precisely captured RNA structural features such as base-stacking and base-pairing. Comparisons with existing potential methods show that the proposed potential is very reliable and accurate in RNA 3D structure evaluation. Project supported by the National Science Foundation of China (Grants Nos. 11605125, 11105054, 11274124, and 11401448).

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

    International Nuclear Information System (INIS)

    Amusia, M.Y.; Dolmatov, V.K.

    1995-01-01

    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

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

    Directory of Open Access Journals (Sweden)

    Elisee Ilunga-Mbuyamba

    2016-04-01

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

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

    International Nuclear Information System (INIS)

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

    2010-01-01

    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

  17. Human stem cell based corneal tissue mimicking structures using laser-assisted 3D bioprinting and functional bioinks.

    Science.gov (United States)

    Sorkio, Anni; Koch, Lothar; Koivusalo, Laura; Deiwick, Andrea; Miettinen, Susanna; Chichkov, Boris; Skottman, Heli

    2018-07-01

    There is a high demand for developing methods to produce more native-like 3D corneal structures. In the present study, we produced 3D cornea-mimicking tissues using human stem cells and laser-assisted bioprinting (LaBP). Human embryonic stem cell derived limbal epithelial stem cells (hESC-LESC) were used as a cell source for printing epithelium-mimicking structures, whereas human adipose tissue derived stem cells (hASCs) were used for constructing layered stroma-mimicking structures. The development and optimization of functional bioinks was a crucial step towards successful bioprinting of 3D corneal structures. Recombinant human laminin and human sourced collagen I served as the bases for the functional bioinks. We used two previously established LaBP setups based on laser induced forward transfer, with different laser wavelengths and appropriate absorption layers. We bioprinted three types of corneal structures: stratified corneal epithelium using hESC-LESCs, lamellar corneal stroma using alternating acellular layers of bioink and layers with hASCs, and finally structures with both a stromal and epithelial part. The printed constructs were evaluated for their microstructure, cell viability and proliferation, and key protein expression (Ki67, p63α, p40, CK3, CK15, collagen type I, VWF). The 3D printed stromal constructs were also implanted into porcine corneal organ cultures. Both cell types maintained good viability after printing. Laser-printed hESC-LESCs showed epithelial cell morphology, expression of Ki67 proliferation marker and co-expression of corneal progenitor markers p63α and p40. Importantly, the printed hESC-LESCs formed a stratified epithelium with apical expression of CK3 and basal expression of the progenitor markers. The structure of the 3D bioprinted stroma demonstrated that the hASCs had organized horizontally as in the native corneal stroma and showed positive labeling for collagen I. After 7 days in porcine organ cultures, the 3D bioprinted

  18. Finding and tracing human MSC in 3D microenvironments with the photoconvertible protein Dendra2

    Science.gov (United States)

    Caires, Hugo R.; Gomez-Lazaro, Maria; Oliveira, Carla M.; Gomes, David; Mateus, Denisa D.; Oliveira, Carla; Barrias, Cristina C.; Barbosa, Mário A.; Almeida, Catarina R.

    2015-05-01

    Mesenchymal Stem/Stromal Cells (MSC) are a promising cell type for cell-based therapies - from tissue regeneration to treatment of autoimmune diseases - due to their capacity to migrate to damaged tissues, to differentiate in different lineages and to their immunomodulatory and paracrine properties. Here, a simple and reliable imaging technique was developed to study MSC dynamical behavior in natural and bioengineered 3D matrices. Human MSC were transfected to express a fluorescent photoswitchable protein, Dendra2, which was used to highlight and follow the same group of cells for more than seven days, even if removed from the microscope to the incubator. This strategy provided reliable tracking in 3D microenvironments with different properties, including the hydrogels Matrigel and alginate as well as chitosan porous scaffolds. Comparison of cells mobility within matrices with tuned physicochemical properties revealed that MSC embedded in Matrigel migrated 64% more with 5.2 mg protein/mL than with 9.6 mg/mL and that MSC embedded in RGD-alginate migrated 51% faster with 1% polymer concentration than in 2% RGD-alginate. This platform thus provides a straightforward approach to characterize MSC dynamics in 3D and has applications in the field of stem cell biology and for the development of biomaterials for tissue regeneration.

  19. 3DSwap: Curated knowledgebase of proteins involved in 3D domain swapping

    KAUST Repository

    Shameer, Khader; Shingate, Prashant N.; Manjunath, S. C. P.; Karthika, M.; Pugalenthi, Ganesan; Sowdhamini, Ramanathan

    2011-01-01

    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

  20. Rapid fabrication of 2D and 3D photonic crystals and their inversed structures

    International Nuclear Information System (INIS)

    Huang, C-K; Chan, C-H; Chen, C-Y; Tsai, Y-L; Chen, C-C; Han, J-L; Hsieh, K-H

    2007-01-01

    In this paper a new technique is proposed for the fabrication of two-dimensional (2D) and three-dimensional (3D) photonic crystals using monodisperse polystyrene microspheres as the templates. In addition, the approaches toward the creation of their corresponding inversed structures are described. The inversed structures were prepared by subjecting an introduced silica source to a sol-gel process; programmed heating was then performed to remove the template without spoiling the inversed structures. Utilizing these approaches, 2D and 3D photonic crystals and their highly ordered inversed hexagonal multilayer or monolayer structures were obtained on the substrate

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

    Science.gov (United States)

    Warmuth, Franziska; Körner, Carolin

    2015-12-02

    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.

  2. The study on evaluation method for primary stress of 3-D structure

    International Nuclear Information System (INIS)

    Sadahiro, Daisuke; Shibamoto, Hiroshi; Nagashima, Hideaki; Inoue, Kazuhiko; Kasahara, Naoto

    2005-01-01

    This paper describes an evaluation method of primary stress in 3-D structures. In 'Design by Analysis' for nuclear components, the stresses in structures are classified into the primary and the secondary stresses. The primary stress in axisymmetric structures can be evaluated by linearization of stress distribution in the specified section, but it is difficult to define the evaluation section in the 3-D structures, and to evaluate the primary stress with the conventional procedure. From this reason, the alternative evaluation method is needed. In this paper, the evaluation method of primary stress in 3-D structures is presented utilizing the feature of primary stress that is independent from stress re-distribution. (author)

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Chen Si

    2015-06-01

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

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

    Science.gov (United States)

    Montes-Grajales, Diana; Olivero-Verbel, Jesus

    2015-01-02

    Endocrine disrupting chemicals (EDCs) are a group of compounds that affect the endocrine system, frequently found in everyday products and epidemiologically associated with several diseases. The purpose of this work was to develop EDCs DataBank, the only database of EDCs with three-dimensional structures. This database was built on MySQL using the EU list of potential endocrine disruptors and TEDX list. It contains the three-dimensional structures available on PubChem, as well as a wide variety of information from different databases and text mining tools, useful for almost any kind of research regarding EDCs. The web platform was developed employing HTML, CSS and PHP languages, with dynamic contents in a graphic environment, facilitating information analysis. Currently EDCs DataBank has 615 molecules, including pesticides, natural and industrial products, cosmetics, drugs and food additives, among other low molecular weight xenobiotics. Therefore, this database can be used to study the toxicological effects of these molecules, or to develop pharmaceuticals targeting hormone receptors, through docking studies, high-throughput virtual screening and ligand-protein interaction analysis. EDCs DataBank is totally user-friendly and the 3D-structures of the molecules can be downloaded in several formats. This database is freely available at http://edcs.unicartagena.edu.co. Copyright © 2014. Published by Elsevier Ireland Ltd.

  6. 3D-printing and mechanics of bio-inspired articulated and multi-material structures.

    Science.gov (United States)

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

    2017-09-01

    3D-printing technologies allow researchers to build simplified physical models of complex biological systems to more easily investigate their mechanics. In recent years, a number of 3D-printed structures inspired by the dermal armors of various fishes have been developed to study their multiple mechanical functionalities, including flexible protection, improved hydrodynamics, body support, or tail prehensility. Natural fish armors are generally classified according to their shape, material and structural properties as elasmoid scales, ganoid scales, placoid scales, carapace scutes, or bony plates. Each type of dermal armor forms distinct articulation patterns that facilitate different functional advantages. In this paper, we highlight recent studies that developed 3D-printed structures not only to inform the design and application of some articulated and multi-material structures, but also to explain the mechanics of the natural biological systems they mimic. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2016-04-01

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

  8. 3D observation of the solidified structures by x-ray micro computerized tomography

    International Nuclear Information System (INIS)

    Yasuda, Hideyuki; Ohnaka, Itsuo; Tsuchiyama, Akira; Nakano, Tsukasa; Uesugi, Kentaro

    2003-01-01

    The high flux density of the monochromatized and well-collimated X-ray and the high-resolution detector provide a new 3D observation tool for microstructures of metallic alloys and ceramics. The X-ray micro computerized tomography in BL47XU of SPring-8 (SP-μCT) was applied to observe microstructures produced through the eutectic reaction for Sn-based alloys and an Al 2 O 3 -Y 2 O 3 oxide system. The constituent phases in the eutectic structures were three-dimensionally identified, in which the lamellar spacing ranged from several to 10 μm. Since the 3D structure of the unidirectionally solidified specimens contains history of the eutectic structure formation, the 3D structure obtained by SP-μCT gives useful information to consider the microstructure evolution. (author)

  9. 3-D seismic velocity and attenuation structures in the geothermal field

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-09-09

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

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

    Science.gov (United States)

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

    2016-04-01

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

  11. A 3D Photothermal Structure toward Improved Energy Efficiency in Solar Steam Generation

    KAUST Repository

    Shi, Yusuf

    2018-04-18

    Summary The energy efficiency in solar steam generation by 2D photothermal materials has approached its limit. In this work, we fabricated 3D cylindrical cup-shaped structures of mixed metal oxide as solar evaporator, and the 3D structure led to a high energy efficiency close to 100% under one-sun illumination due to the capability of the cup wall to recover the diffuse reflectance and thermal radiation heat loss from the 2D cup bottom. Additional heat was gained from the ambient air when the 3D structure was exposed under one-sun illumination, leading to an extremely high steam generation rate of 2.04 kg m−2 h−1. The 3D structure has a high thermal stability and shows great promise in practical applications including domestic wastewater volume reduction and seawater desalination. The results of this work inspire further research efforts to use 3D photothermal structures to break through the energy efficiency limit of 2D photothermal materials.

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

    DEFF Research Database (Denmark)

    Ochmann, Sebastian; Vock, Richard; Wessel, Raoul

    2013-01-01

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

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

    Science.gov (United States)

    Fantino, Erika; Chiappone, Annalisa; Calignano, Flaviana; Fontana, Marco; Pirri, Fabrizio; Roppolo, Ignazio

    2016-01-01

    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. PMID:28773716

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

    Directory of Open Access Journals (Sweden)

    Erika Fantino

    2016-07-01

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

  15. One-Step Solvent Evaporation-Assisted 3D Printing of Piezoelectric PVDF Nanocomposite Structures.

    Science.gov (United States)

    Bodkhe, Sampada; Turcot, Gabrielle; Gosselin, Frederick P; Therriault, Daniel

    2017-06-21

    Development of a 3D printable material system possessing inherent piezoelectric properties to fabricate integrable sensors in a single-step printing process without poling is of importance to the creation of a wide variety of smart structures. Here, we study the effect of addition of barium titanate nanoparticles in nucleating piezoelectric β-polymorph in 3D printable polyvinylidene fluoride (PVDF) and fabrication of the layer-by-layer and self-supporting piezoelectric structures on a micro- to millimeter scale by solvent evaporation-assisted 3D printing at room temperature. The nanocomposite formulation obtained after a comprehensive investigation of composition and processing techniques possesses a piezoelectric coefficient, d 31 , of 18 pC N -1 , which is comparable to that of typical poled and stretched commercial PVDF film sensors. A 3D contact sensor that generates up to 4 V upon gentle finger taps demonstrates the efficacy of the fabrication technique. Our one-step 3D printing of piezoelectric nanocomposites can form ready-to-use, complex-shaped, flexible, and lightweight piezoelectric devices. When combined with other 3D printable materials, they could serve as stand-alone or embedded sensors in aerospace, biomedicine, and robotic applications.

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

    Directory of Open Access Journals (Sweden)

    Zhu Ji-Hong

    2016-01-01

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

  17. Automated 3D-Printed Unibody Immunoarray for Chemiluminescence Detection of Cancer Biomarker Proteins

    Science.gov (United States)

    Tang, C. K.; Vaze, A.; Rusling, J. F.

    2017-01-01

    A low cost three-dimensional (3D) printed clear plastic microfluidic device was fabricated for fast, low cost automated protein detection. The unibody device features three reagent reservoirs, an efficient 3D network for passive mixing, and an optically transparent detection chamber housing a glass capture antibody array for measuring chemiluminescence output with a CCD camera. Sandwich type assays were built onto the glass arrays using a multi-labeled detection antibody-polyHRP (HRP = horseradish peroxidase). Total assay time was ~30 min in a complete automated assay employing a programmable syringe pump so that the protocol required minimal operator intervention. The device was used for multiplexed detection of prostate cancer biomarker proteins prostate specific antigen (PSA) and platelet factor 4 (PF-4). Detection limits of 0.5 pg mL−1 were achieved for these proteins in diluted serum with log dynamic ranges of four orders of magnitude. Good accuracy vs ELISA was validated by analyzing human serum samples. This prototype device holds good promise for further development as a point-of-care cancer diagnostics tool. PMID:28067370

  18. 3D micro-structures by piezoelectric inkjet printing of gold nanofluids

    KAUST Repository

    Kullmann, Carmen; Schirmer, Niklas C; Lee, Ming-Tsang; Ko, Seung Hwan; Hotz, Nico; Grigoropoulos, Costas P; Poulikakos, Dimos

    2012-01-01

    -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

  19. Formation of coherent structures in a class of realistic 3D unsteady flows

    NARCIS (Netherlands)

    Speetjens, M.F.M.; Clercx, H.J.H.; Klapp, J.; Medina, A.; Cros, A.; Vargas, C.

    2013-01-01

    The formation of coherent structures in three-dimensional (3D) unsteady laminar flows in a cylindrical cavity is reviewed. The discussion concentrates on two main topics: the role of symmetries and fluid inertia in the formation of coherent structures and the ramifications for the Lagrangian

  20. 3D OCT imaging in clinical settings: toward quantitative measurements of retinal structures

    Science.gov (United States)

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

    2006-02-01

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

  1. 3D Biomimetic Magnetic Structures for Static Magnetic Field Stimulation of Osteogenesis

    Directory of Open Access Journals (Sweden)

    Irina Alexandra Paun

    2018-02-01

    Full Text Available We designed, fabricated and optimized 3D biomimetic magnetic structures that stimulate the osteogenesis in static magnetic fields. The structures were fabricated by direct laser writing via two-photon polymerization of IP-L780 photopolymer and were based on ellipsoidal, hexagonal units organized in a multilayered architecture. The magnetic activity of the structures was assured by coating with a thin layer of collagen-chitosan-hydroxyapatite-magnetic nanoparticles composite. In vitro experiments using MG-63 osteoblast-like cells for 3D structures with gradients of pore size helped us to find an optimum pore size between 20–40 µm. Starting from optimized 3D structures, we evaluated both qualitatively and quantitatively the effects of static magnetic fields of up to 250 mT on cell proliferation and differentiation, by ALP (alkaline phosphatase production, Alizarin Red and osteocalcin secretion measurements. We demonstrated that the synergic effect of 3D structure optimization and static magnetic stimulation enhances the bone regeneration by a factor greater than 2 as compared with the same structure in the absence of a magnetic field.

  2. 3D Biomimetic Magnetic Structures for Static Magnetic Field Stimulation of Osteogenesis.

    Science.gov (United States)

    Paun, Irina Alexandra; Popescu, Roxana Cristina; Calin, Bogdan Stefanita; Mustaciosu, Cosmin Catalin; Dinescu, Maria; Luculescu, Catalin Romeo

    2018-02-07

    We designed, fabricated and optimized 3D biomimetic magnetic structures that stimulate the osteogenesis in static magnetic fields. The structures were fabricated by direct laser writing via two-photon polymerization of IP-L780 photopolymer and were based on ellipsoidal, hexagonal units organized in a multilayered architecture. The magnetic activity of the structures was assured by coating with a thin layer of collagen-chitosan-hydroxyapatite-magnetic nanoparticles composite. In vitro experiments using MG-63 osteoblast-like cells for 3D structures with gradients of pore size helped us to find an optimum pore size between 20-40 µm. Starting from optimized 3D structures, we evaluated both qualitatively and quantitatively the effects of static magnetic fields of up to 250 mT on cell proliferation and differentiation, by ALP (alkaline phosphatase) production, Alizarin Red and osteocalcin secretion measurements. We demonstrated that the synergic effect of 3D structure optimization and static magnetic stimulation enhances the bone regeneration by a factor greater than 2 as compared with the same structure in the absence of a magnetic field.

  3. BranchAnalysis2D/3D automates morphometry analyses of branching structures.

    Science.gov (United States)

    Srinivasan, Aditya; Muñoz-Estrada, Jesús; Bourgeois, Justin R; Nalwalk, Julia W; Pumiglia, Kevin M; Sheen, Volney L; Ferland, Russell J

    2018-01-15

    Morphometric analyses of biological features have become increasingly common in recent years with such analyses being subject to a large degree of observer bias, variability, and time consumption. While commercial software packages exist to perform these analyses, they are expensive, require extensive user training, and are usually dependent on the observer tracing the morphology. To address these issues, we have developed a broadly applicable, no-cost ImageJ plugin we call 'BranchAnalysis2D/3D', to perform morphometric analyses of structures with branching morphologies, such as neuronal dendritic spines, vascular morphology, and primary cilia. Our BranchAnalysis2D/3D algorithm allows for rapid quantification of the length and thickness of branching morphologies, independent of user tracing, in both 2D and 3D data sets. We validated the performance of BranchAnalysis2D/3D against pre-existing software packages using trained human observers and images from brain and retina. We found that the BranchAnalysis2D/3D algorithm outputs results similar to available software (i.e., Metamorph, AngioTool, Neurolucida), while allowing faster analysis times and unbiased quantification. BranchAnalysis2D/3D allows inexperienced observers to output results like a trained observer but more efficiently, thereby increasing the consistency, speed, and reliability of morphometric analyses. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Geometric Structure of 3D Spinal Curves: Plane Regions and Connecting Zones

    Science.gov (United States)

    Berthonnaud, E.; Hilmi, R.; Dimnet, J.

    2012-01-01

    This paper presents a new study of the geometric structure of 3D spinal curves. The spine is considered as an heterogeneous beam, compound of vertebrae and intervertebral discs. The spine is modeled as a deformable wire along which vertebrae are beads rotating about the wire. 3D spinal curves are compound of plane regions connected together by zones of transition. The 3D spinal curve is uniquely flexed along the plane regions. The angular offsets between adjacent regions are concentrated at level of the middle zones of transition, so illustrating the heterogeneity of the spinal geometric structure. The plane regions along the 3D spinal curve must satisfy two criteria: (i) a criterion of minimum distance between the curve and the regional plane and (ii) a criterion controlling that the curve is continuously plane at the level of the region. The geometric structure of each 3D spinal curve is characterized by the sizes and orientations of regional planes, by the parameters representing flexed regions and by the sizes and functions of zones of transition. Spinal curves of asymptomatic subjects show three plane regions corresponding to spinal curvatures: lumbar, thoracic and cervical curvatures. In some scoliotic spines, four plane regions may be detected. PMID:25031873

  5. VP-Nets : Efficient automatic localization of key brain structures in 3D fetal neurosonography.

    Science.gov (United States)

    Huang, Ruobing; Xie, Weidi; Alison Noble, J

    2018-04-23

    Three-dimensional (3D) fetal neurosonography is used clinically to detect cerebral abnormalities and to assess growth in the developing brain. However, manual identification of key brain structures in 3D ultrasound images requires expertise to perform and even then is tedious. Inspired by how sonographers view and interact with volumes during real-time clinical scanning, we propose an efficient automatic method to simultaneously localize multiple brain structures in 3D fetal neurosonography. The proposed View-based Projection Networks (VP-Nets), uses three view-based Convolutional Neural Networks (CNNs), to simplify 3D localizations by directly predicting 2D projections of the key structures onto three anatomical views. While designed for efficient use of data and GPU memory, the proposed VP-Nets allows for full-resolution 3D prediction. We investigated parameters that influence the performance of VP-Nets, e.g. depth and number of feature channels. Moreover, we demonstrate that the model can pinpoint the structure in 3D space by visualizing the trained VP-Nets, despite only 2D supervision being provided for a single stream during training. For comparison, we implemented two other baseline solutions based on Random Forest and 3D U-Nets. In the reported experiments, VP-Nets consistently outperformed other methods on localization. To test the importance of loss function, two identical models are trained with binary corss-entropy and dice coefficient loss respectively. Our best VP-Net model achieved prediction center deviation: 1.8 ± 1.4 mm, size difference: 1.9 ± 1.5 mm, and 3D Intersection Over Union (IOU): 63.2 ± 14.7% when compared to the ground truth. To make the whole pipeline intervention free, we also implement a skull-stripping tool using 3D CNN, which achieves high segmentation accuracy. As a result, the proposed processing pipeline takes a raw ultrasound brain image as input, and output a skull-stripped image with five detected key brain

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    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...... 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...

  7. Streamlining the Process of 3D Printing a Brain From a Structural MRI

    Directory of Open Access Journals (Sweden)

    Daniel Peterson

    2017-05-01

    Full Text Available Currently, the process of obtaining a 3D model from a structural MRI requires specialized knowlege and skills. This is not due to the fundamental difficulty and complexity of the process, but is a result of the fact that the neccessary tools were developed for and by neuroimaging researchers. This project describes a publically available utility implemented as a Docker image that takes a structural MRI as input, and gives files for 3D printing as output, along with a rendered image of the surface.

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

    DEFF Research Database (Denmark)

    Nikolov, Ivan Adriyanov; Madsen, Claus B.

    2016-01-01

    Structure from Motion 3D reconstruction has become widely used in recent years in a number of fields such as industrial surface in- inspection, archeology, cultural heritage preservation and geomapping. A number of software solutions have been released using variations of this technique. In this ......Structure from Motion 3D reconstruction has become widely used in recent years in a number of fields such as industrial surface in- inspection, archeology, cultural heritage preservation and geomapping. A number of software solutions have been released using variations of this technique...

  9. Integration of High-Resolution Laser Displacement Sensors and 3D Printing for Structural Health Monitoring

    Directory of Open Access Journals (Sweden)

    Shu-Wei Chang

    2017-12-01

    Full Text Available This paper presents a novel experimental design for complex structural health monitoring (SHM studies achieved by integrating 3D printing technologies, high-resolution laser displacement sensors, and multiscale entropy SHM theory. A seven-story structure with a variety of composite bracing systems was constructed using a dual-material 3D printer. A wireless Bluetooth vibration speaker was used to excite the ground floor of the structure, and high-resolution laser displacement sensors (1-μm resolution were used to monitor the displacement history on different floors. Our results showed that the multiscale entropy SHM method could detect damage on the 3D-printed structures. The results of this study demonstrate that integrating 3D printing technologies and high-resolution laser displacement sensors enables the design of cheap, fast processing, complex, small-scale civil structures for future SHM studies. The novel experimental design proposed in this study provides a suitable platform for investigating the validity and sensitivity of SHM in different composite structures and damage conditions for real life applications in the future.

  10. Integration of High-Resolution Laser Displacement Sensors and 3D Printing for Structural Health Monitoring.

    Science.gov (United States)

    Chang, Shu-Wei; Lin, Tzu-Kang; Kuo, Shih-Yu; Huang, Ting-Hsuan

    2017-12-22

    This paper presents a novel experimental design for complex structural health monitoring (SHM) studies achieved by integrating 3D printing technologies, high-resolution laser displacement sensors, and multiscale entropy SHM theory. A seven-story structure with a variety of composite bracing systems was constructed using a dual-material 3D printer. A wireless Bluetooth vibration speaker was used to excite the ground floor of the structure, and high-resolution laser displacement sensors (1-μm resolution) were used to monitor the displacement history on different floors. Our results showed that the multiscale entropy SHM method could detect damage on the 3D-printed structures. The results of this study demonstrate that integrating 3D printing technologies and high-resolution laser displacement sensors enables the design of cheap, fast processing, complex, small-scale civil structures for future SHM studies. The novel experimental design proposed in this study provides a suitable platform for investigating the validity and sensitivity of SHM in different composite structures and damage conditions for real life applications in the future.

  11. 3D flexible NiTi-braided elastomer composites for smart structure applications

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  12. Fabrication of 3D SiO x structures using patterned PMMA sacrificial layer

    Science.gov (United States)

    Li, Zhiqin; Xiang, Quan; Zheng, Mengjie; Bi, Kaixi; Chen, Yiqin; Chen, Keqiu; Duan, Huigao

    2018-02-01

    Three-dimensional (3D) nanofabrication based on electron-beam lithography (EBL) has drawn wide attention for various applications with its high patterning resolution and design flexibility. In this work, we present a bilayer EBL process to obtain 3D freestanding SiO x structures via the release of the bottom sacrificial layer. This new kind of bilayer process enables us to define various 3D freestanding SiO x structures with high resolution and low edge roughness. As a proof of concept for applications, metal-coated freestanding SiO x microplates with an underlying air gap were fabricated to form asymmetric Fabry-Perot resonators, which can be utilized for colorimetric refractive index sensing and thus also have application potential for biochemical detection, anti-counterfeiting and smart active nano-optical devices.

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

    Science.gov (United States)

    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.

  14. Estimation of the 3D positioning of anatomic structures from radiographic projection and volume knowledge

    Energy Technology Data Exchange (ETDEWEB)

    Bifulco, P; Cesarelli, M; Roccasalva Firenze, M; Verso, E; Sansone, M; Bracale, M [University of Naples, Federico II, Electronic Engineering Department, Bioengineering Unit, Via Claudio, 21 - 80125 Naples (Italy)

    1999-12-31

    The aim of this study is to develop a method to estimate the 3D positioning of an anatomic structure using the knowledge of its volume (provided by CT or MRI) combined with a single radiographic projection. This method could be applied in stereotactic surgery or in the study of 3D body joints kinematics. The knowledge of the 3D anatomical structure, available from CT (or in future MRI) is used to estimate the orientation of the projection that better match the actual 2D available projection. For this purpose it was necessary to develop an algorithm to simulate the radiographic projections. The radiographic image formation process has been simulated utilizing the geometrical characteristics of a real radiographic device and the volumetric anatomical data of the patient, obtained by 3D diagnostic CT images. The position of the patient volume respect to the radiological device is estimated comparing the actual radiographic projection with those simulated, maximising a similarity index. To assess the estimation, the 3D positioning of a segmented vertebra has been used as a test volume. The assessment has been carried out only by means of simulation. Estimation errors have been statistically evaluated. Conditions of mispositioning and noise have been also considered. The results relative to the simulation show the feasibility of the method. From the analysis of the errors emerges that the searching procedure results robust respect to the addition of white Gaussian noise. (authors) 13 fers., 4 figs., 1 tabs.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kramar, Maxim [Physics Department, The Catholic University of America, Washington, DC (United States); Airapetian, Vladimir [Department of Physics and Astronomy, George Mason University, Fairfax, VA (United States); NASA/Goddard Space Flight Center, Code 671, Greenbelt, MD (United States); Lin, Haosheng, E-mail: vladimir.airapetian@nasa.gov [College of Natural Sciences, Institute for Astronomy, University of Hawaii at Manoa, Pukalani, HI (United States)

    2016-08-09

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

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

    Directory of Open Access Journals (Sweden)

    Maxim Kramar

    2016-08-01

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

  17. Estimation of the 3D positioning of anatomic structures from radiographic projection and volume knowledge

    International Nuclear Information System (INIS)

    Bifulco, P.; Cesarelli, M.; Roccasalva Firenze, M.; Verso, E.; Sansone, M.; Bracale, M.

    1998-01-01

    The aim of this study is to develop a method to estimate the 3D positioning of an anatomic structure using the knowledge of its volume (provided by CT or MRI) combined with a single radiographic projection. This method could be applied in stereotactic surgery or in the study of 3D body joints kinematics. The knowledge of the 3D anatomical structure, available from CT (or in future MRI) is used to estimate the orientation of the projection that better match the actual 2D available projection. For this purpose it was necessary to develop an algorithm to simulate the radiographic projections. The radiographic image formation process has been simulated utilizing the geometrical characteristics of a real radiographic device and the volumetric anatomical data of the patient, obtained by 3D diagnostic CT images. The position of the patient volume respect to the radiological device is estimated comparing the actual radiographic projection with those simulated, maximising a similarity index. To assess the estimation, the 3D positioning of a segmented vertebra has been used as a test volume. The assessment has been carried out only by means of simulation. Estimation errors have been statistically evaluated. Conditions of mispositioning and noise have been also considered. The results relative to the simulation show the feasibility of the method. From the analysis of the errors emerges that the searching procedure results robust respect to the addition of white Gaussian noise. (authors)

  18. Large-scale Comparative Study of Hi-C-based Chromatin 3D Structure Modeling Methods

    KAUST Repository

    Wang, Cheng

    2018-05-17

    Chromatin is a complex polymer molecule in eukaryotic cells, primarily consisting of DNA and histones. Many works have shown that the 3D folding of chromatin structure plays an important role in DNA expression. The recently proposed Chro- mosome Conformation Capture technologies, especially the Hi-C assays, provide us an opportunity to study how the 3D structures of the chromatin are organized. Based on the data from Hi-C experiments, many chromatin 3D structure modeling methods have been proposed. However, there is limited ground truth to validate these methods and no robust chromatin structure alignment algorithms to evaluate the performance of these methods. In our work, we first made a thorough literature review of 25 publicly available population Hi-C-based chromatin 3D structure modeling methods. Furthermore, to evaluate and to compare the performance of these methods, we proposed a novel data simulation method, which combined the population Hi-C data and single-cell Hi-C data without ad hoc parameters. Also, we designed a global and a local alignment algorithms to measure the similarity between the templates and the chromatin struc- tures predicted by different modeling methods. Finally, the results from large-scale comparative tests indicated that our alignment algorithms significantly outperform the algorithms in literature.

  19. Generating Free-Form Grid Truss Structures from 3D Scanned Point Clouds

    Directory of Open Access Journals (Sweden)

    Hui Ding

    2017-01-01

    Full Text Available Reconstruction, according to physical shape, is a novel way to generate free-form grid truss structures. 3D scanning is an effective means of acquiring physical form information and it generates dense point clouds on surfaces of objects. However, generating grid truss structures from point clouds is still a challenge. Based on the advancing front technique (AFT which is widely used in Finite Element Method (FEM, a scheme for generating grid truss structures from 3D scanned point clouds is proposed in this paper. Based on the characteristics of point cloud data, the search box is adopted to reduce the search space in grid generating. A front advancing procedure suit for point clouds is established. Delaunay method and Laplacian method are used to improve the quality of the generated grids, and an adjustment strategy that locates grid nodes at appointed places is proposed. Several examples of generating grid truss structures from 3D scanned point clouds of seashells are carried out to verify the proposed scheme. Physical models of the grid truss structures generated in the examples are manufactured by 3D print, which solidifies the feasibility of the scheme.

  20. Fabrication of Gold-coated 3-D Woodpile Structures for Mid-IR Thermal Emitters

    Science.gov (United States)

    Li, Shengkai; Moridani, Amir; Kothari, Rohit; Lee, Jae-Hwang; Watkins, James

    3-D metallic woodpile nanostructures possess enhancements in thermal radiation that are both wavelength and polarization specific and are promising for thermal-optical devices for various applications including thermal photovoltaics, self-cooling devices, and chemical and bio-sensors. However, current fabrication techniques for such structures are limited by slow speed, small area capability, the need for expensive facilities and, in general, are not suitable for high-throughput mass production. Here we demonstrate a new strategy for the fabrication of 3D metallic woodpile structures. Well-defined TiO2 woodpile structures were fabricated using a layer-by-layer nanoimprint method using TiO2 nanoparticle ink dispersions. The TiO2 woodpile was then coated with a high purity, conformal gold film via reactive deposition in supercritical carbon dioxide. The final gold-coated woodpile structures exhibit strong spectral and polarization specific thermal emission enhancements. The fabrication method demonstrated here is promising for high-throughput, low-cost preparation of 3D metallic woodpile structures and other 3D nanostructures. Center for Hierarchical Manufacturing, NSF.

  1. SEGMENTATION OF 3D MODELS FOR CULTURAL HERITAGE STRUCTURAL ANALYSIS – SOME CRITICAL ISSUES

    Directory of Open Access Journals (Sweden)

    S. Gonizzi Barsanti

    2017-08-01

    Full Text Available Cultural Heritage documentation and preservation has become a fundamental concern in this historical period. 3D modelling offers a perfect aid to record ancient buildings and artefacts and can be used as a valid starting point for restoration, conservation and structural analysis, which can be performed by using Finite Element Methods (FEA. The models derived from reality-based techniques, made up of the exterior surfaces of the objects captured at high resolution, are - for this reason - made of millions of polygons. Such meshes are not directly usable in structural analysis packages and need to be properly pre-processed in order to be transformed in volumetric meshes suitable for FEA. In addition, dealing with ancient objects, a proper segmentation of 3D volumetric models is needed to analyse the behaviour of the structure with the most suitable level of detail for the different sections of the structure under analysis. Segmentation of 3D models is still an open issue, especially when dealing with ancient, complicated and geometrically complex objects that imply the presence of anomalies and gaps, due to environmental agents such as earthquakes, pollution, wind and rain, or human factors. The aims of this paper is to critically analyse some of the different methodologies and algorithms available to segment a 3D point cloud or a mesh, identifying difficulties and problems by showing examples on different structures.

  2. Segmentation of 3d Models for Cultural Heritage Structural Analysis - Some Critical Issues

    Science.gov (United States)

    Gonizzi Barsanti, S.; Guidi, G.; De Luca, L.

    2017-08-01

    Cultural Heritage documentation and preservation has become a fundamental concern in this historical period. 3D modelling offers a perfect aid to record ancient buildings and artefacts and can be used as a valid starting point for restoration, conservation and structural analysis, which can be performed by using Finite Element Methods (FEA). The models derived from reality-based techniques, made up of the exterior surfaces of the objects captured at high resolution, are - for this reason - made of millions of polygons. Such meshes are not directly usable in structural analysis packages and need to be properly pre-processed in order to be transformed in volumetric meshes suitable for FEA. In addition, dealing with ancient objects, a proper segmentation of 3D volumetric models is needed to analyse the behaviour of the structure with the most suitable level of detail for the different sections of the structure under analysis. Segmentation of 3D models is still an open issue, especially when dealing with ancient, complicated and geometrically complex objects that imply the presence of anomalies and gaps, due to environmental agents such as earthquakes, pollution, wind and rain, or human factors. The aims of this paper is to critically analyse some of the different methodologies and algorithms available to segment a 3D point cloud or a mesh, identifying difficulties and problems by showing examples on different structures.

  3. Experimental validation of 3D printed material behaviors and their influence on the structural topology design

    Science.gov (United States)

    Yang, Kai Ke; Zhu, Ji Hong; Wang, Chuang; Jia, Dong Sheng; Song, Long Long; Zhang, Wei Hong

    2018-05-01

    The purpose of this paper is to investigate the structures achieved by topology optimization and their fabrications by 3D printing considering the particular features of material microstructures and macro mechanical performances. Combining Digital Image Correlation and Optical Microscope, this paper experimentally explored the anisotropies of stiffness and strength existing in the 3D printed polymer material using Stereolithography (SLA) and titanium material using Selective Laser Melting (SLM). The standard specimens and typical structures obtained by topology optimization were fabricated along different building directions. On the one hand, the experimental results of these SLA produced structures showed stable properties and obviously anisotropic rules in stiffness, ultimate strengths and places of fractures. Further structural designs were performed using topology optimization when the particular mechanical behaviors of SLA printed materials were considered, which resulted in better structural performances compared to the optimized designs using `ideal' isotropic material model. On the other hand, this paper tested the mechanical behaviors of SLM printed multiscale lattice structures which were fabricated using the same metal powder and the same machine. The structural stiffness values are generally similar while the strength behaviors show a difference, which are mainly due to the irregular surface quality of the tiny structural branches of the lattice. The above evidences clearly show that the consideration of the particular behaviors of 3D printed materials is therefore indispensable for structural design and optimization in order to improve the structural performance and strengthen their practical significance.

  4. Experimental validation of 3D printed material behaviors and their influence on the structural topology design

    Science.gov (United States)

    Yang, Kai Ke; Zhu, Ji Hong; Wang, Chuang; Jia, Dong Sheng; Song, Long Long; Zhang, Wei Hong

    2018-02-01

    The purpose of this paper is to investigate the structures achieved by topology optimization and their fabrications by 3D printing considering the particular features of material microstructures and macro mechanical performances. Combining Digital Image Correlation and Optical Microscope, this paper experimentally explored the anisotropies of stiffness and strength existing in the 3D printed polymer material using Stereolithography (SLA) and titanium material using Selective Laser Melting (SLM). The standard specimens and typical structures obtained by topology optimization were fabricated along different building directions. On the one hand, the experimental results of these SLA produced structures showed stable properties and obviously anisotropic rules in stiffness, ultimate strengths and places of fractures. Further structural designs were performed using topology optimization when the particular mechanical behaviors of SLA printed materials were considered, which resulted in better structural performances compared to the optimized designs using `ideal' isotropic material model. On the other hand, this paper tested the mechanical behaviors of SLM printed multiscale lattice structures which were fabricated using the same metal powder and the same machine. The structural stiffness values are generally similar while the strength behaviors show a difference, which are mainly due to the irregular surface quality of the tiny structural branches of the lattice. The above evidences clearly show that the consideration of the particular behaviors of 3D printed materials is therefore indispensable for structural design and optimization in order to improve the structural performance and strengthen their practical significance.

  5. 3D Biomimetic Magnetic Structures for Static Magnetic Field Stimulation of Osteogenesis

    OpenAIRE

    Irina Alexandra Paun; Roxana Cristina Popescu; Bogdan Stefanita Calin; Cosmin Catalin Mustaciosu; Maria Dinescu; Catalin Romeo Luculescu

    2018-01-01

    We designed, fabricated and optimized 3D biomimetic magnetic structures that stimulate the osteogenesis in static magnetic fields. The structures were fabricated by direct laser writing via two-photon polymerization of IP-L780 photopolymer and were based on ellipsoidal, hexagonal units organized in a multilayered architecture. The magnetic activity of the structures was assured by coating with a thin layer of collagen-chitosan-hydroxyapatite-magnetic nanoparticles composite. In vitro experime...

  6. Toward 3D structural information from quantitative electron exit wave analysis

    International Nuclear Information System (INIS)

    Borisenko, Konstantin B; Moldovan, Grigore; Kirkland, Angus I; Wang, Amy; Van Dyck, Dirk; Chen, Fu-Rong

    2012-01-01

    Simulations show that using a new direct imaging detector and accurate exit wave restoration algorithms allows nearly quantitative restoration of electron exit wave phase, which can be regarded as only qualitative for conventional indirect imaging cameras. This opens up a possibility of extracting accurate information on 3D atomic structure of the sample even from a single projection.

  7. 3D micro-structures by piezoelectric inkjet printing of gold nanofluids

    International Nuclear Information System (INIS)

    Kullmann, Carmen; Lee, Ming-Tsang; Grigoropoulos, Costas P; Schirmer, Niklas C; Poulikakos, Dimos; Ko, Seung Hwan; Hotz, Nico

    2012-01-01

    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)

  8. Mechanical performance of wall structures in 3D printing processes: theory, design tools and experiments

    NARCIS (Netherlands)

    Suiker, A.S.J.

    2018-01-01

    In the current contribution for the first time a mechanistic model is presented that can be used for analysing and optimising the mechanical performance of straight wall structures in 3D printing processes. The two failure mechanisms considered are elastic buckling and plastic collapse. The model

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

    Directory of Open Access Journals (Sweden)

    Claudia eHänel

    2014-05-01

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

  10. Outlook for NanoInside Theme "3D nano-structuring and metrology"

    NARCIS (Netherlands)

    Kruit, P.; Kroon, M.G.M. de; Maas, D.J.; Baumer, S.M.B.; Spruit, W.E.T.

    2017-01-01

    Het vakgebied van 3D nano-structurering en metrologie ontwikkelt zich razendsnel, zowel in Nederland als in de rest van de wereld. Het niveau van de Nederlandse betrokken onderzoekers, kennisinstituten en bedrijven is van wereldklasse. Veel Nederlandse academische groepen, kennisinstituten en

  11. 3D micro-structures by piezoelectric inkjet printing of gold nanofluids

    KAUST Repository

    Kullmann, Carmen

    2012-04-18

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

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  13. Morphology and characterization of 3D micro-porous structured chitosan scaffolds for tissue engineering.

    Science.gov (United States)

    Hsieh, Wen-Chuan; Chang, Chih-Pong; Lin, Shang-Ming

    2007-06-15

    This research studies the morphology and characterization of three-dimensional (3D) micro-porous structures produced from biodegradable chitosan for use as scaffolds for cells culture. The chitosan 3D micro-porous structures were produced by a simple liquid hardening method, which includes the processes of foaming by mechanical stirring without any chemical foaming agent added, and hardening by NaOH cross linking. The pore size and porosity were controlled with mechanical stirring strength. This study includes the morphology of chitosan scaffolds, the characterization of mechanical properties, water absorption properties and in vitro enzymatic degradation of the 3D micro-porous structures. The results show that chitosan 3D micro-porous structures were successfully produced. Better formation samples were obtained when chitosan concentration is at 1-3%, and concentration of NaOH is at 5%. Faster stirring rate would produce samples of smaller pore diameter, but when rotation speed reaches 4000 rpm and higher the changes in pore size is minimal. Water absorption would reduce along with the decrease of chitosan scaffolds' pore diameter. From stress-strain analysis, chitosan scaffolds' mechanical properties are improved when it has smaller pore diameter. From in vitro enzymatic degradation results, it shows that the disintegration rate of chitosan scaffolds would increase along with the processing time increase, but approaching equilibrium when the disintegration rate reaches about 20%.

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

    DEFF Research Database (Denmark)

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

    2010-01-01

    Patient motion during scanning deteriorates image quality, especially for high resolution PET scanners. A new proposal for a 3D head tracking system for motion correction in high resolution PET brain imaging is set up and demonstrated. A prototype tracking system based on structured light with a ...

  15. Predicted stability, structures, and magnetism of 3d transition metal nitrides: the M4N phases

    NARCIS (Netherlands)

    Fang, C.M.; Koster, R.S.; Li, W.F.; van Huis, M.A.

    2014-01-01

    The 3d transition metal nitrides M4N (Sc4N, Ti4N, V4N, Cr4N, Mn4N, Fe4N, Co4N, Ni4N, and Cu4N) have unique phase relationships, crystal structures, and electronic and magnetic properties. Here we present a systematic density functional theory (DFT) study on these transition metal nitrides, assessing

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

    International Nuclear Information System (INIS)

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

    2009-01-01

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

  17. A wave-bending structure at Ka-band using 3D-printed metamaterial

    Science.gov (United States)

    Wu, Junqiang; Liang, Min; Xin, Hao

    2018-03-01

    Three-dimensional printing technologies enable metamaterials of complex structures with arbitrary inhomogeneity. In this work, a 90° wave-bending structure at the Ka-band (26.5-40 GHz) based on 3D-printed metamaterials is designed, fabricated, and measured. The wave-bending effect is realized through a spatial distribution of varied effective dielectric constants. Based on the effective medium theory, different effective dielectric constants are accomplished by special, 3D-printable unit cells, which allow different ratios of dielectric to air at the unit cell level. In contrast to traditional, metallic-structure-included metamaterial designs, the reported wave-bending structure here is all dielectric and implemented by the polymer-jetting technique, which features rapid, low-cost, and convenient prototyping. Both simulation and experiment results demonstrate the effectiveness of the wave-bending structure.

  18. Comparison of two structured illumination techniques based on different 3D illumination patterns

    Science.gov (United States)

    Shabani, H.; Patwary, N.; Doblas, A.; Saavedra, G.; Preza, C.

    2017-02-01

    Manipulating the excitation pattern in optical microscopy has led to several super-resolution techniques. Among different patterns, the lateral sinusoidal excitation was used for the first demonstration of structured illumination microscopy (SIM), which provides the fastest SIM acquisition system (based on the number of raw images required) compared to the multi-spot illumination approach. Moreover, 3D patterns that include lateral and axial variations in the illumination have attracted more attention recently as they address resolution enhancement in three dimensions. A threewave (3W) interference technique based on coherent illumination has already been shown to provide super-resolution and optical sectioning in 3D-SIM. In this paper, we investigate a novel tunable technique that creates a 3D pattern from a set of multiple incoherently illuminated parallel slits that act as light sources for a Fresnel biprism. This setup is able to modulate the illumination pattern in the object space both axially and laterally with adjustable modulation frequencies. The 3D forward model for the new system is developed here to consider the effect of the axial modulation due to the 3D patterned illumination. The performance of 3D-SIM based on 3W interference and the tunable system are investigated in simulation and compared based on two different criteria. First, restored images obtained for both 3D-SIM systems using a generalized Wiener filter are compared to determine the effect of the illumination pattern on the reconstruction. Second, the effective frequency response of both systems is studied to determine the axial and lateral resolution enhancement that is obtained in each case.

  19. The Implications of 3D Thermal Structure on 1D Atmospheric Retrieval

    Energy Technology Data Exchange (ETDEWEB)

    Blecic, Jasmina; Dobbs-Dixon, Ian [NYU Abu Dhabi, Abu Dhabi (United Arab Emirates); Greene, Thomas, E-mail: jasmina@nyu.edu [NASA Ames Research Center, Space Sciece and Astrobiology Division, M.S. 245-6, Moffett Field, CA 94035 (United States)

    2017-10-20

    Using the atmospheric structure from a 3D global radiation-hydrodynamic simulation of HD 189733b and the open-source Bayesian Atmospheric Radiative Transfer (BART) code, we investigate the difference between the secondary-eclipse temperature structure produced with a 3D simulation and the best-fit 1D retrieved model. Synthetic data are generated by integrating the 3D models over the Spitzer , the Hubble Space Telescope ( HST ), and the James Web Space Telescope ( JWST ) bandpasses, covering the wavelength range between 1 and 11 μ m where most spectroscopically active species have pronounced features. Using the data from different observing instruments, we present detailed comparisons between the temperature–pressure profiles recovered by BART and those from the 3D simulations. We calculate several averages of the 3D thermal structure and explore which particular thermal profile matches the retrieved temperature structure. We implement two temperature parameterizations that are commonly used in retrieval to investigate different thermal profile shapes. To assess which part of the thermal structure is best constrained by the data, we generate contribution functions for our theoretical model and each of our retrieved models. Our conclusions are strongly affected by the spectral resolution of the instruments included, their wavelength coverage, and the number of data points combined. We also see some limitations in each of the temperature parametrizations, as they are not able to fully match the complex curvatures that are usually produced in hydrodynamic simulations. The results show that our 1D retrieval is recovering a temperature and pressure profile that most closely matches the arithmetic average of the 3D thermal structure. When we use a higher resolution, more data points, and a parametrized temperature profile that allows more flexibility in the middle part of the atmosphere, we find a better match between the retrieved temperature and pressure profile and

  20. The Implications of 3D Thermal Structure on 1D Atmospheric Retrieval

    Science.gov (United States)

    Blecic, Jasmina; Dobbs-Dixon, Ian; Greene, Thomas

    2017-10-01

    Using the atmospheric structure from a 3D global radiation-hydrodynamic simulation of HD 189733b and the open-source Bayesian Atmospheric Radiative Transfer (BART) code, we investigate the difference between the secondary-eclipse temperature structure produced with a 3D simulation and the best-fit 1D retrieved model. Synthetic data are generated by integrating the 3D models over the Spitzer, the Hubble Space Telescope (HST), and the James Web Space Telescope (JWST) bandpasses, covering the wavelength range between 1 and 11 μm where most spectroscopically active species have pronounced features. Using the data from different observing instruments, we present detailed comparisons between the temperature-pressure profiles recovered by BART and those from the 3D simulations. We calculate several averages of the 3D thermal structure and explore which particular thermal profile matches the retrieved temperature structure. We implement two temperature parameterizations that are commonly used in retrieval to investigate different thermal profile shapes. To assess which part of the thermal structure is best constrained by the data, we generate contribution functions for our theoretical model and each of our retrieved models. Our conclusions are strongly affected by the spectral resolution of the instruments included, their wavelength coverage, and the number of data points combined. We also see some limitations in each of the temperature parametrizations, as they are not able to fully match the complex curvatures that are usually produced in hydrodynamic simulations. The results show that our 1D retrieval is recovering a temperature and pressure profile that most closely matches the arithmetic average of the 3D thermal structure. When we use a higher resolution, more data points, and a parametrized temperature profile that allows more flexibility in the middle part of the atmosphere, we find a better match between the retrieved temperature and pressure profile and the

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

    Energy Technology Data Exchange (ETDEWEB)

    Richter, T.S.

    2007-12-03

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

  2. Development of 3D CFD code based on structured non-orthogonal grids

    International Nuclear Information System (INIS)

    Vaidya, Abhijeet Mohan; Maheshwari, Naresh Kumar; Rama Rao, A.

    2016-01-01

    Most of the nuclear industry problems involve complex geometries. Solution of flow and heat transfer over complex geometries is a very important requirement for designing new reactor systems. Hence development of a general purpose three dimensional (3D) CFD code is undertaken. For handling complex shape of computational domain, implementation on structured non-orthogonal coordinates is being done. The code is validated by comparing its results for 3D inclined lid driven cavity at different inclination angles and Reynolds numbers with OpenFOAM results. This paper contains formulation and validation of the new code developed. (author)

  3. Fiber Bragg grating sensor based on cantilever structure embedded in polymer 3D printed material

    Science.gov (United States)

    Lima, Rita; Tavares, R.; Silva, S. O.; Abreu, P.; Restivo, Maria T.; Frazão, O.

    2017-04-01

    A cantilever structure in 3D printed based on a fiber Bragg grating (FBG) sensor embedded in polymer material is proposed. The FBG sensor was embedded in 3D printed coating and was tested under three physical parameters: displacement, temperature and vibration. The sensor was tested in displacement in two different regions of the cantilever, namely, on its midpoint and end point. The maximum displacement sensitivity achieved was (3 +/- 0.1) pm/mm for end point displacement, and a temperature sensitivity of (30 +/- 1) pm/°C was also attained. In the case of vibration measurements it was possible to obtain a 10.23Hz-low frequency oscillation.

  4. Smart release of doxorubicin loaded on polyetheretherketone (PEEK) surface with 3D porous structure.

    Science.gov (United States)

    Ouyang, Liping; Sun, Zhenjie; Wang, Donghui; Qiao, Yuqin; Zhu, Hongqin; Ma, Xiaohan; Liu, Xuanyong

    2018-03-01

    It is important to fabricate an implant possessing environment sensitive drug delivery. In this work, the construction of 3D porous structure on polyetheretherketone (PEEK) surface and pH sensitive polymer, chitosan, was introduced. The smart release of doxorubicin can be realized on the 3D porous surface of PEEK loading chitosan. We give a feasible explanation for the effect of chitosan on smart drug release according to Henderson-Hasselbalch equation. Furthermore, the intracellular drug content of the cell cultured on the samples with highest chitosan is significantly higher at pH 4.0, whereas lower at pH 7.4 than other samples. The smart release of doxorubicin via modification with chitosan onto 3D porous PEEK surface paves the way for the application of PEEK in drug loading platform for recovering bone defect caused by malignant bone tumor. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2016-08-09

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

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

    International Nuclear Information System (INIS)

    Boukarri, Bachir

    1989-01-01

    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) [fr

  7. 3D-printing porosity: A new approach to creating elevated porosity materials and structures.

    Science.gov (United States)

    Jakus, A E; Geisendorfer, N R; Lewis, P L; Shah, R N

    2018-05-01

    We introduce a new process that enables the ability to 3D-print high porosity materials and structures by combining the newly introduced 3D-Painting process with traditional salt-leaching. The synthesis and resulting properties of three 3D-printable inks comprised of varying volume ratios (25:75, 50:50, 70:30) of CuSO 4 salt and polylactide-co-glycolide (PLGA), as well as their as-printed and salt-leached counterparts, are discussed. The resulting materials are comprised entirely of PLGA (F-PLGA), but exhibit porosities proportional to the original CuSO 4 content. The three distinct F-PLGA materials exhibit average porosities of 66.6-94.4%, elastic moduli of 112.6-2.7 MPa, and absorbency of 195.7-742.2%. Studies with adult human mesenchymal stem cells (hMSCs) demonstrated that elevated porosity substantially promotes cell adhesion, viability, and proliferation. F-PLGA can also act as carriers for weak, naturally or synthetically-derived hydrogels. Finally, we show that this process can be extended to other materials including graphene, metals, and ceramics. Porosity plays an essential role in the performance and function of biomaterials, tissue engineering, and clinical medicine. For the same material chemistry, the level of porosity can dictate if it is cell, tissue, or organ friendly; with low porosity materials being far less favorable than high porosity materials. Despite its importance, it has been difficult to create three-dimensionally printed structures that are comprised of materials that have extremely high levels of internal porosity yet are surgically friendly (able to handle and utilize during surgical operations). In this work, we extend a new materials-centric approach to 3D-printing, 3D-Painting, to 3D-printing structures made almost entirely out of water-soluble salt. The structures are then washed in a specific way that not only extracts the salt but causes the structures to increase in size. With the salt removed, the resulting medical polymer

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-01-15

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

  9. 3D printing PLA and silicone elastomer structures with sugar solution support material

    Science.gov (United States)

    Hamidi, Armita; Jain, Shrenik; Tadesse, Yonas

    2017-04-01

    3D printing technology has been used for rapid prototyping since 1980's and is still developing in a way that can be used for customized products with complex design and miniature features. Among all the available 3D printing techniques, Fused Deposition Modeling (FDM) is one of the most widely used technologies because of its capability to build different structures by employing various materials. However, complexity of parts made by FDM is greatly limited by restriction of using support materials. Support materials are often used in FDM for several complex geometries such as fully suspended shapes, overhanging surfaces and hollow features. This paper describes an approach to 3D print a structure using silicone elastomer and polylactide fiber (PLA) by employing a novel support material that is soluble in water. This support material is melted sugar which can easily be prepared at a low cost. Sugar is a carbohydrate, which is found naturally in plants such as sugarcane and sugar beets; therefore, it is completely organic and eco-friendly. As another advantage, the time for removing this material from the part is considerably less than other commercially available support materials and it can be removed easily by warm water without leaving any trace. Experiments were done using an inexpensive desktop 3D printer to fabricate complex structures for use in soft robots. The results envision that further development of this system would contribute to a method of fabrication of complex parts with lower cost yet high quality.

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

    International Nuclear Information System (INIS)

    Yang, Xiaoqing; Huang, Hong; Zhang, Guoqing; Li, Xinxi; Wu, Dingcai; Fu, Ruowen

    2015-01-01

    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 −1 for 80 cycles, much higher than the theoretical capacity of commercial graphite (372 mAh g −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 2  g −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

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

    Directory of Open Access Journals (Sweden)

    Bai Shiye

    2016-05-01

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

  12. Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity.

    Science.gov (United States)

    Lee, Karen J I; Calder, Grant M; Hindle, Christopher R; Newman, Jacob L; Robinson, Simon N; Avondo, Jerome J H Y; Coen, Enrico S

    2017-01-01

    Optical projection tomography (OPT) is a well-established method for visualising gene activity in plants and animals. However, a limitation of conventional OPT is that the specimen upper size limit precludes its application to larger structures. To address this problem we constructed a macro version called Macro OPT (M-OPT). We apply M-OPT to 3D live imaging of gene activity in growing whole plants and to visualise structural morphology in large optically cleared plant and insect specimens up to 60 mm tall and 45 mm deep. We also show how M-OPT can be used to image gene expression domains in 3D within fixed tissue and to visualise gene activity in 3D in clones of growing young whole Arabidopsis plants. A further application of M-OPT is to visualise plant-insect interactions. Thus M-OPT provides an effective 3D imaging platform that allows the study of gene activity, internal plant structures and plant-insect interactions at a macroscopic scale. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  13. Complex metrology on 3D structures using multi-channel OCD

    Science.gov (United States)

    Kagalwala, Taher; Mahendrakar, Sridhar; Vaid, Alok; Isbester, Paul K.; Cepler, Aron; Kang, Charles; Yellai, Naren; Sendelbach, Matthew; Ko, Mihael; Ilgayev, Ovadia; Katz, Yinon; Tamam, Lilach; Osherov, Ilya

    2017-03-01

    Device scaling has not only driven the use of measurements on more complex structures, in terms of geometry, materials, and tighter ground rules, but also the need to move away from non-patterned measurement sites to patterned ones. This is especially of concern for very thin film layers that have a high thickness dependence on structure geometry or wafer pattern factor. Although 2-dimensional (2D) sites are often found to be sufficient for process monitoring and control of very thin films, sometimes 3D sites are required to further simulate structures within the device. The measurement of film thicknesses only a few atoms thick on complex 3D sites, however, are very challenging. Apart from measuring thin films on 3D sites, there is also a critical need to measure parameters on 3D sites, which are weak and less sensitive for OCD (Optical Critical Dimension) metrology, with high accuracy and precision. Thus, state-ofthe-art methods are needed to address such metrology challenges. This work introduces the concept of Enhanced OCD which uses various methods to improve the sensitivity and reduce correlations for weak parameters in a complex measurement. This work also describes how more channels of information, when used correctly, can improve the precision and accuracy of weak, non-sensitive or complex parameters of interest.

  14. STRUCTURED-LIGHT BASED 3D LASER SCANNING OF SEMI-SUBMERGED STRUCTURES

    Directory of Open Access Journals (Sweden)

    J. van der Lucht

    2018-05-01

    Full Text Available In this work we look at 3D acquisition of semi-submerged structures with a triangulation based underwater laser scanning system. The motivation is that we want to simultaneously capture data above and below water to create a consistent model without any gaps. The employed structured light scanner consist of a machine vision camera and a green line laser. In order to reconstruct precise surface models of the object it is necessary to model and correct for the refraction of the laser line and camera rays at the water-air boundary. We derive a geometric model for the refraction at the air-water interface and propose a method for correcting the scans. Furthermore, we show how the water surface is directly estimated from sensor data. The approach is verified using scans captured with an industrial manipulator to achieve reproducible scanner trajectories with different incident angles. We show that the proposed method is effective for refractive correction and that it can be applied directly to the raw sensor data without requiring any external markers or targets.

  15. Structured-Light Based 3d Laser Scanning of Semi-Submerged Structures

    Science.gov (United States)

    van der Lucht, J.; Bleier, M.; Leutert, F.; Schilling, K.; Nüchter, A.

    2018-05-01

    In this work we look at 3D acquisition of semi-submerged structures with a triangulation based underwater laser scanning system. The motivation is that we want to simultaneously capture data above and below water to create a consistent model without any gaps. The employed structured light scanner consist of a machine vision camera and a green line laser. In order to reconstruct precise surface models of the object it is necessary to model and correct for the refraction of the laser line and camera rays at the water-air boundary. We derive a geometric model for the refraction at the air-water interface and propose a method for correcting the scans. Furthermore, we show how the water surface is directly estimated from sensor data. The approach is verified using scans captured with an industrial manipulator to achieve reproducible scanner trajectories with different incident angles. We show that the proposed method is effective for refractive correction and that it can be applied directly to the raw sensor data without requiring any external markers or targets.

  16. Advanced Structures and Compositions for 3D Forming of Cellulosic Fibers

    OpenAIRE

    Khakalo, Alexey

    2017-01-01

    The objective of this thesis was to systematically investigate strategies to endow fiber-based materials with toughness and formability. Bio-based polymers and green treatments were applied to develop 3D packaging structures. Formability, the material's ability for three-dimensional shaping, was achieved by plastic deformations in paper structures that were defect-free in terms of appearance and functionality. A set of methods to improve paper toughness was explored, including: (a) combined m...

  17. Optical fibre sensing in metals by embedment in 3D printed metallic structures

    Science.gov (United States)

    Maier, R. R. J.; Havermann, D.; Schneller, O.; Mathew, J.; Polyzos, D.; MacPherson, W. N.; Hand, D. P.

    2014-05-01

    Additive manufacturing or 3D printing of structural components in metals has potential to revolutionise the manufacturing industry. Embedded sensing in such structures opens a route towards SMART metals, providing added functionality, intelligence and enhanced performance in many components. Such embedded sensors would be capable of operating at extremely high temperatures by utilizing regenerated fibre Bragg gratings and in-fibre Fabry-Perot cavities.

  18. 3D-Structured Stretchable Strain Sensors for Out-of-Plane Force Detection.

    Science.gov (United States)

    Liu, Zhiyuan; Qi, Dianpeng; Leow, Wan Ru; Yu, Jiancan; Xiloyannnis, Michele; Cappello, Leonardo; Liu, Yaqing; Zhu, Bowen; Jiang, Ying; Chen, Geng; Masia, Lorenzo; Liedberg, Bo; Chen, Xiaodong

    2018-05-17

    Stretchable strain sensors, as the soft mechanical interface, provide the key mechanical information of the systems for healthcare monitoring, rehabilitation assistance, soft exoskeletal devices, and soft robotics. Stretchable strain sensors based on 2D flat film have been widely developed to monitor the in-plane force applied within the plane where the sensor is placed. However, to comprehensively obtain the mechanical feedback, the capability to detect the out-of-plane force, caused by the interaction outside of the plane where the senor is located, is needed. Herein, a 3D-structured stretchable strain sensor is reported to monitor the out-of-plane force by employing 3D printing in conjunction with out-of-plane capillary force-assisted self-pinning of carbon nanotubes. The 3D-structured sensor possesses large stretchability, multistrain detection, and strain-direction recognition by one single sensor. It is demonstrated that out-of-plane forces induced by the air/fluid flow are reliably monitored and intricate flow details are clearly recorded. The development opens up for the exploration of next-generation 3D stretchable sensors for electronic skin and soft robotics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors.

    Science.gov (United States)

    Venkatraman, Vishwesh; Sael, Lee; Kihara, Daisuke

    2009-01-01

    With structure databases expanding at a rapid rate, the task at hand is to provide reliable clues to their molecular function and to be able to do so on a large scale. This, however, requires suitable encodings of the molecular structure which are amenable to fast screening. To this end, moment-based representations provide a compact and nonredundant description of molecular shape and other associated properties. In this article, we present an overview of some commonly used representations with specific focus on two schemes namely spherical harmonics and their extension, the 3D Zernike descriptors. Key features and differences of the two are reviewed and selected applications are highlighted. We further discuss recent advances covering aspects of shape and property-based comparison at both global and local levels and demonstrate their applicability through some of our studies.

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

    Institute of Scientific and Technical Information of China (English)

    TAO Jun

    2006-01-01

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

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

    Science.gov (United States)

    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.

  2. Toward the identification of a reliable 3D-QSAR model for the protein tyrosine phosphatase 1B inhibitors

    Science.gov (United States)

    Wang, Fangfang; Zhou, Bo

    2018-04-01

    Protein tyrosine phosphatase 1B (PTP1B) is an intracellular non-receptor phosphatase that is implicated in signal transduction of insulin and leptin pathways, thus PTP1B is considered as potential target for treating type II diabetes and obesity. The present article is an attempt to formulate the three-dimensional quantitative structure-activity relationship (3D-QSAR) modeling of a series of compounds possessing PTP1B inhibitory activities using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques. The optimum template ligand-based models are statistically significant with great CoMFA (R2cv = 0.600, R2pred = 0.6760) and CoMSIA (R2cv = 0.624, R2pred = 0.8068) values. Molecular docking was employed to elucidate the inhibitory mechanisms of this series of compounds against PTP1B. In addition, the CoMFA and CoMSIA field contour maps agree well with the structural characteristics of the binding pocket of PTP1B active site. The knowledge of structure-activity relationship and ligand-receptor interactions from 3D-QSAR model and molecular docking will be useful for better understanding the mechanism of ligand-receptor interaction and facilitating development of novel compounds as potent PTP1B inhibitors.

  3. Conforming to interface structured adaptive mesh refinement: 3D algorithm and implementation

    Science.gov (United States)

    Nagarajan, Anand; Soghrati, Soheil

    2018-03-01

    A new non-iterative mesh generation algorithm named conforming to interface structured adaptive mesh refinement (CISAMR) is introduced for creating 3D finite element models of problems with complex geometries. CISAMR transforms a structured mesh composed of tetrahedral elements into a conforming mesh with low element aspect ratios. The construction of the mesh begins with the structured adaptive mesh refinement of elements in the vicinity of material interfaces. An r-adaptivity algorithm is then employed to relocate selected nodes of nonconforming elements, followed by face-swapping a small fraction of them to eliminate tetrahedrons with high aspect ratios. The final conforming mesh is constructed by sub-tetrahedralizing remaining nonconforming elements, as well as tetrahedrons with hanging nodes. In addition to studying the convergence and analyzing element-wise errors in meshes generated using CISAMR, several example problems are presented to show the ability of this method for modeling 3D problems with intricate morphologies.

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

    Science.gov (United States)

    Shen, Da; Lin, Zhipeng; Xue, Lei; Zheng, Qiang; Wang, Zichi

    2014-01-01

    In order to accurately realize the defect detection of pipeline inwall, this paper proposes a measurement system made up of cross structured light, single CCD camera and a smart car, etc. Based on structured light measurement technology, this paper mainly introduces the structured light measurement system, the imaging mathematical model, and the parameters and method of camera calibration. Using these measuring principles and methods, the camera in remote control car platform achieves continuous shooting of objects and real-time rebound processing as well as utilizing established model to extract 3D point cloud coordinate to reconstruct pipeline defects, so it is possible to achieve 3D automatic measuring, and verifies the correctness and feasibility of this system. It has been found that this system has great measurement accuracy in practice.

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

    DEFF Research Database (Denmark)

    Ochmann, Sebastian; Vock, Richard; Wessel, Raoul

    2013-01-01

    We present a new method for automatic semantic structuring of 3D point clouds representing buildings. In contrast to existing approaches which either target the outside appearance like the facade structure or rather low-level geometric structures, we focus on the building’s interior using indoor...... scans to derive high-level architectural entities like rooms and doors. Starting with a registered 3D point cloud, we probabilistically model the affiliation of each measured point to a certain room in the building. We solve the resulting clustering problem using an iterative algorithm that relies...... on the estimated visibilities between any two locations within the point cloud. With the segmentation into rooms at hand, we subsequently determine the locations and extents of doors between adjacent rooms. In our experiments, we demonstrate the feasibility of our method by applying it to synthetic as well...

  6. Finding the displacement of wood structure in heritage building by 3D laser scanner

    Science.gov (United States)

    Lee, M. C.; Tsai, Y. L.; Wang, R. Z.; Lin, M. L.

    2015-08-01

    Heritage buildings are highly prone to long term damage from the microclimate, scourge and vandalism, which can result in damaged materials, structures, painting and cultural heritage items. This study will focus on finding the displacement of wood structural members through the use of a 3D laser scanner and the 4D concept of time. The results will compare the scans from different periods to find the difference (if any) in the structural member position. Wood structures usually consist of numerous wood members connected to form the structure. However, these members can be damaged in various ways such as physical mechanisms, chemical reactions, and biological corrosion. When damage to the wood structure occurs, the structural displacement can be affected, and if affected severely, can lead to a building collapse. Monitoring of the structural displacement is the best way to discover damage immediately and to preserve the heritage building. However, the Cultural Heritage Preservation Law in Taiwan prohibits the installation of monitoring instruments (e.g strain gauge, accelerometer) in historic structures (heritage buildings). Scanning the wood structure with 3D lasers is the most non-intrusive method and quickly achieves displacement through visualization. The displacement scan results can be compared with different periods and different members to analyze the severity of damage. Once the 3D scanner is installed, the whole building is scanned, and point clouds created to build the visual building model. The structural displacement can be checked via the building model and the differences are measured between each member to find the high risk damaged areas or members with large displacement. Early detection of structural damage is the most effective way means of preservation.

  7. 3D structure and conductive thermal field of the Upper Rhine Graben

    Science.gov (United States)

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

    2016-04-01

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

  8. A substructure method to compute the 3D fluid-structure interaction during blowdown

    International Nuclear Information System (INIS)

    Guilbaud, D.; Axisa, F.; Gantenbein, F.; Gibert, R.J.

    1983-08-01

    The waves generated by a sudden rupture of a PWR primary pipe have an important mechanical effect on the internal structures of the vessel. This fluid-structure interaction has a strong 3D aspect. 3D finite element explicit methods can be applied. These methods take into account the non linearities of the problem but the calculation is heavy and expensive. We describe in this paper another type of method based on a substructure procedure: the vessel, internals and contained fluid are axisymmetrically described (AQUAMODE computer code). The pipes and contained fluid are monodimensionaly described (TEDEL-FLUIDE Computer Code). These substructures are characterized by their natural modes. Then, they are connected to another (connection of both structural and fluid nodes) the TRISTANA Computer Code. This method allows to compute correctly and cheaply the 3D fluid-structure effects. The treatment of certain non linearities is difficult because of the modal characterization of the substructures. However variations of contact conditions versus time can be introduced. We present here some validation tests and comparison with experimental results of the litterature

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

    Directory of Open Access Journals (Sweden)

    Carlos Morón

    2015-05-01

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

  10. Direct-write/cure conductive polymer nanocomposites for 3D structural electronics

    International Nuclear Information System (INIS)

    Lu, Yanfeng; Vatani, Morteza; Choi, Jae Won

    2013-01-01

    The use of direct-write (DW) in the fabrication of conductive structures offers dramatic benefits over traditional technologies in terms of low-cost, print-on-demand conformal manufacturing. This DW process can be combined with direct-cure (DC) process as one-step manufacturing of conducting elements, whereas conventional methods need a manufacturing process of conducting elements followed by a relatively long time post-curing/baking process. A hybrid technology combined with direct-write/cure (DWC) and projection microstereolithography (PμSL) is presented in this work. Carbon nanotubes (CNTs) were dispersed in a photopolymer solution to introduce conductivity. The developed PμSL was used to create 3D structures, and DWC of conductive photopolymers with CNTs was utilized to produce conductive paths. To show the capabilities of the developed system and materials, a 3D structure with embedded conductive paths was designed and fabricated. Based on the experiments, it is thought that the suggested manufacturing process and materials are promising to produce 3D structural electronics.

  11. Direct-write/cure conductive polymer nanocomposites for 3D structural electronics

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Yanfeng; Vatani, Morteza; Choi, Jae Won [The University of Akron, Akron, Ohio (United States)

    2013-10-15

    The use of direct-write (DW) in the fabrication of conductive structures offers dramatic benefits over traditional technologies in terms of low-cost, print-on-demand conformal manufacturing. This DW process can be combined with direct-cure (DC) process as one-step manufacturing of conducting elements, whereas conventional methods need a manufacturing process of conducting elements followed by a relatively long time post-curing/baking process. A hybrid technology combined with direct-write/cure (DWC) and projection microstereolithography (PμSL) is presented in this work. Carbon nanotubes (CNTs) were dispersed in a photopolymer solution to introduce conductivity. The developed PμSL was used to create 3D structures, and DWC of conductive photopolymers with CNTs was utilized to produce conductive paths. To show the capabilities of the developed system and materials, a 3D structure with embedded conductive paths was designed and fabricated. Based on the experiments, it is thought that the suggested manufacturing process and materials are promising to produce 3D structural electronics.

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

    Science.gov (United States)

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

    2014-03-01

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

  13. Mapping Cortical Laminar Structure in the 3D BigBrain.

    Science.gov (United States)

    Wagstyl, Konrad; Lepage, Claude; Bludau, Sebastian; Zilles, Karl; Fletcher, Paul C; Amunts, Katrin; Evans, Alan C

    2018-07-01

    Histological sections offer high spatial resolution to examine laminar architecture of the human cerebral cortex; however, they are restricted by being 2D, hence only regions with sufficiently optimal cutting planes can be analyzed. Conversely, noninvasive neuroimaging approaches are whole brain but have relatively low resolution. Consequently, correct 3D cross-cortical patterns of laminar architecture have never been mapped in histological sections. We developed an automated technique to identify and analyze laminar structure within the high-resolution 3D histological BigBrain. We extracted white matter and pial surfaces, from which we derived histologically verified surfaces at the layer I/II boundary and within layer IV. Layer IV depth was strongly predicted by cortical curvature but varied between areas. This fully automated 3D laminar analysis is an important requirement for bridging high-resolution 2D cytoarchitecture and in vivo 3D neuroimaging. It lays the foundation for in-depth, whole-brain analyses of cortical layering.

  14. 3D structure tensor analysis of light microscopy data for validating diffusion MRI.

    Science.gov (United States)

    Khan, Ahmad Raza; Cornea, Anda; Leigland, Lindsey A; Kohama, Steven G; Jespersen, Sune Nørhøj; Kroenke, Christopher D

    2015-05-01

    Diffusion magnetic resonance imaging (d-MRI) is a powerful non-invasive and non-destructive technique for characterizing brain tissue on the microscopic scale. However, the lack of validation of d-MRI by independent experimental means poses an obstacle to accurate interpretation of data acquired using this method. Recently, structure tensor analysis has been applied to light microscopy images, and this technique holds promise to be a powerful validation strategy for d-MRI. Advantages of this approach include its similarity to d-MRI in terms of averaging the effects of a large number of cellular structures, and its simplicity, which enables it to be implemented in a high-throughput manner. However, a drawback of previous implementations of this technique arises from it being restricted to 2D. As a result, structure tensor analyses have been limited to tissue sectioned in a direction orthogonal to the direction of interest. Here we describe the analytical framework for extending structure tensor analysis to 3D, and utilize the results to analyze serial image "stacks" acquired with confocal microscopy of rhesus macaque hippocampal tissue. Implementation of 3D structure tensor procedures requires removal of sources of anisotropy introduced in tissue preparation and confocal imaging. This is accomplished with image processing steps to mitigate the effects of anisotropic tissue shrinkage, and the effects of anisotropy in the point spread function (PSF). In order to address the latter confound, we describe procedures for measuring the dependence of PSF anisotropy on distance from the microscope objective within tissue. Prior to microscopy, ex vivo d-MRI measurements performed on the hippocampal tissue revealed three regions of tissue with mutually orthogonal directions of least restricted diffusion that correspond to CA1, alveus and inferior longitudinal fasciculus. We demonstrate the ability of 3D structure tensor analysis to identify structure tensor orientations that

  15. Subdiffraction Multicolor Imaging of the Nuclear Periphery with 3D Structured Illumination Microscopy

    Science.gov (United States)

    Schermelleh, Lothar; Carlton, Peter M.; Haase, Sebastian; Shao, Lin; Winoto, Lukman; Kner, Peter; Burke, Brian; Cardoso, M. Cristina; Agard, David A.; Gustafsson, Mats G. L.; Leonhardt, Heinrich; Sedat, John W.

    2010-01-01

    Fluorescence light microscopy allows multicolor visualization of cellular components with high specificity, but its utility has until recently been constrained by the intrinsic limit of spatial resolution. We applied three-dimensional structured illumination microscopy (3D-SIM) to circumvent this limit and to study the mammalian nucleus. By simultaneously imaging chromatin, nuclear lamina, and the nuclear pore complex (NPC), we observed several features that escape detection by conventional microscopy. We could resolve single NPCs that colocalized with channels in the lamin network and peripheral heterochromatin. We could differentially localize distinct NPC components and detect double-layered invaginations of the nuclear envelope in prophase as previously seen only by electron microscopy. Multicolor 3D-SIM opens new and facile possibilities to analyze subcellular structures beyond the diffraction limit of the emitted light. PMID:18535242

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

    Energy Technology Data Exchange (ETDEWEB)

    Juvin, D. [CEA Centre d`Etudes de Saclay, 91 - Gif-sur-Yvette (France). Dept. d`Electronique et d`Instrumentation Nucleaire; Boukir, S.; Chaumette, F.; Bouthemy, P. [Rennes-1 Univ., 35 (France)

    1993-10-01

    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.

  17. PDBlocal: A web-based tool for local inspection of biological macromolecular 3D structures

    Directory of Open Access Journals (Sweden)

    Pan Wang

    2018-03-01

    Full Text Available Functional research on biological macromolecules must focus on specific local regions. PDBlocal is a web-based tool developed to overcome the limitations of traditional molecular visualization tools for three-dimensional (3D inspection of local regions. PDBlocal provides an intuitive and easy-to-manipulate web page interface and some new useful functions. It can keep local regions flashing, display sequence text that is dynamically consistent with the 3D structure in local appearance under multiple local manipulations, use two scenes to help users inspect the same local region with different statuses, list all historical manipulation statuses with a tree structure, allow users to annotate regions of interest, and save all historical statuses and other data to a web server for future research. PDBlocal has met expectations and shown satisfactory performance for both expert and novice users. This tool is available at http://labsystem.scuec.edu.cn/pdblocal/.

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

    International Nuclear Information System (INIS)

    Juvin, D.

    1993-01-01

    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

  19. Pyridones as NNRTIs against HIV-1 mutants: 3D-QSAR and protein informatics

    Science.gov (United States)

    Debnath, Utsab; Verma, Saroj; Jain, Surabhi; Katti, Setu B.; Prabhakar, Yenamandra S.

    2013-07-01

    CoMFA and CoMSIA based 3D-QSAR of HIV-1 RT wild and mutant (K103, Y181C, and Y188L) inhibitory activities of 4-benzyl/benzoyl pyridin-2-ones followed by protein informatics of corresponding non-nucleoside inhibitors' binding pockets from pdbs 2BAN, 3MED, 1JKH, and 2YNF were analysed to discover consensus features of the compounds for broad-spectrum activity. The CoMFA/CoMSIA models indicated that compounds with groups which lend steric-cum-electropositive fields in the vicinity of C5, hydrophobic field in the vicinity of C3 of pyridone region and steric field in aryl region produce broad-spectrum anti-HIV-1 RT activity. Also, a linker rendering electronegative field between pyridone and aryl moieties is common requirement for the activities. The protein informatics showed considerable alteration in residues 181 and 188 characteristics on mutation. Also, mutants' isoelectric points shifted in acidic direction. The study offered fresh avenues for broad-spectrum anti-HIV-1 agents through designing new molecules seeded with groups satisfying common molecular fields and concerns of mutating residues.

  20. A 3D visualization of spatial relationship between geological structure and groundwater chemical profile around Iwate volcano, Japan: based on the ARCGIS 3D Analyst

    Science.gov (United States)

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

    2009-12-01

    We established 3D geological and hydrological model around Iwate volcano to visualize 3D relationships between subsurface structure and groundwater profile. Iwate volcano is a typical polygenetic volcano located in NE Japan, and its body is composed of two stratovolcanoes which have experienced sector collapses several times. Because of this complex structure, groundwater flow around Iwate volcano is strongly restricted by subsurface construction. For example, Kazahaya and Yasuhara (1999) clarified that shallow groundwater in north and east flanks of Iwate volcano are recharged at the mountaintop, and these flow systems are restricted in north and east area because of the structure of younger volcanic body collapse. In addition, Ohwada et al. (2006) found that these shallow groundwater in north and east flanks have relatively high concentration of major chemical components and high 3He/4He ratios. In this study, we succeeded to visualize the spatial relationship between subsurface structure and chemical profile of shallow and deep groundwater system using 3D model on the GIS. In the study region, a number of geological and hydrological datasets, such as boring log data and groundwater chemical profile, were reported. All these paper data are digitized and converted to meshed data on the GIS, and plotted in the three dimensional space to visualize spatial distribution. We also inputted digital elevation model (DEM) around Iwate volcano issued by the Geographical Survey Institute of Japan, and digital geological maps issued by Geological Survey of Japan, AIST. All 3D models are converted into VRML format, and can be used as a versatile dataset on personal computer.

  1. CAD-Based Modeling of Advanced Rotary Wing Structures for Integrated 3-D Aeromechanics Analysis

    Science.gov (United States)

    Staruk, William

    This dissertation describes the first comprehensive use of integrated 3-D aeromechanics modeling, defined as the coupling of 3-D solid finite element method (FEM) structural dynamics with 3-D computational fluid dynamics (CFD), for the analysis of a real helicopter rotor. The development of this new methodology (a departure from how rotor aeroelastic analysis has been performed for 40 years), its execution on a real rotor, and the fundamental understanding of aeromechanics gained from it, are the key contributions of this dissertation. This work also presents the first CFD/CSD analysis of a tiltrotor in edgewise flight, revealing many of its unique loading mechanisms. The use of 3-D FEM, integrated with a trim solver and aerodynamics modeling, has the potential to enhance the design of advanced rotors by overcoming fundamental limitations of current generation beam-based analysis tools and offering integrated internal dynamic stress and strain predictions for design. Two primary goals drove this research effort: 1) developing a methodology to create 3-D CAD-based brick finite element models of rotors including multibody joints, controls, and aerodynamic interfaces, and 2) refining X3D, the US Army's next generation rotor structural dynamics solver featuring 3-D FEM within a multibody formulation with integrated aerodynamics, to model a tiltrotor in the edgewise conversion flight regime, which drives critical proprotor structural loads. Prior tiltrotor analysis has primarily focused on hover aerodynamics with rigid blades or forward flight whirl-flutter stability with simplified aerodynamics. The first goal was met with the development of a detailed methodology for generating multibody 3-D structural models, starting from CAD geometry, continuing to higher-order hexahedral finite element meshing, to final assembly of the multibody model by creating joints, assigning material properties, and defining the aerodynamic interface. Several levels of verification and

  2. A theoretical study of the structure and stability of borohydride on 3d transition metals

    Science.gov (United States)

    Arevalo, Ryan Lacdao; Escaño, Mary Clare Sison; Gyenge, Elod; Kasai, Hideaki

    2012-12-01

    The adsorption of borohydride on 3d transition metals (Cr, Mn, Fe, Co, Ni and Cu) was studied using first principles calculations within spin-polarized density functional theory. Magnetic effect on the stability of borohydride is noted. Molecular adsorption is favorable on Co, Ni and Cu, which is characterized by the strong s-dzz hybridization of the adsorbate-substrate states. Dissociated adsorption structure yielding one or two H adatom fragments on the surface is observed for Cr, Mn and Fe.

  3. 3D reconstruction of internal structure of animal body using near-infrared light

    Science.gov (United States)

    Tran, Trung Nghia; Yamamoto, Kohei; Namita, Takeshi; Kato, Yuji; Shimizu, Koichi

    2014-03-01

    To realize three-dimensional (3D) optical imaging of the internal structure of animal body, we have developed a new technique to reconstruct CT images from two-dimensional (2D) transillumination images. In transillumination imaging, the image is blurred due to the strong scattering in the tissue. We had developed a scattering suppression technique using the point spread function (PSF) for a fluorescent light source in the body. In this study, we have newly proposed a technique to apply this PSF for a light source to the image of unknown light-absorbing structure. The effectiveness of the proposed technique was examined in the experiments with a model phantom and a mouse. In the phantom experiment, the absorbers were placed in the tissue-equivalent medium to simulate the light-absorbing organs in mouse body. Near-infrared light was illuminated from one side of the phantom and the image was recorded with CMOS camera from another side. Using the proposed techniques, the scattering effect was efficiently suppressed and the absorbing structure can be visualized in the 2D transillumination image. Using the 2D images obtained in many different orientations, we could reconstruct the 3D image. In the mouse experiment, an anesthetized mouse was held in an acrylic cylindrical holder. We can visualize the internal organs such as kidneys through mouse's abdomen using the proposed technique. The 3D image of the kidneys and a part of the liver were reconstructed. Through these experimental studies, the feasibility of practical 3D imaging of the internal light-absorbing structure of a small animal was verified.

  4. 3-D Structure of the Slave and Rae Cratons Provides Clues to Their Construction

    Science.gov (United States)

    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.

  5. 3-D Digitization of Stereoscopic Jet-in-Crossflow Vortex Structure Images via Augmented Reality

    Science.gov (United States)

    Sigurdson, Lorenz; Strand, Christopher; Watson, Graeme; Nault, Joshua; Tucker, Ryan

    2006-11-01

    Stereoscopic images of smoke-laden vortex flows have proven useful for understanding the topology of the embedded 3-D vortex structures. Images from two cameras allow a perception of the 3-D structure via the use of red/blue eye glasses. The human brain has an astonishing capacity to calculate and present to the observer the complex turbulent smoke volume. We have developed a technique whereby a virtual cursor is introduced to the perception, which creates an ``augmented reality.'' The perceived position of this cursor in the 3-D field can be precisely controlled by the observer. It can be brought near a characteristic vortex structure in order to digitally estimate the spatial coordinates of that feature. A calibration procedure accounts for camera positioning. Vortex tubes can be traced and recorded for later or real time supersposition of tube skeleton models. These models can be readily digitally obtained for display in graphics systems to allow complete exploration from any location or perspective. A unique feature of this technology is the use of the human brain to naturally perform the difficult computation of the shape of the translucent smoke volume. Examples are given of application to low velocity ratio and Reynolds number elevated jets-in-crossflow.

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

    Science.gov (United States)

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

    2016-04-01

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    The methods to manufacture micro- or nano- structures on surfaces have been an area of intense investigation. Demands are shown for technologies for surface structuring on real 3D parts in many fields. However, most technologies for the fabrication of micro-structured functional surfaces are still...... 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 this way micro holes (Ø4 μm) was obtained. The second approach is to produce the cavity part using anodizing process chain, and in this way sub-micro structures can be obtained all over the cavity surface. The third approach is to machine the surface inside the cavity directly by femtosecond laser combined...

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

    Science.gov (United States)

    Challapalli, Adithya

    Cellular materials, often called lattice materials, are increasingly receiving attention for their ultralight structures with high specific strength, excellent impact absorption, acoustic insulation, heat dissipation media and compact heat exchangers. In alignment with emerging additive manufacturing (AM) technology, realization of the structural applications of the lattice materials appears to be becoming faster. Considering the direction dependent material properties of the products with AM, by directionally dependent printing resolution, effective moduli of lattice structures appear to be directionally dependent. In this paper, a constitutive model of a lattice structure, which is an octet-truss with a base material having an orthotropic material property considering AM is developed. In a case study, polyjet based 3D printing material having an orthotropic property with a 9% difference in the principal direction provides difference in the axial and shear moduli in the octet-truss by 2.3 and 4.6%. Experimental validation for the effective properties of a 3D printed octet-truss is done for uniaxial tension and compression test. The theoretical value based on the micro-buckling of truss member are used to estimate the failure strength. Modulus value appears a little overestimate compared with the experiment. Finite element (FE) simulations for uniaxial compression and tension of octettruss lattice materials are conducted. New effective properties for the octet-truss lattice structure are developed considering the observed behavior of the octet-truss structure under macroscopic compression and tension trough simulations.

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

    Science.gov (United States)

    Przybycin, Anna M.; Scheck-Wenderoth, Magdalena; Schneider, Michael

    2014-05-01

    The North Alpine Foreland Basin is situated in the northern front of the European Alps and extends over parts of France, Switzerland, Germany and Austria. It formed as a wedge shaped depression since the Tertiary in consequence of the Euro - Adriatic continental collision and the Alpine orogeny. The basin is filled with clastic sediments, the Molasse, originating from erosional processes of the Alps and underlain by Mesozoic sedimentary successions and a Paleozoic crystalline crust. For our study we have focused on the German part of the basin. To investigate the deep structure, the isostatic state and the load distribution of this region we have constructed a 3D structural model of the basin and the Alpine area using available depth and thickness maps, regional scale 3D structural models as well as seismic and well data for the sedimentary part. The crust (from the top Paleozoic down to the Moho (Grad et al. 2008)) has been considered as two-parted with a lighter upper crust and a denser lower crust; the partition has been calculated following the approach of isostatic equilibrium of Pratt (1855). By implementing a seismic Lithosphere-Asthenosphere-Boundary (LAB) (Tesauro 2009) the crustal scale model has been extended to the lithospheric-scale. The layer geometry and the assigned bulk densities of this starting model have been constrained by means of 3D gravity modelling (BGI, 2012). Afterwards the 3D load distribution has been calculated using a 3D finite element method. Our results show that the North Alpine Foreland Basin is not isostatically balanced and that the configuration of the crystalline crust strongly controls the gravity field in this area. Furthermore, our results show that the basin area is influenced by varying lateral load differences down to a depth of more than 150 km what allows a first order statement of the required compensating horizontal stress needed to prevent gravitational collapse of the system. BGI (2012). The International

  10. A 3D moisture-stress FEM analysis for time dependent problems in timber structures

    Science.gov (United States)

    Fortino, Stefania; Mirianon, Florian; Toratti, Tomi

    2009-11-01

    This paper presents a 3D moisture-stress numerical analysis for timber structures under variable humidity and load conditions. An orthotropic viscoelastic-mechanosorptive material model is specialized on the basis of previous models. Both the constitutive model and the equations needed to describe the moisture flow across the structure are implemented into user subroutines of the Abaqus finite element code and a coupled moisture-stress analysis is performed for several types of mechanical loads and moisture changes. The presented computational approach is validated by analyzing some wood tests described in the literature and comparing the computational results with the reported experimental data.

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

    DEFF Research Database (Denmark)

    Klank, Henning; Goranovic, Goran; Kutter, Jörg Peter

    2002-01-01

    . 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 stereoscopic principle was applied to obtain all three velocity components, showing the feasibility of obtaining full volume mapping (x, y, z, U, V, W) from micro-PIV measurements. The results are compared with computational fluid dynamics (CFD) simulations....

  12. Methods and uncertainty estimations of 3-D structural modelling in crystalline rocks: a case study

    Directory of Open Access Journals (Sweden)

    R. Schneeberger

    2017-09-01

    Full Text Available Exhumed basement rocks are often dissected by faults, the latter controlling physical parameters such as rock strength, porosity, or permeability. Knowledge on the three-dimensional (3-D geometry of the fault pattern and its continuation with depth is therefore of paramount importance for applied geology projects (e.g. tunnelling, nuclear waste disposal in crystalline bedrock. The central Aar massif (Central Switzerland serves as a study area where we investigate the 3-D geometry of the Alpine fault pattern by means of both surface (fieldwork and remote sensing and underground ground (mapping of the Grimsel Test Site information. The fault zone pattern consists of planar steep major faults (kilometre scale interconnected with secondary relay faults (hectometre scale. Starting with surface data, we present a workflow for structural 3-D modelling of the primary faults based on a comparison of three extrapolation approaches based on (a field data, (b Delaunay triangulation, and (c a best-fitting moment of inertia analysis. The quality of these surface-data-based 3-D models is then tested with respect to the fit of the predictions with the underground appearance of faults. All three extrapolation approaches result in a close fit (> 10 % when compared with underground rock laboratory mapping. Subsequently, we performed a statistical interpolation based on Bayesian inference in order to validate and further constrain the uncertainty of the extrapolation approaches. This comparison indicates that fieldwork at the surface is key for accurately constraining the geometry of the fault pattern and enabling a proper extrapolation of major faults towards depth. Considerable uncertainties, however, persist with respect to smaller-sized secondary structures because of their limited spatial extensions and unknown reoccurrence intervals.

  13. Methods and uncertainty estimations of 3-D structural modelling in crystalline rocks: a case study

    Science.gov (United States)

    Schneeberger, Raphael; de La Varga, Miguel; Egli, Daniel; Berger, Alfons; Kober, Florian; Wellmann, Florian; Herwegh, Marco

    2017-09-01

    Exhumed basement rocks are often dissected by faults, the latter controlling physical parameters such as rock strength, porosity, or permeability. Knowledge on the three-dimensional (3-D) geometry of the fault pattern and its continuation with depth is therefore of paramount importance for applied geology projects (e.g. tunnelling, nuclear waste disposal) in crystalline bedrock. The central Aar massif (Central Switzerland) serves as a study area where we investigate the 3-D geometry of the Alpine fault pattern by means of both surface (fieldwork and remote sensing) and underground ground (mapping of the Grimsel Test Site) information. The fault zone pattern consists of planar steep major faults (kilometre scale) interconnected with secondary relay faults (hectometre scale). Starting with surface data, we present a workflow for structural 3-D modelling of the primary faults based on a comparison of three extrapolation approaches based on (a) field data, (b) Delaunay triangulation, and (c) a best-fitting moment of inertia analysis. The quality of these surface-data-based 3-D models is then tested with respect to the fit of the predictions with the underground appearance of faults. All three extrapolation approaches result in a close fit ( > 10 %) when compared with underground rock laboratory mapping. Subsequently, we performed a statistical interpolation based on Bayesian inference in order to validate and further constrain the uncertainty of the extrapolation approaches. This comparison indicates that fieldwork at the surface is key for accurately constraining the geometry of the fault pattern and enabling a proper extrapolation of major faults towards depth. Considerable uncertainties, however, persist with respect to smaller-sized secondary structures because of their limited spatial extensions and unknown reoccurrence intervals.

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

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  15. Modeling of DNA and Protein Organization Levels with Cn3D Software

    Science.gov (United States)

    Stasinakis, Panagiotis K.; Nicolaou, Despoina

    2017-01-01

    The molecular structure of living organisms and the complex interactions amongst its components are the basis for the diversity observed at the macroscopic level. Proteins and nucleic acids are some of the major molecular components, and play a key role in several biological functions, such as those of development and evolution. This article…

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

    Science.gov (United States)

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

    2013-01-01

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

  17. 3D Geo-Structures Visualization Education Project (3dgeostructuresvis.ucdavis.edu)

    Science.gov (United States)

    Billen, M. I.

    2014-12-01

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

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

    Directory of Open Access Journals (Sweden)

    Md. Anowar Hossain

    2014-01-01

    Full Text Available beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330 and Glu(331 could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom.

  19. Molecular phylogeny and predicted 3D structure of plant beta-D-N-acetylhexosaminidase.

    Science.gov (United States)

    Hossain, Md Anowar; Roslan, Hairul Azman

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    M.-F. Robbe

    2006-01-01

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

  1. Application of Characterization, Modeling, and Analytics Towards Understanding Process Structure Linkages in Metallic 3D Printing (Postprint)

    Science.gov (United States)

    2017-08-01

    METALLIC 3D PRINTING (POSTPRINT) M.A. Groeber, E. Schwalbach, S. Donegan, K. Chaput, T. Butler, and J. Miller AFRL/RX 27 JULY...MODELING, AND ANALYTICS TOWARDS UNDERSTANDING PROCESS- STRUCTURE LINKAGES IN METALLIC 3D PRINTING (POSTPRINT) 5a. CONTRACT NUMBER IN-HOUSE 5b...characterization, modelling, and analytics towards understanding process-structure linkages in metallic 3D printing M A Groeber, E Schwalbach, S Donegan, K

  2. Determination of ICRF antenna fields in the vicinity of a 3-D Faraday shield structure

    Energy Technology Data Exchange (ETDEWEB)

    Ryan, P M; Rothe, K E; Whealton, J H; Shepard, T D [Oak Ridge National Lab., TN (USA)

    1990-04-01

    A three-dimensional (3-D) magnetostatic analysis developed at Oak Ridge National Laboratory has been used to calculate the electromagnetic transmission properties of representative Faraday shield designs. The analysis uses the long-wavelength approximation to obtain a 3-D Laplace solution for the magnetic scalar potential over one poloidal period of the Faraday shield, from which the complete magnetic field distribution may be obtained. Once the magnetic field distributions in the presence and absence of a Faraday shield are known, the flux transmission coefficient can be found, as well as any change in the distributed inductance of the current strap. The distrbuted capacitance of the strap can be found from an analogous 3-D electrostatic calculation, enabling the phase velocity of the slow-wave structure to be determined. Power dissipation in the shield may be estimated by equating the surface current on a perfect conductor with the surface magnetic field and using this surface current in conjunction with the finite conductivities of the shield materials to obtain the power distribution due to eddy current heating. (orig.).

  3. TLS-Based Feature Extraction and 3D Modeling for Arch Structures

    Directory of Open Access Journals (Sweden)

    Xiangyang Xu

    2017-01-01

    Full Text Available Terrestrial laser scanning (TLS technology is one of the most efficient and accurate tools for 3D measurement which can reveal surface-based characteristics of objects with the aid of computer vision and programming. Thus, it plays an increasingly important role in deformation monitoring and analysis. Automatic data extraction and high efficiency and accuracy modeling from scattered point clouds are challenging issues during the TLS data processing. This paper presents a data extraction method considering the partial and statistical distribution of the point clouds scanned, called the window-neighborhood method. Based on the point clouds extracted, 3D modeling of the boundary of an arched structure was carried out. The ideal modeling strategy should be fast, accurate, and less complex regarding its application to large amounts of data. The paper discusses the accuracy of fittings in four cases between whole curve, segmentation, polynomial, and B-spline. A similar number of parameters was set for polynomial and B-spline because the number of unknown parameters is essential for the accuracy of the fittings. The uncertainties of the scanned raw point clouds and the modeling are discussed. This process is considered a prerequisite step for 3D deformation analysis with TLS.

  4. Using Openstreetmap Data to Generate Building Models with Their Inner Structures for 3d Maps

    Science.gov (United States)

    Wang, Z.; Zipf, A.

    2017-09-01

    With the development of Web 2.0, more and more data related to indoor environments has been collected within the volunteered geographic information (VGI) framework, which creates a need for construction of indoor environments from VGI. In this study, we focus on generating 3D building models from OpenStreetMap (OSM) data, and provide an approach to support construction and visualization of indoor environments on 3D maps. In this paper, we present an algorithm which can extract building information from OSM data, and can construct building structures as well as inner building components (e.g., doors, rooms, and windows). A web application is built to support the processing and visualization of the building models on a 3D map. We test our approach with an indoor dataset collected from the field. The results show the feasibility of our approach and its potentials to provide support for a wide range of applications, such as indoor and outdoor navigation, urban planning, and incident management.

  5. Tensor decomposition in electronic structure calculations on 3D Cartesian grids

    International Nuclear Information System (INIS)

    Khoromskij, B.N.; Khoromskaia, V.; Chinnamsetty, S.R.; Flad, H.-J.

    2009-01-01

    In this paper, we investigate a novel approach based on the combination of Tucker-type and canonical tensor decomposition techniques for the efficient numerical approximation of functions and operators in electronic structure calculations. In particular, we study applicability of tensor approximations for the numerical solution of Hartree-Fock and Kohn-Sham equations on 3D Cartesian grids. We show that the orthogonal Tucker-type tensor approximation of electron density and Hartree potential of simple molecules leads to low tensor rank representations. This enables an efficient tensor-product convolution scheme for the computation of the Hartree potential using a collocation-type approximation via piecewise constant basis functions on a uniform nxnxn grid. Combined with the Richardson extrapolation, our approach exhibits O(h 3 ) convergence in the grid-size h=O(n -1 ). Moreover, this requires O(3rn+r 3 ) storage, where r denotes the Tucker rank of the electron density with r=O(logn), almost uniformly in n. For example, calculations of the Coulomb matrix and the Hartree-Fock energy for the CH 4 molecule, with a pseudopotential on the C atom, achieved accuracies of the order of 10 -6 hartree with a grid-size n of several hundreds. Since the tensor-product convolution in 3D is performed via 1D convolution transforms, our scheme markedly outperforms the 3D-FFT in both the computing time and storage requirements.

  6. USING OPENSTREETMAP DATA TO GENERATE BUILDING MODELS WITH THEIR INNER STRUCTURES FOR 3D MAPS

    Directory of Open Access Journals (Sweden)

    Z. Wang

    2017-09-01

    Full Text Available With the development of Web 2.0, more and more data related to indoor environments has been collected within the volunteered geographic information (VGI framework, which creates a need for construction of indoor environments from VGI. In this study, we focus on generating 3D building models from OpenStreetMap (OSM data, and provide an approach to support construction and visualization of indoor environments on 3D maps. In this paper, we present an algorithm which can extract building information from OSM data, and can construct building structures as well as inner building components (e.g., doors, rooms, and windows. A web application is built to support the processing and visualization of the building models on a 3D map. We test our approach with an indoor dataset collected from the field. The results show the feasibility of our approach and its potentials to provide support for a wide range of applications, such as indoor and outdoor navigation, urban planning, and incident management.

  7. Polypyrrole shell@3D-Ni metal core structured electrodes for high-performance supercapacitors.

    Science.gov (United States)

    Chen, Gao-Feng; Su, Yu-Zhi; Kuang, Pan-Yong; Liu, Zhao-Qing; Chen, Dao-Yi; Wu, Xu; Li, Nan; Qiao, Shi-Zhang

    2015-03-16

    Three-dimensional (3D) nanometal films serving as current collectors have attracted much interest recently owing to their promising application in high-performance supercapacitors. In the process of the electrochemical reaction, the 3D structure can provide a short diffusion path for fast ion transport, and the highly conductive nanometal may serve as a backbone for facile electron transfer. In this work, a novel polypyrrole (PPy) shell@3D-Ni-core composite is developed to enhance the electrochemical performance of conventional PPy. With the introduction of a Ni metal core, the as-prepared material exhibits a high specific capacitance (726 F g(-1) at a charge/discharge rate of 1 A g(-1)), good rate capability (a decay of 33% in Csp with charge/discharge rates increasing from 1 to 20 A g(-1)), and high cycle stability (only a small decrease of 4.2% in Csp after 1000 cycles at a scan rate of 100 mV s(-1)). Furthermore, an aqueous symmetric supercapacitor device is fabricated by using the as-prepared composite as electrodes; the device demonstrates a high energy density (≈21.2 Wh kg(-1)) and superior long-term cycle ability (only 4.4% and 18.6% loss in Csp after 2000 and 5000 cycles, respectively). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. 3D cinematic rendering of the calvarium, maxillofacial structures, and skull base: preliminary observations.

    Science.gov (United States)

    Rowe, Steven P; Zinreich, S James; Fishman, Elliot K

    2018-06-01

    Three-dimensional (3D) visualizations of volumetric data from CT have gained widespread clinical acceptance and are an important method for evaluating complex anatomy and pathology. Recently, cinematic rendering (CR), a new 3D visualization methodology, has become available. CR utilizes a lighting model that allows for the production of photorealistic images from isotropic voxel data. Given how new this technique is, studies to evaluate its clinical utility and any potential advantages or disadvantages relative to other 3D methods such as volume rendering have yet to be published. In this pictorial review, we provide examples of normal calvarial, maxillofacial, and skull base anatomy and pathological conditions that highlight the potential for CR images to aid in patient evaluation and treatment planning. The highly detailed images and nuanced shadowing that are intrinsic to CR are well suited to the display of the complex anatomy in this region of the body. We look forward to studies with CR that will ascertain the ultimate value of this methodology to evaluate calvarium, maxillofacial, and skull base morphology as well as other complex anatomic structures.

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

    Directory of Open Access Journals (Sweden)

    Michaël Hinderdael

    2017-02-01

    Full Text Available Currently, research on structural health monitoring systems is focused on direct integration of the system into a component or structure. The latter results in a so-called smart structure. One example of a smart structure is a component with integrated strain sensing for continuous load monitoring. Additive manufacturing, or 3D printing, now also enables such integration of functions inside components. As a proof-of-concept, the Fused Deposition Modeling (FDM technique was used to integrate a strain sensing element inside polymer (ABS tensile test samples. The strain sensing element consisted of a closed capillary filled with a fluid and connected to an externally mounted pressure sensor. The volumetric deformation of the integrated capillary resulted in pressure changes in the fluid. The obtained pressure measurements during tensile testing are reported in this paper and compared to state-of-the-art extensometer measurements. The sensitivity of the 3D printed pressure-based strain sensor is primarily a function of the compressibility of the capillary fluid. Air- and watertightness are of critical importance for the proper functioning of the 3D printed pressure-based strain sensor. Therefore, the best after-treatment procedure was selected on basis of a comparative analysis. The obtained pressure measurements are linear with respect to the extensometer readings, and the uncertainty on the strain measurement of a capillary filled with water (incompressible fluid is ±3.1 µstrain, which is approximately three times less sensitive than conventional strain gauges (±1 µstrain, but 32 times more sensitive than the same sensor based on air (compressible fluid (±101 µstrain.

  10. Error analysis for creating 3D face templates based on cylindrical quad-tree structure

    Science.gov (United States)

    Gutfeter, Weronika

    2015-09-01

    Development of new biometric algorithms is parallel to advances in technology of sensing devices. Some of the limitations of the current face recognition systems may be eliminated by integrating 3D sensors into these systems. Depth sensing devices can capture a spatial structure of the face in addition to the texture and color. This kind of data is yet usually very voluminous and requires large amount of computer resources for being processed (face scans obtained with typical depth cameras contain more than 150 000 points per face). That is why defining efficient data structures for processing spatial images is crucial for further development of 3D face recognition methods. The concept described in this work fulfills the aforementioned demands. Modification of the quad-tree structure was chosen because it can be easily transformed into less dimensional data structures and maintains spatial relations between data points. We are able to interpret data stored in the tree as a pyramid of features which allow us to analyze face images using coarse-to-fine strategy, often exploited in biometric recognition systems.

  11. Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints.

    Science.gov (United States)

    Liu, Jie; Su, Minyi; Liu, Zhihai; Li, Jie; Li, Yan; Wang, Renxiao

    2017-07-18

    In structure-based drug design, binding affinity prediction remains as a challenging goal for current scoring functions. Development of target-biased scoring functions provides a new possibility for tackling this problem, but this approach is also associated with certain technical difficulties. We previously reported the Knowledge-Guided Scoring (KGS) method as an alternative approach (BMC Bioinformatics, 2010, 11, 193-208). The key idea is to compute the binding affinity of a given protein-ligand complex based on the known binding data of an appropriate reference complex, so the error in binding affinity prediction can be reduced effectively. In this study, we have developed an upgraded version, i.e. KGS2, by employing 3D protein-ligand interaction fingerprints in reference selection. KGS2 was evaluated in combination with four scoring functions (X-Score, ChemPLP, ASP, and GoldScore) on five drug targets (HIV-1 protease, carbonic anhydrase 2, beta-secretase 1, beta-trypsin, and checkpoint kinase 1). In the in situ scoring test, considerable improvements were observed in most cases after application of KGS2. Besides, the performance of KGS2 was always better than KGS in all cases. In the more challenging molecular docking test, application of KGS2 also led to improved structure-activity relationship in some cases. KGS2 can be applied as a convenient "add-on" to current scoring functions without the need to re-engineer them, and its application is not limited to certain target proteins as customized scoring functions. As an interpolation method, its accuracy in principle can be improved further with the increasing knowledge of protein-ligand complex structures and binding affinity data. We expect that KGS2 will become a practical tool for enhancing the performance of current scoring functions in binding affinity prediction. The KGS2 software is available upon contacting the authors.

  12. The Plasmodium falciparum exported protein PF3D7_0402000 binds to erythrocyte ankyrin and band 4.1

    Energy Technology Data Exchange (ETDEWEB)

    Shakya, Bikash; Penn, Wesley D.; Nakayasu, Ernesto S.; Lacount, Douglas J.

    2017-09-01

    Plasmodium falciparum extensively modifies the infected red blood cell (RBC), resulting in changes in deformability, shape and surface properties. These alterations suggest that the RBC cytoskeleton is a major target for modification during infection. However, the molecular mechanisms leading to these changes are largely unknown. To begin to address this question, we screened for exported P. falciparum proteins that bound to the erythrocyte cytoskeleton proteins ankyrin 1 (ANK1) and band 4.1 (4.1R), which form critical interactions with other cytoskeletal proteins that contribute to the deformability and stability of RBCs. Yeast two-hybrid screens with ANK1 and 4.1R identified eight interactions with P. falciparum exported proteins, including an interaction between 4.1R and PF3D7_0402000 (PFD0090c). This interaction was first identified in a large-scale screen (Vignali et al., Malaria J, 7:211, 2008), which also reported an interaction between PF3D7_0402000 and ANK1. We confirmed the interactions of PF3D7_0402000 with 4.1R and ANK1 in pair-wise yeast two-hybrid and co-precipitation assays. In both cases, an intact PHIST domain in PF3D7_0402000 was required for binding. Complex purification followed by mass spectrometry analysis provided additional support for the interaction of PF3D7_0402000 with ANK1 and 4.1R. RBC ghost cells loaded with maltose-binding protein (MBP)-PF3D7_0402000 passed through a metal microsphere column less efficiently than mock- or MBP-loaded controls, consistent with an effect of PF3D7_0402000 on RBC rigidity or membrane stability. This study confirmed the interaction of PF3D7_0402000 with 4.1R in multiple independent assays, provided the first evidence that PF3D7_0402000 also binds to ANK1, and suggested that PF3D7_0402000 affects deformability or membrane stability of uninfected RBC ghosts.

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

    Science.gov (United States)

    Boudard, Mélanie; Bernauer, Julie; Barth, Dominique; Cohen, Johanne; Denise, Alain

    2015-01-01

    Cellular processes involve large numbers of RNA molecules. The functions of these RNA molecules and their binding to molecular machines are highly dependent on their 3D structures. One of the key challenges in RNA structure prediction and modeling is predicting the spatial arrangement of the various structural elements of RNA. As RNA folding is generally hierarchical, methods involving coarse-grained models hold great promise for this purpose. We present here a novel coarse-grained method for sampling, based on game theory and knowledge-based potentials. This strategy, GARN (Game Algorithm for RNa sampling), is often much faster than previously described techniques and generates large sets of solutions closely resembling the native structure. GARN is thus a suitable starting point for the molecular modeling of large RNAs, particularly those with experimental constraints. GARN is available from: http://garn.lri.fr/.

  14. Parallel 3D Simulation of Seismic Wave Propagation in the Structure of Nobi Plain, Central Japan

    Science.gov (United States)

    Kotani, A.; Furumura, T.; Hirahara, K.

    2003-12-01

    We performed large-scale parallel simulations of the seismic wave propagation to understand the complex wave behavior in the 3D basin structure of the Nobi Plain, which is one of the high population cities in central Japan. In this area, many large earthquakes occurred in the past, such as the 1891 Nobi earthquake (M8.0), the 1944 Tonankai earthquake (M7.9) and the 1945 Mikawa earthquake (M6.8). In order to mitigate the potential disasters for future earthquakes, 3D subsurface structure of Nobi Plain has recently been investigated by local governments. We referred to this model together with bouguer anomaly data to construct a detail 3D basin structure model for Nobi plain, and conducted computer simulations of ground motions. We first evaluated the ground motions for two small earthquakes (M4~5); one occurred just beneath the basin edge at west, and the other occurred at south. The ground motions from these earthquakes were well recorded by the strong motion networks; K-net, Kik-net, and seismic intensity instruments operated by local governments. We compare the observed seismograms with simulations to validate the 3D model. For the 3D simulation we sliced the 3D model into a number of layers to assign to many processors for concurrent computing. The equation of motions are solved using a high order (32nd) staggered-grid FDM in horizontal directions, and a conventional (4th-order) FDM in vertical direction with the MPI inter-processor communications between neighbor region. The simulation model is 128km by 128km by 43km, which is discritized at variable grid size of 62.5-125m in horizontal directions and of 31.25-62.5m in vertical direction. We assigned a minimum shear wave velocity is Vs=0.4km/s, at the top of the sedimentary basin. The seismic sources for the small events are approximated by double-couple point source and we simulate the seismic wave propagation at maximum frequency of 2Hz. We used the Earth Simulator (JAMSTEC, Yokohama Inst) to conduct such

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

    Directory of Open Access Journals (Sweden)

    Ernie G. Kalnins

    2012-06-01

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

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

    International Nuclear Information System (INIS)

    Shi, Linlin; Liu, Na; Zhou, Jianyang; Zhou, Yuanguo; Wang, Jiamin; Liu, Qing Huo

    2016-01-01

    The spectral element method (SEM) is a special kind of high-order finite element method (FEM) which combines the flexibility of a finite element method with the accuracy of a spectral method. In contrast to the traditional FEM, the SEM exhibits advantages in the high-order accuracy as the error decreases exponentially with the increase of interpolation degree by employing the Gauss–Lobatto–Legendre (GLL) polynomials as basis functions. In this study, the spectral element method is developed for the first time for the determination of band structures of 3D isotropic/anisotropic phononic crystals (PCs). Based on the Bloch theorem, we present a novel, intuitive discretization formulation for Navier equation in the SEM scheme for periodic media. By virtue of using the orthogonal Legendre polynomials, the generalized eigenvalue problem is converted to a regular one in our SEM implementation to improve the efficiency. Besides, according to the specific geometry structure, 8-node and 27-node hexahedral elements as well as an analytic mesh have been used to accurately capture curved PC models in our SEM scheme. To verify its accuracy and efficiency, this study analyses the phononic-crystal plates with square and triangular lattice arrangements, and the 3D cubic phononic crystals consisting of simple cubic (SC), bulk central cubic (BCC) and faced central cubic (FCC) lattices with isotropic or anisotropic scatters. All the numerical results considered demonstrate that SEM is superior to the conventional FEM and can be an efficient alternative method for accurate determination of band structures of 3D phononic crystals. (paper)

  17. Spiral-structured, nanofibrous, 3D scaffolds for bone tissue engineering.

    Science.gov (United States)

    Wang, Junping; Valmikinathan, Chandra M; Liu, Wei; Laurencin, Cato T; Yu, Xiaojun

    2010-05-01

    Polymeric nanofiber matrices have already been widely used in tissue engineering. However, the fabrication of nanofibers into complex three-dimensional (3D) structures is restricted due to current manufacturing techniques. To overcome this limitation, we have incorporated nanofibers onto spiral-structured 3D scaffolds made of poly (epsilon-caprolactone) (PCL). The spiral structure with open geometries, large surface areas, and porosity will be helpful for improving nutrient transport and cell penetration into the scaffolds, which are otherwise limited in conventional tissue-engineered scaffolds for large bone defects repair. To investigate the effect of structure and fiber coating on the performance of the scaffolds, three groups of scaffolds including cylindrical PCL scaffolds, spiral PCL scaffolds (without fiber coating), and spiral-structured fibrous PCL scaffolds (with fiber coating) have been prepared. The morphology, porosity, and mechanical properties of the scaffolds have been characterized. Furthermore, human osteoblast cells are seeded on these scaffolds, and the cell attachment, proliferation, differentiation, and mineralized matrix deposition on the scaffolds are evaluated. The results indicated that the spiral scaffolds possess porosities within the range of human trabecular bone and an appropriate pore structure for cell growth, and significantly lower compressive modulus and strength than cylindrical scaffolds. When compared with the cylindrical scaffolds, the spiral-structured scaffolds demonstrated enhanced cell proliferation, differentiation, and mineralization and allowed better cellular growth and penetration. The incorporation of nanofibers onto spiral scaffolds further enhanced cell attachment, proliferation, and differentiation. These studies suggest that spiral-structured nanofibrous scaffolds may serve as promising alternatives for bone tissue engineering applications. Copyright 2009 Wiley Periodicals, Inc.

  18. 3D velocity structure of upper crust beneath NW Bohemia/Vogtland

    Science.gov (United States)

    Javad Fallahi, Mohammad; Mousavi, Sima; Korn, Michael; Sens-Schönfelder, Christoph; Bauer, Klaus; Rößler, Dirk

    2013-04-01

    The 3D structure of the upper crust beneath west Bohemia/Vogtland region, analyzed with travel time tomography and ambient noise surface wave tomography using existing data. This region is characterized by a series of phenomena like occurrence of repeated earthquake swarms, surface exhalation, CO2 enriched fluids, mofettes, mineral springs and enhanced heat flow, and has been proposed as an excellent location for an ICDP drilling project targeted to a better understanding of the crust in an active magmatic environment. We performed a 3D tomography using P-and S-wave travel times of local earthquakes and explosions. The data set were taken from permanent and temporary seismic networks in Germany and Czech Republic from 2000 to 2010, as well as active seismic experiments like Celebration 2000 and quarry blasts. After picking P and S wave arrival times, 399 events which were recorded by 9 or more stations and azimuthal gap<160° were selected for inversion. A simultaneous inversion of P and S wave 1D velocity models together with relocations of hypocenters and station corrections was performed. The obtained minimum 1D velocity model was used as starting model for the 3D Vp and Vp/Vs velocity models. P and S wave travel time tomography employs damped least-square method and ray tracing by pseudo-bending algorithm. For model parametrization different cell node spacings have been tested to evaluate the resolution in each node. Synthetic checkerboard tests have been done to check the structural resolution. Then Vp and Vp/Vs in the preferred 3D grid model have been determined. Earthquakes locations in iteration process change till the hypocenter adjustments and travel time residuals become smaller than the defined threshold criteria. Finally the analysis of the resolution depicts the well resolved features for interpretation. We observed lower Vp/Vs ratio in depth of 5-10 km close to the foci of earthquake swarms and higher Vp/Vs ratio is observed in Saxoturingian zone and

  19. Co-simulation coupling spectral/finite elements for 3D soil/structure interaction problems

    Science.gov (United States)

    Zuchowski, Loïc; Brun, Michael; De Martin, Florent

    2018-05-01

    The coupling between an implicit finite elements (FE) code and an explicit spectral elements (SE) code has been explored for solving the elastic wave propagation in the case of soil/structure interaction problem. The coupling approach is based on domain decomposition methods in transient dynamics. The spatial coupling at the interface is managed by a standard coupling mortar approach, whereas the time integration is dealt with an hybrid asynchronous time integrator. An external coupling software, handling the interface problem, has been set up in order to couple the FE software Code_Aster with the SE software EFISPEC3D.

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

    Science.gov (United States)

    Holness, F. Benjamin; Price, Aaron D.

    2016-04-01

    The intractable nature of intrinsically conductive polymers (ICP) leads to practical limitations in the fabrication of ICP-based transducers having complex three-dimensional geometries. Conventional ICP device fabrication processes have focused primarily on thin-film deposition techniques; therefore this study explores novel additive manufacturing processes specifically developed for ICP with the ultimate goal of increasing the functionality of ICP sensors and actuators. Herein we employ automated polymer paste extrusion processes for the direct ink writing of 3D conductive polyaniline (PANI) structures. Realization of these structures is enabled through a modified fused filament fabrication delta robot equipped with an integrated polymer paste extruder. This unique robot-controlled additive manufacturing platform is capable of fabricating high-resolution 3D conductive PANI and has been utilized to produce structures with a minimum feature size of 1.5 mm. The required processability of PANI is achieved by means of a counter-ion induced thermal doping method. Using this method, a viscous paste is formulated as the extrudate and a thermo-chemical treatment is applied post extrusion to finalize the complexation.

  1. Direct ink writing of 3D conductive polyaniline structures and rheological modelling

    Science.gov (United States)

    Holness, F. Benjamin; Price, Aaron D.

    2018-01-01

    The intractable nature of conjugated polymers (CP) leads to practical limitations in the fabrication of CP-based transducers having complex three-dimensional geometries. Conventional CP device fabrication processes have focused primarily on thin-film deposition techniques; this study explores novel additive manufacturing processes specifically developed for CP with the ultimate goal of increasing the functionality of CP sensors and actuators. Herein we employ automated polymer paste extrusion processes for the direct ink writing of 3D conductive polyaniline (PANI) structures. Realization of these structures was enabled through a modified fused filament fabrication delta robot equipped with an integrated polymer paste extruder to fabricate high-resolution 3D conductive PANI structures. The required processability of PANI was achieved by means of a counterion-induced thermal doping method. The effect of thermal doping on the PANI-DBSA paste by means of a constitutive relationship to describe the paste flow as a function of the thermal doping time is explored. This relationship is incorporated within a flow model to predict the extruded track width as a function of various process parameters including: print speed, gauge pressure, nozzle diameter, and pre-extrusion thermal doping time.

  2. Point-Structured Human Body Modeling Based on 3D Scan Data

    Directory of Open Access Journals (Sweden)

    Ming-June Tsai

    2018-01-01

    Full Text Available A novel point-structured geometrical modelling for realistic human body is introduced in this paper. This technique is based on the feature extraction from the 3D body scan data. Anatomic feature such as the neck, the arm pits, the crotch points, and other major feature points are recognized. The body data is then segmented into 6 major parts. A body model is then constructed by re-sampling the scanned data to create a point-structured mesh. The body model contains body geodetic landmarks in latitudinal and longitudinal curves passing through those feature points. The body model preserves the perfect body shape and all the body dimensions but requires little space. Therefore, the body model can be used as a mannequin in garment industry, or as a manikin in various human factor designs, but the most important application is to use as a virtue character to animate the body motion in mocap (motion capture systems. By adding suitable joint freedoms between the segmented body links, kinematic and dynamic properties of the motion theories can be applied to the body model. As a result, a 3D virtual character that is fully resembled the original scanned individual is vividly animating the body motions. The gaps between the body segments due to motion can be filled up by skin blending technique using the characteristic of the point-structured model. The model has the potential to serve as a standardized datatype to archive body information for all custom-made products.

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

    Science.gov (United States)

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

    2015-03-01

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

  4. A novel 3D shape descriptor for automatic retrieval of anatomical structures from medical images

    Science.gov (United States)

    Nunes, Fátima L. S.; Bergamasco, Leila C. C.; Delmondes, Pedro H.; Valverde, Miguel A. G.; Jackowski, Marcel P.

    2017-03-01

    Content-based image retrieval (CBIR) aims at retrieving from a database objects that are similar to an object provided by a query, by taking into consideration a set of extracted features. While CBIR has been widely applied in the two-dimensional image domain, the retrieval of3D objects from medical image datasets using CBIR remains to be explored. In this context, the development of descriptors that can capture information specific to organs or structures is desirable. In this work, we focus on the retrieval of two anatomical structures commonly imaged by Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) techniques, the left ventricle of the heart and blood vessels. Towards this aim, we developed the Area-Distance Local Descriptor (ADLD), a novel 3D local shape descriptor that employs mesh geometry information, namely facet area and distance from centroid to surface, to identify shape changes. Because ADLD only considers surface meshes extracted from volumetric medical images, it substantially diminishes the amount of data to be analyzed. A 90% precision rate was obtained when retrieving both convex (left ventricle) and non-convex structures (blood vessels), allowing for detection of abnormalities associated with changes in shape. Thus, ADLD has the potential to aid in the diagnosis of a wide range of vascular and cardiac diseases.

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

    Directory of Open Access Journals (Sweden)

    Feng Xu

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

  6. 3D printing in chemical engineering and catalytic technology: structured catalysts, mixers and reactors.

    Science.gov (United States)

    Parra-Cabrera, Cesar; Achille, Clement; Kuhn, Simon; Ameloot, Rob

    2018-01-02

    Computer-aided fabrication technologies combined with simulation and data processing approaches are changing our way of manufacturing and designing functional objects. Also in the field of catalytic technology and chemical engineering the impact of additive manufacturing, also referred to as 3D printing, is steadily increasing thanks to a rapidly decreasing equipment threshold. Although still in an early stage, the rapid and seamless transition between digital data and physical objects enabled by these fabrication tools will benefit both research and manufacture of reactors and structured catalysts. Additive manufacturing closes the gap between theory and experiment, by enabling accurate fabrication of geometries optimized through computational fluid dynamics and the experimental evaluation of their properties. This review highlights the research using 3D printing and computational modeling as digital tools for the design and fabrication of reactors and structured catalysts. The goal of this contribution is to stimulate interactions at the crossroads of chemistry and materials science on the one hand and digital fabrication and computational modeling on the other.

  7. Building 3D structures of vanadium pentoxide nanosheets and application as electrodes in supercapacitors.

    Science.gov (United States)

    Zhu, Jixin; Cao, Liujun; Wu, Yingsi; Gong, Yongji; Liu, Zheng; Hoster, Harry E; Zhang, Yunhuai; Zhang, Shengtao; Yang, Shubin; Yan, Qingyu; Ajayan, Pulickel M; Vajtai, Robert

    2013-01-01

    Various two-dimensional (2D) materials have recently attracted great attention owing to their unique properties and wide application potential in electronics, catalysis, energy storage, and conversion. However, large-scale production of ultrathin sheets and functional nanosheets remains a scientific and engineering challenge. Here we demonstrate an efficient approach for large-scale production of V2O5 nanosheets having a thickness of 4 nm and utilization as building blocks for constructing 3D architectures via a freeze-drying process. The resulting highly flexible V2O5 structures possess a surface area of 133 m(2) g(-1), ultrathin walls, and multilevel pores. Such unique features are favorable for providing easy access of the electrolyte to the structure when they are used as a supercapacitor electrode, and they also provide a large electroactive surface that advantageous in energy storage applications. As a consequence, a high specific capacitance of 451 F g(-1) is achieved in a neutral aqueous Na2SO4 electrolyte as the 3D architectures are utilized for energy storage. Remarkably, the capacitance retention after 4000 cycles is more than 90%, and the energy density is up to 107 W·h·kg(-1) at a high power density of 9.4 kW kg(-1).

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

    KAUST Repository

    Ceylan, Duygu

    2014-01-01

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

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

    Science.gov (United States)

    Vogt, Dominik Walter; Leonhardt, Rainer

    2016-11-01

    We demonstrate broadband, low loss, and close-to-zero dispersion guidance of terahertz (THz) radiation in a dielectric tube with an anti-reflection structure (AR-tube waveguide) in the frequency range from 0.2 to 1.0 THz. The anti-reflection structure (ARS) consists of close-packed cones in a hexagonal lattice arranged on the outer surface of the tube cladding. The feature size of the ARS is in the order of the wavelength between 0.2 and 1.0 THz. The waveguides are fabricated with the versatile and cost efficient 3D-printing method. Terahertz time-domain spectroscopy (THz-TDS) measurements as well as 3D finite-difference time-domain simulations (FDTD) are performed to extensively characterize the AR-tube waveguides. Spectrograms, attenuation spectra, effective phase refractive indices, and the group-velocity dispersion parameters β 2 of the AR-tube waveguides are presented. Both the experimental and numerical results confirm the extended bandwidth and smaller group-velocity dispersion of the AR-tube waveguide compared to a low loss plain dielectric tube THz waveguide. The AR-tube waveguide prototypes show an attenuation spectrum close to the theoretical limit given by the infinite cladding tube waveguide.

  10. Numerical modeling of 3D halo current path in ITER structures

    Energy Technology Data Exchange (ETDEWEB)

    Bettini, Paolo; Marconato, Nicolò; Furno Palumbo, Maurizio; Peruzzo, Simone [Consorzio RFX, EURATOM-ENEA Association, C.so Stati Uniti 4, 35127 Padova (Italy); Specogna, Ruben, E-mail: ruben.specogna@uniud.it [DIEGM, Università di Udine, Via delle Scienze, 208, 33100 Udine (Italy); Albanese, Raffaele; Rubinacci, Guglielmo; Ventre, Salvatore; Villone, Fabio [Consorzio CREATE, EURATOM-ENEA Association, Via Claudio 21, 80125 Napoli (Italy)

    2013-10-15

    Highlights: ► Two numerical codes for the evaluation of halo currents in 3D structures are presented. ► A simplified plasma model is adopted to provide the input (halo current injected into the FW). ► Two representative test cases of ITER symmetric and asymmetric VDEs have been analyzed. ► The proposed approaches provide results in excellent agreement for both cases. -- Abstract: Disruptions represent one of the main concerns for Tokamak operation, especially in view of fusion reactors, or experimental test reactors, due to the electro-mechanical loads induced by halo and eddy currents. The development of a predictive tool which allows to estimate the magnitude and spatial distribution of the halo current forces is of paramount importance in order to ensure robust vessel and in-vessel component design. With this aim, two numerical codes (CARIDDI, CAFE) have been developed, which allow to calculate the halo current path (resistive distribution) in the passive structures surrounding the plasma. The former is based on an integral formulation for the eddy currents problem particularized to the static case; the latter implements a pair of 3D FEM complementary formulations for the solution of the steady-state current conduction problem. A simplified plasma model is adopted to provide the inputs (halo current injected into the first wall). Two representative test cases (ITER symmetric and asymmetric VDEs) have been selected to cross check the results of the proposed approaches.

  11. 3D Structure of Iran and Surrounding Areas From The Simultaneous Inversion of Complementary Geophysical Observations

    Science.gov (United States)

    Ammon, C. J.; Maceira, M.; Cleveland, M.

    2010-12-01

    We present a three-dimensional seismic-structure model of the Arabian-Eurasian collision zone obtained via simultaneous, joint inversion of surface-wave dispersion measurements, teleseismic P-wave receiver functions, and gravity observations. We use a simple, approximate relationship between density and seismic velocities so that the three data sets may be combined in a single inversion. The sensitivity of the different data sets are well known: surface waves provide information on the smooth variations in elastic properties, receiver functions provide information on abrupt velocity contrasts, and gravity measurements provide information on broad-wavenumber shallow density variations and long-wavenumber components of deeper density structures. The combination of the data provides improved resolution of shallow-structure variations, which in turn help produce the smooth features at depth with less contamination from the strong heterogeneity often observed in the upper crust. We also explore geologically based smoothness constraints to help resolve sharp features in the underlying shallow 3D structure. Our focus is on the region surrounding Iran from east Turkey and Iraq in the west, to Pakistan and Afghanistan in the east. We use Bouguer gravity anomalies derived from the global gravity model extracted from the GRACE satellite mission. Surface-wave dispersion velocities in the period range between 7 and 150 s are taken from previously published tomographic maps for the region. Preliminary results show expected strong variations in the Caspian region as well as the deep sediment regions of the Persian Gulf. Regions constrained with receiver-function information generally show sharper crust-mantle boundary structure than that obtained by inversion of the surface waves alone (with thin layers and smoothing constraints). Final results of the simultaneous inversion will help us to better understand one of the most prominent examples of continental collision. Such models

  12. Electrically heated 3D-macro cellular SiC structures for ignition and combustion application

    International Nuclear Information System (INIS)

    Falgenhauer, Ralf; Rambacher, Patrick; Schlier, Lorenz; Volkert, Jochen; Travitzky, Nahum; Greil, Peter; Weclas, Miroslaw

    2017-01-01

    Highlights: • 3D-printed macro cellular SiC structure. • Directly integrated electrically heated ignition element used in combustion reactor. • Experimental investigation of the ignition process. - Abstract: The paper describes different aspects of porous combustion reactor operation especially at cold start conditions. Under cold start conditions it is necessary to increase the internal energy of the combustion reactor, to accumulate enough energy inside its solid phase and to reach at least the ignition temperature on the reactors inner surface. The most practicable method to preheat a cold porous reactor is to use its surface as a flame holder and to apply free flame combustion as a heat source for the preheating process. This paper presents a new electrically heated ignition element, which gets integrated in a three dimensional macro-cellular SiSiC reactor structure. For the development of the ignition element it was assumed, that the element is made of the same material as the combustion reactor itself and is fully integrated within the three-dimensional macro-cellular structure of the combustion reactor. Additive manufacturing like three-dimensional (3D) printing permits the production of regular SiSiC structures with constant strut thickness and a defined current flow path. To get a controlled temperature distribution on the ignition element it is necessary to control the current density distribution in the three-dimensional macro-cellular reactor structure. The ignition element used is designed to be an electrical resistance in an electric current system, converting flowing current into heat with the goal to get the highest temperature in the ignition region (glow plug). First experiments show that the ignition element integrated in a combustion reactor exhibits high dynamics and can be heated to the temperatures much above 1000 °C in a very short time (approx. 800 ms) for current of I = 150 A.

  13. Curvilinear immersed boundary method for simulating fluid structure interaction with complex 3D rigid bodies

    Science.gov (United States)

    Borazjani, Iman; Ge, Liang; Sotiropoulos, Fotis

    2008-08-01

    The sharp-interface CURVIB approach of Ge and Sotiropoulos [L. Ge, F. Sotiropoulos, A numerical method for solving the 3D unsteady incompressible Navier-Stokes equations in curvilinear domains with complex immersed boundaries, Journal of Computational Physics 225 (2007) 1782-1809] is extended to simulate fluid structure interaction (FSI) problems involving complex 3D rigid bodies undergoing large structural displacements. The FSI solver adopts the partitioned FSI solution approach and both loose and strong coupling strategies are implemented. The interfaces between immersed bodies and the fluid are discretized with a Lagrangian grid and tracked with an explicit front-tracking approach. An efficient ray-tracing algorithm is developed to quickly identify the relationship between the background grid and the moving bodies. Numerical experiments are carried out for two FSI problems: vortex induced vibration of elastically mounted cylinders and flow through a bileaflet mechanical heart valve at physiologic conditions. For both cases the computed results are in excellent agreement with benchmark simulations and experimental measurements. The numerical experiments suggest that both the properties of the structure (mass, geometry) and the local flow conditions can play an important role in determining the stability of the FSI algorithm. Under certain conditions the FSI algorithm is unconditionally unstable 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

  14. Web-based three-dimensional Virtual Body Structures: W3D-VBS.

    Science.gov (United States)

    Temkin, Bharti; Acosta, Eric; Hatfield, Paul; Onal, Erhan; Tong, Alex

    2002-01-01

    Major efforts are being made to improve the teaching of human anatomy to foster cognition of visuospatial relationships. The Visible Human Project of the National Library of Medicine makes it possible to create virtual reality-based applications for teaching anatomy. Integration of traditional cadaver and illustration-based methods with Internet-based simulations brings us closer to this goal. Web-based three-dimensional Virtual Body Structures (W3D-VBS) is a next-generation immersive anatomical training system for teaching human anatomy over the Internet. It uses Visible Human data to dynamically explore, select, extract, visualize, manipulate, and stereoscopically palpate realistic virtual body structures with a haptic device. Tracking user's progress through evaluation tools helps customize lesson plans. A self-guided "virtual tour" of the whole body allows investigation of labeled virtual dissections repetitively, at any time and place a user requires it.

  15. Static/dynamic fluid-structure interaction analysis for 3-D rotary blade model

    International Nuclear Information System (INIS)

    Kim, Dong Hyun; Kim, Yu Sung; Kim, Dong Man; Park, Kang Kyun

    2009-01-01

    In this study, static/dynamic fluid-structure interaction analyses have been conducted for a 3D rotary blade model like a turbo-machinery or wind turbine blade. Advanced computational analysis system based on Computational Fluid Dynamics (CFD) and Computational Structural Dynamics (CSD) has been developed in order to investigate detailed dynamic responses of rotary type models. Fluid domains are modeled using the computational grid system with local grid deforming techniques. Reynolds-averaged Navier-Stokes equations with various turbulence model are solved for unsteady flow problems of the rotating blade model. Detailed static/dynamic responses and instantaneous pressure contours on the blade surfaces considering flow-separation effects are presented to show the multi-physical phenomenon of the rotating blades.

  16. 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography

    Science.gov (United States)

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

    2005-01-01

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

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

    Science.gov (United States)

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

    2017-03-28

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

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

    International Nuclear Information System (INIS)

    Franca, Fernando

    1995-01-01

    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)

  19. Usability of aerial video footage for 3-D scene reconstruction and structural damage assessment

    Science.gov (United States)

    Cusicanqui, Johnny; Kerle, Norman; Nex, Francesco

    2018-06-01

    Remote sensing has evolved into the most efficient approach to assess post-disaster structural damage, in extensively affected areas through the use of spaceborne data. For smaller, and in particular, complex urban disaster scenes, multi-perspective aerial imagery obtained with unmanned aerial vehicles and derived dense color 3-D models are increasingly being used. These type of data allow the direct and automated recognition of damage-related features, supporting an effective post-disaster structural damage assessment. However, the rapid collection and sharing of multi-perspective aerial imagery is still limited due to tight or lacking regulations and legal frameworks. A potential alternative is aerial video footage, which is typically acquired and shared by civil protection institutions or news media and which tends to be the first type of airborne data available. Nevertheless, inherent artifacts and the lack of suitable processing means have long limited its potential use in structural damage assessment and other post-disaster activities. In this research the usability of modern aerial video data was evaluated based on a comparative quality and application analysis of video data and multi-perspective imagery (photos), and their derivative 3-D point clouds created using current photogrammetric techniques. Additionally, the effects of external factors, such as topography and the presence of smoke and moving objects, were determined by analyzing two different earthquake-affected sites: Tainan (Taiwan) and Pescara del Tronto (Italy). Results demonstrated similar usabilities for video and photos. This is shown by the short 2 cm of difference between the accuracies of video- and photo-based 3-D point clouds. Despite the low video resolution, the usability of these data was compensated for by a small ground sampling distance. Instead of video characteristics, low quality and application resulted from non-data-related factors, such as changes in the scene, lack of

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

    Science.gov (United States)

    Zhang, Z.; Tian, J.; Qiu, B.; Zhao, W.

    2016-12-01

    South China Sea (SCS), the largest marginal sea in the western Pacific, is abundant with strong mesoscale eddies as revealed by both satellite and in situ observations. The 3D structure, generation and dissipation mechanisms of the SCS mesoscale eddies, however, are still not well understood at present due to the lack of well-designed and comprehensive field observations. In order to address the above scientific issues, the SCS Mesoscale Eddy Experiment (S-MEE for short) was designed and conducted in the period from October 2013 to June 2014. As part of S-MEE, two bottom-anchored subsurface mooring arrays with one consisting of 10 moorings and the other 7 moorings, were deployed along the historical pathway of the mesoscale eddies in the northern SCS. All the moorings were equipped with ADCPs, RCMs, CTDs and temperature chains to make continues measurements of horizontal current velocity and temperature/salinity in the whole water column. In addition to moored observations, we also conducted two transects across the center of one anticyclonic eddy (AE) and made high-resolution hydrographic and turbulent mixing measurements. Based on the data collected by the S-MEE, we obtained the full-depth 3D structures of one AE and one cyclonic eddy (CE) and revealed their generation and dissipation mechanisms. For the first time we found that the eddies in the northern SCS extend from the surface to the sea bottom and display prominent tilted structures in the vertical. The AE was suggested to be shed from the Kuroshio current, which intruded into the SCS through Luzon Strait in winter. For the CE, its generation was associated with the barotropic instability of the Kuroshio current. By conducting an eddy energy budget analysis, we further identified that generation of submesoscale motions constitutes the dominant mechanism for the eddy dissipation. The findings in this study, not only provides new insights into the 3D structure of oceanic eddies, but also contributes to

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

    Science.gov (United States)

    Dolžan, Erazem; Vrabec, Marko

    2015-04-01

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

  2. An Investigation of the 3D Electrical Resistivity Structure in the Chingshui Geothermal Area, NE Taiwan

    Directory of Open Access Journals (Sweden)

    Chih-Wen Chiang

    2015-01-01

    Full Text Available The Chingshui geothermal area southwest of the Ilan plain is identified as a western extension of the Okinawa Trough in the northern Taiwan subduction system. Numerous geophysical, geological and geochemical investigations have been conducted since the 1970s by the Industrial Technology Research Institute, the Chinese Petroleum Corporation of Taiwan and the National Science Council of Taiwan. These studies indicated that the Chingshui stream is one of the largest geothermal areas for electricity generation in Taiwan. However, the power generation efficiency has not met initial expectations. Magnetotelluric (MT data analyses show that the Chingshui geothermal region is a geologically complex area. A full three-dimensional (3D inversion was therefore applied to reprocess the MT data and provide the detailed electrical structure beneath the Chingshui geothermal region. The 3D geoelectrical model displays an improved image that clearly delineates the Chingshui geothermal system geometry. Two conductive anomalies are imaged that possibly indicate high potential areas for geothermal energy in the Chingshui geothermal system. One of the potential areas is located in the eastern part of the Chingshui Fault at shallow depths. A significant conductive anomaly is associated with high heat flow and fluid content situations southwest of the geothermal manifest area at depth. A higher interconnected fluid indicates that this area contains the highest potential for geothermal energy in the Chingshui geothermal system.

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

    Science.gov (United States)

    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.

  4. Real time 3D structural and Doppler OCT imaging on graphics processing units

    Science.gov (United States)

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

    2013-03-01

    In this report the application of graphics processing unit (GPU) programming for real-time 3D Fourier domain Optical Coherence Tomography (FdOCT) imaging with implementation of Doppler algorithms for visualization of the flows in capillary vessels is presented. Generally, the time of the data processing of the FdOCT data on the main processor of the computer (CPU) constitute a main limitation for real-time imaging. Employing additional algorithms, such as Doppler OCT analysis, makes this processing even more time consuming. Lately developed GPUs, which offers a very high computational power, give a solution to this problem. Taking advantages of them for massively parallel data processing, allow for real-time imaging in FdOCT. The presented software for structural and Doppler OCT allow for the whole processing with visualization of 2D data consisting of 2000 A-scans generated from 2048 pixels spectra with frame rate about 120 fps. The 3D imaging in the same mode of the volume data build of 220 × 100 A-scans is performed at a rate of about 8 frames per second. In this paper a software architecture, organization of the threads and optimization applied is shown. For illustration the screen shots recorded during real time imaging of the phantom (homogeneous water solution of Intralipid in glass capillary) and the human eye in-vivo is presented.

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

    Science.gov (United States)

    Cowley, Aidan

    2016-07-01

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

  6. A genetically modified protein-based hydrogel for 3D culture of AD293 cells.

    Directory of Open Access Journals (Sweden)

    Xiao Du

    Full Text Available Hydrogels have strong application prospects for drug delivery, tissue engineering and cell therapy because of their excellent biocompatibility and abundant availability as scaffolds for drugs and cells. In this study, we created hybrid hydrogels based on a genetically modified tax interactive protein-1 (TIP1 by introducing two or four cysteine residues in the primary structure of TIP1. The introduced cysteine residues were crosslinked with a four-armed poly (ethylene glycol having their arm ends capped with maleimide residues (4-armed-PEG-Mal to form hydrogels. In one form of the genetically modification, we incorporated a peptide sequence 'GRGDSP' to introduce bioactivity to the protein, and the resultant hydrogel could provide an excellent environment for a three dimensional cell culture of AD293 cells. The AD293 cells continued to divide and displayed a polyhedron or spindle-shape during the 3-day culture period. Besides, AD293 cells could be easily separated from the cell-gel constructs for future large-scale culture after being cultured for 3 days and treating hydrogel with trypsinase. This work significantly expands the toolbox of recombinant proteins for hydrogel formation, and we believe that our hydrogel will be of considerable interest to those working in cell therapy and controlled drug delivery.

  7. Detection, characterization and evolution of internal repeats in Chitinases of known 3-D structure.

    Directory of Open Access Journals (Sweden)

    Manigandan Sivaji

    Full Text Available Chitinase proteins have evolved and diversified almost in all organisms ranging from prokaryotes to eukaryotes. During evolution, internal repeats may appear in amino acid sequences of proteins which alter the structural and functional features. Here we deciphered the internal repeats from Chitinase and characterized the structural similarities between them. Out of 24 diverse Chitinase sequences selected, six sequences (2CJL, 2DSK, 2XVP, 2Z37, 3EBV and 3HBE did not contain any internal repeats of amino acid sequences. Ten sequences contained repeats of length <50, and the remaining 8 sequences contained repeat length between 50 and 100 residues. Two Chitinase sequences, 1ITX and 3SIM, were found to be structurally similar when analyzed using secondary structure of Chitinase from secondary and 3-Dimensional structure database of Protein Data Bank. Internal repeats of 3N17 and 1O6I were also involved in the ligand-binding site of those Chitinase proteins, respectively. Our analyses enhance our understanding towards the identification of structural characteristics of internal repeats in Chitinase proteins.

  8. Contact force structure and force chains in 3D sheared granular systems

    Science.gov (United States)

    Mair, Karen; Jettestuen, Espen; Abe, Steffen

    2010-05-01

    Faults often exhibit accumulations of granular debris, ground up to create a layer of rock flour or fault gouge separating the rigid fault walls. Numerical simulations and laboratory experiments of sheared granular materials, suggest that applied loads are preferentially transmitted across such systems by transient force networks that carry enhanced forces. The characterisation of such features is important since their nature and persistence almost certainly influence the macroscopic mechanical stability of these systems and potentially that of natural faults. 3D numerical simulations of granular shear are a valuable investigation tool since they allow us to track individual particle motions, contact forces and their evolution during applied shear, that are difficult to view directly in laboratory experiments or natural fault zones. In characterising contact force distributions, it is important to use global structure measures that allow meaningful comparisons of granular systems having e.g. different grain size distributions, as may be expected at different stages of a fault's evolution. We therefore use a series of simple measures to characterise the structure, such as distributions and correlations of contact forces that can be mapped onto a force network percolation problem as recently proposed by Ostojic and coworkers for 2D granular systems. This allows the use of measures from percolation theory to both define and characterise the force networks. We demonstrate the application of this method to 3D simulations of a sheared granular material. Importantly, we then compare our measure of the contact force structure with macroscopic frictional behaviour measured at the boundaries of our model to determine the influence of the force networks on macroscopic mechanical stability.

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Renata Ferrari

    2016-02-01

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

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

    Science.gov (United States)

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

    2016-04-01

    We present a 3D radially anisotropic velocity model of the crust and uppermost mantle structure beneath the Sea of Marmara and surroundings based on the full waveform inversion method. The intense seismic activity and crustal deformation are observed in the Northwest Turkey due to transition tectonics between the strike-slip North Anatolian Fault (NAF) and the extensional Aegean region. We have selected and simulated complete waveforms of 62 earthquakes (Mw > 4.0) occurred during 2007-2015, and recorded at (Δ Technological Research Council of Turkey (TUBITAK Project No: ÇAYDAG-114Y066), and EU-HORIZON-2020: COST Actions: Earth System Science and Environmental Management: ES1401 - Time Dependent Seismology (TIDES).

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

    Science.gov (United States)

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

    2008-12-01

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

  13. 3D NEAREST NEIGHBOUR SEARCH USING A CLUSTERED HIERARCHICAL TREE STRUCTURE

    Directory of Open Access Journals (Sweden)

    A. Suhaibah

    2016-06-01

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

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

    Science.gov (United States)

    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.

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

    KAUST Repository

    Coluccio, M. L.

    2015-05-01

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

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

    Science.gov (United States)

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

    2015-10-01

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

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

    International Nuclear Information System (INIS)

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

    2015-01-01

    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. (technical note)

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

    International Nuclear Information System (INIS)

    Gischkat, Thomas

    2010-01-01

    The present thesis deals with the usage of the ion-beam enhanced etching (IBEE) for the 3D structuration of lithium niobate (LiNbO 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 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 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 3 . This is exemplarily shown for a microresonator and for a 2D photonic crystal with below lying air slit. [de

  19. Crystalline Hybrid Polyphenylene Macromolecules from Octaalkynylsilsesquioxanes, Crystal Structures, and a Potential Route to 3-D Graphenes

    Energy Technology Data Exchange (ETDEWEB)

    Roll, Mark F; Kampf, Jeffrey W.; Laine, Richard M

    2011-05-10

    We report here the Diels–Alder reaction of octa(diphenylacetylene)silsesquioxane [DPA₈OS] with tetraphenylcyclopentadienone or tetra(p-tolyl)cyclopentadienone to form octa(hexaphenylbenzene)octasilsesquioxane, (Ph₆C₆)₈OS, or octa(tetratolyldiphenylbenzene)octasilsesquioxane, (p-Tolyl₄Ph₂C₆)₈OS. Likewise, tetra(p-tolyl)cyclopentadienone reacts with octa(p-tolylethynylphenyl)OS to form octa(pentatolylphenylbenzene)octasilsesquioxane (p-Tolyl₅PhC₆)₈OS. These compounds, with molecular weights of 4685–5245 Da, were isolated and characterized using a variety of analytical methods. The crystal structure of DPA₈OS offers a 3 nm³ unit cell with Z = 1. The crystal structure of (Ph₆C₆)₈OS was determined to have a triclinic unit cell of 11 nm³ with Z = 1. The latter structure is believed to be the largest discrete molecular structure reported with 330 carbons. Efforts to dehydrogenatively cyclize (Scholl reaction) the hexaarylbenzene groups to form 3-D octgraphene compounds are described.

  20. Statistics on Near Wall Structures and Shear Stress Distribution from 3D Holographic Measurement.

    Science.gov (United States)

    Sheng, J.; Malkiel, E.; Katz, J.

    2007-11-01

    Digital Holographic Microscopy performs 3D velocity measurement in the near-wall region of a turbulent boundary layer in a square channel over a smooth wall at Reτ=1,400. Resolution of ˜1μm over a sample volume of 1.5x2x1.5mm (x^+=50, y^+=60, z^+=50) is sufficient for resolving buffer layer and lower log layer structures, and for measuring instantaneous wall shear stress distributions from velocity gradients in the viscous sublayer. Results, based on 700 instantaneous realizations, provide detailed statistics on the spatial distribution of both wall stress components along with characteristic flow structures. Conditional sampling based on maxima and minima of wall shear stresses, as well as examination of instantaneous flow structures, lead to development of a conceptual model for a characteristic flow phenomenon that seems to generating extreme stress events. This structure develops as an initially spanwise vortex element rises away from the surface, due to local disturbance, causing a local stress minimum. Due to increasing velocity with elevation, this element bends downstream, forming a pair of inclined streamwise vortices, aligned at 45^0 to freestream, with ejection-like flow between them. Entrainment of high streamwise momentum on the outer sides of this vortex pair generates streamwise shear stress maxima, 70 δν downstream, which are displaced laterally by 35 δν from the local minimum.

  1. DeepSite: protein-binding site predictor using 3D-convolutional neural networks.

    Science.gov (United States)

    Jiménez, J; Doerr, S; Martínez-Rosell, G; Rose, A S; De Fabritiis, G

    2017-10-01

    An important step in structure-based drug design consists in the prediction of druggable binding sites. Several algorithms for detecting binding cavities, those likely to bind to a small drug compound, have been developed over the years by clever exploitation of geometric, chemical and evolutionary features of the protein. Here we present a novel knowledge-based approach that uses state-of-the-art convolutional neural networks, where the algorithm is learned by examples. In total, 7622 proteins from the scPDB database of binding sites have been evaluated using both a distance and a volumetric overlap approach. Our machine-learning based method demonstrates superior performance to two other competitive algorithmic strategies. DeepSite is freely available at www.playmolecule.org. Users can submit either a PDB ID or PDB file for pocket detection to our NVIDIA GPU-equipped servers through a WebGL graphical interface. gianni.defabritiis@upf.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  2. Applying a foil queue micro-electrode in micro-EDM to fabricate a 3D micro-structure

    Science.gov (United States)

    Xu, Bin; Guo, Kang; Wu, Xiao-yu; Lei, Jian-guo; Liang, Xiong; Guo, Deng-ji; Ma, Jiang; Cheng, Rong

    2018-05-01

    Applying a 3D micro-electrode in a micro electrical discharge machining (micro-EDM) can fabricate a 3D micro-structure with an up and down reciprocating method. However, this processing method has some shortcomings, such as a low success rate and a complex process for fabrication of 3D micro-electrodes. By focusing on these shortcomings, this paper proposed a novel 3D micro-EDM process based on the foil queue micro-electrode. Firstly, a 3D micro-electrode was discretized into several foil micro-electrodes and these foil micro-electrodes constituted a foil queue micro-electrode. Then, based on the planned process path, foil micro-electrodes were applied in micro-EDM sequentially and the micro-EDM results of each foil micro-electrode were able to superimpose the 3D micro-structure. However, the step effect will occur on the 3D micro-structure surface, which has an adverse effect on the 3D micro-structure. To tackle this problem, this paper proposes to reduce this adverse effect by rounded corner wear at the end of the foil micro-electrode and studies the impact of machining parameters on rounded corner wear and the step effect on the micro-structure surface. Finally, using a wire cutting voltage of 80 V, a current of 0.5 A and a pulse width modulation ratio of 1:4, the foil queue micro-electrode was fabricated by wire electrical discharge machining. Also, using a pulse width of 100 ns, a pulse interval of 200 ns, a voltage of 100 V and workpiece material of 304# stainless steel, the foil queue micro-electrode was applied in micro-EDM for processing of a 3D micro-structure with hemispherical features, which verified the feasibility of this process.

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

    Science.gov (United States)

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

    2017-01-15

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

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

    Science.gov (United States)

    2015-11-17

    fabricated using 3D printer . The fill factor decreases radially outwards and the voids are visible in the unit cells as you approach the periphery of the...fabricated in 3D PhC template. The height of letters is 0.7 mm as designed in the motion stage control program [110...with thin walls) [29]. Figure 6: Examples of lenses fabricated with AM (a) GRIN lens fabricated using 3D printer . The fill factor decreases

  5. 3D Modelling of Inaccessible Areas using UAV-based Aerial Photography and Structure from Motion

    Science.gov (United States)

    Obanawa, Hiroyuki; Hayakawa, Yuichi; Gomez, Christopher

    2014-05-01

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

  6. Topology optimization aided structural design: Interpretation, computational aspects and 3D printing.

    Science.gov (United States)

    Kazakis, Georgios; Kanellopoulos, Ioannis; Sotiropoulos, Stefanos; Lagaros, Nikos D

    2017-10-01

    Construction industry has a major impact on the environment that we spend most of our life. Therefore, it is important that the outcome of architectural intuition performs well and complies with the design requirements. Architects usually describe as "optimal design" their choice among a rather limited set of design alternatives, dictated by their experience and intuition. However, modern design of structures requires accounting for a great number of criteria derived from multiple disciplines, often of conflicting nature. Such criteria derived from structural engineering, eco-design, bioclimatic and acoustic performance. The resulting vast number of alternatives enhances the need for computer-aided architecture in order to increase the possibility of arriving at a more preferable solution. Therefore, the incorporation of smart, automatic tools in the design process, able to further guide designer's intuition becomes even more indispensable. The principal aim of this study is to present possibilities to integrate automatic computational techniques related to topology optimization in the phase of intuition of civil structures as part of computer aided architectural design. In this direction, different aspects of a new computer aided architectural era related to the interpretation of the optimized designs, difficulties resulted from the increased computational effort and 3D printing capabilities are covered here in.

  7. Impact of 3D Canopy Structure on Remote Sensing Vegetation Index and Solar Induced Chlorophyll Fluorescence

    Science.gov (United States)

    Zeng, Y.; Berry, J. A.; Jing, L.; Qinhuo, L.

    2017-12-01

    Terrestrial ecosystem plays a critical role in removing CO2 from atmosphere by photosynthesis. Remote sensing provides a possible way to monitor the Gross Primary Production (GPP) at the global scale. Vegetation Indices (VI), e.g., NDVI and NIRv, and Solar Induced Fluorescence (SIF) have been widely used as a proxy for GPP, while the impact of 3D canopy structure on VI and SIF has not be comprehensively studied yet. In this research, firstly, a unified radiative transfer model for visible/near-infrared reflectance and solar induced chlorophyll fluorescence has been developed based on recollision probability and directional escape probability. Then, the impact of view angles, solar angles, weather conditions, leaf area index, and multi-layer leaf angle distribution (LAD) on VI and SIF has been studied. Results suggest that canopy structure plays a critical role in distorting pixel-scale remote sensing signal from leaf-scale scattering. In thin canopy, LAD affects both of the remote sensing estimated GPP and real GPP, while in dense canopy, SIF variations are mainly due to canopy structure, instead of just due to physiology. At the microscale, leaf angle reflects the plant strategy to light on the photosynthesis efficiency, and at the macroscale, a priori knowledge of leaf angle distribution for specific species can improve the global GPP estimation by remote sensing.

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

    Directory of Open Access Journals (Sweden)

    Mihai V. Putz

    2016-07-01

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

  9. 3D QSAR models built on structure-based alignments of Abl tyrosine kinase inhibitors.

    Science.gov (United States)

    Falchi, Federico; Manetti, Fabrizio; Carraro, Fabio; Naldini, Antonella; Maga, Giovanni; Crespan, Emmanuele; Schenone, Silvia; Bruno, Olga; Brullo, Chiara; Botta, Maurizio

    2009-06-01

    Quality QSAR: A combination of docking calculations and a statistical approach toward Abl inhibitors resulted in a 3D QSAR model, the analysis of which led to the identification of ligand portions important for affinity. New compounds designed on the basis of the model were found to have very good affinity for the target, providing further validation of the model itself.The X-ray crystallographic coordinates of the Abl tyrosine kinase domain in its active, inactive, and Src-like inactive conformations were used as targets to simulate the binding mode of a large series of pyrazolo[3,4-d]pyrimidines (known Abl inhibitors) by means of GOLD software. Receptor-based alignments provided by molecular docking calculations were submitted to a GRID-GOLPE protocol to generate 3D QSAR models. Analysis of the results showed that the models based on the inactive and Src-like inactive conformations had very poor statistical parameters, whereas the sole model based on the active conformation of Abl was characterized by significant internal and external predictive ability. Subsequent analysis of GOLPE PLS pseudo-coefficient contour plots of this model gave us a better understanding of the relationships between structure and affinity, providing suggestions for the next optimization process. On the basis of these results, new compounds were designed according to the hydrophobic and hydrogen bond donor and acceptor contours, and were found to have improved enzymatic and cellular activity with respect to parent compounds. Additional biological assays confirmed the important role of the selected compounds as inhibitors of cell proliferation in leukemia cells.

  10. Imidazole-containing farnesyltransferase inhibitors: 3D quantitative structure-activity relationships and molecular docking

    Science.gov (United States)

    Xie, Aihua; Odde, Srinivas; Prasanna, Sivaprakasam; Doerksen, Robert J.

    2009-07-01

    One of the most promising anticancer and recent antimalarial targets is the heterodimeric zinc-containing protein farnesyltransferase (FT). In this work, we studied a highly diverse series of 192 Abbott-initiated imidazole-containing compounds and their FT inhibitory activities using 3D-QSAR and docking, in order to gain understanding of the interaction of these inhibitors with FT to aid development of a rational strategy for further lead optimization. We report several highly significant and predictive CoMFA and CoMSIA models. The best model, composed of CoMFA steric and electrostatic fields combined with CoMSIA hydrophobic and H-bond acceptor fields, had r 2 = 0.878, q 2 = 0.630, and r pred 2 = 0.614. Docking studies on the statistical outliers revealed that some of them had a different binding mode in the FT active site based on steric bulk and available active site space, explaining why the predicted activities differed from the experimental activities.

  11. Fluid-structure interaction and structural analyses using a comprehensive mitral valve model with 3D chordal structure.

    Science.gov (United States)

    Toma, Milan; Einstein, Daniel R; Bloodworth, Charles H; Cochran, Richard P; Yoganathan, Ajit P; Kunzelman, Karyn S

    2017-04-01

    Over the years, three-dimensional models of the mitral valve have generally been organized around a simplified anatomy. Leaflets have been typically modeled as membranes, tethered to discrete chordae typically modeled as one-dimensional, non-linear cables. Yet, recent, high-resolution medical images have revealed that there is no clear boundary between the chordae and the leaflets. In fact, the mitral valve has been revealed to be more of a webbed structure whose architecture is continuous with the chordae and their extensions into the leaflets. Such detailed images can serve as the basis of anatomically accurate, subject-specific models, wherein the entire valve is modeled with solid elements that more faithfully represent the chordae, the leaflets, and the transition between the two. These models have the potential to enhance our understanding of mitral valve mechanics and to re-examine the role of the mitral valve chordae, which heretofore have been considered to be 'invisible' to the fluid and to be of secondary importance to the leaflets. However, these new models also require a rethinking of modeling assumptions. In this study, we examine the conventional practice of loading the leaflets only and not the chordae in order to study the structural response of the mitral valve apparatus. Specifically, we demonstrate that fully resolved 3D models of the mitral valve require a fluid-structure interaction analysis to correctly load the valve even in the case of quasi-static mechanics. While a fluid-structure interaction mode is still more computationally expensive than a structural-only model, we also show that advances in GPU computing have made such models tractable. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  12. Shallow structure of the Somma Vesuvius volcano from 3D inversion of gravity data

    Science.gov (United States)

    Cella, Federico; Fedi, Maurizio; Florio, Giovanni; Grimaldi, Marino; Rapolla, Antonio

    2007-04-01

    A gravity investigation was carried out in the Somma-Vesuvius complex area (Campania, Italy) based on a dataset recently enlarged with new measurements. These cover the volcanic top and fill some other important spatial gaps in previous surveys. Besides the new gravity map of the Vesuvius, we also present the results of a 3D inverse modelling, carried out by using constraints from deep well exploration and seismic reflection surveys. The resulting density model provides a complete reconstruction of the top of the carbonate basement. This is relevant mostly on the western side of the survey area, where no significant information was previously available. Other new information regards the Somma-Vesuvius structure. It consists of an annular volume of rocks around the volcanic vent and that extends down to the carbonate basement. It results to be denser with respect to the surrounding sedimentary cover of the Campanian Plain and to the material located just along the central axis of the volcanic structure. The coherence between these features and other geophysical evidences from previous studies, will be discussed together with the other results of this research.

  13. Spatio-temporal structure of turbulent Reynolds stress zonal flow drive in 3D magnetic configuration

    International Nuclear Information System (INIS)

    Schmid, B; Ramisch, M; Manz, P; Stroth, U

    2017-01-01

    The poloidal dependence of the zonal flow drive and the underlying Reynolds stress structure are studied at the stellarator experiment TJ-K by means of a poloidal Langmuir-probe array. This gives the unique possibility to study the locality of the Reynolds stress in a complex toroidal magnetic geometry. It is found that the Reynolds stress is not homogeneously distributed along the flux surface but has a strong poloidal asymmetry where it is concentrated on the outboard side with a maximum above the midplane. The average tilt of the turbulent structures is thereby reflected in the anisotropy of the bivariant velocity distribution. Using a conditional averaging technique the temporal dynamics reveal that the zonal flow drive is also maximal in this particular region. The results suggest an influence of the magnetic field line curvature, which controls the underlying plasma turbulence. The findings are a basis for further comparison with turbulence simulations in 3D geometry and demonstrate the need for a global characterisation of plasma turbulence. (paper)

  14. 3D Measurement Technology by Structured Light Using Stripe-Edge-Based Gray Code

    International Nuclear Information System (INIS)

    Wu, H B; Chen, Y; Wu, M Y; Guan, C R; Yu, X Y

    2006-01-01

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

  15. Reconstruction of 3D Micro Pore Structure of Coal and Simulation of Its Mechanical Properties

    Directory of Open Access Journals (Sweden)

    Guang-zhe Deng

    2017-01-01

    Full Text Available This article takes the low permeability coal seam in the coalfield of South Judger Basin in Xinjiang, as a research object. The pore structure characteristics of coal rock mass in low permeability coal seam were analyzed quantitatively using scanning electron microscopy (SEM through the methods of statistics and digital image analysis. Based on the pore structure parameters and the distribution function of the coal rock mass, a three-dimensional porous cylinder model with different porosity was reconstructed by FLAC3D. The numerical simulation study of reconstructed pore model shows that (1 the porosity and the compressive strength have obvious nonlinear relation and satisfy the negative exponential relation; (2 the porosity significantly affects the stress distribution; with the increase of micro porosity, the stress distribution becomes nonuniform; (3 the compressive failures of different models are mainly shear failures, and the shape of fracture section is related to porosity; (4 the variation of seepage coefficient of the pore reconstruction model is consistent with the development of micro cracks. The micro mechanism of the deformation and failure of coal and the interaction of multiphase flow with porosity are revealed, which provides a theoretical reference for the clean development of the low permeability coal seam.

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

    Energy Technology Data Exchange (ETDEWEB)

    Gischkat, Thomas

    2010-01-12

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

  17. Strategies for Directing the Structure and Function of 3D Collagen Biomaterials across Length Scales

    Science.gov (United States)

    Walters, Brandan D.; Stegemann, Jan P.

    2013-01-01

    Collagen type I is a widely used natural biomaterial that has found utility in a variety of biological and medical applications. Its well characterized structure and role as an extracellular matrix protein make it a highly relevant material for controlling cell function and mimicking tissue properties. Collagen type I is abundant in a number of tissues, and can be isolated as a purified protein. This review focuses on hydrogel biomaterials made by reconstituting collagen type I from a solubilized form, with an emphasis on in vitro studies in which collagen structure can be controlled. The hierarchical structure of collagen from the nanoscale to the macroscale is described, with an emphasis on how structure is related to function across scales. Methods of reconstituting collagen into hydrogel materials are presented, including molding of macroscopic constructs, creation of microscale modules, and electrospinning of nanoscale fibers. The modification of collagen biomaterials to achieve desired structures and functions is also addressed, with particular emphasis on mechanical control of collagen structure, creation of collagen composite materials, and crosslinking of collagenous matrices. Biomaterials scientists have made remarkable progress in rationally designing collagen-based biomaterials and in applying them to both the study of biology and for therapeutic benefit. This broad review illustrates recent examples of techniques used to control collagen structure, and to thereby direct its biological and mechanical functions. PMID:24012608

  18. Modeling the blockage of Lg waves from 3-D variations in crustal structure

    Science.gov (United States)

    Sanborn, Christopher J.; Cormier, Vernon F.

    2018-05-01

    Comprised of S waves trapped in Earth's crust, the high frequency (2-10 Hz) Lg wave is important to discriminating earthquakes from explosions by comparing its amplitude and waveform to those of Pg and Pn waves. Lateral variations in crustal structure, including variations in crustal thickness, intrinsic attenuation, and scattering, affect the efficiency of Lg propagation and its consistency as a source discriminant at regional (200-1500 km) distances. To investigate the effects of laterally varying Earth structure on the efficiency of propagation of Lg and Pg, we apply a radiative transport algorithm to model complete, high-frequency (2-4 Hz), regional coda envelopes. The algorithm propagates packets of energy with ray theory through large-scale 3-D structure, and includes stochastic effects of multiple-scattering by small-scale heterogeneities within the large-scale structure. Source-radiation patterns are described by moment tensors. Seismograms of explosion and earthquake sources are synthesized in canonical models to predict effects on waveforms of paths crossing regions of crustal thinning (pull-apart basins and ocean/continent transitions) and thickening (collisional mountain belts), For paths crossing crustal thinning regions, Lg is amplified at receivers within the thinned region but strongly disrupted and attenuated at receivers beyond the thinned region. For paths crossing regions of crustal thickening, Lg amplitude is attenuated at receivers within the thickened region, but experiences little or no reduction in amplitude at receivers beyond the thickened region. The length of the Lg propagation within a thickened region and the complexity of over- and under-thrust crustal layers, can produce localized zones of Lg amplification or attenuation. Regions of intense scattering within laterally homogeneous models of the crust increase Lg attenuation but do not disrupt its coda shape.

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

    Science.gov (United States)

    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

  20. Modeling and Reconstruction of Micro-structured 3D Chitosan/Gelatin Porous Scaffolds Using Micro-CT

    Science.gov (United States)

    Gong, Haibo; Li, Dichen; He, Jiankang; Liu, Yaxiong; Lian, Qin; Zhao, Jinna

    2008-09-01

    Three dimensional (3D) channel networks are the key to promise the uniform distribution of nutrients inside 3D hepatic tissue engineering scaffolds and prompt elimination of metabolic products out of the scaffolds. 3D chitosan/gelatin porous scaffolds with predefined internal channels were fabricated and a combination of light microscope, laser confocal microscopy and micro-CT were employed to characterize the structure of porous scaffolds. In order to evaluate the flow field distribution inside the micro-structured 3D scaffolds, a computer reconstructing method based on Micro-CT was proposed. According to this evaluating method, a contrast between 3D porous scaffolds with and without predefined internal channels was also performed to assess scaffolds' fluid characters. Results showed that the internal channel of the 3D scaffolds formed the 3D fluid channel network; the uniformity of flow field distribution of the scaffolds fabricated in this paper was better than the simple porous scaffold without micro-fluid channels.

  1. A Review on the 3D Printing of Functional Structures for Medical Phantoms and Regenerated Tissue and Organ Applications

    Directory of Open Access Journals (Sweden)

    Kan Wang

    2017-10-01

    Full Text Available Medical models, or “phantoms,” have been widely used for medical training and for doctor-patient interactions. They are increasingly used for surgical planning, medical computational models, algorithm verification and validation, and medical devices development. Such new applications demand high-fidelity, patient-specific, tissue-mimicking medical phantoms that can not only closely emulate the geometric structures of human organs, but also possess the properties and functions of the organ structure. With the rapid advancement of three-dimensional (3D printing and 3D bioprinting technologies, many researchers have explored the use of these additive manufacturing techniques to fabricate functional medical phantoms for various applications. This paper reviews the applications of these 3D printing and 3D bioprinting technologies for the fabrication of functional medical phantoms and bio-structures. This review specifically discusses the state of the art along with new developments and trends in 3D printed functional medical phantoms (i.e., tissue-mimicking medical phantoms, radiologically relevant medical phantoms, and physiological medical phantoms and 3D bio-printed structures (i.e., hybrid scaffolding materials, convertible scaffolds, and integrated sensors for regenerated tissues and organs.

  2. 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

    International Nuclear Information System (INIS)

    Rodt, T.; Ratiu, P.; Kacher, D.F.; Anderson, M.; Jolesz, F.A.; Kikinis, R.; Becker, H.; Bartling, S.

    2002-01-01

    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.)

  3. Very Deep inside the SN 1987A Core Ejecta: Molecular Structures Seen in 3D

    Energy Technology Data Exchange (ETDEWEB)

    Abellán, F. J.; Marcaide, J. M. [Departamento de Astronomía y Astrofísica, Universidad de Valencia, C/Dr. Moliner 50, E-46100 Burjassot (Spain); Indebetouw, R.; Chevalier, R. [Department of Astronomy, University of Virginia, P.O. Box 400325, Charlottesville, VA 22904 (United States); Gabler, M.; Janka, H.-Th. [Max-Planck-Institut für Astrophysik, Karl-Schwarzschild-Straße 1, D-85748 Garching (Germany); Fransson, C.; Lundqvist, P. [Department of Astronomy, The Oskar Klein Centre, Stockholm University, Alba Nova University Centre, SE-106 91 Stockholm (Sweden); Spyromilio, J. [ESO, Karl-Schwarzschild-Straße 2, D-85748 Garching (Germany); Burrows, D. N. [Department of Astronomy and Astrophysics, The Pennsylvania State University, University Park, PA 16802 (United States); Cigan, P.; Gomez, H. L.; Matsuura, M. [School of Physics and Astronomy, Cardiff University, Queens Buildings, The Parade, Cardiff CF24 3AA (United Kingdom); Gaensler, B. M. [Dunlap Institute for Astronomy and Astrophysics, University of Toronto, Toronto, ON M5S 3H4 (Canada); Kirshner, R. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Larsson, J. [KTH, Department of Physics, and the Oskar Klein Centre, AlbaNova, SE-106 91 Stockholm (Sweden); McCray, R. [Department of Astronomy, University of California, Berkeley, CA 94720-3411 (United States); Ng, C.-Y. [Department of Physics, The University of Hong Kong, Pokfulam Road, Hong Kong (China); Park, S. [Department of Physics, University of Texas at Arlington, 108 Science Hall, Box 19059, Arlington, TX 76019 (United States); Roche, P., E-mail: francisco.abellan@uv.es [Department of Physics, University of Oxford, Oxford OX1 3RH (United Kingdom); and others

    2017-06-20

    Most massive stars end their lives in core-collapse supernova explosions and enrich the interstellar medium with explosively nucleosynthesized elements. Following core collapse, the explosion is subject to instabilities as the shock propagates outward through the progenitor star. Observations of the composition and structure of the innermost regions of a core-collapse supernova provide a direct probe of the instabilities and nucleosynthetic products. SN 1987A in the Large Magellanic Cloud is one of very few supernovae for which the inner ejecta can be spatially resolved but are not yet strongly affected by interaction with the surroundings. Our observations of SN 1987A with the Atacama Large Millimeter/submillimeter Array are of the highest resolution to date and reveal the detailed morphology of cold molecular gas in the innermost regions of the remnant. The 3D distributions of carbon and silicon monoxide (CO and SiO) emission differ, but both have a central deficit, or torus-like distribution, possibly a result of radioactive heating during the first weeks (“nickel heating”). The size scales of the clumpy distribution are compared quantitatively to models, demonstrating how progenitor and explosion physics can be constrained.

  4. Very Deep inside the SN 1987A Core Ejecta: Molecular Structures Seen in 3D

    International Nuclear Information System (INIS)

    Abellán, F. J.; Marcaide, J. M.; Indebetouw, R.; Chevalier, R.; Gabler, M.; Janka, H.-Th.; Fransson, C.; Lundqvist, P.; Spyromilio, J.; Burrows, D. N.; Cigan, P.; Gomez, H. L.; Matsuura, M.; Gaensler, B. M.; Kirshner, R.; Larsson, J.; McCray, R.; Ng, C.-Y.; Park, S.; Roche, P.

    2017-01-01

    Most massive stars end their lives in core-collapse supernova explosions and enrich the interstellar medium with explosively nucleosynthesized elements. Following core collapse, the explosion is subject to instabilities as the shock propagates outward through the progenitor star. Observations of the composition and structure of the innermost regions of a core-collapse supernova provide a direct probe of the instabilities and nucleosynthetic products. SN 1987A in the Large Magellanic Cloud is one of very few supernovae for which the inner ejecta can be spatially resolved but are not yet strongly affected by interaction with the surroundings. Our observations of SN 1987A with the Atacama Large Millimeter/submillimeter Array are of the highest resolution to date and reveal the detailed morphology of cold molecular gas in the innermost regions of the remnant. The 3D distributions of carbon and silicon monoxide (CO and SiO) emission differ, but both have a central deficit, or torus-like distribution, possibly a result of radioactive heating during the first weeks (“nickel heating”). The size scales of the clumpy distribution are compared quantitatively to models, demonstrating how progenitor and explosion physics can be constrained.

  5. Polymer structure-property requirements for stereolithographic 3D printing of soft tissue engineering scaffolds.

    Science.gov (United States)

    Mondschein, Ryan J; Kanitkar, Akanksha; Williams, Christopher B; Verbridge, Scott S; Long, Timothy E

    2017-09-01

    This review highlights the synthesis, properties, and advanced applications of synthetic and natural polymers 3D printed using stereolithography for soft tissue engineering applications. Soft tissue scaffolds are of great interest due to the number of musculoskeletal, cardiovascular, and connective tissue injuries and replacements humans face each year. Accurately replacing or repairing these tissues is challenging due to the variation in size, shape, and strength of different types of soft tissue. With advancing processing techniques such as stereolithography, control of scaffold resolution down to the μm scale is achievable along with the ability to customize each fabricated scaffold to match the targeted replacement tissue. Matching the advanced manufacturing technique to polymer properties as well as maintaining the proper chemical, biological, and mechanical properties for tissue replacement is extremely challenging. This review discusses the design of polymers with tailored structure, architecture, and functionality for stereolithography, while maintaining chemical, biological, and mechanical properties to mimic a broad range of soft tissue types. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

    Karthikeyan, Muthukumarasamy; Vyas, Renu

    2016-01-01

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

  7. 3-D Printed Anti-Reflection Structures for the Terahertz Region

    Science.gov (United States)

    Bomba, Jarosław; Suszek, Jarosław; Makowski, Michał; Sobczyk, Artur; Sypek, Maciej

    2018-01-01

    Terahertz radiation has a growing number of applications in material characterization, where spectral fingerprinting and diffractive effects are the carriers of information. On the other hand, electromagnetic waves in the range of millimeters exhibit strong unwanted specular reflections, resulting in uncontrolled interferences. This problem is especially disturbing in the goniometric time-domain spectroscopy (TDS) configuration, where angular distribution of the field modified by the sample is altered by unwanted reflections. For this reason, low-cost anti-reflection layers are desired. Here, we present a simple way of designing and manufacturing one-sided and two-sided anti-reflection polyamide layers for the THz range. The structures were fabricated using 3-D printers based on selective laser sintering. We demonstrate experimentally in the goniometric time-domain spectroscopy the significant reduction of wavelength-dependent oscillations in Fabry-Perot configuration in the range between 0.1 and 0.3 THz. We also examine the influence of the anti-reflection layers on the distribution of THz energy in reflected, transmitted, and diffracted fields.

  8. Porous Structures in Stacked, Crumpled and Pillared Graphene-Based 3D Materials.

    Science.gov (United States)

    Guo, Fei; Creighton, Megan; Chen, Yantao; Hurt, Robert; Külaots, Indrek

    2014-01-01

    Graphene, an atomically thin material with the theoretical surface area of 2600 m 2 g -1 , has great potential in the fields of catalysis, separation, and gas storage if properly assembled into functional 3D materials at large scale. In ideal non-interacting ensembles of non-porous multilayer graphene plates, the surface area can be adequately estimated using the simple geometric law ~ 2600 m 2 g -1 /N, where N is the number of graphene sheets per plate. Some processing operations, however, lead to secondary plate-plate stacking, folding, crumpling or pillaring, which give rise to more complex structures. Here we show that bulk samples of multilayer graphene plates stack in an irregular fashion that preserves the 2600/N surface area and creates regular slot-like pores with sizes that are multiples of the unit plate thickness. In contrast, graphene oxide deposits into films with massive area loss (2600 to 40 m 2 g -1 ) due to nearly perfect alignment and stacking during the drying process. Pillaring graphene oxide sheets by co-deposition of colloidal-phase particle-based spacers has the potential to partially restore the large monolayer surface. Surface areas as high as 1000 m 2 g -1 are demonstrated here through colloidal-phase deposition of graphene oxide with water-dispersible aryl-sulfonated ultrafine carbon black as a pillaring agent.

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

    Science.gov (United States)

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

    2016-03-01

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

  10. Liquid immersion thermal crosslinking of 3D polymer nanopatterns for direct carbonisation with high structural integrity

    Science.gov (United States)

    Kang, Da-Young; Kim, Cheolho; Park, Gyurim; Moon, Jun Hyuk

    2015-12-01

    The direct pyrolytic carbonisation of polymer patterns has attracted interest for its use in obtaining carbon materials. In the case of carbonisation of nanopatterned polymers, the polymer flow and subsequent pattern change may occur in order to relieve their high surface energies. Here, we demonstrated that liquid immersion thermal crosslinking of polymer nanopatterns effectively enhanced the thermal resistance and maintained the structure integrity during the heat treatment. We employed the liquid immersion thermal crosslinking for 3D porous SU8 photoresist nanopatterns and successfully converted them to carbon nanopatterns while maintaining their porous features. The thermal crosslinking reaction and carbonisation of SU8 nanopatterns were characterised. The micro-crystallinity of the SU8-derived carbon nanopatterns was also characterised. The liquid immersion heat treatment can be extended to the carbonisation of various polymer or photoresist nanopatterns and also provide a facile way to control the surface energy of polymer nanopatterns for various purposes, for example, to block copolymer or surfactant self-assemblies.

  11. Femtosecond laser pulses for fast 3-D surface profilometry of microelectronic step-structures.

    Science.gov (United States)

    Joo, Woo-Deok; Kim, Seungman; Park, Jiyong; Lee, Keunwoo; Lee, Joohyung; Kim, Seungchul; Kim, Young-Jin; Kim, Seung-Woo

    2013-07-01

    Fast, precise 3-D measurement of discontinuous step-structures fabricated on microelectronic products is essential for quality assurance of semiconductor chips, flat panel displays, and photovoltaic cells. Optical surface profilers of low-coherence interferometry have long been used for the purpose, but the vertical scanning range and speed are limited by the micro-actuators available today. Besides, the lateral field-of-view extendable for a single measurement is restricted by the low spatial coherence of broadband light sources. Here, we cope with the limitations of the conventional low-coherence interferometer by exploiting unique characteristics of femtosecond laser pulses, i.e., low temporal but high spatial coherence. By scanning the pulse repetition rate with direct reference to the Rb atomic clock, step heights of ~69.6 μm are determined with a repeatability of 10.3 nm. The spatial coherence of femtosecond pulses provides a large field-of-view with superior visibility, allowing for a high volume measurement rate of ~24,000 mm3/s.

  12. CamMedNP: building the Cameroonian 3D structural natural products database for virtual screening.

    Science.gov (United States)

    Ntie-Kang, Fidele; Mbah, James A; Mbaze, Luc Meva'a; Lifongo, Lydia L; Scharfe, Michael; Hanna, Joelle Ngo; Cho-Ngwa, Fidelis; Onguéné, Pascal Amoa; Owono Owono, Luc C; Megnassan, Eugene; Sippl, Wolfgang; Efange, Simon M N

    2013-04-16

    Computer-aided drug design (CADD) often involves virtual screening (VS) of large compound datasets and the availability of such is vital for drug discovery protocols. We present CamMedNP - a new database beginning with more than 2,500 compounds of natural origin, along with some of their derivatives which were obtained through hemisynthesis. These are pure compounds which have been previously isolated and characterized using modern spectroscopic methods and published by several research teams spread across Cameroon. In the present study, 224 distinct medicinal plant species belonging to 55 plant families from the Cameroonian flora have been considered. About 80 % of these have been previously published and/or referenced in internationally recognized journals. For each compound, the optimized 3D structure, drug-like properties, plant source, collection site and currently known biological activities are given, as well as literature references. We have evaluated the "drug-likeness" of this database using Lipinski's "Rule of Five". A diversity analysis has been carried out in comparison with the ChemBridge diverse database. CamMedNP could be highly useful for database screening and natural product lead generation programs.

  13. (¹⁵N ± ¹³C') edited (4, 3)D-H(CC)CONH TOCSY and (4, 3)D-NOESY HNCO experiments for unambiguous side chain and NOE assignments of proteins with high shift degeneracy.

    Science.gov (United States)

    Kumar, Dinesh; Arora, Ashish

    2011-11-01

    Well-resolved and unambiguous through-bond correlations and NOE data are crucial for high-quality protein structure determination by NMR. In this context, we present here (4, 3)D reduced dimensionality (RD) experiments: H(CC)CONH TOCSY and NOESY HNCO--which instead of (15)N shifts exploit the linear combination of (15)N(i) and (13)C'(i-1) shifts (where i is a residue number) to resolve the through-bond (1)H-(1)H correlations and through-space (1)H-(1)H NOEs. The strategy makes use of the fact that (15)N and (13)C' chemical shifts when combined linearly provide a dispersion which is better compared to those of the individual chemical shifts. The extended dispersion thus available in these experiments will help to obtain the unambiguous side chain and accurate NOE assignments especially for medium-sized alpha-helical or partially unstructured proteins [molecular weight (MW) between 12-15 kDa] as well as higher MW (between 15-25 kDa) folded proteins where spectral overlap renders inaccurate and ambiguous NOEs. Further, these reduced dimensionality experiments in combination with routinely used (15)N and (13)C' edited TOCSY and NOESY experiments will provide an alternative way for high-quality NMR structure determination of large unstable proteins (with very high shift degeneracy), which are not at all amenable to 4D NMR. The utility of these experiments has been demonstrated here using (13)C/(15)N labeled ubiquitin (76 aa) protein. Copyright © 2011 John Wiley & Sons, Ltd.

  14. Layout of PWR in-core instrumentation system tubing and support structure with Bechtel 3D-CADD

    International Nuclear Information System (INIS)

    Ichikawa, T.; Pfeifer, B.W.; Mulay, J.N.

    1987-01-01

    The optimization study of the PWR In-Core Instrumentation System (ICIS) tubing layout and support structure presented an opportunity to utilize the Bechtel 3D-CADD program to perform this task. This paper provides a brief summary of the Bechtel 3D-CADD program development and capabilities and outlines the process of developing and optimizing the ICIS tube layout. Specific aspects relating to the ICIS tube layout criteria, support, alignment, electronic interference check and erection sequence are provided. (orig.)

  15. Fabrication, Characterization, And Deformation of 3D Structural Meta-Materials

    Science.gov (United States)

    Montemayor, Lauren C.

    Current technological advances in fabrication methods have provided pathways to creating architected structural meta-materials similar to those found in natural organisms that are structurally robust and lightweight, such as diatoms. Structural meta-materials are materials with mechanical properties that are determined by material properties at various length scales, which range from the material microstructure (nm) to the macro-scale architecture (mum -- mm). It is now possible to exploit material size effect, which emerge at the nanometer length scale, as well as structural effects to tune the material properties and failure mechanisms of small-scale cellular solids, such as nanolattices. This work demonstrates the fabrication and mechanical properties of 3-dimensional hollow nanolattices in both tension and compression. Hollow gold nanolattices loaded in uniaxial compression demonstrate that strength and stiffness vary as a function of geometry and tube wall thickness. Structural effects were explored by increasing the unit cell angle from 30° to 60° while keeping all other parameters constant; material size effects were probed by varying the tube wall thickness, t, from 200nm to 635nm, at a constant relative density and grain size. In-situ uniaxial compression experiments reveal an order-of-magnitude increase in yield stress and modulus in nanolattices with greater lattice angles, and a 150% increase in the yield strength without a concomitant change in modulus in thicker-walled nanolattices for fixed lattice angles. These results imply that independent control of structural and material size effects enables tunability of mechanical properties of 3-dimensional architected meta-materials and highlight the importance of material, geometric, and microstructural effects in small-scale mechanics. This work also explores the flaw tolerance of 3D hollow-tube alumina kagome nanolattices with and without pre-fabricated notches, both in experiment and simulation

  16. 3D P and S Wave Velocity Structure and Tremor Locations in the Parkfield Region

    Science.gov (United States)

    Zeng, X.; Thurber, C. H.; Shelly, D. R.; Bennington, N. L.; Cochran, E. S.; Harrington, R. M.

    2014-12-01

    We have assembled a new dataset to refine the 3D seismic velocity model in the Parkfield region. The S arrivals from 184 earthquakes recorded by the Parkfield Experiment to Record MIcroseismicity and Tremor array (PERMIT) during 2010-2011 were picked by a new S wave picker, which is based on machine learning. 74 blasts have been assigned to four quarries, whose locations were identified with Google Earth. About 1000 P and S wave arrivals from these blasts at permanent seismic network were also incorporated. Low frequency earthquakes (LFEs) occurring within non-volcanic tremor (NVT) are valuable for improving the precision of NVT location and the seismic velocity model at greater depths. Based on previous work (Shelley and Hardebeck, 2010), waveforms of hundreds of LFEs in same family were stacked to improve signal qualify. In a previous study (McClement et al., 2013), stacked traces of more than 30 LFE families at the Parkfileld Array Seismic Observatory (PASO) have been picked. We expanded our work to include LFEs recorded by the PERMIT array. The time-frequency Phase Weight Stacking (tf-PWS) method was introduced to improve the stack quality, as direct stacking does not produce clear S-wave arrivals on the PERMIT stations. This technique uses the coherence of the instantaneous phase among the stacked signals to enhance the signal-to-noise ratio (SNR) of the stack. We found that it is extremely effective for picking LFE arrivals (Thurber et al., 2014). More than 500 P and about 1000 S arrivals from 58 LFE families were picked at the PERMIT and PASO arrays. Since the depths of LFEs are much deeper than earthquakes, we are able to extend model resolution to lower crustal depths. Both P and S wave velocity structure have been obtained with the tomoDD method. The result suggests that there is a low velocity zone (LVZ) in the lower crust and the location of the LVZ is consistent with the high conductivity zone beneath the southern segment of the Rinconada fault that

  17. Coupling effects in 3D plasmonic structures templated by Morpho butterfly wings.

    Science.gov (United States)

    He, Jiaqing; Shen, Qingchen; Yang, Shuai; He, Gufeng; Tao, Peng; Song, Chengyi; Wu, Jianbo; Deng, Tao; Shang, Wen

    2018-01-03

    This paper presents the study of the coupling effects of three dimensional (3D) plasmonic nanostructures templated by Morpho butterfly wings. Different from the random deposition of metallic nanoparticles (NPs) or conformal coating of metallic layers on butterfly wings reported previously, the 3D plasmonic nanostructures studied in this work consist of gold (Au) nanostrips quasi-periodically arranged in 3D, which allows us to investigate the plasmonic coupling effects. Through refractive index (RI) matching, the plasmonic coupling can be differentiated from the optical contribution of butterfly wings. By tuning the deposition thickness of Au from 30 to 90 nm, the plasmonic coupling effects between the 3D Au nanostrips are gradually enhanced. In particular, the near-field coupling results in two resonant modes and enhances the surface-enhanced Raman scattering (SERS) signals.

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

    Science.gov (United States)

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

    2016-01-01

    Surface gravity surveys can detect subsurface density variations that can reveal subsurface geologic features. In 1972, the Apollo 17 (A17) mission conducted the Traverse Gravimeter Experiment (TGE) using a gravimeter that measured the local gravity field near Taurus Littrow Valley (TLV), located on the south-eastern rim of the Serenitatis basin. TLV is hypothesized to be a basaltfilled radial graben resulting from the impact that formed Mare Serenitatis. It is bounded by both the North and South Massifs (NM and SM) as well as other smaller mountains to the East that are thought to be mainly composed of brecciated highland material. The TGE is the first and only successful gravity survey on the surface of the Moon. Other more recent satellite surveys, such as NASA's Gravity Recovery and Interior Laboratory (GRAIL) mission (2011- 2012), have produced the best global gravity field to date (approx. 13km resolution). However, these satellite surveys are not sensitive enough to detect fine-scale (<1km) lunar subsurface structures. This underscores the value of the data collected at the surface by A17. In the original analysis of the data a 2D forward-modelling approach was used to derive a thickness of the subsurface basalt layer of 1.0 km by assuming a simple flat-faced rectangular geometry and using densities derived from Apollo lunar samples. We are investigating whether modern 3D modelling techniques in combination with high-resolution topographical and image datasets can reveal additional fine-scale subsurface structure in TLV.

  19. From 3D to 2D: a review of the molecular imprinting of proteins.

    Science.gov (United States)

    Turner, Nicholas W; Jeans, Christopher W; Brain, Keith R; Allender, Christopher J; Hlady, Vladimir; Britt, David W

    2006-01-01

    Molecular imprinting is a generic technology that allows for the introduction of sites of specific molecular affinity into otherwise homogeneous polymeric matrices. Commonly this technique has been shown to be effective when targeting small molecules of molecular weight proteins has proven difficult. A number of key inherent problems in protein imprinting have been identified, including permanent entrapment, poor mass transfer, denaturation, and heterogeneity in binding pocket affinity, which have been addressed using a variety of approaches. This review focuses on protein imprinting in its various forms, ranging from conventional bulk techniques to novel thin film and monolayer surface imprinting approaches.

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

    DEFF Research Database (Denmark)

    Joergensen, Louise; Turner, Louise; Magistrado, Pamela

    2006-01-01

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

  1. 2D and 3D GPR imaging of structural ceilings in historic and existing constructions

    Science.gov (United States)

    Colla, Camilla

    2014-05-01

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

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

    Science.gov (United States)

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

    2016-04-20

    RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.

    Directory of Open Access Journals (Sweden)

    Radhakrishna Bettadapura

    2015-10-01

    Full Text Available There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data, and 3D reconstructed cryo-electron microscopy (3D EM maps (albeit at coarser resolution of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2 fit (Polar Fast Fourier Fitting for the best possible structural alignment of atomistic structures with 3D EM. While PF(2 fit enables only a rigid, six dimensional (6D alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2 fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2 fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2 fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2 fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search.

  4. Cell and protein compatible 3D bioprinting of mechanically strong constructs for bone repair

    International Nuclear Information System (INIS)

    Sawkins, M J; Mistry, P; Shakesheff, K M; Yang, J; Brown, B N; Bonassar, L J

    2015-01-01

    Rapid prototyping of bone tissue engineering constructs often utilizes elevated temperatures, organic solvents and/or UV light for materials processing. These harsh conditions may prevent the incorporation of cells and therapeutic proteins in the fabrication processes. Here we developed a method for using bioprinting to produce constructs from a thermoresponsive microparticulate material based on poly(lactic-co-glycolic acid) at ambient conditions. These constructs could be engineered with yield stresses of up to 1.22 MPa and Young’s moduli of up to 57.3 MPa which are within the range of properties of human cancellous bone. Further study showed that protein-releasing microspheres could be incorporated into the bioprinted constructs. The release of the model protein lysozyme from bioprinted constructs was sustainted for a period of 15 days and a high degree of protein activity could be measured up to day 9. This work suggests that bioprinting is a viable route to the production of mechanically strong constructs for bone repair under mild conditions which allow the inclusion of viable cells and active proteins. (paper)

  5. Mapping of coma anisotropies to plasma structures of weak comets: a 3-D hybrid simulation study

    Directory of Open Access Journals (Sweden)

    N. Gortsas

    2009-04-01

    Full Text Available The effects of coma anisotropies on the plasma environment of comets have been studied by means of a 3-D hybrid model which treats electrons as a massless, charge-neutralizing fluid, whereas ion dynamics are covered by a kinetic approach. From Earth-based observations as well as from in-situ spacecraft measurements the shape of the coma of many comets is ascertained to be anisotropic. However, most plasma simulation studies deploy a spherically symmetric activity pattern. In this paper anisotropy is studied by considering three different coma shape models. The first model is derived from the Haser model and is characterised by spherically symmetry. This reference model is then compared with two different neutral gas shape models: the dayside restricted model with no nightside activity and a cone shaped model with opening angle of π/2. In all models the integrated surface activity is kept constant. The simulations have been done for the Rosetta target comet 67P/Churyumov-Gerasimenko for two heliocentric distances, 1.30 AU and 3.25 AU. It is found that shock formation processes are modified as a result of increasing spatial confinement. Characteristic plasma structures of comets such as the bow shock, magnetic barrier region and the ion composition boundary exhibit a shift towards the sun. In addition, the cone shaped model leads to a strong increase of the mass-loaded region which in turn leads to a smooth deceleration of the solar wind flow and an increasing degree of mixture between the solar wind and cometary ion species. This creates an additional transport channel of the magnetic field from the magnetic barrier region away which in turn leads to a broadening of this region. In addition, it leads to an ion composition boundary which is only gradually developed.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-04-24

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

  7. High resolution 3-D shear wave velocity structure in South China from surface wave tomography

    Science.gov (United States)

    Ning, S.; Guo, Z.; Chen, Y. J.

    2017-12-01

    Using continuous data from a total of 638 seismic stations, including 484 from CEArray between 2008 and 2013 and 154 from SINOPROBE between 2014 and 2015, we perform both ambient noise and earthquake Rayleigh wave tomography across South China. Combining Rayleigh wave phase velocity between 6and 40s periods from ambient noise tomography and Rayleigh wave phase velocity between 20and 140s from teleseismic two-plane-wave tomography, we obtain phase velocity maps between 6 and140 s periods. We then invert Rayleigh wave phase velocity to construct a 3-D shear wave velocity structure of South China by Markov Chain Monte Carlo method. Similar to other inversion results, our results correspond topography well. Moreover, our results also reveal that velocity structure of the eastern South China in mantle depth is similar to eastern North China, the core of the western South China, Sichuan Block (SB),still exists thick lithosphere. However, owing to much more data employed and some data quality control techniques in this research, our results reveal more detailed structures. Along Qinling-Dabie Orogenic Belt (QDOB), North-South Gravity Lineament (NSGL) and the Sichuan-Yunnan Rhombic Block (SYRB), there are obvious high speed anomalies in depths of 10-20 km, which possibly imply ancient intrusions. Moreover, it seems that Tancheng-Lujiang Fault Zone (TLFZ) has already cut through QDOB, forming a deep fracture cutting through the crust of the whole China continent. Although SB still exists thick lithosphere, there are indications for thermal erosion. At the same time, the lithosphere of the central SYRB seems to be experiencing delamination process, obviously forming a barrier to prevent the hot Tibetan Plateau (TP) mantle material from flowing further southeast. Upwelling hot mantle material possibly triggered by this delamination process might be the cause of the Emeishan Large Igneous Province. There exists an intercontinental low velocity layer in the crust of the TP

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

    Directory of Open Access Journals (Sweden)

    Vivek Nandakumar

    Full Text Available 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.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.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.Our results provide a new perspective on nuclear structure variations associated with malignancy and point to the

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

    Science.gov (United States)

    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

    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. 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. 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 pfibrocystic from the metastatic cell populations. Our results provide a new perspective on nuclear structure variations associated with malignancy and point to the value of automated quantitative 3D nuclear morphometry as an objective tool to enable development of sensitive and specific nuclear grade classification in breast cancer diagnosis.

  10. CCDC 1025419: Experimental Crystal Structure Determination : bisthieno[3,2-b:2',3'-d]thiophene

    KAUST Repository

    Castañ eda, Raú l; Khrustalev, Victor N.; Fonari, Alexandr; Bredas, Jean-Luc; Getmanenko, Yulia A.; Timofeeva, Tatiana V.

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

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

    Science.gov (United States)

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

    2015-08-01

    In this study, we present a correlative microscopy workflow to combine detailed 3D fluorescence light microscopy data with ultrastructural information gained by 3D focused ion beam assisted scanning electron microscopy. The workflow is based on an optimized high pressure freezing/freeze substitution protocol that preserves good ultrastructural detail along with retaining the fluorescence signal in the resin embedded specimens. Consequently, cellular structures of interest can readily be identified and imaged by state of the art 3D confocal fluorescence microscopy and are precisely referenced with respect to an imprinted coordinate system on the surface of the resin block. This allows precise guidance of the focused ion beam assisted scanning electron microscopy and limits the volume to be imaged to the structure of interest. This, in turn, minimizes the total acquisition time necessary to conduct the time consuming ultrastructural scanning electron microscope imaging while eliminating the risk to miss parts of the target structure. We illustrate the value of this workflow for targeting virus compartments, which are formed in HIV-pulsed mature human dendritic cells. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  12. Investigating the Importance of 3D Structure & Topography in Seismic Deformation Modeling: Case Study of the April 2015 Nepal Earthquake

    Science.gov (United States)

    Langer, L.; Gharti, H. N.; Tromp, J.

    2017-12-01

    In recent years, observations of deformation at plate boundaries have been greatly improved by the development of techniques in space geodesy. However, models of seismic deformation remain limited and are unable to account for realistic 3D structure in topography and material properties. We demonstrate the importance of 3D structure using a spectral-element method that incorporates fault geometry, topography, and heterogeneous material properties in a (non)linear viscoelastic domain. Our method is benchmarked against Okada's analytical technique and the PyLith software package. The April 2015 Nepal earthquake is used as a case study to examine whether 3D structure can affect the predictions of seismic deformation models. We find that the inclusion of topography has a significant effect on our results.

  13. 3D cellular structures and co-cultures formed through the contactless magnetic manipulation of cells on adherent surfaces.

    Science.gov (United States)

    Abdel Fattah, Abdel Rahman; Mishriki, Sarah; Kammann, Tobias; Sahu, Rakesh P; Geng, Fei; Puri, Ishwar K

    2018-02-27

    A magnet array is employed to manipulate diamagnetic cells that are contained in paramagnetic medium to demonstrate for the first time the contactless bioprinting of three-dimensional (3D) cellular structures and co-cultures of breast cancer MCF-7 and endothelial HUVEC at prescribed locations on tissue culture treated well plates. Sequential seeding of different cell lines and the spatial displacement of the magnet array creates co-cultured cellular structures within a well without using physically intrusive well inserts. Both monotypic and co-culture experiments produce morphologically rich 3D cell structures that are otherwise absent in regular monolayer cell cultures. The magnetic contactless bioprinting of cells provides further insight into cell behaviour, invasion strategies and transformations that are useful for potential applications in drug screening, 3D cell culture formation and tissue engineering.

  14. 2D virtual texture on 3D real object with coded structured light

    Science.gov (United States)

    Molinier, Thierry; Fofi, David; Salvi, Joaquim; Gorria, Patrick

    2008-02-01

    Augmented reality is used to improve color segmentation on human body or on precious no touch artifacts. We propose a technique to project a synthesized texture on real object without contact. Our technique can be used in medical or archaeological application. By projecting a suitable set of light patterns onto the surface of a 3D real object and by capturing images with a camera, a large number of correspondences can be found and the 3D points can be reconstructed. We aim to determine these points of correspondence between cameras and projector from a scene without explicit points and normals. We then project an adjusted texture onto the real object surface. We propose a global and automatic method to virtually texture a 3D real object.

  15. 3D Crustal Velocity Structure Model of the Middle-eastern North China Craton

    Science.gov (United States)

    Duan, Y.; Wang, F.; Lin, J.; Wei, Y.

    2017-12-01

    Lithosphere thinning and destruction in the middle-eastern North China Craton (NCC), a region susceptible to strong earthquakes, is one of the research hotspots in solid earth science. Up to 42 wide-angle reflection/refraction deep seismic sounding (DSS) profiles have been completed in the middle-eastern NCC, we collect all the 2D profiling results and perform gridding of the velocity and interface depth data, and build a 3D crustal velocity structure model for the middle-eastern NCC, named HBCrust1.0, using the Kriging interpolation method. In this model, four layers are divided by three interfaces: G is the interface between the sedimentary cover and crystalline crust, with velocities of 5.0-5.5 km/s above and 5.8-6.0 km/s below. C is the interface of the upper and lower crust, with velocity jump from 6.2-6.4 km/s to 6.5-6.6 km/s. M is the interface between the crust and upper mantle, with velocity 6.7-7.0 km/s at the crust bottom and 7.9-8.0 km/s on mantle top. Our results show that the first arrival time calculated from HBCust1.0 fit well with the observation. It also demonstrates that the upper crust is the main seismogenic layer, and the brittle-ductile transition occurs at depths near interface C. The depth of interface Moho varies beneath the source area of the Tangshan earth-quake, and a low-velocity structure is found to extend from the source area to the lower crust. Based on these observations, it can be inferred that stress accumulation responsible for the Tangshan earthquake may have been closely related to the migration and deformation of the mantle materials. Comparisons of the average velocities of the whole crust, the upper and the lower crust show that the average velocity of the lower crust under the central part of the North China Basin (NCB) in the east of the craton is obviously higher than the regional average, this high-velocity probably results from longterm underplating of the mantle magma. This research is founded by the Natural Science

  16. An efficient depth map preprocessing method based on structure-aided domain transform smoothing for 3D view generation.

    Directory of Open Access Journals (Sweden)

    Wei Liu

    Full Text Available Depth image-based rendering (DIBR, which is used to render virtual views with a color image and the corresponding depth map, is one of the key techniques in the 2D to 3D conversion process. Due to the absence of knowledge about the 3D structure of a scene and its corresponding texture, DIBR in the 2D to 3D conversion process, inevitably leads to holes in the resulting 3D image as a result of newly-exposed areas. In this paper, we proposed a structure-aided depth map preprocessing framework in the transformed domain, which is inspired by recently proposed domain transform for its low complexity and high efficiency. Firstly, our framework integrates hybrid constraints including scene structure, edge consistency and visual saliency information in the transformed domain to improve the performance of depth map preprocess in an implicit way. Then, adaptive smooth localization is cooperated and realized in the proposed framework to further reduce over-smoothness and enhance optimization in the non-hole regions. Different from the other similar methods, the proposed method can simultaneously achieve the effects of hole filling, edge correction and local smoothing for typical depth maps in a united framework. Thanks to these advantages, it can yield visually satisfactory results with less computational complexity for high quality 2D to 3D conversion. Numerical experimental results demonstrate the excellent performances of the proposed method.

  17. Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins

    Directory of Open Access Journals (Sweden)

    Selbig Joachim

    2009-04-01

    Full Text Available Abstract Background Phosphorylation of proteins plays a crucial role in the regulation and activation of metabolic and signaling pathways and constitutes an important target for pharmaceutical intervention. Central to the phosphorylation process is the recognition of specific target sites by protein kinases followed by the covalent attachment of phosphate groups to the amino acids serine, threonine, or tyrosine. The experimental identification as well as computational prediction of phosphorylation sites (P-sites has proved to be a challenging problem. Computational methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding phosphorylation sites. Results We characterized the spatial context of phosphorylation sites and assessed its usability for improved phosphorylation site predictions. We identified 750 non-redundant, experimentally verified sites with three-dimensional (3D structural information available in the protein data bank (PDB and grouped them according to their respective kinase family. We studied the spatial distribution of amino acids around phosphorserines, phosphothreonines, and phosphotyrosines to extract signature 3D-profiles. Characteristic spatial distributions of amino acid residue types around phosphorylation sites were indeed discernable, especially when kinase-family-specific target sites were analyzed. To test the added value of using spatial information for the computational prediction of phosphorylation sites, Support Vector Machines were applied using both sequence as well as structural information. When compared to sequence-only based prediction methods, a small but consistent performance improvement was obtained when the prediction was informed by 3D-context information. Conclusion While local one-dimensional amino acid sequence information was observed to harbor most of the discriminatory power, spatial context information was identified as

  18. Chondrocytes and stem cells in 3D-bioprinted structures create human cartilage in vivo.

    Science.gov (United States)

    Apelgren, Peter; Amoroso, Matteo; Lindahl, Anders; Brantsing, Camilla; Rotter, Nicole; Gatenholm, Paul; Kölby, Lars

    2017-01-01

    Cartilage repair and replacement is a major challenge in plastic reconstructive surgery. The development of a process capable of creating a patient-specific cartilage framework would be a major breakthrough. Here, we described methods for creating human cartilage in vivo and quantitatively assessing the proliferative capacity and cartilage-formation ability in mono- and co-cultures of human chondrocytes and human mesenchymal stem cells in a three-dimensional (3D)-bioprinted hydrogel scaffold. The 3D-bioprinted constructs (5 × 5 × 1.2 mm) were produced using nanofibrillated cellulose and alginate in combination with human chondrocytes and human mesenchymal stem cells using a 3D-extrusion bioprinter. Immediately following bioprinting, the constructs were implanted subcutaneously on the back of 48 nude mice and explanted after 30 and 60 days, respectively, for morphological and immunohistochemical examination. During explantation, the constructs were easy to handle, and the majority had retained their macroscopic grid appearance. Constructs consisting of human nasal chondrocytes showed good proliferation ability, with 17.2% of the surface areas covered with proliferating chondrocytes after 60 days. In constructs comprising a mixture of chondrocytes and stem cells, an additional proliferative effect was observed involving chondrocyte production of glycosaminoglycans and type 2 collagen. This clinically highly relevant study revealed 3D bioprinting as a promising technology for the creation of human cartilage.

  19. Chondrocytes and stem cells in 3D-bioprinted structures create human cartilage in vivo.

    Directory of Open Access Journals (Sweden)

    Peter Apelgren

    Full Text Available Cartilage repair and replacement is a major challenge in plastic reconstructive surgery. The development of a process capable of creating a patient-specific cartilage framework would be a major breakthrough. Here, we described methods for creating human cartilage in vivo and quantitatively assessing the proliferative capacity and cartilage-formation ability in mono- and co-cultures of human chondrocytes and human mesenchymal stem cells in a three-dimensional (3D-bioprinted hydrogel scaffold. The 3D-bioprinted constructs (5 × 5 × 1.2 mm were produced using nanofibrillated cellulose and alginate in combination with human chondrocytes and human mesenchymal stem cells using a 3D-extrusion bioprinter. Immediately following bioprinting, the constructs were implanted subcutaneously on the back of 48 nude mice and explanted after 30 and 60 days, respectively, for morphological and immunohistochemical examination. During explantation, the constructs were easy to handle, and the majority had retained their macroscopic grid appearance. Constructs consisting of human nasal chondrocytes showed good proliferation ability, with 17.2% of the surface areas covered with proliferating chondrocytes after 60 days. In constructs comprising a mixture of chondrocytes and stem cells, an additional proliferative effect was observed involving chondrocyte production of glycosaminoglycans and type 2 collagen. This clinically highly relevant study revealed 3D bioprinting as a promising technology for the creation of human cartilage.

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

    KAUST Repository

    Ceylan, Duygu; Mitra, Niloy J.; Zheng, Youyi; Pauly, Mark

    2014-01-01

    . 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

  1. An Innovative Cell Microincubator for Drug Discovery Based on 3D Silicon Structures

    Directory of Open Access Journals (Sweden)

    Francesca Aredia

    2016-01-01

    Full Text Available We recently employed three-dimensional (3D silicon microstructures (SMSs consisting in arrays of 3 μm-thick silicon walls separated by 50 μm-deep, 5 μm-wide gaps, as microincubators for monitoring the biomechanical properties of tumor cells. They were here applied to investigate the in vitro behavior of HT1080 human fibrosarcoma cells driven to apoptosis by the chemotherapeutic drug Bleomycin. Our results, obtained by fluorescence microscopy, demonstrated that HT1080 cells exhibited a great ability to colonize the narrow gaps. Remarkably, HT1080 cells grown on 3D-SMS, when treated with the DNA damaging agent Bleomycin under conditions leading to apoptosis, tended to shrink, reducing their volume and mimicking the normal behavior of apoptotic cells, and were prone to leave the gaps. Finally, we performed label-free detection of cells adherent to the vertical silicon wall, inside the gap of 3D-SMS, by exploiting optical low coherence reflectometry using infrared, low power radiation. This kind of approach may become a new tool for increasing automation in the drug discovery area. Our results open new perspectives in view of future applications of the 3D-SMS as the core element of a lab-on-a-chip suitable for screening the effect of new molecules potentially able to kill tumor cells.

  2. Fabrication of scalable and structured tissue engineering scaffolds using water dissolvable sacrificial 3D printed moulds

    DEFF Research Database (Denmark)

    Mohanty, Soumyaranjan; Larsen, Layla Bashir; Trifol Guzman, Jon

    2015-01-01

    One of the major challenges in producing large scale engineered tissue is the lack of ability to create large highly perfused scaffolds in which cells can grow at a high cell density and viability. Here, we explore 3D printed polyvinyl alcohol (PVA) as a sacrificial mould in a polymer casting...

  3. PRONTO3D users` instructions: A transient dynamic code for nonlinear structural analysis

    Energy Technology Data Exchange (ETDEWEB)

    Attaway, S.W.; Mello, F.J.; Heinstein, M.W.; Swegle, J.W.; Ratner, J.A. [Sandia National Labs., Albuquerque, NM (United States); Zadoks, R.I. [Univ. of Texas, El Paso, TX (United States)

    1998-06-01

    This report provides an updated set of users` instructions for PRONTO3D. PRONTO3D is a three-dimensional, transient, solid dynamics code for analyzing large deformations of highly nonlinear materials subjected to extremely high strain rates. This Lagrangian finite element program uses an explicit time integration operator to integrate the equations of motion. Eight-node, uniform strain, hexahedral elements and four-node, quadrilateral, uniform strain shells are used in the finite element formulation. An adaptive time step control algorithm is used to improve stability and performance in plasticity problems. Hourglass distortions can be eliminated without disturbing the finite element solution using either the Flanagan-Belytschko hourglass control scheme or an assumed strain hourglass control scheme. All constitutive models in PRONTO3D are cast in an unrotated configuration defined using the rotation determined from the polar decomposition of the deformation gradient. A robust contact algorithm allows for the impact and interaction of deforming contact surfaces of quite general geometry. The Smooth Particle Hydrodynamics method has been embedded into PRONTO3D using the contact algorithm to couple it with the finite element method.

  4. Robust and Elastic Lunar and Martian Structures from 3D-Printed Regolith Inks

    Science.gov (United States)

    Jakus, Adam E.; Koube, Katie D.; Geisendorfer, Nicholas R.; Shah, Ramille N.

    2017-03-01

    Here, we present a comprehensive approach for creating robust, elastic, designer Lunar and Martian regolith simulant (LRS and MRS, respectively) architectures using ambient condition, extrusion-based 3D-printing of regolith simulant inks. The LRS and MRS powders are characterized by distinct, highly inhomogeneous morphologies and sizes, where LRS powder particles are highly irregular and jagged and MRS powder particles are rough, but primarily rounded. The inks are synthesized via simple mixing of evaporant, surfactant, and plasticizer solvents, polylactic-co-glycolic acid (30% by solids volume), and regolith simulant powders (70% by solids volume). Both LRS and MRS inks exhibit similar rheological and 3D-printing characteristics, and can be 3D-printed at linear deposition rates of 1-150 mm/s using 300 μm to 1.4 cm-diameter nozzles. The resulting LRS and MRS 3D-printed materials exhibit similar, but distinct internal and external microstructures and material porosity (~20-40%). These microstructures contribute to the rubber-like quasi-static and cyclic mechanical properties of both materials, with young’s moduli ranging from 1.8 to 13.2 MPa and extension to failure exceeding 250% over a range of strain rates (10-1-102 min-1). Finally, we discuss the potential for LRS and MRS ink components to be reclaimed and recycled, as well as be synthesized in resource-limited, extraterrestrial environments.

  5. The structural feasibility of 3D-printing houses using printable polymers

    NARCIS (Netherlands)

    Van der Veen, A.C.; Coenders, J.L.; Veer, F.A.; Nijsse, R.; Houtman, R.; Schonwalder, J.

    2015-01-01

    At this point in time, 3D-printing techniques in general, but especially applied for the building industry, still are in a phase of early experiments. One of the experimental attempts is to print a full-scale, three-story high, house in Amsterdam, using an up scaled version of a FDM-printer that is

  6. Unleash the building bots: 3d printing structures with an autonomous robot swarm

    Directory of Open Access Journals (Sweden)

    Aant van der Zee

    2017-12-01

    Full Text Available 3D printing techniques for the building industry are developing fast. Concepts like Contour printing, concrete printing concepts of the TU/E and D Shape are examples. Despite the range of techniques is broad (and vary from a large gantry system, to a supersized Delta printer for example, many of the developed 3D printing machines are constraint in their movement. Mobile 3D printers however show advantages in flexibility, as they can move outside the constraint of a large 3D printer and they can move in the highly unstructured and hazardous environment of the building site, which can be dangerous for people to work in. The Institute for advanced architecture of Catalonia developed vehicles, which they call minibuilders, each designed for a special task in the building process, printing the foundation, printing a wall, smoothing the outer-wall etc. The minibuilders are used in succession according the building process. However they are still limited in their autonomy and capability. The minibuilders are tethered with a hose to a vehicle, which carries the concrete supply.

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

    DEFF Research Database (Denmark)

    Saparin, Peter I.; Thomsen, Jesper Skovhus; Prohaska, Steffen

    2005-01-01

    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...

  8. A 3D Photothermal Structure toward Improved Energy Efficiency in Solar Steam Generation

    KAUST Repository

    Shi, Yusuf; Li, Renyuan; Jin, Yong; Zhuo, Sifei; Shi, Le; Chang, Jian; Hong, Seunghyun; Ng, Kim Choon; Wang, Peng

    2018-01-01

    high energy efficiency close to 100% under one-sun illumination due to the capability of the cup wall to recover the diffuse reflectance and thermal radiation heat loss from the 2D cup bottom. Additional heat was gained from the ambient air when the 3D

  9. Protein structure database search and evolutionary classification.

    Science.gov (United States)

    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].

  10. Molecular And 3D-Structural Characterization Of Fructose-1,6-Bisphosphate Aldolase Derived From Metroxylon Sagu

    Directory of Open Access Journals (Sweden)

    Hairul Azman Roslan

    2017-06-01

    Full Text Available ABSTRACT Fructose-1,6-bisphosphate aldolase (FBAld is an enzyme that catalyzes the cleavage of D-fructose-1,6-phosphate (FBP to D-glyceraldehyde-3-phosphate (G3P and dihydroxyacetone phosphate (DHAP, and plays vital role in glycolysis and gluconeogenesis. However, molecular characterization and functional roles of FBAld remain unknown in sago palm. Here we report a modified CTAB-RNA extraction method was developed for the isolation of good quality RNA (RIN>8 from sago leaves and the isolation of FBAld cDNA from sago palm. The isolated sago FBAld (msFBAld cDNA has total length of 1288 bp with an open reading frame of 1020 bp and a predicted to encode for a protein of 340 amino acid resides. The predicted protein shared a high degree of homology with Class-I FBAld from other plants. Meanwhile, the msFBAld gene spanned 2322 bp and consisted of five exons. Conserved domain search identified fifteen catalytically important amino acids at the active site and phylogenetic tree revealed localization of msFBAld in the chloroplast. A molecular 3D-structure of msFBAld was generated by homology modeling and a Ramachandran plot with 86.7% of the residues in the core region, 13.4% in the allowed region with no residues in the disallowed region. The modeled structure is a homotetramer containing an (/(-TIM-barrel at the center. Superimposition of the model with Class-I aldolases identified a catalytic dyad, Lys209-Glu167, which could be involved in the Schiff's base formation and aldol condensation. Apart from that, overproduction of the recombinant msFBAld in Escherichia coli resulted in increased tolerance towards salinity.

  11. A series of novel lanthanide carboxyphosphonates with a 3D framework structure: synthesis, structure, and luminescent and magnetic properties.

    Science.gov (United States)

    Chen, Kai; Dong, Da-Peng; Sun, Zhen-Gang; Jiao, Cheng-Qi; Li, Chao; Wang, Cheng-Lin; Zhu, Yan-Yu; Zhao, Yan; Zhu, Jiang; Sun, Shou-Hui; Zheng, Ming-Jing; Tian, Hui; Chu, Wei

    2012-08-28

    By introduction of 1,4-benzenedicarboxylic acid as the second organic ligand, a series of novel lanthanide carboxyphosphonates with a 3D framework structure, namely, [Ln(3)(H(2)L)(HL)(2)(bdc)(2)(H(2)O)]·7H(2)O (Ln = La (1), Ce (2), Pr (3), Nd (4), Sm (5), Eu (6), Gd (7), Tb (8); H(3)L = H(2)O(3)PCH(2)NC(5)H(9)COOH; H(2)bdc = HOOCC(6)H(4)COOH) have been synthesized under hydrothermal conditions. Compounds are isostructural and feature a 3D framework in which Ln(III) polyhedra are interconnected by bridging {CPO(3)} tetrahedra into 2D inorganic layers parallel to the ab plane. The organic groups of H(2)L(-) are grafted on the two sides of the layer. These layers are further cross-linked by the bdc(2-) ligands from one layer to the Ln atoms from the other into a pillared-layered architecture with one-dimensional channel system along the a axis. The thermal stability of compounds has been investigated. Luminescent properties of compounds , and the magnetic properties of compound have also been studied.

  12. Genome-Wide Prediction and Analysis of 3D-Domain Swapped Proteins in the Human Genome from Sequence Information.

    Science.gov (United States)

    Upadhyay, Atul Kumar; Sowdhamini, Ramanathan

    2016-01-01

    3D-domain swapping is one of the mechanisms of protein oligomerization and the proteins exhibiting this phenomenon have many biological functions. These proteins, which undergo domain swapping, have acquired much attention owing to their involvement in human diseases, such as conformational diseases, amyloidosis, serpinopathies, proteionopathies etc. Early realisation of proteins in the whole human genome that retain tendency to domain swap will enable many aspects of disease control management. Predictive models were developed by using machine learning approaches with an average accuracy of 78% (85.6% of sensitivity, 87.5% of specificity and an MCC value of 0.72) to predict putative domain swapping in protein sequences. These models were applied to many complete genomes with special emphasis on the human genome. Nearly 44% of the protein sequences in the human genome were predicted positive for domain swapping. Enrichment analysis was performed on the positively predicted sequences from human genome for their domain distribution, disease association and functional importance based on Gene Ontology (GO). Enrichment analysis was also performed to infer a better understanding of the functional importance of these sequences. Finally, we developed hinge region prediction, in the given putative domain swapped sequence, by using important physicochemical properties of amino acids.

  13. Analysis and Compensation for Lateral Chromatic Aberration in a Color Coding Structured Light 3D Measurement System

    Science.gov (United States)

    Huang, Junhui; Xue, Qi; Wang, Zhao; Gao, Jianmin

    2016-01-01

    While color-coding methods have improved the measuring efficiency of a structured light three-dimensional (3D) measurement system, they decreased the measuring accuracy significantly due to lateral chromatic aberration (LCA). In this study, the LCA in a structured light measurement system is analyzed, and a method is proposed to compensate the error caused by the LCA. Firstly, based on the projective transformation, a 3D error map of LCA is constructed in the projector images by using a flat board and comparing the image coordinates of red, green and blue circles with the coordinates of white circles at preselected sample points within the measurement volume. The 3D map consists of the errors, which are the equivalent errors caused by LCA of the camera and projector. Then in measurements, error values of LCA are calculated and compensated to correct the projector image coordinates through the 3D error map and a tri-linear interpolation method. Eventually, 3D coordinates with higher accuracy are re-calculated according to the compensated image coordinates. The effectiveness of the proposed method is verified in the following experiments. PMID:27598174

  14. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.

    2016-01-01

    operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching

  15. Structure in the 3D Galaxy Distribution. III. Fourier Transforming the Universe: Phase and Power Spectra

    Energy Technology Data Exchange (ETDEWEB)

    Scargle, Jeffrey D.; Way, M. J.; Gazis, P. R., E-mail: Jeffrey.D.Scargle@nasa.gov, E-mail: Michael.J.Way@nasa.gov, E-mail: PGazis@sbcglobal.net [NASA Ames Research Center, Astrobiology and Space Science Division, Moffett Field, CA 94035 (United States)

    2017-04-10

    We demonstrate the effectiveness of a relatively straightforward analysis of the complex 3D Fourier transform of galaxy coordinates derived from redshift surveys. Numerical demonstrations of this approach are carried out on a volume-limited sample of the Sloan Digital Sky Survey redshift survey. The direct unbinned transform yields a complex 3D data cube quite similar to that from the Fast Fourier Transform of finely binned galaxy positions. In both cases, deconvolution of the sampling window function yields estimates of the true transform. Simple power spectrum estimates from these transforms are roughly consistent with those using more elaborate methods. The complex Fourier transform characterizes spatial distributional properties beyond the power spectrum in a manner different from (and we argue is more easily interpreted than) the conventional multipoint hierarchy. We identify some threads of modern large-scale inference methodology that will presumably yield detections in new wider and deeper surveys.

  16. Structure in the 3D Galaxy Distribution. III. Fourier Transforming the Universe: Phase and Power Spectra

    International Nuclear Information System (INIS)

    Scargle, Jeffrey D.; Way, M. J.; Gazis, P. R.

    2017-01-01

    We demonstrate the effectiveness of a relatively straightforward analysis of the complex 3D Fourier transform of galaxy coordinates derived from redshift surveys. Numerical demonstrations of this approach are carried out on a volume-limited sample of the Sloan Digital Sky Survey redshift survey. The direct unbinned transform yields a complex 3D data cube quite similar to that from the Fast Fourier Transform of finely binned galaxy positions. In both cases, deconvolution of the sampling window function yields estimates of the true transform. Simple power spectrum estimates from these transforms are roughly consistent with those using more elaborate methods. The complex Fourier transform characterizes spatial distributional properties beyond the power spectrum in a manner different from (and we argue is more easily interpreted than) the conventional multipoint hierarchy. We identify some threads of modern large-scale inference methodology that will presumably yield detections in new wider and deeper surveys.

  17. Chondrocytes and stem cells in 3D-bioprinted structures create human cartilage in vivo

    OpenAIRE

    Apelgren, Peter; Amoroso, Matteo; Lindahl, Anders; Brantsing, Camilla; Rotter, Nicole; Gatenholm, Paul; Kölby, Lars

    2017-01-01

    Cartilage repair and replacement is a major challenge in plastic reconstructive surgery. The development of a process capable of creating a patient-specific cartilage framework would be a major breakthrough. Here, we described methods for creating human cartilage in vivo and quantitatively assessing the proliferative capacity and cartilage-formation ability in mono- and co-cultures of human chondrocytes and human mesenchymal stem cells in a three-dimensional (3D)-bioprinted hydrogel scaffold....

  18. Oculomotor paralysis: 3D-CISS MR imaging with MPR in the evaluation of neuralgic manifestation and the adjacent structures

    Energy Technology Data Exchange (ETDEWEB)

    Sun Xiaoli; Liang Changhu [Shandong Medical Imaging Research Institute, Shandong University, Jing-wu Road No. 324, Jinan 250021 (China); Liu Cheng [Shandong Medical Imaging Research Institute, Shandong University, Jing-wu Road No. 324, Jinan 250021 (China)], E-mail: sdsxl2005@126.com; Liu Shuwei; Deng Kai; He Jingzhen [Shandong Medical Imaging Research Institute, Shandong University, Jing-wu Road No. 324, Jinan 250021 (China)

    2010-02-15

    Purpose: To evaluate the value of three-dimensional (3D) constructive interference in steady-state (CISS) magnetic resonance (MR) imaging with multi-planar reconstruction (MPR) in displaying the relationship between the oculomotor nerve and its adjacent structures for patients with oculomotor paralysis. Materials and methods: 17 consecutive patients with oculomotor paralysis were examined with 3D-CISS and conventional spin-echo (SE) sequences on a 1.5-Tesla MR system. Original transverse and MPR images were used for image interpretation. The features of the oculomotor nerve and its adjacent structures were identified. The diagnosis was surgically confirmed in all patients. Results: Through 3D-CISS with MPR images, obvious relationship of the oculomotor nerve and its adjacent structures was demonstrated on 17 patients. Of those oculomotor nerves, 15 were compressed by the arteries (n = 15), one by the craniopharyngioma (n = 1), and another one by the neurofibroma (n = 1). Conclusion: 3D-CISS MR imaging with MPR provides an excellent way to characterize the relationship between the nerve and its adjacent structures in the cisternal segment of the oculomotor nerve in the patients with oculomotor paralysis. Moreover, this method shows anatomical details for imaging diagnosis and surgical procedure.

  19. Atomic force microscopy imaging and 3-D reconstructions of serial thin sections of a single cell and its interior structures

    International Nuclear Information System (INIS)

    Chen Yong; Cai Jiye; Zhao Tao; Wang Chenxi; Dong Shuo; Luo Shuqian; Chen, Zheng W.

    2005-01-01

    The thin sectioning has been widely applied in electron microscopy (EM), and successfully used for an in situ observation of inner ultrastructure of cells. This powerful technique has recently been extended to the research field of atomic force microscopy (AFM). However, there have been no reports describing AFM imaging of serial thin sections and three-dimensional (3-D) reconstruction of cells and their inner structures. In the present study, we used AFM to scan serial thin sections approximately 60 nm thick of a mouse embryonic stem (ES) cell, and to observe the in situ inner ultrastructure including cell membrane, cytoplasm, mitochondria, nucleus membrane, and linear chromatin. The high-magnification AFM imaging of single mitochondria clearly demonstrated the outer membrane, inner boundary membrane and cristal membrane of mitochondria in the cellular compartment. Importantly, AFM imaging on six serial thin sections of a single mouse ES cell showed that mitochondria underwent sequential changes in the number, morphology and distribution. These nanoscale images allowed us to perform 3-D surface reconstruction of interested interior structures in cells. Based on the serial in situ images, 3-D models of morphological characteristics, numbers and distributions of interior structures of the single ES cells were validated and reconstructed. Our results suggest that the combined AFM and serial-thin-section technique is useful for the nanoscale imaging and 3-D reconstruction of single cells and their inner structures. This technique may facilitate studies of proliferating and differentiating stages of stem cells or somatic cells at a nanoscale

  20. How Students and Field Geologists Reason in Integrating Spatial Observations from Outcrops to Visualize a 3-D Geological Structure

    Science.gov (United States)

    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…

  1. From 1D to 3D: A new route to fabricate tridimensional structures via photo-generation of silver networks

    NARCIS (Netherlands)

    Wang, Zhanhua; Shen, Huaizhong; Wu, Yuxin; Fang, Liping; Ye, Shunsheng; Wang, Zhaoyi; Liu, Wendong; Cheng, Zhongkai; Zhang, Junhu; Yang, Bai

    2015-01-01

    A rapid and cost effective method has been developed to fabricate 3 dimensional (3D) ordered structures by photo-generating silver networks inside a 1D layered heterogeneous laminate composed of poly(vinyl alcohol) (PVA) and poly(methyl methacrylate) (PMMA). By designing the photo-mask meticulously,

  2. Oculomotor paralysis: 3D-CISS MR imaging with MPR in the evaluation of neuralgic manifestation and the adjacent structures

    International Nuclear Information System (INIS)

    Sun Xiaoli; Liang Changhu; Liu Cheng; Liu Shuwei; Deng Kai; He Jingzhen

    2010-01-01

    Purpose: To evaluate the value of three-dimensional (3D) constructive interference in steady-state (CISS) magnetic resonance (MR) imaging with multi-planar reconstruction (MPR) in displaying the relationship between the oculomotor nerve and its adjacent structures for patients with oculomotor paralysis. Materials and methods: 17 consecutive patients with oculomotor paralysis were examined with 3D-CISS and conventional spin-echo (SE) sequences on a 1.5-Tesla MR system. Original transverse and MPR images were used for image interpretation. The features of the oculomotor nerve and its adjacent structures were identified. The diagnosis was surgically confirmed in all patients. Results: Through 3D-CISS with MPR images, obvious relationship of the oculomotor nerve and its adjacent structures was demonstrated on 17 patients. Of those oculomotor nerves, 15 were compressed by the arteries (n = 15), one by the craniopharyngioma (n = 1), and another one by the neurofibroma (n = 1). Conclusion: 3D-CISS MR imaging with MPR provides an excellent way to characterize the relationship between the nerve and its adjacent structures in the cisternal segment of the oculomotor nerve in the patients with oculomotor paralysis. Moreover, this method shows anatomical details for imaging diagnosis and surgical procedure.

  3. 3D printing the pterygopalatine fossa: a negative space model of a complex structure.

    Science.gov (United States)

    Bannon, Ross; Parihar, Shivani; Skarparis, Yiannis; Varsou, Ourania; Cezayirli, Enis

    2018-02-01

    The pterygopalatine fossa is one of the most complex anatomical regions to understand. It is poorly visualized in cadaveric dissection and most textbooks rely on schematic depictions. We describe our approach to creating a low-cost, 3D model of the pterygopalatine fossa, including its associated canals and foramina, using an affordable "desktop" 3D printer. We used open source software to create a volume render of the pterygopalatine fossa from axial slices of a head computerised tomography scan. These data were then exported to a 3D printer to produce an anatomically accurate model. The resulting 'negative space' model of the pterygopalatine fossa provides a useful and innovative aid for understanding the complex anatomical relationships of the pterygopalatine fossa. This model was designed primarily for medical students; however, it will also be of interest to postgraduates in ENT, ophthalmology, neurosurgery, and radiology. The technical process described may be replicated by other departments wishing to develop their own anatomical models whilst incurring minimal cos